Molecular Structure and Reactivity (Pharmacy) Credit Points: 30 Course Aims Level: 1 Semester AB

Code: 1PHA0003 2009/2010

The aims of this module are to enable students to . . . appreciate the central role of inorganic, physical and organic chemistry in the determination of molecular structure; to develop the ability to predict molecular reactivity from the basis of a structural understanding; to understand the chemistry associated with the key organic functional groups that are present in biologically active molecules. Learning Outcomes Knowledge and Understanding: Successful students will be able to: describe spectroscopy and its role in structure determination demonstrate a knowledge of kinetic and thermodynamics describe the structures of organic and inorganic molecules demonstrate a knowledge of periodicity and basic inorganic chemistry describe the chemistry of alkenes, alkanes, halides; carbonyls, amines, alcohols, ethers, sulfides and the benzene aromatics

Skills and Attributes: Successful students will be able to: predict how a given reaction should proceed use functional group chemistry to design simple synthetic reaction sequences conduct simple laboratory based syntheses and perform experiments to determine properties of different compounds communicate scientific data, locate information relevant to studies in molecular structure and reactivity at Level 1 manipulate quantitative information related to molecular structure and reactivity at Level 1 Brief Description Chemical equations, valency and formulae, moles and related calculations, ionic and covalent bond and associated molecular shapes, based on s,p,d (and associated hybrid) orbitals (VSERP). Foundations of organic chemistry including nomenclature, bonding and structure, reaction of organic molecules and factors affecting, stereo chemistry. (E/Z ,R/S and d/l (D/L) systems, introduction to types of mechanism (SN1,2 etc) chemistry of functional groups (eg carbonyl, nucleophilic groups, Chemistry of Benzene, alkenes, organic halides. Introduction to spectroscopy.

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Module Co-ordinator: Paul Bassin (PB) (e-mail j.p.bassin@herts.ac.uk) Module Team: Sara Evans (SE) Steve Hall (SH) Suzanne Fergus (SF) David Griffiths (DG) Sharon Rossiter (SR) Jacque Stair (JS) Andrew Hutt (AJH) Theo Berkhout (TB) Stewart Kirton (SK)

Lecture and Workshop Timetable - Tuesday Precise week numbers and timetable information may change.
Week Lecture Tuesday 14.00-15.00 Prince Edward Hall
Thermodynamics SK

Lecture Tuesday 15.00-16.00 Prince Edward Hall

Workshop 16.00-17.00 Room B400

Tuesday

Workshop 17.00-18.00 Room B400

Tuesday

2 3 4 5 6 7 8 9 10 11 12 13 -15 16 17 18 19 20 21 22 23 24 25 26 27 28-29 30 31 32-36

INDUCTION WEEK Structure, equations moles and calculation TB Structure, equations moles and calculation TB Thermodynamics SK Organic lecture 1 Organic lecture 2 Organic lecture 3 Organic lecture 4 Organic lecture 5 PB PB PB PB AJH MSR W3 Group 1,2,3 MSR W3 Group 4,5,6 TB TB TB TB DG DG DG MSR W4 Group 1,2,3 MSR W4 Group 4,5,6 MSR W4 Group 7,8,9 MSR W4 Group 10,11,12 MSR W6 Group 1,2,3 MSR W6 Group 4,5,6 MSR W6 Group 7,8,9 SF SF SF SF AJH AJH AJH

Structure, equations moles and calculation TB Thermodynamics SK Lab lecture MSR 2 PB pH & Buffers TB

MSR W1 Group 1,2,3 MSR W1 Group 4,5,6 MSR W1 Group 7,8,9

SK SK SK

MSR W2 Group 1,2,3 MSR W2 Group 4,5,6 MSR W2 Group 7,8,9

TB TB TB

MSR W1 Group 10.11.12 SK

MSR W2 Group 10,11,12 TB

Atomic and Molecular Orbitals and Molecular Shape DG Radioactivity Radioactivity Kinetics SH SH DG

Atomic and Molecular Orbitals Radioactivity SH Organic lecture 6

CHRISTMAS VACATION AJH MSR W3 Group 7,8,9

INTERSEMESTER EXAMINATIONS Organic lecture 7 AJH MSR W3 Group 10.11.12 Organic lecture 8 AJH Lab lecture MSR 4 PB PB PB SR SR SF JS MSR W7 Group 1,2,3 MSR W7 Group 4,5,6 MSR W7 Group 7,8,9 MSR W7 Group 10.11.12 REVISION Organic lecture 10 Organic lecture 12 Organic lecture 14 Organic lecture 16 Organic lecture 18 Organic lecture 20 MSR W5 Group 1,2,3 MSR W5 Group 4,5,6 MSR W5 Group 7,8,9

Organic lecture 9 Organic lecture 11 Organic lecture 13 Organic lecture 15 Organic lecture 17 Organic lecture 19 Spectroscopy Spectroscopy REVISION

SF SF SR SR SR JS SE SE

MSR W5 Group 10.11.12 DG SF SF SF SF

MSR W6 Group 10,11,12 AJH MSR W8 Group 1,2,3 MSR W8 Group 4,5,6 MSR W8 Group 7,8,9 SR SR SR

Spectroscopy SE EASTER VACATION Spectroscopy REVISION SE

MSR W8 Group 10,11,12 SR REVISION

SEMESTER B EXAMINATIONS

Revision Sessions: Students should be prepared to raise any questions they wish on any aspect of the curriculum.

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Practical timetable
Week Friday 14.00-18.00 Groups 1,2,3,4 Lockers (1C104) MSR 1 TB/AJH Friday 14.00-18.00 Groups 5,6,7,8 INDUCTION WEEK Lockers (1C104) MSR 1 MSR 2 PB/TB MSR 2 PB/SR TB/SH/MJF MSR 1 TB/AJH/MJF Friday 14.00-18.00 Groups 9,10,11,12 Lockers (1C104)

2 3 4 5 6 7 8 9 10 11 12 13 - 15 16 17 18 19 20 21 22 23 24 25 26 27 28-30 31 32 33 - 36

MSR 2 PB/SR Use of Crossfire and ISIS Draw, H150, 2-6 pm/PB/LC. See studyNet for details MSR3 SF/TB/MJF MSR 3 TB/AJH/MJF MSR 3 SF/TB/MJF CHRISTMAS VACATION INTERSEMESTER EXAMINATIONS

MSR 4

SH/DG MSR 4 DG/SR/MJF MSR 4 DG/SE

MSR 7

All staff

MSR 7

All staff MSR 7 All staff

Good Friday No Practicals EASTER VACATION

SEMESTER B EXAMINATIONS

MSR 6 will run on Wednesday mornings from 9.00-13.00 in 2G168 in C.P.Snow building Week 23 (group 1,2,3) (Staff; DG/JS/TB) Week 24 (group 4,5,6) (Staff; DG/JS/TB) Week 25 (group 7,8,9) (Staff; DG/JS/TB) Week 30 (group 10,11,12) (Staff; DG/JS/TB) ASSESSMENT (25% examination, 75% coursework) A pass is normally required in both examination and coursework All work for assessment must be accompanied by a coversheet available from the CP Snow reception. Marked work will generally be returned in class or through the CP Snow reception. NSA laboratory work will be discussed/marked in the laboratory session.

The nature and value of the assignments are shown below.

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Nature of assessment Beilstein Kinetic

Code MSR 8 MSR 9

Deadline Week 21 Week 27

Staff PB DG

Value 10% 15%

Details on Assignments MSR 8 and MSR 9 The use of ISIS & Beilstein. MSR 8 Titles will be issued in week 10. Deadline week 21. This is a scientific data exercise. You will be individually assigned a compound and be expected to carry out a data search using Crossfire Beilstein. We would normally expect you to spend approximately 10 hours on this work in addition to your regular studies on this module. Kinetics Assignment MSR 9 (to be handed in week 27) Assignment will be put on studynet in week 20. This is a calculation based activity where students determine the initial rate, order, rate constant and half- life for one component of a particular reaction (in this case the hydrolysis of a commonly used pharmaceutical excipient (sucrose) under acidic conditions). You should expect to spend a minimum of 10 hours on this piece of work.
Laboratory Classes

Weeks

Code

Title Redox Reactions (NH2OH/Fe2+) Benzocaine Influence of pH on drugs absorption Eugenol isolation Friedel-Crafts Alkylation Preparation of radioactive solution Practical Test

Lab.

Report

3,4,5 6,7,8 10.11,12 20,21,22 25 23, 24,25, 30 25,26

MSR 1 MSR2 MSR3 MSR4 MSR5 MSR6 MSR7

1C100 1C100 1C100 1C100 1C100 2G168 1C100 Full Full

Assessed SA NSA * * * *

* SA - summative assessment NSA - compulsory but not summative assessment Timetabled feedback sessions Feedback on assignments and practicals will occur during the workshops and practical sessions. Details will also be posted on Studynet

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PTS assessment Code Title PTS Assessment 2+ MSR 1 Redox Reactions (NH2OH/Fe ) COM, NUM, PS MSR 2 Benzocaine A, COM, GW, NUM MSR 3 Influence of pH on drugs absorption COM, A,GW MSR 4 Eugenol isolation A, COM, NUM MSR 5 Friedel-Crafts Alkylation COM, A, MSR 6 Preparation of radioactive solution COM, NUM, PS MSR 7 Practical Test COM, A,NUM,PS MSR 8 The use of ISIS & Beilstein . A, IM, MSR 9 Kinetics Assignment COM, NUM NB These are the skills that we think you will use while carrying out the assignments. You can ask for other skills to be assessed if you think they are appropriate. Key to PTS skills Autonomy taking responsibility for themselves Information management COM Oral and written communication SERP Self evaluation and reflective practice
A

IM

NUM Numeracy GW Group working PS Problem solving

Workshop subjects It is essential to prepare for workshops and to be prepared to contribute to them. Consult your workshop booklet and bring it with you to the class. Workshops are compulsory. Your record of attendance will be taken into account at the Board of Examiners when deciding your grade. You must attend at least 75% of these workshops in order to pass A for PTS1. You will be required to record your workshops in a log book which will be assessed periodically by your personal tutor. Workshop No MSR W1 MSR W2 MSR W3 MSR W4 MSR W5 MSR W6 MSR W7 MSR W8 Topic Thermodynamics Chemical equations and calculations Solutions, electrolytes, pH and Buffers Structures, resonance & aromatics Kinetics Stereochemistry Substitution and elimination reactions Functional groups Staff SK TB TB SF DG AJH SF SR

Performance in laboratory classes In order to meet the learning outcomes for the module you must attend all laboratory classes. If you miss a laboratory class (both SA or NSA) it is your responsibility to contact the module coordinator by email immediately giving the reason for your lack of attendance. If you have a legitimate reason for missing a session, the module coordinator may be able to arrange your attendance at a subsequent running of the practical session or ask you to do alternative work (alternative work will be posted on studynet). Failure to inform the module coordinator and submit the alternative work will result in you being penalised by deduction of 5% of your coursework mark.

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You must use your logbook for making notes and recording data for all laboratory experiments. Logbooks should normally be completed during the practical. If data are not available (e.g. because of experimental constraints) written work can be completed either before or during the following laboratory session. Logbooks should briefly record Aims, Results and Conclusion. Proforma reports involve using notes in logbooks to fill in a prepared sheet. Proformas may need to be completed within the laboratory session or outside the session as instructed by academic staff. Logbooks and Proformas may be marked either at the end of a practical session or in a subsequent session as instructed. Full reports should have an Abstract, Introduction, Aims, Materials and Methods (do not reproduce the schedule), Results, Discussion and References as detailed in the student handbook. The Results should show calculations where appropriate and the Discussion should interpret data put into context with textbook information. To avoid plagiarism when working in pairs, you should discuss the results of your experiments with your laboratory partner but the report should always be your own work, in your own words. Work done as a group may, in some cases, be submitted as a group report but the structure of the report should follow the same format. Full reports must be completed on or before deadlines specified which is normally 2 weeks (for full time students) and 3 weeks for part time students) after the last session of that practical. However, you are strongly encouraged to submit practical reports as soon as possible. Late submission of up to 1 week will result in a maximum mark of D3. Extensions must be requested from Pathway Tutor or Associate Head of Department (see the student handbook for detail of the procedure). Unsatisfactory completion of laboratory assignments or lack of attendance will result in a reduction of 5 percentage points from the % coursework mark, for each omission i.e. 2.5 percentage points from the overall module mark. Thus, you will risk FAILURE of the module by not attending a practical or not completing satisfactorily non-summatively assessed exercises. In the past, students have failed modules because of this penalty and, as a result, put their progression to the next level, and even their degree, at risk. Plagiarism Plagiarized work will be given zero marks. You may also be reported to the Faculty Academic Conduct Officer which may result in disciplinary action taken against you (see Departmental Handbook for further details). Coursework Laboratory reports: 2 Full reports (15% each) Practical Test Assignments: Kinetic Beilstein 8 Random drop-quizzes 30% 10% 15% 10% 10% Examination One unseen 2 hour written examination 25%

A PASS IS NORMALLY REQUIRED IN BOTH EXAMINATION AND COURSEWORK

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Learning Outcomes

Exm

PRACTICALS (MSR 1-7) Assignments (MSR 8, MSR 9) & Drop Quizzes (10)
1 2 3 4 5 6 7 8 9 10

describe spectroscopy and its role in structure determination demonstrate a knowledge of kinetic and thermodynamics describe the structures of organic and inorganic molecules demonstrate a knowledge of periodicity and basic inorganic chemistry describe the chemistry of alkenes, alkanes, halides; carbonyls, amines, alcohols, ethers, sulfides and the benzene aromatics predict how a given reaction should proceed use functional group chemistry to design simple synthetic reaction sequences conduct simple laboratory based syntheses and perform experiments to determine properties of different compounds communicate scientific data, locate information relevant to studies in molecular structure and reactivity at Level 1 manipulate quantitative information related to molecular structure and reactivity at Level 1

BOOK LIST RECOMMENDED PURCHASE Housecroft C.E & Constable E.C. (2006) Chemistry (3th edition) Pearson Prentice Hall. RECOMMENDED READING

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Dewick, P.M. (2006) Essentials of Organic Chemistry for Students of Pharmacy, Medicinal Chemistry and Biological Chemistry, Wiley Zatz J.L. and Teixeira M.G., (2005) Pharmaceutical Calculations (4 th Edition) Wiley Interscience. Blein, I and Odian, G. (1999) General Organic and Biochemistry W.F.Freeman. Brown W.H. (1995) Organic Chemistry Saunders College Publishing. Carey F.A. (2000) Organic Chemistry (4th edition) McGraw-Hill Inc. Chang, R (2000) Physical Chemistry for the Chemical and Biological Sciences University Publishers Inc Patrick G. (2000) Instant Notes in Organic Chemistry Bios Scientific Publishers Thomas, Gareth (1996) Chemistry for Pharmacy and the Life Sciences Prentice Hall Atkins, P. and Jones, L. (2005) Chemical Principles The Quest for Insight. 3 rd Edition W.H.Freeman. Atkins, P. and Jones, L. (2000) Molecules, Matter and Change. W.F.Freeman Handbook of Chemistry & Physics, CRC Press

In addition there are many organic chemistry/synthetic chemistry books available in the library you are advised to extensively delve into these books. Communication All communication concerning this module will be via StudyNet. You should check the module site at least weekly.
The information given in this module guide is believed correct at the time of going to press, but the Department reserves the right, at its discretion, and for any reason, to make changes to the guide without prior notice, and in particular: (a) to make changes to syllabuses and modules for reasons including meeting technological or academic developments or employers' requirements particularly in specialist options. (b) not to offer options, specialisms or elective modules within a programme of study, where there is insufficient student demand.

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