Course Links (still under construction & to be updated)

PH425: Fluorescence Spectroscopy:

Fluorescence Spectroscopy,  Course Outline:

This part of the PH425 lecture course gives a more detailed insight into the key aspects of Fluorescence Spectroscopy.  Specific topics to be covered include:

• Excited States: What governs the absorption of radiation and what happens to the molecule in the excited state.
• Fluorescence Spectroscopy: Basic concepts -- Jablonski diagram, Franck-Condon principle, characteristics of fluorescence emission, solvent effects.
• Fluorescence anisotropy.  A very useful measurement method particularly for protein studies that allows one to determine size changes. 
• Fluorescence Lifetime measurements.  Measuring the fluorescence decay on nanosecond timeframes. 
• Förster Resonance Energy Transfer (FRET). A very useful technique for measuring distance on the Angstrom length scale and studying protein binding. 
• Quenching & the Stern-Volmer analysis.  Molecular interactions that reduce fluorescence intensity. 
• Fluorophores: A short overview of what types of molecules and materials fluorescence (small molecule, proteins, and quantum dots).

 Reading Lists:

The recommended textbooks are Physical Chemistry, Atkins & de Paula, 8th edition and Principles of Fluorescence Spectroscopy, Lakowicz, 3rd edition.  Both of these are available in the library.  I will also provide handouts at the lectures.
L1  will give you a good introductory background to the various concepts covered in this topic.
 
Level 1 (Introductory & revision):

Elements of Physical Chemistry, Atkins & de Paula, 4th Edition: Chapter 20: Electronic transitions and photochemistry.
This is a basic introduction to spectroscopy. But it does not cover any of the topics in sufficient detail.
Revise 2y spectroscopy notes.

Level 2 (Core course):

The course is based on the course outline and lecture notes.
Atkins does not cover in detail all the topics which we will cover, so there are a list of additional texts that should be consulted.  Some reviews are also included for some of the specific topics to help.
Physical Chemistry, Atkins & de Paula, 8th Edition (recommended textbook). Chapters 14:  electronic transitions/excited states.  Chapter 23:  23.7-23.8: Photochemistry/Fluorescence.
Principles of Fluorescence Spectroscopy, J.R. Lakowicz (2nd or 3rd edition): Elements of Chapters 1, 3, 6, 8.

Fluorescence Polarization/Anisotropy in Diagnostics and Imaging.  D.M. Jameson and J.A. Ross, Chem. Rev. 2010, 110, 2685-2708.  DOI:  10.1021/cr900267p

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Internet Resources:

The following websites have useful online demos and graphics for illustrating many of the concepts covered in the lectures.

For Fluorescence spectroscopy:

• Molecular Probes (now owned by Invitrogen): This manufacturer of fluorescent dyes has a very comprehensive website with a lot of resources useful for understanding fluorescence techniques. The Handbook covers most of what we will cover.  The handbook covers a lot of the basics of fluorescence and applications in life sciences. The introduction section covers a lot of what you need to know. The spectral viewer is very useful for selecting fluorescent probes. 
• Fluorescence tutorials by Invitrogen.  You are strongly encouraged to view the tutorials on fluorescence from Invitrogen.

Rutgers have brief notes on most of what we will do.

Fluorescence Lifetimes:

ISS tech note and data:  This company make lifetime spectrometers and microscopes.  There are 2 in the NBL labs.
Fluorescence Lifetime Imaging Microscopy (FLIM) introduction from Olympus resource centre.

Fluorescence Anisotropy:

This link has a brief review (5 pages) article on the method.
Nice intro and examples at Rochester.
Technical note from JY-Horiba.

Fluorescence Correlation Spectroscopy (FCS):

FCS expert:  a series of tutorials and examples covering FCS (very good company website).

I'll add more later.

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Fluorescence Microscopy:

This course covers some of the basics of microscopy and optical instrumentation.  This is not being given at the moment (2024-25). 

 Fluorescence Microscopy: course  outline.

Reading List: 

• Principles of Fluorescence Spectroscopy, 3rd ed. (2006), J.R. Lakowicz, Springer.
• Handbook of Biological Confocal Microscopy, 3rd ed. (2006) Pawley, Springer.

Internet Resources: 

• Institute of Molecular Biophysics (IMB), Florida State University.
• Keck Biophysics facility, Northwestern University
• Laser spectroscopy and microinstrumentation group, Oak Ridge National Laboratory.
• Molecular Biophysics group, Utrecht, Holland.
• Regional Laser and Biomedical Technology Laboratories (RLBL) of the University of Pennsylvania.
• Wadsworth Centre, visualization of biological complexity.

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Microspectroscopy

• MicroSpectroscopy Centre Wageningen-Leiden,
• Microscopy introduction, the basics,
• Microscopy portal at the University of Wisconsin,
• Microscopical Society of Ireland, good info about the different microscopy activities in Ireland.

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Spectroscopy Lecture Material:

In third year I lecture two different elements of spectroscopy.

Analytical techniques: X-Ray Fluorescence (XRF), surface analytical, and thermal analysis techniques (8 lectures).

Spectroscopy: General spectroscopy (Rotational & Vibrational).

The course descriptions and lecture notes for each are listed below;

Analytical Chemistry &  Structure:  X-Ray Fluorescence (XRF).

This year there will be 8 lectures on XRF and surface analysis techniques. This is still being developed, so check back later.

The full set of notes will be available later for download from blackboard prior to the lectures.

Course outline:

XRF: This course gives a reasonably detailed insight into X-Ray fluorescence spectroscopy.  Specific topics to be covered include:

• General theory of X-Ray Fluorescence Spectroscopy.
• Instrumentation (sources & detectors, wavelength dispersive and energy dispersive spectrometers).
• Instrumentation (wavelength dispersive and energy dispersive spectrometers)..
• Matrix effects,
• Sampling & standards.

Surface Analysis: This will give an introduction into the use of electron based techniques for surface analysis in a chemistry context.

• A basic understanding of the workings of a secondary ion mass spectrometer (SIMS), an x-ray photoelectron spectrometer (XPS), a scanning electron microscope (SEM) and an energy dispersive x-ray analysis system (EDS).
• An understanding of the kinds of chemical and structural information that these instruments can provide about the surface of materials.
• Their application to the analysis of the surface of biomaterials.

YouTube Videos:

These are a collection of videos that show various aspects of XRF in operation. 
USM chem Club. This shows how easy it is to collect XRF data. 
HandHeld XRF from Innov-X, with reasonable soundtrack. Using XRF to check gold purity.
Lab-X system from Oxford Instruments, similar to the NBL system. Another video from Oxford shows oil & cement analysis.
Testing Children's toys for lead using handheld XRF. 
Analyzing solder using micro-XRF (from Spectro).

An XRF tube video from the 1940's.....in black & white.

Animations demonstrating Bremsstrahlung radiation, K-alpha rays, Characteristic radiation ( with fruit & vegetables)

Reading Lists:

The following texts are recommended for this course:

• " Analytical Chemistry: a modern approach to analytical science, 2nd. edition.", edited by Kellner/Mermet?Otto, etc. Chapter 24.4 (all of this for XRF), chapter 27 (selected sections for surface analysis).  There are 4 copies in the library. This is the recommended textbook.
• X-Ray Fluorescence Spectroscopy, 2nd edition, Ron Jenkins. John Wiley. (This is vol. 152 in Chemical Analysis). 

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Internet resources:

The following online tutorials cover all of the course plus a lot extra.  They are good sources of information about the XRF method if you want to learn more:

• Micro- and Trace Analysis Centre (MiTAC) at the University of Antwerp (UA) , the ChemometriX group:
  http://www.chemometrix.ua.ac.be/xrftrain/  [An excellent set of lecture notes].
• Bruker, a manufacturer of XRF instrumentation has a very good online tutorial available at:
  www.bruker-axs.de/fileadmin/user_upload/xrfintro/index.html 
• Amptek, a manufacturer of detectors and compact XRF systems have a lot of good information available at:
  www.amptek.com/xrf.html  Includes details about the XRF system on the Mars pathfinder system.

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General Spectroscopy 

Spectroscopy Course Outline :

This course gives a detailed insight into Rotational, Vibrational &  Molecular spectroscopy.  Specific topics to be covered include:

• General Features of Spectroscopy.
• Pure Rotational (Microwave) spectroscopy.
• Vibrational Spectroscopy.
• Vibrational Rotational Spectroscopy,
• Raman Spectroscopy.

A detailed description of the syllabus is available here.

Lecture Notes

Not available yet.

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Reading Lists

The reading is broken down into level 1 (introductory & 2Y revision) and level 2(core course).  L1  will give you a good introductory background to the various concepts covered in 3rd year, while L2 texts will give you the necessary detail and tools to be able to understand and answer the questions. 

Required Reading: 

Elements of Physical Chemistry, Atkins & de Paula, 4th Edition:
Vibrational & Rotational spectroscopy:  Chapter 19
Physical Chemistry, Atkins & de Paula, 8^th Edition (recommended textbook).
Chapter 13: Molecular spectroscopy 1; rotational & vibrational spectra. 

Level 1 (introductory & 2Y Revision):
Revision of second year spectroscopy. Notes available here. 

Elements of Physical Chemistry, Atkins & de Paula, 4th Edition: Chapter 19: Molecular Rotations and Vibrations (Revision of second year topics).  

Level 2 (core course):
Elements of Physical Chemistry, Atkins & de Paula, 4th Edition: Chapter 19: Molecular Rotations and Vibrations  
This is a reasonable introduction to spectroscopy. But it does not cover all the required topics in sufficient detail.

Physical Chemistry, Atkins & de Paula, 8^th Edition (recommended textbook). Chapter 13. 
There are a lot of electronic resources available in the ebook which are very useful for understanding quantum mechanics.  

Suggested Reading: 
The following sources are useful if you want to find out more about these methods.
Foundations of Spectroscopy, Duckett & Gilbert, Oxford Chemistry Primers. Chapters 2 and 3. 
Molecular Spectroscopy, J.M. Brown, Oxford Chemistry Primers. Chapters 1-6.
Fundamentals of Molecular Spectroscopy, Banwell & McCash, Chapters 1-4. 

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Problem Sheet

Handed out at first quantum lecture.

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Internet resources

The following websites have useful online demos and graphics for illustrating many of the concepts covered in the lectures. 

General Spectroscopic Info: 
From MIT, basic intro to spectroscopy handout. 

Microwave (rotational) spectroscopy: 

Steve Kukolich, at Arizona University: study of molecular structure through microwave spectroscopy. 
Interstellar Microwave Spectroscopy at NASA, JPL lab. (includes simple explanation).
Eastern Illinois University have a nice page with pics of a microwave spectrometer.
List of Rotational Spectroscopy groups.

Vibrational-Rotational Spectroscopy:

MIT website has lecture notes available at http://web.mit.edu/5.33/www/lec/spec5.pdf 
Description of Vib-Rot experiment. New Mexico State University. 
Explanation of why water is blue. J. Chem. Edu., 1993, 70(8), 612.
Internet Journal of Vibrational Spectroscopy.  Lots of interesting articles online. 

Raman spectroscopy: 
University wesbsites, mixture of teaching and research:
Chemsoc. Org.  Basic tutorial.
Virtual Raman.  Nice pictures of setup and tutorial.

The following manufacturer sites give tutorials on Raman & applications:
Kaiser Optical Systems. 
Avalon Instruments, part of Perkin-Elmer. We have one of these systems in NUIG. Some nice application notes on the use of Raman.
Horiba Jobin-Yvon.  We have one of their confocal Raman systems at NUIG.
Renishaw.  Nice list of indicative applications of Raman analysis. 
Delta Nu. Application Notes, Forensics, and portable systems.  

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3rd year Quantum Chemistry Lecture Material

Quantum Chemistry : Course Outline

This course gives a detailed insight into Quantum Chemistry.  Specific topics to be covered include:

• Failure of classical mechanics.
• Schrodinger Wave equation (SWE).
• 1D Translational motion: Particle in a box.
• Tunnelling.
• 2D Translational motion.
• 2D Translational motion:  Quantum dots.
• Rotational Motion. 
• Vibrational Motion.

The detailed syllabus is available to download here

Lecture Notes

These are only study aids, you are required to read the various textbooks. 
The current lecture notes are available on blackboard.

 Required Reading 

Elements of Physical Chemistry, Atkins & de Paula, 4th Edition: Chapter 12: Quantum Theory  
This is a good introduction to what we will cover. But it does not cover all the topics in complete detail.
Physical Chemistry, Atkins & de Paula, 8^th Edition (recommended textbook).
Chapter 8 and 9 (up to section & including section 9.6).

Physical Chemistry, Atkins & de Paula, 9^th Edition, Chapter 7 and 8 (up to section & including section 8.6).
If you purchase the book there are a lot of electronic resources available in the ebook which are very useful for understanding quantum mechanics.  

Suggested Reading: 
An Introduction to Quantum Theory and Atomic Structure, P.A. Cox, Oxford Chemistry Primers. Chapters 1-3.

Internet resources

The following websites have useful online demos and graphics for illustrating many of the concepts covered in the lectures. You are advised to take a look.

Quantum physics online, This has a range of excellent visualizations of wave-particle duality (topic 1.1), barriers (topic 1.5), Harmonic oscillator (topic 3.6), and other concepts.
Quantum aspects of the world, contains links to notes and tutorials. 
3D quantum solution explained here from MIT OpenCourseWare.

Videos:  some interesting bits & bobs....worth a couple of minutes.

Quantum tunneling. Quantum Dot LEDs. Invention of Quantum dots. QM-C4 (dodgy animation at the beginning). Wave-Particle duality.

Problem Sheet : This problem sheet contains indicative problems from the course.  You should attempt these prior to the scheduled tutorials. The sheet will be handed out during the first lecture. 
My strong advice is for people to work individually first and then in small groups.

Basic level introduction to spectroscopy.

Spectroscopy is covered in two modules during second year.  3 lectures in CH203 (Sem I) and 6 lectures in CH205 (Sem II).    [Webpage still a work in progress]

 2nd year Physical Chemistry (CH203):  Spectroscopy & Equilibrium 

Two topics, 3 lectures on each topic, 2 questions in exam paper.  The handouts are available for downloading on blackboard, no guarantees with regard to content, the required reading has to be undertaken.

Spectroscopy (CH203):  This course gives an introduction to Molecular, & Vibrational spectroscopy.  Specific topics to be covered include:

• Introduction to Spectroscopy.
• Quantitative Spectroscopy (Beer-Lambert Law).
• Electronic spectroscopy.
• Vibrational Spectroscopy (FT-IR and Raman spectroscopy).
• Energies of Vibrational transitions.
• Polyatomic Vibrational spectroscopy.

The syllabus and learning outcomes for this section can be downloaded from blackboard.

Lecture Notes: These are only study aids, please also study the required texts. The notes are downloadable from Blackboard only.

Required Reading: 

Elements of Physical Chemistry, Atkins & de Paula, 4th Edition:
Chapter 19: Molecular rotations and vibrations, sections 19.1-19.3/19.9-19.13 & 19.15
Chapter 20: Electronic transitions and photochemistry, sections 20.1/20.4/20.5.

Optional Texts: 

Foundations of Spectroscopy, Duckett & Gilbert, Chapters 2,3, and 4. 
Physical Chemistry for the Life Sciences, Atkins & de Paula, Chapter 13.

Internet resources:  The following websites have various documents and tutorials covering various aspects of spectroscopy.

Foundations of spectroscopy, Colorado State University. pdf handout that covers some of the basics.
Raman spectroscopy, tutorial and history, from Horiba Jobin Yvon.
FT-IR spectroscopy, links page. 
UV-Visible, tutorial from MSU, 
Fluorescence spectroscopy, tutorial (1), tutorial (2) molecular probes.
Virtual Textbook of Organic Chemistry,  sections on spectroscopy. 
Optics of Spectroscopy, From Horiba Jobin Yvon, a detailed resource on spectrometers and the physics behind the instrumentation.

Video Links:  The following videos on Youtube are useful for illustrating various aspects of the course: RSC-UV-VIS tutorial. Beer-Lambert experiment demonstration (very similar to lab practical)

RSC-MIR tutorial.  Assigning MIR spectra. Molecular spectroscopy in the dark ages (e.g. before PCs).

Hand-held Raman spectrometers ( Thermo company).  Molecular fingerprinting (plastic recycling application). Forensic Ink analysis by Raman.

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