Advanced Higher Chemistry Unit 2

Unit 2 - Organic Chemistry and Instrumental Analysis

Sigma and Pi bonds - a bit of an explanation - although really you will hopefully only need to know about Carbon's hybrid orbitals hopefully :
https://www.youtube.com/watch?v=HKyobMewXBw
and a good explanation of bonding with sigma bonds formed in methane etc.
http://www.chemguide.co.uk/basicorg/bonding/methane.html

Chromophore Experiment
Really easy chromophore experiment using the chromophore lycopene which gives the red colour in tomatoes - and adding Bromine water to get a rainbow of colour (watch out its a noisy video!) http://chemicalsareyourfriends.com/sliders/tomato-juice-rainbow-explained/

Chromophores and Bleach 
https://chem.ku.edu/sites/chem.ku.edu/files/docs/CHEM190/stain_removal.pdf
How bleach breaks up a chromophore

Chromophores - a tricky explanation
The explanation here about how Chromophores absorb light etc. is probably more advanced than you need for Advanced Higher but it makes for quite interesting reading if you don't worry too much about trying to learn it ! It also talks about indicators for acids and alkalis which is quite interesting .. and also how the Colour Wheel is not always quite as simple as it seems ...
http://www.chemguide.co.uk/analysis/uvvisible/theory.html

Chromophores with some interesting examples and graphs (I like this link)
http://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/spectrpy/uv-vis/spectrum.htm

another chromophore link : https://people.chem.umass.edu/samal/269/color.pdf

Dyes - see page 5 of this Mole magazine from Royal Society of Chemistry - v interesting - https://issuu.com/rsc_eic/docs/the-mole-november-2016

Enantiomers
http://www.oit.edu/docs/default-source/library-documents/library-publishing/che102-intro-organic-chemistry/chapter-2-4.pdf?sfvrsn=2

There is a picture of plane polarised light on this link - and also what two enantiomers do to this-
http://www.wiredchemist.com/chemistry/instructional/an-introduction-to-chemistry/structure/geometric-and-optical-isomers

Limonene - an optical stereo-isomer (enantiomer) - one optical isomer has a lemon smell, the other has a pine smell :
http://www.chm.bris.ac.uk/motm/limonene/limoneneh.htm

Explaining about amino acids being stereo-isomers - this is a little beyond Adv H level but if you are doing biology as well then you might be interested in the fact that all amino acids in the body are of one type of enantiomer - L-amino acids http://www.chemguide.co.uk/organicprops/aminoacids/background.html

Understanding the curly arrows used in Organic chemistry reaction diagrams :
http://www.masterorganicchemistry.com/2012/02/29/curved-arrows-2-initial-tails-and-final-heads/

Amines
Determining how Basic they are - eg methylamine, phenylamine etc. - are they good bases ?
http://www.chemguide.co.uk/basicorg/acidbase/bases.html

Reaction Pathways
This is an interesting website with the reaction pathways we need to know. I haven't completely examined the site yet but it pretty much seems to cover what is in Advanced Higher Chemistry :
http://www.reactionpathways.chemistry-teaching-resources.com/New_Reaction_Pathways.html

Alcohols vs Ethers
Discussing hydrogen bonding (or lack of !), boiling points, behaviour of these two molecules which can have same molecular formulas but quite different behaviours.
http://www.4college.co.uk/as/df/alcohols.php

Alcohols - Ethers - Esters - Alkanes
Comparing boiling points -
Useful table in green, yellow, blue and orange colour half way down this page.
http://www.masterorganicchemistry.com/2010/10/25/3-trends-that-affect-boiling-points/

Esters
Some information about Esters, including which smells/flavours you can get from different esters -
http://2012books.lardbucket.org/books/introduction-to-chemistry-general-organic-and-biological/s18-07-physical-properties-of-esters.html

Haloalkanes
Naming Rules - Follow Link to excellent page
Naming rules - http://www.ausetute.com.au/namhaloa.html - this hopefully goes a little beyond the types of compounds you might have to name so don't panic ! ...
rules also here : http://www.docbrown.info/page06/halogenoalkanes1.htm
and a quiz to try :
http://www.docbrown.info/page06/Ahaloalkanes/haloalkaneQsa.htm

Forcing Benzene to Undergo Nucleophillic Substitution reactions ...
An explanation of why we need to use FeBr3 to encourage Br-Br to react with benzene ...




Also more details at:
http://www.chemguide.co.uk/mechanisms/elsub/whatis.html
and http://www.chemguide.co.uk/mechanisms/elsub/halogenation.html

Mass Spectrometry
Really good animation / explanation
http://www.rsc.org/learn-chemistry/collections/spectroscopy/introduction#MassSpectrometry

Experimental Determination of Structure :
Elemental Microanalysis - lots of calculations to try on this technique that is mentioned in Bright Red book p72  :
http://www.chemteam.info/Mole/CombustionAnalysis.html

Gas Chromatography
Quite a nice 5 minute video about Gas Chromatography :
http://www.youtube.com/watch?v=08YWhLTjlfo&list=PLbNovFNl4Fxj25YJ8LvufVC8k8SO142gP
Nice explanation of Gas Chromatography - I would say you just need general ideas about this so DO NOT WORRY ABOUT THE DETAILS here !! But there is some interesting information :
http://chemguide.co.uk/analysis/chromatography/gas.html

Extra of interest :
IR Spectroscopy
The lower parts of this page are not relevant but the top half is very readable and has good examples which we will use during tutoring.
http://www.rsc.org/learn-chemistry/collections/spectroscopy/introduction#IRSpectroscopy
Interesting link: https://instruct.uwo.ca/chemistry/020/calvin/Chem020IR.pdf

NMR - Here is quite a nice resource - I think pages 1,4, 6,7 and 8 are the most useful, and basically you do not need to know all this detail but read the first bit and then have a look at all the graphs on pages 6,7 and 8 to get an idea how to interpret them.
http://www.chem.ucalgary.ca/courses/350/Carey5th/Ch13/ch13-nmr-1.html

NMR animation from Royal Society of Chemistry  :  http://sod-a.rsc-cdn.org/www.rsc.org/learn-chemistry/Collections/spectroscopy/Content/FileRepository/NMR/NMR%20002.swf

Here are some more examples of NMR spectra :
http://legacy.chemgym.net/as_a2/topics/nmr_intro/introduction.html

Drugs and Medicines

Plant tours of chemical plants ...
https://www.abpischools.org.uk/topic/labpilotplant

The design of drugs and medicines are considered. Whether they are agonists, which mimic the body's own biological molecules or ant-agonists which block the body's receptors to get their effect are all considered.
Beta blockers is one group of medicines which were originally designed to block the β receptors in the heart. They were designed by a Scot, James Black who received a Nobel Prize.
http://www.nobelprize.org/nobel_prizes/medicine/laureates/1988/black-bio.html
Propanolol is the drug he discovered :
You do not appear to need to memorise these structures but you may have to compare them with other structures to look for similarites or you may be expected to recognise groups within them such as amine groups etc.
Affects of Adrenaline and a small animation : 

Robots helping us to discover/design new medicines - very interesting video from the Royal Society of Chemistry: https://www.youtube.com/watch?v=RY7uS9bm3Zk

Medicines that affect neurotransmitters :

Drug design - some interesting reading about "The Rule of Five" and other considerations when designing drugs - http://www.rsc.org/images/Breaking%20the%20rules_tcm18-121442.pdf
and


This is quite interesting - a short video from "Periodic Videos" about the chemical structure of various painkillers - and the associated illegal drug as well - morphine, diamorphine, codeine, etc 
- interesting to read this as well after watching this video - about Andanamide - the natural "bliss" molecule - (mentioned in Course and Unit Support notes) -http://antoine.frostburg.edu/chem/senese/101/features/anandamide.shtml

Andanamide - the Bliss molecule (also this article links to the medicine and drug section below)
http://antoine.frostburg.edu/chem/senese/101/features/anandamide.shtml (this is probably really just background reading - it will make more sense too if you are studying Biology as well so don't panic if you are not - just have a bit of a read of it and see what you pick up)

Medicines - structures
There are a few interesting bits about medicines and drugs on the first few pages of this reference: https://courses.edx.org/c4x/DavidsonX/001x/asset/Week_1__DavidsonX_001x_Medicinal_Chemistry_Weekly_Summary_.pdf

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