Chemistry Living and Systems: 123.101 Lecture 1

Chemistryand living systems123.101Gareth Rowlands

anintroduction tochemistry and...

...howit relates to living things

the study guide contains all the information you need

my lectures containexplanationand examples

but as I’m not here... ! ...the Prof will have to do

my notes are available from:www.massey.ac.nz/~gjrowlan/teaching.html

my notes are available from:http://www.slideshare.net/gjr2323

Slideshare is an awesome resourcefor learning about presentations

read each chapter in advance I will give different examples. Do not expect me to read it to you... ©Noukka Signe@Flickr

Ready?

Unit One Part 1: introduction pic: Aquarium of the Paciﬁc

Unit One Part 1: introduction these are not random pictures; the molecule is a potential painkiller called epibatidine which is isolated from poison dart frogs... pic: Aquarium of the Paciﬁc

why do we needorganic chemistry?

...because its fun?? why do we need organic chemistry?

why do we needorganic chemistry? ...it keeps me in a job? Or...

if w e want tounderstandliving systems...

we need tounderstand theindividual organs...

...to understandorgans, we have tounderstand cells...

...and still we have to get smaller and smaller...

...and to do this we must understand themolecules that make up these systems Me N Me Me N Fe N HO2C(H2C)2 N HO2C(H2C)2 Me haem

...lets stop with atoms & electrons! And none of this maths malarkey. but we dont needImage Credit: NIST/University of Colorado to get carried away...

simple chemicalprinciples control biology

Me Me Me 11 12 Me Me Rhodopsin H 11-cis-retinal N (aldehyde not imine) Opsin photon Me Me Me Meisomers and the Me N Hvisual cascade all trans-retinal starts VISUAL CASCADE Opsin

$chemistryand medicine

penicillin G antibacterial H H N S Me O N Me O CO2Hhttp://staff.science.uva.nl/~dcslob/lesbrieven/maarten/Bacterien.html

penicillin G Chemistry explains how penicillin blocks antibacterial bacterial cell wall synthesis. H H N S Me O N Me O CO2Hhttp://staff.science.uva.nl/~dcslob/lesbrieven/maarten/Bacterien.html

F OH OH OH N O Ca2+N O Me Me 2 Liptor cholesterol treatment US$ 12.9 billion

the languageof chemistry...

First we need to be able to communicate with each other...the languageof chemistry...

There are three ways of talking about chemicals...the languageof chemistry...

MACROSCOPIC bulk propertiesMICROSCOPIC SYMBOLIC atoms & chemical molecules formulae

macroscopicrepresentation physical properities©DC Comics

macroscopicrepresentation physical properities obviously important (if you happen to get dunked in a vat of the stuff)©DC Comics

macroscopicrepresentation physical properities but ignored in this lecture...lets just leave it for the lab...©DC Comics

how do we represent molecules?

microscopicrepresentation

how we represent the actual molecules themselves... microscopic representation

hexane molecular orbital representation

hexane electrons spread over entire molecule...true but not very useful! molecular orbital representation

hexane space ﬁlling representation

hexane shows us the atoms and their relative size...but bonds hard to see space ﬁlling representation

hexane ball and stick representation

hexane atoms, bonds, shape, it has it all. Time consuming to draw so... ball and stick representation

symbolicrepresentation

symbolic representationquick and dirty ways to represent molecules

C3H7empiricalformula

C3H7 just the ratio of atoms...empiricalformula

C3H7 ...too many possibilities!C6H14C24H56 12H28 C C15H35C30H70 C27H63 3H7 C18H42 C C21H49formula 33H77 9H21 C Cempirical

C6H14 molecular formula

C6H14exact number of atoms... molecular formula

C6H14 ...but not how they H H H H are connected H H H HH C C H H C H H H H C H H H C C C H C C H C C H C C H H HH C H H C C C H H H H H C H H H H H H H H H H H H H H H H H C C C C C C H molecular H H H H H H formula

CH3CH2CH2CH2CH2CH3condensedformula

CH3CH2CH2CH2CH2CH3 bonding sorted...condensedformula

CH3CH2CH2CH2CH2CH3 H H O Me H C H H H Me N N H C C C C H (CH3)2CHCH(CH3)CH3 O N N H H H C H H H ...but bulky...and Me some structurescondensed would be confusing!formula

H H H H H H C C C HH C C C H H H H H H structural formula

H H H H H H C C C H H C C C H H H H H H now we’re talking; atoms, bonding,shape. It has it all. But... structural formula

H H H H H H C C C H H C C C H H H H H H ...can be messy and time consuming... H C H2C CH OH OH H2C N H H2C C CH2 H C C N CH HC C H C 2N H N C C CH OMe HC C CH3 structural formula C O H

skeletal(structural) formula

Quick, easy and tells me everything...but do you understand what it means?skeletal(structural) formula

otherrepresentations H H C H O O H H C C CHO H C C H H H H H OH Et H CHO Et H H OH HO Ph CH3 H CH3 H CH3 Ph Fischer Newman Sawhorse projection projection projection

do not use thisrepresentation! H H H H H HH C C C C C C H H H H H H H

...key to this course is understanding / interpreting these symbols ©Lucasﬁlms

understandingskeletal (structural)formulae

4 H H C H H H H C C H H H C C HCARBON O H C H C O H H

4 H H C H Hcarbon always has H H four bonds... C C H H H C C HCARBON O H C H C O H H

why? a good question & one we will partially answer later©ultraBobban@Flickr

1 H H C H HHYDROGEN H C C H H H O H C H C O H H H H O C C H H C O H N H H

1 H H C H HHYDROGEN H C C H H H O H C H C O H Hhydrogen always has one bond... H H O C C H H C O H N H H

2 H H C O H C H H H H H H H C C H C C H H O H H H O C C H H C OOXYGEN H N H H

3 H H ONITROGEN H C C C O H H N H H H H C N H H C C H H H H C C N H

so how do we drawskeletal formulae?

HO HO OH O O O NH2 O Cl OH O O HO Cl OH O O O H H H O N N N N N N H H H HN O O O O HO NH2 OH HO OH C CH Vancomycin can beall and removed

HO HO OH O O O O assume each corner NH2 Cl OH O O is a carbon... HO Cl OH O O O H H H O N N N N N N H H H HN O O O O HO NH2 OH HO OH C CH Vancomycin can beall and removed

HO HO OH O O O NH2 O Cl OH O O HO Cl OH O O O H H H O N N N N N N H H H HN O O O O NH2 ...and it will always HO have four bonds. OH HO OH C CH Vancomycin can beall and removed

exampleone H H H C C CH C H H

exampleone remove H H H H C C C C C CH C C H H –H

exampleone H H H C C C C C CH C C H H –H –C now remove C

exampletwo HH C H C C C CH C H H

exampletwo H remove HH C H C C C C C C C C CH C H C –H H

exampletwo HH C H C C C C C C C C CH C H C –H –C H now remove C

examplethree H OH C HH C O H N H H

examplethree remove C–H BUT H O O leave all others!H C H C C HH C O C O H N H N H H H only remove CH

examplethree This is key. We can only remove C–H bonds. We must leave all others... H O OH C H C C HH C O C O H N H N H H H only remove CH

examplethree O H O O OHH C H C C H NH2H C O C O H N H N H CO2H H H NH2 only remove –C CH now remove C

example very im p ortantfourreverse CO2HHO NH2

examplefourreverse add C to corners CO2H C CO2HHO HO C +C NH2 NH2

examplefourreverse H H CO2H C CO2HHO HO C C CO2H HO C +C +H NH2 NH2 H NH2 Add H to make all C have four bonds

examplefour remember C hasreverse four; O has two bonds and H has one H H CO2H C CO2HHO HO C C CO2H HO C +C +H NH2 NH2 H NH2 H H O H H O H H O H C C C C H C C HHO C O HO C O HO C O H NH2 H NH2 H NH2

2examplefourreverse H H O H C C HO C O H NH2 neither of the O has OXYGEN two bonds

2examplefourreverse H H O C C H HO C O O still does not have two bonds. This structure is wrong H NH2 OXYGEN

4examplefourreverse H H O C C H HO C O CARBON H NH2 C still does not have four bonds. This structure is wrong

CHONC CO2Hexampleﬁvereverse

H CHO H C CHO C C H H C C CNC CO2H NC C C CO2H H H H add C to corners and H to make four bondsexampleﬁvereverse

H CHO H C CHO C C H H C C CNC CO2H NC C C CO2H now get three bonds H H H to N; two bonds to O and one to H H O H C C C C H H H C C C Oexample N C C C C Hﬁve H H H Oreverse

OH O OH OOHC OHC C C +C CO2H C C CO2H OH OH OH OH +H O H OH O H OH O C C C O OHC C CH C C C H C C CO2H HO H H OH O HO H H OHexamplesix

4what have....we learnt? o r ga n i c c h e m i s try is easy if we can count to...

4what have....we learnt? oh, and it’s really important! o r ga n i c c h e m i s try is easy if we can count to...

Acknowledgmentsgareth(Dr. GJ Rowlands) would to like thank Trevor Kitson Massey University & the 101 students www.massey.ac.nz/~gjrowlan

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Chemistry Living and Systems: 123.101 Lecture 1

by Gareth Rowlands on Jul 22, 2008

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Chemistry Living and Systems: 123.101 Lecture 1 — Presentation Transcript