3D Structure and Bonding: Crash Course Organic Chemistry #4 - Free Educational videos for Students in K-12

3D Structure and Bonding: Crash Course Organic Chemistry #4 - By CrashCourse

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00:0-1	You can review content from Crash course Organic Chemistry with
00:02	the Crash course app available now for android and IOS
00:05	devices . Hi , I'm Debbie Chakravarty and welcome back
00:09	to Crash Course Organic Chemistry . Imagine for a second
00:12	that you've never seen a real life cat , not
00:14	even a picture or a single Youtube video . You've
00:18	only seen simple two D drawings of them , like
00:21	a stick figure drawn out by your cousin or a
00:23	misshapen fuzzy blob from those drawings . You get a
00:26	sense of an average cat , two ears , some
00:29	whiskers for legs and a tail , but without imagining
00:33	a three D . Cat , you wouldn't have a
00:35	great idea of how they fit into the world ,
00:37	including things like they're fluffy for chunky Belize or sharp
00:41	retractable claws . The organic molecules that make up cats
00:44	and everything living on earth aren't the flat , lifeless
00:48	structures . We've been drawing either from the simplest organic
00:50	molecule methane to the most complex proteins are . All
00:54	of these compounds can be plotted on a three D
00:57	, Cartesian coordinate system with X , Y and Z
00:59	axes . By understanding how molecules have three D shapes
01:03	. We can better understand how the structure of any
01:05	molecule affects what it can do . Some compounds fit
01:09	together like puzzle pieces and other combinations are like trying
01:12	to force a square peg into a round hole .
01:23	Yeah , if you're super rusty on vesper and no
01:29	worries . If you are or if you haven't heard
01:31	of hybridization or valence bond theory , you may want
01:34	to watch crash course General Chemistry episodes 24 25 .
01:39	Hank did a really good job explaining those ideas .
01:42	So I'm just going to do a quick refresher and
01:44	build from there . Since organic chemistry became a thing
01:47	, there have been lots of improvements to theories about
01:49	how atoms interact and form chemical bonds with each other
01:52	to make molecules , it's like the quote standing on
01:54	the shoulders of Giants . Each theory explains and observed
01:58	phenomenon that the previous theory couldn't quite nail down in
02:01	1916 . Lewis structures helped us think about how atoms
02:04	and electrons are arranged in a molecule . There are
02:07	powerful tool , which is why we still use them
02:09	today for simple two D drawings . These structures use
02:12	straight lines to represent covalin bonds and dots for an
02:16	bonded valence electrons , valence shell electron pair repulsion theory
02:20	, or vesper , was first proposed in 1957 and
02:23	started to explain the observed three D shapes of these
02:26	molecular structures . Vesper is the theory that the three
02:29	D shape of a molecule is determined by a central
02:32	atoms , lone pairs of electrons and the other atoms
02:36	X bonded to . There are five generally accepted vesper
02:39	electron pair geometries , which are the three D shapes
02:42	that take lone pairs of electrons and bonds into account
02:46	in organic chemistry , we use three of these five
02:48	geometries , linear tribunal planer and tetra hydro . On
02:52	the other hand , there are lots of molecular shapes
02:55	which describe how atoms in a molecule relate to each
02:58	other and pretend that lone pairs are invisible . For
03:01	example , we say that water has a bent molecular
03:04	shape in a water molecule . The central oxygen atom
03:07	has two lone pairs of electrons and two hydrogen is
03:10	bonded to it . The bond angles and the lone
03:13	pairs are important . They locked the molecule into its
03:16	three D shape . But when we call it Ben
03:19	, that only describes the atoms as scientists started to
03:22	widely accept vesper as a way to explain the molecular
03:25	shapes that they saw experimentally . Quantum theory became a
03:29	thing . And so did the idea of orbital's places
03:32	where we're most likely to find electrons around atoms .
03:35	There are four distinct atomic orbital names and shapes .
03:38	S . P . D and F . Because of
03:40	how orbital's are positioned . Even orbital's couldn't completely explain
03:45	the three D shapes predicted by vesper and observed experimentally
03:49	. Something was still missing . That something was an
03:51	idea called orbital hybridization . Basically you can mix one
03:56	s orbital with its spherical shape and one P orbital
03:59	with its three D . Figure eight shape to make
04:02	two hybrid atomic orbital's that sort of look like both
04:06	kind of like mixing a donkey and horse to get
04:08	a mule . It's important to pay attention to the
04:10	number of atomic orbital's we mix because that's how many
04:14	hybrid orbital's are produced . In other words , if
04:17	we mix one s orbital and one p orbital we
04:20	get to sp orbital's . If we mix one s
04:23	orbital and two p orbital's we get three sp two
04:27	orbital's . And if we mix one S orbital and
04:30	three P orbital's we get four sp three orbital's orbital
04:34	hybridization helps explain the three D geometry is predicted by
04:37	vesper . For example . Let's look at the tetra
04:40	usual shape of a methane molecule . Carbon atom has
04:43	four valence electrons . Which all need to be unfair
04:46	to bond to make sure they're all impaired . It
04:49	makes four sp three hybrid orbital's and we can just
04:52	imagine sticking one electron in each . Each hydrogen atom
04:55	has a one S orbital with one UNP aired electron
04:59	. So when these five atoms unite to form methane
05:02	, each hydrogen is one s orbital overlaps with the
05:05	carbons . Sp three hybrid orbital's to form chemical bonds
05:08	called sigma bonds . Signal bonds are sort of like
05:11	a handshake made by the direct overlap of two orbital's
05:15	that point at each other . This idea of overlapping
05:17	orbital's is the foundation of valence bond theory . These
05:20	bonds give methane a tetra hydro molecular shape . So
05:24	it's basically the same as these four balloons tied together
05:27	at the base . These aren't Hanks balloons from seven
05:29	years ago , but they're just as good at showing
05:31	the shape and the science behind it . Now ,
05:34	methane is a relatively simple way to think about orbital
05:37	hybridization and valence bond theory . But we can use
05:40	these same ideas to explain the three D shapes of
05:42	molecules with double and triple bonds to for double bonds
05:46	. Let's look at the if you've been paying attention
05:48	to all this nomenclature , we've been doing that's C
05:51	two H four . The carbon atoms are double bonded
05:54	to each other . Here's the LewiS structure which shows
05:56	that each carbon has three things connected to it .
05:59	So each carbon needs to hybridize three atomic orbital's to
06:03	make three sp two hybrid orbital's two SB two orbital's
06:07	overlap with two hydrogen one s orbital's and one sp
06:11	two orbital overlaps with one of the other carbons .
06:14	Sp two orbital's that makes three sigma bonds . Because
06:18	each carbon made three SB two hybrid orbital's , each
06:21	carbon still has one p orbital left . The leftover
06:24	p orbital's on the two carbons are close enough to
06:26	say , hey , what's up ? If we share
06:29	our electrons we can make a bond to this is
06:32	called a pie von where the orbital's line up next
06:35	to each other in sort of overlap sideways . More
06:38	valence bond theory . Every double bond will be in
06:40	the series has a sigma bond with orbital's that overlap
06:43	end to end and a pi bond with orbital's that
06:46	overlap sideways . This leads to the three D molecular
06:49	geometry of ethylene . Attritional planer arrangement around each of
06:52	the carbon atoms . Now for triple bonds , let's
06:55	take a look at death in So we're all on
06:57	the same page with names . This one C two
06:59	H two with the carbon atoms triple bonded to each
07:02	other . In this lewis structure we can see that
07:04	each carbon has two things connected to it , one
07:06	hydrogen and the other carbon . That's how we know
07:09	. They'll combine two atomic orbital's to make two sp
07:12	hybrid orbital's . Each carbon has to pee orbital's left
07:16	which all lean over and share their electrons in two
07:19	pi bonds . So the triple bonds that will meet
07:21	in this course will always have one sigma bond and
07:24	two pi bonds . This makes the three D .
07:26	Molecular geometry linear around the carbon atoms . When we
07:29	draw all kinds the groups they're bonded to should always
07:32	be in a straight line at 180 degree angles .
07:35	So like this not this now . Organic chemistry is
07:39	all about carbon . So we've been focusing on orbital
07:42	hybridization and valence bond theory in carbon containing compounds ,
07:46	but other elements have their own electron pair geometries and
07:49	hybrid orbital's going on to . For example , oxygen
07:53	and a water molecule is kind of similar to methane
07:56	. In water , the central oxygen atom is sp
07:58	three hybridized , it has sigma bonds with two hydrogen
08:01	atoms and has two lone pairs hanging out . This
08:04	gives water a tetra federal electron pair geometry and a
08:08	bent molecular shape . Remember oxygen is often sp three
08:12	hybridized informed single bonds in organic compounds like alcohols and
08:16	ethers too . But it can also be sp two
08:19	hybridized and form double bonds as a carbon Neil group
08:23	, which we see an alga hides ketones in carb
08:25	oxalic acids . In fact , carbon he'll groups in
08:28	valence bond theory were super important to figuring out the
08:31	structure of a little molecule known as D . N
08:33	. A . You know , just the thing that
08:35	holds our genetic information and provides the blueprints for ourselves
08:38	to grow and stay alive . To see how let's
08:41	go to the thought bubble . Our story begins in
08:44	18 69 . When Swiss physiological chemist Friedrich Mischer isolated
08:49	a novel substance from the nucleus of a cell .
08:52	In 1919 . Russian biochemist fetus Levin was able to
08:56	prove that D . N . A . Had three
08:57	main pieces , five carbon sugars , phosphate groups and
09:01	organic ring compounds called nitrogenous bases . By 1944 we
09:06	knew that our genetic information was held in DNA molecules
09:09	and Austrian biochemist Irwin Charge off found a relationship in
09:13	the ratios of the nitrogenous bases A . T .
09:16	G . And C . But researchers struggled to figure
09:18	out the three D . Shape of D . N
09:19	. A . They worked with the idea that nitrogenous
09:22	bases needed to be in the center of a double
09:24	helix and bond with each other . Any bond that
09:26	formed between the basis had to be strong enough to
09:29	hold the double helix together , but weak enough that
09:32	the helix could open up for things like reading the
09:34	genetic code or copying DNA strands . Some scientists presented
09:38	evidence that the bonds between bases were hydrogen bonds ,
09:41	A relatively weak inter molecular force . Other scientists ,
09:45	like Rosalind franklin , made three D representations that suggested
09:49	the same . But there was a problem at that
09:51	time . The agreed upon structure for nitrogenous bases meant
09:55	some oxygen and nitrogen atoms wouldn't have the correct orbital
09:58	hybridization and geometry to form hydrogen bonds . American crystallography
10:03	. For jerry Donohue eventually suggested that the text books
10:06	were wrong and proposed a different structure , an oxygen
10:09	atom that was sp two hybridized instead of an alcohol
10:13	group . It was a carbon Neil group . With
10:15	this key structural change . DNS nitrogenous bases could hydrogen
10:19	bond to each other After this , the now famous
10:22	1953 report on the structure of DNA was published helping
10:25	change the way we thought about genetics . Talk about
10:28	standing on the shoulders of giants . Thanks , thought
10:30	bubble . So it's pretty clear that the bonds of
10:32	a molecule affected structure . We use the word is
10:35	immersed to describe molecules that have the same molecular formula
10:39	, but different arrangements of atoms . To help remember
10:41	this , the word is summer comes from the greek
10:44	root , IsIS meaning same from general chemistry . We
10:48	have words like isotope meaning same number of protons or
10:51	isil electronic meaning same number of electrons . Then we
10:54	had the greek root more meaning part . It shows
10:58	up in words like polymer meaning many parts and monomer
11:01	meaning a single part . So the term is summer
11:04	means the same parts and two major kinds of customers
11:07	in organic chemistry are Constitutionalist summers , which are more
11:10	common and geometric I Summers . Constitutionalist Summers also called
11:15	structuralist summers are where two molecules have the same number
11:18	and types of atoms as each other , but the
11:20	connections between the atoms can be super different . Like
11:23	we just saw what the oxygen atom indiana . Let's
11:26	use a more straightforward example though . In the first
11:29	episode of this series , we mentioned octane and iso
11:32	octane , two components of gasoline . Their Constitutional I
11:36	summers because they both have eight carbons and 18 hydrogen
11:39	. In fact , that's how iso octane got its
11:42	name . Past chemists just stuck on the prefix I
11:44	so to mean same as octane , but their structures
11:47	are pretty different and octane the carbons are attached in
11:51	a long chain without any branches . So it checks
11:54	out as an aipac systematic name . Iso octane is
11:57	branch though . And if we're going by I you
12:00	pack rules . It isn't octane at all . It
12:02	has three carbon chain . Substitue ints . And we
12:05	rule followers would call it 2 to 4 tri metal
12:08	painting . On the other hand , geometric I summers
12:11	have the same number in types of atoms and the
12:13	same connections between them . But these compounds differ in
12:16	how the bonds are spatially arranged . To sort of
12:19	visualize this , I can put the tips of my
12:21	index fingers together and rotate one hand as far as
12:24	I can see . I can twist one hand about
12:27	180 degrees without breaking contact . And if my fingers
12:31	were a single bond and my hand atoms weren't held
12:34	back by my arms , I could rotate it a
12:37	full 360 degrees . This is known as free rotation
12:40	when Adams can completely rotate around the axis of a
12:43	bond , the carbons on an ethane molecule can do
12:46	this . So ethane doesn't have any geometric is immersed
12:50	. However , if I touch to fingertips from each
12:52	hand , I can't rotate one hand without breaking a
12:56	connection . So a double bond between atoms doesn't have
12:59	free rotation . And molecules with double bonds can how
13:03	geometric I summers that are spatially different . Take ,
13:05	for example , the simple alkaline pen . To in
13:08	in one geometric I simmer the ethyl group and the
13:11	metal group are on the same side of the double
13:13	bond , which we use the prefix cyst to describe
13:16	. But in the other , these groups are opposite
13:18	each other , which we use the prefix trans to
13:21	describe . For more complex Calkins . And to stick
13:23	with our trusty aipac rules . We use the prefixes
13:26	, E and Z . But don't worry about that
13:29	for now . We'll learn about NZ nomenclature in another
13:31	episode . All this to say electron orbital's and atomic
13:34	bonds determine the shape of molecules which determines what they
13:38	can do , which determines basically every chemical reaction that
13:41	keeps us in our universe going even though it can
13:44	be a little brain bendy to imagine tiny molecules in
13:47	three D . Like you would a fluffy cat without
13:50	them . We wouldn't exist to pet cats or watch
13:53	youtube videos or take organic chemistry tests . In this
13:57	episode , we learned that orbital hybridization and valence bond
14:00	theory can help us explain three D . Molecular structures
14:03	. Constitutional listeners have the same atoms but different atom
14:07	to atom connections and geometric customers have different spatial arrangements
14:12	. Next time we'll learn some techniques to understand customers
14:15	and adam connections even better . Thanks for watching this
14:17	episode of Crash Course Organic Chemistry . If you want
14:20	to help keep all crash Course free for everybody forever
14:24	, you can join our community on Patreon . Yeah
00:0-1	.

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