Principles of Biochemistry 1 |Chiral, Orbital| Class Notes |HarvardX

Unit 1, introduction

Course in Edx

Why so much carbon is needed for organism

• It is facility for organism use one molecule for versatility of functions.
• Carbon can build different shape and geometry of molecules:
  • linear chain
  • branched chain
  • cyclical structure
• Structure diversity leads to functional diversity.

Carbon’s versatility

hybrid orbital

© courses.lumenlearning.com 3 barbell shape orbital of carbon: 2px, 2py, 2pz
There are 2 shells for Carbon. 1s and 2s. In 2s, there is an inner subshell, 2s/2ns, 3 orbital in outer subshell, 2px, 2py, and 2pz

More for Carbon electron orbital: Chemical Assignment

© chemistry-assignment.com

1. Ground state:
   6C: $1s2\ |\ 2s2\ |\ 2px1\ |\ 2py1\ |\ 2pz0$
2. $sp^3$-Hybridization:
   6C: $1s2\ |\ 2s1\ |\ 2px1\ |\ 2py1\ |\ 2pz1$; ($2pz1$ from $2s$)
3. $sp^2$ Hybridization:
   6C: $1s2\ |\ sp^23\ |\ 2px0\ |\ 2py0\ |\ 2pz1$; ($sp^23$ comes from $2s1\ |\ 2px1\ |\ 2py1$)
4. $sp$-Hybridization:
   6C: $1s2\ |\ sp2\ |\ 2px0\ |\ 2py1\ |\ 2pz1$

Ground state

In Ground state, there are two electrons unpaired orbiting in 2p and leaving the 3sd unoccupied orbital 2pz. And this how Covalent Bond formed: one orbital for each atom carrying an unpaired electron.
Hence that, carbon can only from two covalent bonds.

Exited state

The electron in carbon can shift around and so, one electron from 2s promoted into 2spz orbital, to form 4 unpaired electrons.

sp³-Hybridization: Mathane (CH₄)

$sp^23 = 2s1+2px1+2py1$

4 unpaired electrons are unstable since the orbitals are not identity. So, they have to went through a process name as hybridization to form $sp^3$ orbital. The newly formed $sp^3$ orbital has 25% s character and 75% of p character. For forming a methane, they apart from each other as they can and forming four identical $190.5^{\circ}$ from each other. Which is a tetrahedron.

© chemistry-assignment.com

sp²-Hybridization: ethylene (C₂H₄)

$sp^2 3= 2s 1 + 2p 2 $

© chemistry-assignment.com

• $sp^2$ has 33% s character and 67% p character and arranged in Trigonal Planar structure. $120^{\circ}$ apart from each other.
• The remaining $2pz$ orbital (Unhybridised 2p-orbital illustrate in the image above.) is orthogonal to the plane containing the $sp2$ orbitals.

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© chemistry-assignment.com	To Make a ethylene, 2 $sp^2$ orbit fuse head to head form a $\sigma$ covalent. The sideways overlap of the $2pz$ orbits, lead to the formation of new covalent boned called $\pi$ bond between two carbons. Remainning $4*sp2$ orbitals covalent with $H^+$ to form 4 carbon hydrogen bonds. The electrons involved in $\pi$ bond occupy a ring shape space circulate the $\sigma$ bond.

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$\sigma$: sigma

sp-Hybridization: acetylene (C₂H₂)

$sp2 = 2s+ 2px$

© chemistry-assignment.com

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© chemistry-assignment.com	$sp$ orbital are $180^{\circ}$ from each other Other two unpaired electrons are remain on $2py;\ 2pz$ obirtals. Two $sp$ orbital come head to head to form a $\sigma$ covalent bond. Sideways overlap between paires of 2p orbitals on each carbon lead the formation of 2 $\pi$ bonds between carbons. Remainning $sp$ orbitals fuse with hydrogen to form 2 carbon hydrogen covalent bonds.

The geometry and reactivity of the bonds

Bond	Length ($A$)	Bond strength ($kcal/mol$)	$\Delta EN$
$C-H$	1.09	99	0.4
$O-H$	0.96	110	1.4
$N-H$	1.02	84	0.9
$C=O$	1.23	174	1
$C-C$	1.54	88	0
$C=C$	1.34	147	0

Shape: $O-H$ is shorter than $C-C$;
Strength: $C-C$ stronger than $C=C$;
Electronegativity: One electron has a stronger pull on the electrons.

Configuration Isomers

Single bond: enantiomer

Molecule containing a chiral center could exist in different configurations.

Double bond

Maleix acid	Fumaric acid
Cis-configuration	Trans-configuration

As you can see the structure of Maleix acid and Fumaric acid above, they have the same composition but a different structure since the double bond blocked the free rotation of the $C-C$ axis. So, they have the different =configuration=, or =stereoisomers=.

Significant

Same composition with different configuration leads to functional diversity.

exp:
$( R)-Carvone$ and $(S)-Carvone$ bind different neural receptors in your nose.
As a result, $( R)-Carvone$ leads to a fresh spearmint smell, but $(S)-Carvone$ leads to a pungent caraway smell.

$R-Carvone$	$S-Carvone$

Structure Dynamic

Two covalent bonds prohibited rotation. Though single covalent bond made rotation possible and it has infinite number of configurations in theory, majority of them are prefer to stay in a stable structure (low free energy state).

Caffeine from PubChem:

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More reading materials about chiral:
libretexts: 5.1: Chiral Molecules

3D models are embedded from molview.org