Computational Chemistry
Lecture 2
Essential Concepts in
Chemistry
1 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Coordinates
Cartesian coordinates Spherical coordinates
https://wikimedia.org https://wikimedia.org
Distance between two points?
Angle between three points (two lines)?
Dihedral angle between two planes?
2 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Coordinates
Internal coordinate - Geometric parameters
One point → Coordinates
Two points → Distance (D)
Three points (or two lines) → Angle (A)
Four points → Dihedral angle (D)
(4)
(2) (3)
D(1,2,3,4)
A(1,2,3)
(1)
(x1, y1, z1)
3 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Coordinates
Internal coordinate - Geometric parameters
H2O
4 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Coordinates
Redundant Internal coordinate
5 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Degrees of freedom
z
Types of motion
• Translation: Translation degrees of freedom?
• Rotation: Rotation degree of freedom?
• Vibration (number of particles N > 1) O
x
– Example of H2 molecule y
• vibrational degrees of freedom?
• Energy?
Examples:
• Atom
• Molecules: CO and H2O
6 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Chemical formulae (Organic compounds)
7 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Chemical formulae (Organic compounds)
Projection formula
• A wedge-and-dashed projection
• Newman projection
• Fischer projection
• Haworth projection
Lactic acid
8 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Isomers
Classification
• different • same connectivity,
connectivity • different arrangement in space
Nonsuperposable
Nonsuperposable & mirror images non-mirror images
9 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Stereoisomers
Isomers with the same molecular formula and same
connectivity of atoms but different arrangement of
atoms in space
Handedness (≡ chirality)
Our hands are not identical but mirror images
They are non-superimposable → chiral (vs. achiral)
10 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Optical isomers: Optical Activity
Polarimeter
α = 0 → optically inactive
α ≠ 0 → optically active
11 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Optical isomers: Optical Activity
Observed rotation:the number of degrees, α, through which a compound
rotates the plane of polarized light
dextrorotatory (+): refers to a compound that rotates the plane of
polarized light to the right
levorotatory (-): refers to a compound that rotates of the plane of
polarized light to the left
specific rotation:observed rotation when a pure sample is placed in a
tube 1.0 dm in length and concentration in g/mL (density); for a
solution, concentration is expressed in g/ 100 mL
12 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Optical isomers: Optical Activity
Racemic mixture: an equimolar mixture of two enantiomers
A racemic mixture contains equal numbers of
dextrorotatory and levorotatory molecules → its specific
rotation is zero
Resolution: the separation of a racemic mixture into its
enantiomers
13 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Optical isomers - Enantiomers
Superimposable?
14 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Optical isomers - Enantiomers
15 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Optical isomers – Enantiomers: chemical properties
A pair of enantiomers:
shares the same physical/chemical properties
The properties become different when they are interacting
with different chiral substances.
Pharmaceutical:
many of the molecules produced by organisms exhibit a specific
handedness
chemists must be concerned about which enantiomer is the active
one - the one that fits the intended receptor
16 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Enantiomer - Chiral/Stereogenic Center
Chiral center
17 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Enantiomer - Chiral/Stereogenic Center
18 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Enantiomer - Chiral/Stereo/Stereogenic Center
With one chiral center, a molecule will always be chiral.
With two or more chiral centers, a molecule may or may not be chiral
Ex: meso compound which contains a plane of symmetry or a mirror plane
Not optically active
Superposable on its mirror image
Has a plane of symmetry
Not Enantiomers:
Superimposable and has an Internal Mirror Plane
19 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Enantiomer
20 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Enantiomer
21 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Enantiomer – number of isomers?
Maximum number = 2n
n is the number of Chiral/Stereogenic Center
22 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Enantiomer – number of isomers?
23 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Enantiomer – Nomenclature (naming)
Cahn-Ingold-Prelog System
Counter-clockwise Clockwise
Rule 1
A substituent with a higher atomic number takes precedence over a substituent with
a lower atomic number.
1. When dealing with isotopes, the atom with the higher atomic mass receives
higher priority.
2. When visualizing the molecule, the lowest priority substituent should always point
away from the viewer
3. Draw an arrow from the highest priority atom to the 2nd highest priority atom to
the 3rd highest priority atom
24 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Enantiomer – Nomenclature (naming)
Cahn-Ingold-Prelog System:
Counter-clockwise Clockwise
Rule 2
If there are two substituents with equal rank, proceed along the two substituent
chains until there is a point of difference.
First, determine which of the chains has the first connection to an atom with the
highest priority (the highest atomic number). That chain has the higher priority.
If the chains are similar, proceed down the chain, until a point of difference.
25 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Enantiomer – Nomenclature (naming)
Cahn-Ingold-Prelog System:
Counter-clockwise Clockwise
Rule 3
If a chain is connected to the same kind of atom twice or three times, check to see if
the atom it is connected to has a greater atomic number than any of the atoms that
the competing chain is connected to.
If none of the atoms connected to the competing chain(s) at the same point has a
greater atomic number: the chain bonded to the same atom multiple times has the
greater priority
If however, one of the atoms connected to the competing chain has a higher atomic
number: that chain has the higher priority.
26 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Enantiomer – Nomenclature (naming)
Cahn-Ingold-Prelog System: R or S
27 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Optical Isomers - Diastereomers
Different?
Diastereomers are stereoisomers that are not enantiomers
Q: Can diastereomers be separated?
28 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Properties: Enantiomers vs. Diastereomers
• Enantiomers have identical physical and chemical properties in
achiral environments
• Diastereomers are different compounds and have different
physical and chemical properties
29 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Test – Please name the following structure?
H
HO
2 CO2H
3
H 3C
H OH
30 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
Test – Please name the following structures & their relationships?
???
name?
name?
???
???
???
???
name? name?
31 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
The End
32 / Computational Chemistry | Lecture 02 | Semester 2: 2021-2022
