Organic Chem II Lec 1 2

University of Science and Technology of Hanoi
Department of Fundamental and Applied Sciences
Dr. Nguyen Duc Anh

Department of Fundamental and Applied Sciences (FAS)
nguyen-duc.anh@usth.edu.vn
0904888819
September 2020
Something about me Concerned issue Objectives Methods Results and discussion Conclusion and perspectives
Something about me
Name: NGUYEN Duc Anh - PhD

Email: nguyen-duc.anh@usth.edu.vn
Mobile: 0904888819
Position: Lecturer and researcher
At USTH since: 2017/7
Department: Advanced Materials Science and Nanotechnology (until 7/2018)
Fundamental and Applied Sciences (since 8/2018)
Laboratory: NENS (NanoEngineering and NanoScience)
Teaching Subjects: Polymer Chemistry; Organic Chemistry; General Chemistry
Chemical bonding in organic Physical properties and
Something about me Introduction Organic functionalities Summary
chemistry molecular structures
Something about me
Research Works
+ Synthesis of Polymers Conducting polymers
- PEDOT
+ Biocompatible polymers - PANi Catalytic nanoparticles
- PPy - MoSx; MoS2
+ Polymer Composite
Super-adsorption polymer - Spinel transition metal oxides
+ Nanocomposite nanoparticles/conducting polymers - PDA complex
- BiVO4
+ Chemistry of catalysts
+ Functional polymers
Energy conversion and storage

- H2 evolution reaction
- Oxygen reduction and oxygen
evolution reaction
Environmental Treatment
- Superadsorbents
State of the art Introduction Organic functionalities Summary
Something about me
HER reaction 2H+ + 2e → H2
Conventional HER catalysts are rarely metals (Pt, Ru)
+ High and stable catalytic activity

- Rare and expensive
The demand of new

catalysts that cheaper
Something about me
Chemistry of catalysts
- Mechanism of synthesis ?
- Mechanism of catalytic activities?
HOW ???
Proposed mechanism for the synthesis of MoSx from [MoS4]2-
The formation of MoSx from [MoS4]2- go through several

steps:
- 2e S 1. Formation of S bridge with electrode: Oxidation 1e.
-2e -2e
-2e
2. Formation of 1st Mo3S12 by generation of 3 S-S
bridges: Oxidation 6e
-e
-e
3. Elimination of 1 S atom (S2- - 2e  S0): Oxidation 2e
-2e
- 2e -2e -e 4. Formation of S-S sharing with the 4th [MoS4]2-:
-2e -e
-2 e
-e
… Oxidation 2e sharing between 2 cluster Mo3S11
- 2e -e  Repeat from 2 to 4 for each cluster.
-e
-2e
-2 e
- 2e -2 e
-2e
In total: Formation of MoSx is a 10 electrons process
-2 e
S
Something about me
Dissolution in
water How to remain these
clusters?
Electrochemical
corrosion of MoSx
A novel hybrid catalyst for:

1. Enhancement of HER
catalytic activities
2. Enhancement of durability
of catalyst
Something about me
Hydrophilic hydrogel Amphiphilic copolymers
Blend of natural
and synthetics pH-responsive
polymers copolymers
Polydopamine modified Controlled release fertilizers

natural polymers Thermo-responsive
blend polymers
INTRODUCTION OF COURSE
Dr. Nguyen Duc Anh
0904888819
September 2019
Introduction
Chemists invent molecules.

Biologists apply molecules.
Physicists study molecules.
Engineers fabricate molecules.
Public enjoys molecules.
Introduction
What is organic chemistry?
It is a branch of chemistry that deals with the composition, uses

and properties of carbon compounds (organic compounds).
 Organic compounds are carbon compounds that are not carbonates,

diamond, graphite, oxides of carbon, sulfides
 Organic compounds contain mainly carbon and hydrogen with few
other elements like oxygen, halogens, nitrogen or sulfur…
Introduction
Why?
As a central science, chemistry especially

organic chemistry involve in all sides of
human life.
 More than 90% of well-known compounds
are organic.
Where can you find organic compounds?

Introduction
Why?
What do you imagine about the future of organic chemistry?
Problems?
- Can we unravel the puzzle of life’s origins?
- Can we ever beat photosynthesis?
- How do we make chemistry environmentally friendly?
- Can we design the perfect drug?
Challenges
- How to explore new frontiers at the interface of organic
chemistry and other science or technology fields?
Introduction
What is in organic chemistry ?
Functionalities Characterization
Organic
Structures Organic
Bonds Chemistry Skills
Chemistry I
II
Advanced
Reactions reactions
Introduction
How? Hours
Ref./
Class
Contents Assig.(s)
Lect.
Prc.
Exr.
Resources
Introduction of organic chemistry II course.
Tutorial of Addition and Electrophilic subsitutions
Organic Reactions 1 Remind of basic knowledges - Functionalities groups 3 Chap. 1, 2, 3
7 Carbonyland
Structure compounds - Aldehydes and ketones
physical properties 3 Chap. 16
Substitutions reactions Mechanisms
Oxidation – and intermediates
reductions species
reactions 3 Chap. 5
2
Stereochemistry of tetrahedral centers.
Addition reaction/Elimination Carbonyl
Tutorial of compounds - Carboxylic acid
Stereochemistry
Chap. 4
38 Alkanes
Acyl substitution reactions 33 Chap. 17
Chap. 10
Oxidation/Reduction Radical and Radical reactions
Enol and enolated reactions
Alkyl derivatives – alkyl halides / alcohols
Organometallic catalytic reactions Carbonyl compounds
3
Chap. 6
4 Nucleophilic substitution reactions Chap. 19 Reading
Condensation and Conjugate Addition Reactions
High selective reactions – Click Chemistry Elimination reactions
Tutorial of
Tutorials of SN
Carbonyl compounds
and E reactions Chap. 8
Rearrangement reactions 9
5 Aminesand Alkynes
Alkenes 33 Chap.920
Chap.
Diazonium
Addition salts
reactions
Additive “click” reactions Chap. Present. 2
6 Click Azide – alkynes reaction Chap.14
21
10 Aromatic compounds 33 Chap.15 +Present.
3 1
Organometallic compounds in organic reactions Ref. 4: Chap 28
Characterization Electrophilic substitution reactions
Pericyclic reactions Reading
IR; NMR and MS Conjugating unsaturated hydrocarbon system Chap. 13 Reading
Alcohol, ether, epoxy and thiols
Ref 2: Chap 10 Reading
Introduction
Topic of presentation
No. Topic Group
1 Additive “click” reaction: Thiol- Michael reaction Lan, Duc Anh,

(Thiol-enes; thiol-ynes reactions)
2 Click Azide – Alkyne reaction Tai, Huu Binh
3 Olefin metathesis reaction using Grubbs’ and Schrock’s Huy, Duc, The Binh
catalysts
1 hour including questions and answers; Provide and explain mechanisms; Catalysts (if any);
Reaction conditions; and applications
Introduction
Expectation?
+ Classification of the reactions of organic functionalities;
+ Explanation of the reaction mechanisms;
+ Identification and evaluation of factors affected to organic reactions
+ Proposal of synthetic route for an organic product
+ Use of characterization methods for organic chemistry

Introduction
Requirements Attendance/Attitude 10 %
+ Assignment for presentations:
Class exercise(s) – Homeworks 0%
- Work in team
Presentations/Midterm 30 %
- Will be use as midterm mark
Experimental Report(s) 0%
Final exam 60 %
Textbooks
T.W. G. Solomon, C. B.
Fryhle, S. A. Snyder,
Organic Chemistry
11th Edition,
Wiley, 2013
John McMurry, D. Klein Paula Y. Bruice
Organic Chemistry Organic Chemistry Organic Chemistry
9th Edition, 3rd Edition, 8th Edition,
Cengage Learning, Wiley, 2017 Pearson, 2016
2016
THE BASICS OF ORGANIC CHEMISTRY
Dr. Nguyen Duc Anh

0904888819
September 2019
Chemical bonding in organic chemistry
Atomic Structure
 Compounds
● made up of elements combined in different
proportions
 Elements
● made up of atoms
 Atoms
● positively charged nucleus containing protons
and neutrons
● with a surrounding cloud of negatively charged
electrons
 Each element is distinguished by its atomic number (Z)
 Atomic number = number of protons in nucleus
 Isotopes? Inner electrons ? Valence electrons ?

Chemical Bonds
 Ionic (or electrovalent) bonds are formed by the transfer of one or more
electrons from one atom to another to create ions
 Covalent bonds result when atoms of similar electronegativities share

electrons to achieve the configuration of a noble gas
 Metallic bonds: Freely move electrons sea bound metallic nuclear
 Octet Rule
● In forming compounds, they gain, lose, or share electrons to give a
stable electron configuration characterized by 8 valence electrons
● When the octet rule is satisfied for C, N, O and F, they have an
electron configuration analogous to the noble gas Ne
Exceptions to the Octet Rule

 Elements in the 2nd row in the periodic table usually obey the Octet Rule (Li, Be, B, C, N, O, F) since they have one
2s and three 2p orbitals available for bonding
 Elements in the 3rd row in the periodic table have d orbitals that can be used for bonding and may not obey the
Octet Rule
Lewis structure
A Lewis structure is a diagram that shows the covalent bonds and lone electron pairs in a molecule.
1. Lewis structures show the connections between atoms in a molecule or ion using
only the valence electrons of the atoms involved.
2. For main group elements, the number of valence electrons a neutral atom brings to
a Lewis structure is the same as its group number in the periodic table.
3. If the structure we are drawing is a negative ion (an anion), we add one electron for
each negative charge to the original count of valence electrons. if the structure is a
positive ion (a cation), we subtract one electron for each positive charge.
4. In drawing Lewis structures we try to give each atom the electron configuration of a
noble gas.
Formal charge
Formal charge (FC) is the charge assigned to an atom in a molecule, assuming that electrons in all chemical bonds are shared
equally between atoms, regardless of relative electronegativity.
 Calculation of formal charge

Formal charge number of valence electrons 1/2 number of
shared electrons – number of unshared electrons
F : the formal charge,
Z : group number of the element,
F = Z - S /2 - U S : the number of shared electrons
U: the number of unshared electrons
 Why use formal charge  How?

Formal charge can be used as criterion to select - Formal charge of zero is preferable
the most suitable Lewis structure of a compound. - Small formal charge is preferable
- Like charges on adjacent atoms are highly unlikely
- Negative charges reside on higher electronegativity element.
Resonance theory
.
A molecule or ion can be represented by two or more Lewis structures that differ only in the positions of the electrons
● None of these structures, which we call O O O

resonance structures or resonance
C C C
contributors, will be a realistic O O O O O O
representation for the molecule or ion.
None will be in complete accord with the (1) Benzene
physical or chemical properties of the
substance
● The actual molecule or ion will be better (2) Carboxylate ion (RCOO-)
represented by a hybrid (average) of these O O O
structures
R O R O R O
● The energy of the resonance hybrid is
lower than the energy of any contributing (3) Ozone (O3)
structure. Resonance stabilizes a O O
molecule or ion. O O O O
Quantum Mechanics & Atomic Structure
● Each wave function (ψ) corresponds to a different energy state

for an electron.
● Each energy state is a sublevel where one or two electrons can
reside.
● The energy associated with the state of an electron can be
calculated from the wave function.
● The relative probability of finding an electron in a given region of
space can be calculated from the wave function
● The solution to a wave function can be positive, negative, or zero.
● The phase sign of a wave equation indicates whether the solution
is positive or negative when calculated for a given point in space
relative to the nucleus.
Quantum Mechanics & Atomic Structure
● Wave functions, whether they are for sound waves, lake

waves, or the energy of an electron, have the possibility of
constructive interference and destructive interference
o Constructive interference occurs when wave functions
with the same phase sign interact. There is a
reinforcing effect and the amplitude of the wave
function increases
o Destructive interference occurs when wave functions
with opposite phase signs interact. There is a
subtractive effect and the amplitude of the wave
function goes to zero or changes sign

Atomic orbitals
● The square of a wave function (ψ2) for a particular x, y, z location
expresses the probability of finding an electron at that location in space.
● An orbital is a region of space where the probability of finding an
electron is high.
● Atomic orbitals are plots of ψ2 in three dimensions. These plots
generate the familiar s, p, and d orbital shapes
● The + and - signs of wave functions do not imply positive or negative
charge or greater or lesser probability of finding an electron.
Atomic orbitals Electron configuration
Aufbau principle ?
Pauli exclusion principle ?
Hund’s rule ?
Molecular Orbitals
 A bonding molecular orbital (ymolec) results when

two orbitals of the same phase overlap
● A molecular orbital (MO) represents the region of space where one or two
electrons of a molecule are likely to be found.
● An orbital (atomic or molecular) can contain a maximum of two spin-paired

electrons (Pauli exclusion principle).
● When atomic orbitals combine to form molecular orbitals, the number of

molecular orbitals that result always equals the number of atomic orbitals  An antibonding molecular orbital (y*molec) results when
that combine two orbitals of opposite phase overlap
Molecular Orbitals
Two electrons (with their spins opposed) occupy the bonding
molecular orbital, where their total energy is less than in the
separate atomic orbitals. This is the lowest electronic state or
ground state of the hydrogen molecule. An electron may
occupy the antibonding molecular orbital in what is called an
excited state for the molecule. This state forms when the
molecule in the ground state absorbs a photon of light having
the proper energy (ΔE).
Fluorescence probe for cells

and proteins characterization
Nobel Prize 2008
Orbitals Hybridization
Orbital hybridization is the concept of mixing atomic orbitals into new hybrid orbitals.
- Combination of the wave functions of n atomic

orbitals provides mathematical descriptions of n
hybrid atomic orbitals of equal energy.
- Hybrid orbitals are used in the explanation
of molecular geometry and atomic bonding
properties and are symmetrically disposed in
space
Orbitals Hybridization
Sigma (σ) bonds and pi (π) bonds
A sigma bond (σ bond) is a bond formed by the A pi bond (π bond) is a bond formed by the overlap of
overlap of orbitals in an end-to-end fashion, with the orbitals in a side-by-side fashion with the electron
electron density concentrated between the nuclei of density concentrated above and below the plane of the
the bonding atoms nuclei of the bonding atoms
•The extent of overlapping is high, it is a strong bond. •Since the extent of overlapping is low, it is a weak bond.
•High bonding energy •Low bonding energy
•The bond formation can occur between s-p, p-p, s-s, or any •The bond formation is possible only between two p orbitals.
hybrid orbitals. •Formation of pi bond occurs only in the presence of sigma bond.
•Ease of self-rotation •Only pi bonds cannot be formed.
•Prevention of self-rotation
Organic functionalities
Hydrocarbons
- The main type of energy on earth
- The resource of almost chemicals
- The resource of “Plastic Age”
Hydrocarbons
 Hydrocarbons are compounds that contain only carbon and hydrogen atoms
● Alkanes ● Alkynes
 hydrocarbons that do not have multiple bonds  contain at least one carbon–carbon triple bond
between carbon atoms e.g. H C C H
ethyne 1-pentyne
e.g.
pentane cyclohexane
2-pentyne
● Alkenes
● Aromatic compound
 contain at least one carbon–carbon double bond
 contain a special type of ring, the most common
example of which is a benzene ring
e.g.
CH3 COOH
propene cyclohexene
e.g.
benzene toluene benzoic acid

Functional groups
Functional groups are common and specific arrangements of atoms that impart predictable reactivity and properties to
a molecule.
Alkyl groups are groups that would be obtained

by removing a hydrogen atom from an alkane.
This group is used for naming compounds
R is used as a general symbol to represent any

alkyl group
Alkanes = R-H
Compounds of only single bonds: R-X

 Haloalkanes R–X (X = F, Cl, Br, I)  Alcohols R-OH
+ Alkyl halides are compounds in which a halogen atom + Alcohols are compounds in which a hydroxyl group replaces a
(fluorine, chlorine, bromine, or iodine) replaces a hydrogen hydrogen atom of an alkane.
atom of an alkane. + As with alkyl halides, alcohols are classified into three groups:
+ Alkyl halides are classified as being primary (1o), secondary (2o), primary (1o), secondary (2o), or tertiary (3o) alcohols. This
or tertiary (3o). This classification is based on the carbon atom classification is based on the degree of substitution of the
to which the halogen is directly attached. carbon to which the hydroxyl group is directly attached.
Compounds of only single bonds: R-X

 Ethers R-O-R  Amines R-NH2
+ Amines are the derivative of ammonia since hydrogen atoms are
replaced with alkynes groups.
+ Amines are classified as primary, secondary, or tertiary amines. This
classification is based on the number of organic groups that are
attached to the nitrogen atom
Ethers have been used for years in anesthesia

Compounds contain multiple bonds:
Carbonyl compounds
Aldehydes and ketones
Carbonyl compounds
Carboxylic acids and derivatives
O O O
R OH R OR R Cl
(carboxylic (ester) (acid
acid) chloride)
O O O
R NR2 R O R
(amide) (acid
anhydride)
Nitriles
A nitrile has the formula . The carbon and the nitrogen of a nitrile are sp hybridized.
2
2 1 1
3
H3C C N C N C N
Ethanenitrile Propenenitrile Benzenecarbonitrile

(acetonitrile) (acrylonitrile) (benzonitrile)
Summary of Organic Functionalities
Summary of Organic Functionalities
Bio-organic compounds
Main compounds found

in nature
Physical properties and molecular structures
Physical properties terms
Any property you can see, smell, touch, hear or

 The melting point of a solid is the temperature at which
otherwise detect and measure without performing
the vapor pressure of the solid phase equals the vapor
a chemical reaction
pressure of the liquid phase.
• Color  The boiling point of a liquid is the temperature at which

the vapor pressure of the liquid equals the pressure of the
• Shape
atmosphere above it
• Volume
• Density  Solubility is a property referring to the ability for a given
substance, the solute, to dissolve in a solvent
• Melting point
• Boiling point “like dissolves like” rule?
• Viscosity
• Solubility
Polar bonds / Polar molecules

 Covalent bonds result when atoms of similar electronegativities share electrons to achieve the configuration of a noble gas
+ If the same electronegativity, the electrons are  Electronegativity (EN)
shared equally between the atoms  non-polar ● The intrinsic ability of an atom to attract the shared
covalent bond electrons in a covalent bond
● Electronegativities are based on an arbitrary scale, with F
the most electronegative (EN = 4.0) and Cs the least (EN =
0.7)
+ If electronegativity diffrences exist between

two bonded atoms, the electrons are not shared
equally and generate a polar covalent bond
A dipole moment is a measurement of the separation of The overall dipole moment of a molecule is the sum of dipole
two opposite electrical charges moment vectors of individual bonds and lone electron pairs.
Net dipole moment Net dipole moment

(sum) is zero (sum) is non-zero
 non-polar molecule  polar molecule
Dipole moments are expressed in debyes (D),

where 1 D = 3.336  10–30 coulomb meter (C•m)
Explain the differences in physical properties of cis and trans isomers on table ?
Ionic compounds / Ion – ion forces

Compound Structure mp (oC) bp (oC)
(1 atm)
 In an ionic compound, the ion–ion forces that hold the ions
Ethane CH3CH3 -172 -88.2
together in the crystalline state are the strong electrostatic
lattice forces that act between the positive and negative Chloroethane CH3CH2Cl -138.7 13.1
ions in the orderly crystalline structure
Ethyl alcohol CH3CH2OH -114 78.5
 A large amount of thermal energy is required to break up
the orderly structure of the crystal into the disorderly open Acetaldehyde CH3CHO -121 20
structure of a liquid
Acetic acid CH3CO2H 16.6 118
 The boiling points of ionic compounds are higher still, so Sodium
CH3CO2Na 324 dec
high that most ionic organic compounds decompose before acetate
they boil
Intermolecular forces
 The forces that act between molecules are not as Hydrogen bonds
strong as those between ions Dipole-dipole attractions between hydrogen atoms bonded to
 These intermolecular forces are all electrical in small, strongly electronegative atoms (O, N, or F) and
nonbonding electron pairs on other such electronegative
nature
atoms
Dipole-dipole forces (Van der Waals)
Hydrogen bonds (bond dissociation energies of about 4 – 38 kJ
Most organic molecules are not fully ionic but have -1
mol ) are weaker than ordinary covalent bonds but much
insteada permanent dipole moment resulting from a stronger than the dipole–dipole interactions
nonuniform distribution of the bonding electrons
- Dipole – dipole attraction between molecules
The molecules orient themselves so that the positive end of one

molecule is directed toward the negative end of another
Intermolecular forces  The relative surface area of the molecules involved – The
Dispersion forces (London forces) molecular shape
Temporary dipole in one molecule can induce opposite
(attractive) dipoles in surrounding molecules. . These temporary The larger the surface area, the larger is the overall attraction
dipoles change constantly, but the net result of their existence is to between molecules caused by dispersion forces
produce attractive forces between nonpolar molecules
- - -
larger surface d-
Temporary dipole occur since electrons may slightly accumulated - d-d d d -
d -
area
-
d H HH d-
on one part of the molecule because of continuous moving d H H H H d  stronger H H
d- H H d- d- C C -
dispersion forces H H d
H H C H
H C C
+
 The relative polarizability of electrons of the atoms d+ +H H H H + d+ d d+
d d H H H
involved. By polarizability we mean how easily the d+ d+ + d+ d+ d+ d+
d +
d
electrons respond to a changing electric field
- - -
d d -
stronger weaker - d- d d d-
d H H H H d- -
d H HH d-
dispersion forces dispersion forces d- H H d- H
d- d+ + d- d+ + H
- - dF- d+ dF- d+ H H d- C C
H d
-
d d+ d d+ H
d-- I d d-- I d d+
smaller surface
d+ area C H
d- C d- C
+ + H H H
d d+
d d+
F F d F F d +H
d + d
H + + C C
d- I
C I d++ d- I C I d++ d d+ + d+ d+ d d+
- - F F d  weaker H H
d- I d d- I d d- d+ d- d+ H
d - d +
d - d +
dispersion forces d+ +
d+
d d+ d d+ d
Pentane (bp 36oC)
Neopentane
The larger atom, the easier polarizability (bp 9.5oC)
Summary of
interaction forces
ORGANIC REACTIONS - REACTION MECHANISMS
Dr. Nguyen Duc Anh

0904888819
September 2019
Mechanism – Term of
Acid-base reactions Organic reactions Radicals Carbocation – Carbanion Nucleophile - Electrophile
understanding
Acid-base reactions
Bronsted-Lowry acid-base reaction

Bronsted–Lowry acid–base reactions involve the transfer of protons
Base Conjugate Acid

A Bronsted–Lowry base is a substance (H+ acceptor) of H2O
that can accept (or remove) a proton
H O + H Cl H O H + Cl
A Bronsted–Lowry acid is a substance H H

that can donate (or lose) a proton
Acid Conjugate Base
(H+ donor) of HCl
understanding
Acid-base reactions
Lewis acid-base reaction

Lewis Base
(e pair donor)
Lewis Acids are electron pair acceptors

d- d+
Lewis Bases are electron pair donors Cl H + NH3 Cl + H NH3
Lewis Acid
(e pair acceptor)
In Lewis acid–base theory, the attraction of oppositely charged species is fundamental to reactivity
understanding
Acid-base reactions
Chapter 3: Acid and Bases
- Strength of acid and base ?

T.W. G. Solomon, C. B. - Factor affected to strength of acid and base?
Fryhle, S. A. Snyder, - How solvent affect to acidity?
Organic Chemistry -
11th Edition,
Wiley, 2016
understanding
Organic reactions
Organic reactions
• Organic reactions are chemical reactions involving
organic compounds. The basic organic chemistry
reaction types are addition reactions, elimination
reactions, substitution reactions, rearrangement
reactions and redox reactions.
• Main kinds of organic reactions

+ Substitution reactions
+ Addition reactions
+ Elimination reaction
+ Rearrangement reaction
+ Redox reactions
• Factors to consider:
+ Reactants and type of reactions
+ Kinetics
+ Thermodynamics
understanding
Organic reactions
How Organic Reactions Occur: Mechanisms
• In an organic reaction, the transformation has occurred.
• The mechanism describes the steps behind the changes that

we can observe
Nucleophilic substitution to aromatic ring

• Reactions occur in defined steps that lead from reactant to
product.
Steps ?
Intermediate species ? Radical ? Carbocation? Carbanion?
Nucleophile ? Electrophile?
How to use curved arrows?
Addition of HBr into ethylene

understanding
Mechanisms – Terms of understanding
Steps in Mechanisms
• We classify the types of steps in a sequence

• A step involves either the formation or breaking of a covalent bond
• Steps can occur individually or in combination with other steps
• When several steps occur at the same time, they are said to be concerted
• Bond formation or breakage can be symmetrical or unsymmetrical

• Symmetrical- homolytic
• Unsymmetrical- heterolytic
understanding
Organic reactions

Radicals – Radical reactions
A radical is an atom, molecule, or ion that has an unpaired valence electron. Radicals generated by the homolytic
breakage of a single bond under heat, light or catalysts.
Radicals
+ Highly chemically reactive, thus, almost radical has short
lifetimes and spontaneously dimerize.
+ Radical normally are electron deficient, they tend to pair up
with other electrons rich position.
+ A carbon radical is sp2 hybridation with one p orbital bearing
a single electron. Carbon radical is planar geometry .
+ A radical has neutral charge
understanding
Organic reactions

understanding
Organic reactions
Radical – The killers of DNA

Type of common radicals
+ Superoxide anion O22-

+ Hydroperoxide H2O2
+ Hydroxyl radical HO.
+ Alkoxyl radical RO.
+ Peroxyl radical ROO.
+ Nitroxide RNO.
+ Singlet oxygen O.
TEMPO ??
understanding
Organic reactions
Polar bond cleavage

Carbocation – Carbanion
Carbanion: A species contains negative charged carbon atom
Carbocation: A species contains positive charged carbon atom
Diamagnetic
understanding
Organic reactions
Factor affected to stability of intermediate species

Stability of intermediate species (carbocation, carbanion, radicals) depend on electronic effects of molecules as
well as surrounding environment
- The electron density on active carbon
- The steric hindrance of active carbon

understanding
Organic reactions
Electronic effects
Inductive effects Resonance effects

Resonance effect describes the polarity produced in a
•An inductive effect is an electronic effect due to the molecule by interaction between a lone pair electron and
polarisation of σ bonds within a molecule or ion. a pi bond or the interaction of two pi bonds in adjacent
•Inductive effcts are electronic effects transmitted through atoms.
bonds. The inductive effect of a group can be electron donating
or electron withdrawing. Inductive effects weaken as the
distance from the group increases.
understanding
Organic reactions
Polar solvent stabilize carbocation and carbanion

understanding
Organic reactions
Electrophile - Nucleophile
Electrophiles are reagents that seek electrons so as to achieve a A nucleophile is a Lewis base that seeks a positive center such as a
stable shell of electrons like that of a noble gas. positively charged carbon atom
All Lewis acids are electrophiles
Carbon atoms that are electron poor because of bond polarity, but
are not carbocations, can also be electrophiles.
understanding
Organic reactions
Reason?
understanding
Organic reactions
Which of the following is likely to be a nucleophile and which an electrophile?
Which of the following is expected to be the worst nucleophile?
NH3 H 2O BH3 ethylene (CH3)3P

?
Acid-base reactions Organic reactions Radical Reactions Carbocation – Carbanion Nucleophile - Electrophile
understanding
Organic reactions
Polar Reaction
• Polar reactions occur because of the electrical attraction between positively and negatively polarized centers on functional groups in
molecules; or an electrophile, an electron-poor species, combines with a nucleophile, an electron-rich species.
• Molecules can contain local unsymmetrical electron distributions due to differences in electronegativities.
• This causes a partial negative charge on an atom and a compensating partial positive charge on an adjacent atom
understanding
Organic reactions
Example of a Polar Reaction: Addition of HBr to Ethylene
 HBr adds to the π part of C-C double bond

 The π bond is e- rich, allowing it to function as a
nucleophile
 H-Br is electron deficient at the H since Br is
much more electronegative, making HBr an
electrophile
understanding
Organic reactions
Curved arrows
HO H NOT HO H
● show the direction of electron flow in a reaction mechanism

NOT
● point from the source of an electron pair to the atom receiving dO -
d-O
N N
the pair H H
H C H C
● always show the flow of electrons from a site of higher electron H d+ H d+
density to a site of lower electron density O
O
● never show the movement of atoms. Atoms are assumed to O
H3C O +H H
follow the flow of the electron H3C O H+ OH
● A half “head” arrow shows the movement of one electron; a full
“head” arrow shows the movement of an electron pair
understanding
Organic reactions
?
STEREOCHEMISTRY
Dr. Nguyen Duc Anh

0904888819
September 2019
understanding
Stereochemistry
 An object is achiral (not chiral) if the

object and its mirror image are identical,
or the object can superpose its mirror.
 A chiral object is one that cannot be

superposed on its mirror image. Chiral
objects is common in daily lifes.
Stereochemistry - Chiral centers – chiral Racemic forms –
R, S configuration Synthesis of stereoisomers Fischer projection
Stereoisomers molecules Enantiomeric excess
Stereochemistry
Isomerisms
 Isomers: different compounds that have the same molecular formula
Constitutional isomers: isomers that have the same Stereoisomers have their atoms connected in the same
molecular formula but different connectivity –their sequence but they differ in the arrangement of their atoms
atoms are connected in a different order in space. The consideration of such spatial aspects of
molecular structure is called stereochemistry
and
Butane 2-Methylpropane
Cl
Cl
and
1-Chloropropane 2-Chloropropane
O
OCH3
OH and
O
Butanoic acid Methyl propanoate
Stereochemistry
Stereoisomers
● Enantiomers – stereoisomers whose molecules are ● Diastereomers – stereoisomers whose molecules
nonsuperposable mirror images of each other are not mirror images of each other
Stereochemistry
Stereoisomers
e.g.
Ph
 Geometrical isomers Ph Ph and Ph
(cis & trans isomers) are:
(cis) (trans)
● Diastereomers ?
● Enantiomers ? Cl Cl Cl H
and
H H H Cl
(cis) (trans)
Stereochemistry
Summary of isomers
Stereochemistry
Enantiomers and chiral molecules

OH
(2-Butanol)
 Enantiomers occur only with compounds whose
molecules are chiral (I) and (II) are
nonsuperposable
 A chiral molecule is one that is NOT superposable on
H OH HO H mirror images of
its mirror image. each other
 A single chirality center causes a molecule to be chiral (I) (II)

 The relationship between a chiral molecule and its
mirror image is one that is enantiomeric. A chiral
molecule and its mirror image are said to be
enantiomers of each other
Stereochemistry
Chirality Center
+ A chirality center is a tetrahedral carbon atom that is

bonded to four different groups. Such a carbon atom is
called an asymmetric carbon or a chiral center and is
usually designated with an asterisk (*)
+ A molecule that contains one chirality center is chiral

and can exist as a pair of enantiomers.
+ The presence of a single chirality center in a molecule

guarantees that the molecule is chiral and that
enantiomeric forms are possible.
Stereochemistry
Stereogenic Center
Any atom at which an interchange of groups produces a stereoisomer is called a stereogenic center.
(If the atom is a carbon atom it is usually called a stereogenic carbon.)
H OH HO H
 Chirality centers are tetrahedral
stereogenic centers Me * Et Et * Me chiral
(A) (B) (A) & (B) are enantiomers
mirror
 Cis and trans alkene isomers contain Ph H H Ph

trigonal stereogenic centers achiral
H Ph Ph H
(C) (D)
(C) & (D) are identical
mirror
Stereochemistry
Chirality in biological system
HO
O O
NH NH
HO
N O
OMe
(+)-Limonene (-)-Limonene O Tretoquinol
(limonene enantiomer (limonene enantiomer OMe
Thalidomide
found in oranges) found in lemons) OMe
One enantiomer causes birth defects, One enantiomer is a bronchodilator, the
the other cures morning sickness other inhibits platelet aggregation
Most pharmaceuticals are chiral. Usually only one mirror-image form of a drug provides the desired effect.
66% of all drugs in development are chiral, 51% are being studied as a single enantiomer
Stereochemistry
Test for Chirality: Planes of Symmetry
 A molecule will not be chiral if it possesses a

plane of symmetry
 A plane of symmetry (mirror plane) is an
imaginary plane that bisects a molecule such
that the two halves of the molecule are mirror
images of each other
 All molecules with a plane of symmetry in their
most symmetric conformation are achiral
Stereochemistry
R, S system- RS configuration OH H OH HO H
(R) and (S) are from the Latin words rectus and sinister,
Recall:
(I) (II)
meaning right and left, respectively
How to Assign (R) and (S) Configurations O H

● Assign priorities to the four different groups on the stereocenter Step 2: C CH3
from highest to lowest. H3C C
H2
+ Higher atomic number  priority
(H, H, H) (C, H, H)
+ Higher order of Carbon connected with chiral center  priority
+ Double bond and triple bond are consider as 2nd and 3rd order
carbon, respectively
● Visualize the molecule
+ the lowest priority group is directed away from
you
+ trace a path from highest to lowest priority.
+ If the path is a clockwise motion, configuration
at the asymmetric carbon is (R).
+ If the path is a counter-clockwise motion, then
the configuration is (S)
Stereochemistry - Chiral centers – chiral Racemic forms – Synthesis of
Acid-base reactions R, S configuration Fischer projection
Stereoisomers molecules Enantiomeric excess stereoisomers
Stereochemistry
R, S system- RS configuration
Cl Cl Counter-
clockwise
H CH3 HO CH3 (S)
HO
Clockwise
OCH3 OCH3
(R)
H3C CH2CH3 Br CH2CH3

Br
Stereochemistry
Stereochemistry
Properties of enantiomers
H H
* *
Cl CH3 Cl
H3C
H3CH2C CH2CH3
mirror
. Are they different in term of properties ??

Stereochemistry
Pure enantiomers have identical melting and boiling points
Enantiomers show different

behavior only when they
interact with other chiral
substances, including their
own enantiomer
Stereochemistry
• Racemic compound: each enantiomer has a greater affinity

for molecules of the opposite type than for its own kind. The
crystal is thus composed of enantiomer pairs. These racemic
compounds have unique physical properties, including
melting points, solubility, density and solid state spectra,
different from that of either crystalline enantiomer.
• Racemic mixture: each enantiomer has a greater affinity for

molecules of its own kind than for those of the other
enantiomer  conglomerate crystal structure
• Solid solution: a rare racemate modification occurs when

there is little affinity difference between enantiomeric
molecules of like or opposite configuration, Here, the two
enantiomers may be randomly distributed in the crystal,
Stereochemistry
Properties of enantiomers: Optical properties

• When a beam of plane-polarized light passes
through an enantiomer, the plane of polarization
rotates.
• Separate enantiomers rotate the plane of plane-

polarized light equal amounts but in opposite
directions.
• Separate enantiomers are said to be optically active

compounds. Because of their effect on plane-
polarized light
https://www.youtube.com/watch?v=L3qNc8lUdMU
Stereochemistry

Polarimeter
Stereochemistry

Specific Rotation
The number of degrees that the plane of polarization is rotated

as the light passes through a solution of an enantiomer
depends on the number of chiral molecules that it encounters.
Specific rotation: Normalization of rotation angle with [a] = the specific rotation
concentration and length of sample a = the observed rotation
c = the concentration of the solution in grams
per milliliter of solution (or density in g mL-1 for
The specific rotation also depends on the temperature and the neat liquids)
wavelength of light. l = the length of the cell in decimeters (1 dm =
10 cm)
Polarimeter contains the D line of a sodium lamp (l = 589.6 nm); temperature of

25 oC; a sample containing 1.00 g mL-1 of the optically active substance, in a 1
dm tube, produced a rotation of 3.128 in a clockwise direction.*
Stereochemistry

Specific Rotation
• The direction of rotation of plane-polarized light is often

incorporated into the names of optically active
compounds
• No obvious correlation exists between the (R) and (S)

configurations of enantiomers and the direction [(+) or (-)]
in which they rotate plane-polarized light.
• No necessary correlation exists between the (R) and (S)
designation and the direction of rotation of plane-
polarized light.
Stereochemistry
Racemic forms – Enantiomeric excess (ee)

An equimolar mixture of two enantiomers is called a racemic A sample of an optically active substance that consists of a single
mixture (or racemate or racemic form). A racemic mixture enantiomer is said to be enantiomerically pure or to have an
causes no net rotation of plane polarized light enantiomeric excess of 100%
Enantiomeric excess (ee) (Also known as the optical purity)
mole of one moles of other

% enantiomeric enantiomer enantiomer
= x 100
excess total moles of both enantiomers
% enantiomeric observed specific rotation

= x 100
excess * specific rotation of the
pure enantiomers
Stereochemistry
Synthesis of chiral molecules
Reactions carried out with achiral reactants can often lead to

chiral products. In the absence of any chiral influence from a
catalyst, reagent, or solvent, the outcome of such a reaction is a
racemic mixture.
Ni
CH3CH2CCH3 + H H (+
-)-CH3CH2CHCH3
O OH
Butanone Hydrogen (+
- )-2-Butanol
(achiral (achiral (chiral
molecules) molecules) molecules; but
50:50 mixture
(R) & (S))
Stereochemistry
Stereoselective reactions
 Stereoselective reactions are reactions that lead to a preferential formation of one stereoisomer
over other stereoisomers that could possibly be formed
● enantioselective – if a reaction produces preferentially one enantiomer over its mirror
image
● diastereoselective – if a reaction leads preferentially to one diastereomer over others
that are possible
The lipase enzyme reacts selectively with one enantiomer to release the corresponding chiral
carboxylic acid and an alcohol, while the other ester enantiomer remains unchanged or reacts much
more slowly.
Stereochemistry
Molecules with more than one chiral center
In compounds whose stereoisomerism is due to chirality centers,

the total number of stereoisomers will not exceed 2n, where n is
equal to the number of chirality centers
- Assign R,S configuration for all of chiral centers of each molecule.

- Which of them are enantiomers? Diastereomers?
- Would you expect all of them have the same physical properties?
Stereochemistry
Meso compounds
A meso compound is an achiral molecule that contains chirality centers and has an internal plane of symmetry. Meso compounds
are not optically active
Which of the following (X, Y, or Z) is a meso compound?

Stereochemistry
Fischer projection formulas
COOH
COOH
Et Br
HO Ph Br Ph Fischer
Br Ph
Et OH
Projection
H3C COOH Et OH
CH3
CH3
The carbon chain in a Fischer From the vertical formula with the groups at
projection is always drawn from top to each carbon eclipsed we “project” all of the
bottom; only chiral center showed on bonds onto the paper, replacing all solid and
Fischer projection dashed wedges with ordinary lines
COOH COOH
H Me Me OH
COOH H H HO H HO H
Ph Me H Me H
H Ph COOH
OH Ph Ph
Stereochemistry
Erythro- and Threo-isomers

Erythro and Threo are used to distinguish between diastereomers containing only two chiral centers, which are adjacent
and bearing two pairs of common ligands.
In the Fischer projection:
Erythro isomers: ligands are on the same side of the bond linking the chiral centers
Threo isomers: ligands are on the opposite sides of the bond linking the chiral centers
Stereochemistry
Fischer projection formulas
Fischer projections are allowed to rotate them in the

plane of the paper by 180o, but by no other angle.
Fischer projections are not allowed to flip them over

Stereochemistry
Separation of enantiomers: Resolution
Enantiomers have identical solubilities in ordinary solvents, and they

have identical boiling points.
Distillation? Crystallization? – NO, because of racemic forms
Idea: When a racemic mixture reacts

with a single enantiomer of another
compound, a mixture of diastereomers
results, and diastereomers, because
they have different melting points,
boiling points, and solubilities, can be
separated by conventional means.
Stereochemistry
Chiral molecules that do not possess a chirality center
Compounds that have such large rotational barriers between conformers

Stereochemistry
Homeworks
5.33, 5.34, 5.35, 5.39, 5.40, Chap 4

5.43, 5.44, 5.45, 5.46, 5.48 79, 80, 83, 84, 85, 87, 89,
91, 92,

Organic Chem II Lec 1 2

Uploaded by

Document Information

Original Description:

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Organic Chem II Lec 1 2

Uploaded by

Copyright:

Available Formats

University of Science and Technology of Hanoi

Department of Fundamental and Applied Sciences

Dr. Nguyen Duc Anh

Name: NGUYEN Duc Anh - PhD

Energy conversion and storage

HER reaction 2H+ + 2e → H2

Conventional HER catalysts are rarely metals (Pt, Ru)

+ High and stable catalytic activity

The demand of new

Proposed mechanism for the synthesis of MoSx from [MoS4]2-

The formation of MoSx from [MoS4]2- go through several

A novel hybrid catalyst for:

Hydrophilic hydrogel Amphiphilic copolymers

Polydopamine modified Controlled release fertilizers

Chemists invent molecules.

What is organic chemistry?

It is a branch of chemistry that deals with the composition, uses

 Organic compounds are carbon compounds that are not carbonates,

As a central science, chemistry especially

Where can you find organic compounds?

What do you imagine about the future of organic chemistry?

What is in organic chemistry ?

No. Topic Group

1 Additive “click” reaction: Thiol- Michael reaction Lan, Duc Anh,

2 Click Azide – Alkyne reaction Tai, Huu Binh

+ Classification of the reactions of organic functionalities;

+ Explanation of the reaction mechanisms;

+ Identification and evaluation of factors affected to organic reactions

+ Proposal of synthetic route for an organic product

+ Use of characterization methods for organic chemistry

THE BASICS OF ORGANIC CHEMISTRY

Dr. Nguyen Duc Anh

Chemical bonding in organic chemistry

 Atomic number = number of protons in nucleus

 Isotopes? Inner electrons ? Valence electrons ?

Chemical bonding in organic chemistry

 Covalent bonds result when atoms of similar electronegativities share

 Metallic bonds: Freely move electrons sea bound metallic nuclear

Chemical bonding in organic chemistry

Exceptions to the Octet Rule

Chemical bonding in organic chemistry

Chemical bonding in organic chemistry

 Calculation of formal charge

 Why use formal charge  How?

Chemical bonding in organic chemistry

● None of these structures, which we call O O O

Chemical bonding in organic chemistry

Quantum Mechanics & Atomic Structure

● Each wave function (ψ) corresponds to a different energy state

Chemical bonding in organic chemistry

Quantum Mechanics & Atomic Structure

● Wave functions, whether they are for sound waves, lake

Chemical bonding in organic chemistry

Chemical bonding in organic chemistry

Atomic orbitals Electron configuration

Chemical bonding in organic chemistry

 A bonding molecular orbital (ymolec) results when

● An orbital (atomic or molecular) can contain a maximum of two spin-paired

● When atomic orbitals combine to form molecular orbitals, the number of

Chemical bonding in organic chemistry

Fluorescence probe for cells

Chemical bonding in organic chemistry

- Combination of the wave functions of n atomic