Chapter 1 The Basics

CCB1013 Organic Chemistry
By Dr. Oh Pei Ching
Chapter 1: The Basics Bonding & Molecular Structure
The Basics
The Basics
By the end of this weeks lecture, you should be able to apply: Octet rule & Lewis structures Formal charge Resonance Dash and condensed structural formulas Constitutional isomers Wedge-dashed, wedge-line and bond-line formulas Orbital hybridization Typical bond angles and molecular geometry
3
Introduction
The name Organic Chemistry came from the word organism. Organic Chemistry is the study of carbon compounds. Carbon, atomic number 6, is a second-row element. Although carbon is the principal element in organic compounds, most also contain hydrogen, and many contain nitrogen, oxygen, phosphorus, sulfur, chlorine, or other elements.
(found in various citrus fruits)
Introduction
Most of the compounds found in nature - those we rely on for food, medicine, clothing (cotton, wool, silk), and energy (natural gas, petroleum) are organic as well.
Introduction
Important organic compounds are not, however, limited to the ones we find in nature. Chemists have learned to synthesize millions of organic compounds never found in nature, including synthetic fabrics, plastics, synthetic rubber, medicines, and even things like photographic film & Super glue.
Atomic Structure
Compounds made up of elements combined in different proportions Elements made up of atoms
Electron cloud
Atoms positively charged nucleus containing protons and neutrons with a surrounding cloud of negatively charged electrons
Nucleus
Each element is distinguished by its atomic number (Z) Atomic number = number of protons in nucleus
Isotopes
Although all the nuclei of all atoms of the same element will have the same number of protons, some atoms of the same element may have different masses because they have different numbers of neutrons. Such atoms are called isotopes. Example: (1)
12C 13C 14C
(6 protons 6 neutrons)
2H
3H
(2)
1H
Hydrogen (1 protons 0 neutrons)
Deuterium (1 protons 1 neutrons)
Tritium (1 protons 2 neutrons)

Review Problem 1.19
Valence Electrons
Electrons that surround the nucleus exist in shells of increasing energy and at increasing distances from the nucleus. The most important shell, called the valence shell, is the outermost shell because the electrons of this shell are the ones that an atom uses in making chemical bonds with other atoms to form compounds. The number of electrons in the valence shell (called valence electrons) is equal to the group number of the atom. Example: (1) Carbon is in group IVA Carbon has 4 valence electrons (2) Nitrogen is in group VA Nitrogen has 5 valence electrons (3) Halogens are in group VIIA F, Cl, Br, I all have 7 valence electrons
Review Problem 1.2 10
Structural Theory
Atoms in organic compounds form a fixed number of bonds using their valence electrons.
Carbon atom can form one or more bonds to other carbon atoms.
11
Isomers
Isomers are different molecules with the same molecular formula. Many types of isomers exist. Constitutional isomers are different compounds with the same molecular formula but differ in their connectivity. Usually have different physical and chemical properties. Example:
#
Consider two compounds with molecular formula C2H6O.
Dimethyl ether
Ethanol
Ethanol is the alcohol of alcoholic beverages
These compounds cannot be distinguished based on molecular formula; however they have different structures. # The two compounds differ in the connectivity of their atoms.
#
12
Chemical Bonds: The Octet Rule

Atoms form bonds to produce the electron configuration of a noble gas (because the electronic configuration of noble gases is particularly stable). For most atoms of interest this means achieving a valence shell configuration of 8 electrons corresponding to that of the nearest noble gas. Atoms close to helium achieve a valence shell configuration of 2 electrons. Atoms can form either ionic or covalent bonds to satisfy the octet rule. Ionic bonds are formed by the transfer of one or more electrons from one atom to another to create ions. Covalent bonds result when atoms share electrons.
13
Ionic Bonds
When ionic bonds are formed, atoms gain or lose electrons to achieve the electronic configuration of the nearest noble gas.
# In the process the atoms become ionic.
The resulting oppositely charged ions attract and form ionic bonds.
# Lithium loses an electron (to have the configuration of helium) and
becomes positively charged. # Fluoride gains an electron (to have the configuration of neon) and becomes negatively charge. # The positively charged lithium and the negatively charged fluoride form a strong ionic bond.
Ionic compounds form only when atoms of very different electronegativities transfer electrons to become ions
14
Electronegativity
Electronegativity is the ability of an atom to attract electrons. It increases from left to right and from bottom to top in the periodic table (noble gases excluded).
# Fluorine is the most electronegative atom and can stabilize
excess electron density the best.
15
Covalent Bonds
Covalent bonds occur between atoms of similar electronegativity (close to each other in the periodic table). Atoms achieve octets by sharing of valence electrons. Molecules result from this covalent bonding. Valence electrons can be indicated by dots (electron-dot formula or Lewis structures) but this is time-consuming. The usual way to indicate the two electrons in a bond is to use a line (one line = two electrons)
16
How to Write Lewis Structures

Lewis structures show the connections between atoms in a molecule or ion using only the valence electrons of the atoms involved. 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. 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. In drawing Lewis structures we try to give each atom the electron configuration of a noble gas. If necessary, use multiple bonds to satisfy the octet rule.
17
Solved Problem 1.4

Write a Lewis structure of methylamine (CH5N). STRATEGY AND ANSWER 1. Total number of all valence electrons for all atoms:
2. 3.
Use electron pair to join the carbon and nitrogen.
Use 3 pairs to form single bonds between C and three H atoms. 4. Use 2 pairs to form single bonds between N and two H atoms. 5. This leaves one electron pair, use as lone pair on N atom.
18
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. These elements can form more than four covalent bonds. Examples are compounds such as PCl5 and SF6.
Some highly reactive molecules or ions have atoms with fewer than eight electrons in their outer shell. An example is boron trifluoride (BF3).
19
Energy-level diagram of an atom
20
Formal Charges
Many Lewis structures are incomplete until formal charge is assigned. Formal charge = number of valence electrons 1/2 number of shared electrons number of unshared electrons
12
where F is the formal charge, Z is the group number of the element, S equals the number of shared electrons, and U is the number of unshared electrons. The arithmetic sum of all the formal charges in a molecule or ion will equal the overall charge on the molecule or ion.
21
Formal Charges
Example:
#
12
(NH4+).
Consider the ammonium ion
Consider the nitrate ion (NO3-).
22
Formal Charges
Example:
#
12
Consider water and ammonia.
23
Summary of Formal Charges
24
Resonance
Often a single Lewis structure does not accurately represent the true structure of a molecule. The real carbonate ion is not represented by any of the structures 13.
Experimentally carbonate is known not to have two carbon-oxygen single bonds and one double bond; all bonds are equal in length and the charge is spread equally over all three oxygen.
25
Resonance
The real carbonate ion can be represented by a drawing in which partial double bonds to the oxygen are shown and partial negative charge exists on each oxygen. The real structure is a resonance hybrid or mixture of all three Lewis structures. Double headed arrows are used to show that the three Lewis structures are resonance contributors to the true structure.
#
The use of equilibrium arrows is incorrect since the three structures do not equilibrate; the true structure is a hybrid (average) of all three Lewis structures
26
Resonance
One resonance contributor is converted to another by the use of curved arrows which show the movement of electrons.
#
The use of these arrows serves as a bookkeeping device to assure all structures differ only in position of electrons
27
Rules for Resonance

Rules for Resonance: Individual resonance structures exist only on paper.
# The real molecule is a hybrid (average) of all contributing forms # Resonance forms are indicated by the use of double-headed arrows
Only electrons are allowed to move between resonance structures.

# The position of nuclei must remain the same # Only electrons in multiple bonds and nonbonding electrons can be moved
Example: Structure 3 is not a resonance form because an atom has moved.
28
Rules for Resonance

Rules for Resonance:
All structures must be proper Lewis structures.
The energy of the resonance hybrid is lower than the energy of any single contributing form.
# The lowering of energy is called resonance stabilization
Equivalent resonance forms make equal contributions to the structure of the real molecule.
# The structures with equivalent resonance forms tend to be greatly stabilized # Example: The two resonance forms of benzene contribute equally and greatly stabilize it
Unequal resonance structures contribute based on their relative stabilities.

# More stable resonance forms contribute more to the structure of the real molecule
29
Rules for Resonance Stability

Rule 1: The more covalent bonds a structure has, the more stable it is.
Example: For formaldehyde, the resonance hybrid is more like structure A than B
Rule 2: Charge separation decreases stability.

Example: Structure B has separated plus and minus charges, thus it is less stable and
makes a smaller contribution to the hybrid
Rule 3: Structures in which all the atoms have a complete valence shell of electrons (noble gas structure) are more stable.
Example: For structure B, carbon atom has 6 electrons, whereas structure A has 8.
Thus, structure A is more stable and makes a large contribution to the hybrid Solved Problem 1.7
30
Atomic Orbitals
Only s and p orbitals are very important in organic chemistry. Orbital: a region in space where the probability of finding an electron is high.
#
The typical representation of orbitals are those volumes which contain the electron 90-95% of the time
Energy level diagram of an atom

31
Atomic Orbitals
1s and 2s orbitals are spheres centered around the nucleus.
# #
Each orbital can accommodate 2 electrons The 2s orbital is higher in energy and contains a nodal surface (2= 0) in its center One sphere has a positive phase sign and the other a negative phase sign; a nodal plane separates the spheres Each p orbital can accommodate 2 electrons for a total of 6 electrons All three p orbitals are degenerate (equal in energy)
Each 2p orbital has two nearly touching spheres (or lobes).

#
There are three 2p orbitals which are perpendicular (orthoganal) to each other.
# #
The 2p orbitals are higher in energy than 1s or 2s.
32
Electron Configurations
The relative energies of atomic orbitals in the 1st & 2nd principal shells are as follows:
Electrons in 1s orbitals have the lowest energy because they are closest to the positive nucleus. Electrons in 2s orbitals are next lowest in energy. Electrons of the three 2p orbitals have equal but higher energy than the 2s orbital. Orbitals of equal energy (such as the three 2p orbitals) are called degenerate orbitals.
33
Electron Configurations
Aufbau principle:
Orbitals are filled so that those of lowest energy are filled first. A maximum of two electrons may be placed in each orbital but only when the spins of the electrons are paired. For orbitals of equal energy (degenerate orbitals) such as the three p orbitals, we add one electron to each with their spins unpaired until each of the degenerate orbitals contains one electron. Then we begin adding a second electron to each degenerate orbital so that the spins are paired.
Pauli exclusion principle:
Hunds rule:
34
Molecular Orbitals
Atomic orbitals provide a means for understanding how atoms form covalent bonds.
Example: Formation of bond between two hydrogen atoms
Ideal internuclear distance (bond length)
Figure 1.8 The potential energy of the hydrogen molecule as a function of internuclear distance
# State I: When two hydrogen atoms are relatively far apart, total energy is that of two
isolated hydrogen atoms # State II: As two hydrogen atoms move closer together, each nucleus increasingly attracts the others electron # State III: When the attraction compensates for the repulsive force, covalent bond forms # State IV: If the nuclei moved closer together, the repulsion force predominates, increasing the energy of the system CCB1013 Organic Chemistry
35
Molecular Orbitals
Heisenberg uncertainty principle: We cannot simultaneously know the position and momentum of an electron. An atomic orbital represents the region of space where one or two electrons of an isolated atom are likely to be found. 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 spinpaired 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 that combine.
36
Molecular Orbitals
A bonding molecular orbital (molec) results when two orbitals of the same phase overlap.
Figure 1.9: (a) The overlapping of two hydrogen 1s atomic orbitals with the same phase sign to form a bonding molecular orbital
Figure 1.9: (b) The analogous overlapping of two waves with the same phase, resulting in constructive interference and enhanced amplitude
37
Molecular Orbitals
An antibonding molecular orbital (*molec) results when two orbitals of opposite phase overlap.
Figure 1.10: (a) The overlapping of two hydrogen 1s atomic orbitals with opposite phase signs to form an antibonding molecular orbital
Figure 1.10: (b) The analogous overlapping of two waves with opposite sign, resulting in destructive interference and decreased amplitude
38
The Structure of Methane and Ethane: sp3 Hybridization

The Structure of Methane: The structure of methane with its four identical tetrahedral bonds cannot be adequately explained using the electronic configuration of carbon.
Hybridization of the valence orbitals (2s and 2p) provides four new identical orbitals which can be used for the bonding in methane. Orbital hybridization is a mathematical combination of the 2s and 2p wave functions to obtain wave functions for the new orbitals.
Excited state of a carbon atom

39

When one 2s orbital and three 2p orbitals are hybridized, four new and identical 2sp3 hybrid orbitals are obtained.
# # # #
When four orbitals are hybridized, four orbitals must result Each new orbital has one part s character and 3 parts p character The four identical orbitals are oriented in a tetrahedral arrangements The antibonding orbitals are not derived in the following diagram
Figure 1.12: Hybridization of pure atomic orbitals of a carbon atom to produce sp3 hybrid orbitals
40

The four sp3 orbitals are then combined with the 1s orbitals of four hydrogens to give the molecular orbitals of methane. Each new molecular orbital can accommodate 2 electrons.
Figure 1.13: The hypothetical formation of methane from an sp3-hybridized carbon atom and four hydrogen atoms
The bond formed from the overlap of an sp3 orbital and a 1s orbital is an example of a sigma () bond.
41

The Structure of Ethane: The carbon-carbon bond is made from overlap of two sp3 orbitals to form a sigma bond. The molecule is approximately tetrahedral around each carbon.
42

The Structure of Ethane:
(a)
(b)
(c)
Figure 1.19: (a) Structure of ethane based on quantum mechanical calculations (b) A ball-and-stick model of ethane (c) Structural formula for ethane
43
The Structure of Ethene: sp2 Hybridization

Ethene (C2H2) contains a carbon-carbon double bond and is in the class of organic compounds called alkenes.
#
Another example of the alkenes is propene
The geometry around each carbon is called trigonal planar.

# # #
All atoms directly connected to each carbon are in a plane (coplanar) The bonds point towards the corners of a regular triangle The bond angle are approximately 120o
Carbon-carbon double bonds are comprised of sp2-hybridized carbon atoms.

44

There are three bonds around each carbon of ethene and these are formed by using sp2 hybridized orbitals. The three sp2 hybridized orbitals come from mixing one s and two p orbitals.
#
One p orbital is left unhybridized
The sp2 orbitals are arranged in a trigonal planar arrangement.

#
The p orbital is perpendicular (orthogonal) to the plane
Figure 1.21: A process for deriving sp2-hybridized carbon atoms
Figure 1.22: An sp2-hybridized carbon atom

45

Overlap of sp2 orbitals in ethene results in formation of a framework.
#
One sp2 orbital on each carbon overlaps to form a carbon-carbon bond; the remaining sp2 orbitals form bonds to hydrogen
The leftover p orbitals on each carbon overlap to form a bonding bond between the two carbons. A bond results from overlap of p orbitals above and below the plane of the bond.
#
It has a nodal plane passing through the two bonded nuclei and between the two lobes of the molecular orbital
Note: A carbon-carbon double bond consists of one bond and one bond.
Figure 1.23: A model for the bonding molecular orbitals of ethene formed from two sp2 hybridized carbon atoms and four hydrogen atoms
46
Cis-Trans Isomerism
Restricted rotation of groups joined by a double bond causes a new type of isomerism.
These two compounds are isomers (stereoisomers); they are different compounds that have the same molecular formula.
Cis-trans isomerism is not possible if one carbon atom of the double bond bears two identical groups CCB1013 Organic Chemistry
47
The Structure of Ethyne: sp Hybridization

The carbon in ethyne is sp hybridized.
#
Propyne is another typical alkyne
The arrangement of atoms around each carbon is linear with bond angles 180o.
48

Ethyne (acetylene) is a member of a group of compounds called alkynes which all have carbon-carbon triple bonds.
# #
One s and one p orbital are mixed to form two sp orbitals Two p orbitals are left unhybridized
The two sp orbitals are oriented 180o relative to each other around the carbon nucleus.
#
The two p orbitals are perpendicular to the axis that passes through the center of the sp orbitals
Figure 1.27: A process for deriving sp-hybridized carbon atoms
Figure 1.28: An sp-hybridized carbon atom

49

In ethyne the sp orbitals on the two carbons overlap to form a bond.
#
The remaining sp orbitals overlap with hydrogen 1s orbitals
The p orbitals on each carbon overlap to form two bonds. The carbon-carbon triple bond consists of one and two bonds.
Figure 1.29: Formation of the bonding molecular orbitals of ethyne from two sp-hybridized carbon atoms and two hydrogen atoms
50
Bond Lengths of Ethyne, Ethene, and Ethane

Note: The greater the s orbital character, the shorter the bond. The greater the p orbital character, the longer the bond.
Ethyne sp hybrid orbital (50% s character, 50% p character)
Ethene sp2 hybrid orbital (33% s character, 67% p character)

Ethane sp3 hybrid orbital (25% s character, 75% p character)

51
Molecular Geometry
Valence Shell Electron Pair Repulsion (VSEPR) Model To predict the arrangement of atoms in molecules and ions. Electron pairs repel each other, thus electron pairs of valence shell tend to stay as far apart as possible. The repulsion between nonbonding pairs are generally greater than bonding pairs. The geometry of the molecule considers all electron pairs (bonding and nonbonding). The shape of the molecule or ion refers to the positions of the nuclei (or atoms), not positions of the electron pairs.
52
Molecular Geometry: The Valence Shell Electron Pair Repulsion (VSEPR) Model
Methane The valence shell of methane contains four pairs or sets of electrons. To be as far apart from each other as possible they adopt a tetrahedral arrangement (bond angle 109.5o). The molecule methane is therefore tetrahedral.
Figure 1.32: A tetrahedral shape for methane allows maximum separation of electron pairs
53
Ammonia A tetrahedral arrangement of the electron pairs explains the trigonal pyramidal arrangement of the four atoms. The bond angles are 107 (not 109.5) because the nonbonding pair occupies more space than the bonding pairs.
Figure 1.34: The tetrahedral arrangement of the electron pairs of ammonia that results when the nonbonding electron pair is considered to occupy one corner. This arrangement of electron pairs explains the trigonal pyramidal shape of NH3 molecule.
54
Water A molecule of water has an angular or bent shape. The HO H bond angle is 104.5 (close to 109.5).
Figure 1.35: An approximately tetrahedral arrangement of the electron pairs of a molecule of water that results when the pairs of nonbonding electrons are considered to occupy corners. This arrangement accounts for the angular shape of the H2O molecule.
55
Boron Trifluoride (BF3) It has a trigonal planar structure. The bond angles are 120.
Figure 1.36: The triangular (trigonal planar) shape of boron trifluoride maximally separates the three bonding pairs
56
Beryllium Hydride (BeH2) It has a linear geometry. The bond angle is 180.
Carbon Dioxide
57
Review Problem 1.18

58
Representation of Structural Formulas

Dot formulas are more cumbersome to draw than dash formulas and condensed formulas. Lone-pair electrons are often (but not always) drawn in, especially when they are crucial to the chemistry being discussed.
Figure 1.37: Structural formulas for propyl alcohol
59
Dash Structural Formulas

Each dash represents a pair of electrons. This type of representation is meant to emphasize connectivity and does not represent the 3-dimensional nature of the molecule.
#
The dash formulas of propyl alcohol appear to have 90o angles for carbons which actually have tetrahedral bond angles (109.5o)
There is relatively free rotation around single bonds so the dash structures below are all equivalent.
60
Dash Structural Formulas

Constitutional isomers:
#
Constitutional isomers have the same molecular formula but different connectivity Propyl alcohol is a constitutional isomer of isopropyl alcohol
61
Condensed Structural Formulas

In these representations, some or all of the dash lines are omitted. In partially condensed structures all hydrogen attached to an atom are simply written after it but some or all of the other bonds are explicitly shown. In fully condensed structure all bonds are omitted and atoms attached to carbon are written immediately after it. For emphasis, branching groups are often written using vertical lines to connect them to the main chain.
62
Bond-Lind Formulas
A further simplification of drawing organic molecules is to completely omit all carbon and hydrogen and only show heteroatoms (e.g. O, Cl, N) explicitly. Each intersection or end of line in a zig-zag represents a carbon with the appropriate number of hydrogen atoms.
#
Heteroatoms with attached hydrogen atoms must be drawn in explicitly
63
Bond-Lind Formulas
Cyclic compounds are condensed using a drawing of the corresponding polygon.
Multiple bonds are indicated by using the appropriate number of lines connecting the atoms.
64
Three-Dimensional Formulas
Since virtually all organic molecules have a 3-dimensional shape it is often important to be able to convey their shape. The conventions for this are:
# # #
Bonds that lie in the plane of the paper are indicated by a simple line ( ) Bonds that come forward out of the plane of the paper are indicated by a solid wedge ( Bonds that go back out of the plane of the paper are indicated by a dashed wedge ( )
Generally to represent a tetrahedral atom:

# #
Two of the bonds are drawn in the plane of the paper about 109o apart The other two bonds are drawn in the opposite direction to the in-plane bonds but right next to each other
H H C H H Ethane C H H OR H H H C C H H H etc.
H C Br H H OR H
H C Br OR
Br etc. H C H H
H Bromomethane
65
END OF CHAPTER 1
Octet rule & Lewis structures Formal charge Resonance Dash and condensed structural formulas Constitutional isomers Wedge-dashed, wedge-line and bond-line formulas Orbital hybridization Typical bond angles and molecular geometry
Try to solve all review problems

66
Tutorial 1 Questions
All problems are from T.W. Graham Solomons and Craig B. Fryhle, Organic Chemistry, 10th ed., John Wiley & Sons, 2011. Note that the problem numbers are identical to those in the 10th edition, International Student Version. Chapter 1: 1. #1.6(b)(c)(e)(f) 2. #1.8(a)(b)(c) 3. #1.10(a)(c)(f) 4. #1.11(a)(b) 5. #1.22(f)(g)(h) 6. #1.27(b)(d) 7. #1.31(f)(i)(p) 8. #1.32(a)(c)(d) 9. #1.33 10. #1.35(c)(h) 11. #1.38 12. #1.42
67

Chapter 1 The Basics

Uploaded by

Document Information

Original Title

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

Chapter 1 The Basics

Uploaded by

Copyright:

Available Formats

CCB1013 Organic Chemistry

By Dr. Oh Pei Ching