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Transcript of CM1501-Week 1A & 1B-Struc Bonding
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CM1501 Week 1A & 1B – Structure & Bonding
Organic Chemistry, Second EditionJanice Gorzynski Smith
University of Hawai’i
Textbook
Monday Lecture: 45 mins
DR Zeng Huaqiang: [email protected] Ong Yue Ying: [email protected]
Teaching Staff
Thursday Lecture: 90 mins(no break)
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CM1501 Week 1A & 1B – Structure & Bonding
Chapter 1: Structure and BondingChapter 2: Acids and BasesChapter 3: Introduction to Organic Molecules & Functional GroupsChapter 4: AlkanesChapter 5: StereochemistryChapter 6: Understanding Organic ReactionsChapter 7: Alkyl Halides and Nucleophilic SubstitutionChapter 8: Alkyl Halides and Elimination SubstitutionChapter 9: Alcohols, Ethers and EpoxidesChapter 10: AlkenesChapter 11: AlkynesChapter 16: Conjugation, Resonance and DienesChapter 17: Benzene and Aromatic CompoundsChapter 22: Carboxylic acids and Their DerivativesChapter 19: Carboxylic Acids and the Acidity of the O-H BondChapter 21: Aldehydes and KetonesChapter 25: Amines and whole class tutorial
CM1501 Course ScheduleWeek 1Week 2
Week 3
Week 4
Weeks 5-6
Week 7Week 8
Week 12
Week 13
Weeks 9-11
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CM1501 Week 1A & 1B – Structure & Bonding
Mid-Term Exam 30 %
Final Exam 50 %
Practical Section 20 %
Total 100 %
CM1501 Assessments
Final Exam: Monday, 03-12-2012 (1:00-3:00 pm)
CLOSED BOOK EXAMINATION
Mid Exam: 04-10-2012, 4:10-5:50pm at MPSH1, section A+B
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CM1501 Week 1A & 1B – Structure & Bonding
What is Organic Chemistry?
• Organic chemistry is the study of carbon compounds.
• Why is it so special?- 90% of more than 30 million chemical compounds contain
carbon.
- Examination of carbon in periodic chart answers some of
these questions.
- Carbon is group 4A element, it can share 4 valence
electrons and form 4 covalent bonds.
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CM1501 Week 1A & 1B – Structure & Bonding
Silicon As An Alternative Element for Life?
Smaller in size and lighter in mass.
Can form double or triple bonds.
Can form alkane hydrocarbons or long carbon chains
CO2 is gas & soluble in water
Larger in size and heavier in mass.
Difficult to form double or triple bonds.
Silanes, the analogs of alkanehydrocarbons, are highly reactive and may decompose easily
SiO2 is non-soluble solid.
SiliconCarbon126
2814
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CM1501 Week 1A & 1B – Structure & Bonding
The nucleus (very dense; very small: 10-15 m; 1 fm) contains positively charged protons and uncharged neutrons.
The electron cloud (10-10m; ~ 2Ǻ) is composed of negatively charged electrons.
The Periodic Table
Neutral atomprotons = electrons
Cationsprotons > electrons
Anionsprotons < electrons
Atomic number Isotope
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CM1501 Week 1A & 1B – Structure & Bonding
A comparison of two isotopes of the element carbon
Atomic weight: the weighted average of the mass of all isotopes reported in atomic mass units (amu)
Carbon as the example: 12.011 = 12 x 98.9% + 13 x 1.1%
The Periodic Table
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CM1501 Week 1A & 1B – Structure & Bonding
The Periodic Table
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181832
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32http://www.dayah.com/periodic/
1A 2A 3B 4B 5B 6B 7B 8B 8B 8B 1B 2B 3A 4A 5A 6A 7A 8A
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CM1501 Week 1A & 1B – Structure & Bonding
The Periodic Table
• Elements in the same row are similar in size.• Elements in the same column have similar electronic and
chemical properties.
From left to right From top to bottom
Atomic radius
Electronegativity
Ionization energy
Atomic radius
Electronegativity
Ionization energy
Periodic Trends
+-
+-
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CM1501 Week 1A & 1B – Structure & Bonding
The Periodic Table
• Four types: s, p, d, and f
• s and p orbitals most important in organic and biological chemistry.
• There are ONE s orbital, THREE p orbitals, FIVE d orbitals and SEVEN f orbitals.
• Each orbital can hold two electrons.
Atomic Orbital:
A region of space that ishigh in electron density
1s (1)
2s (1)
3s (1)
3d (5)
2p (3)
3p (3)
4f
Energy gradient
Electron fillingpriority
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CM1501 Week 1A & 1B – Structure & Bonding
• Orbitals are grouped in shells of increasing size and energy• Different shells contain different numbers and kinds of orbitals• Each orbital can be occupied by two electrons with opposite spins
The Periodic Table
Orbitals and Shells
1s
2s
3s
3d
2p
3p
Pauli exclusion principle
Hund's rule
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CM1501 Week 1A & 1B – Structure & Bonding
The Periodic Table
Orbitals and Shells
• Orbitals are grouped in shells of increasing size and energy
• Different shells contain different numbers and kinds of orbitals
• Each orbital can be occupied by two electrons with opposite spins
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CM1501 Week 1A & 1B – Structure & Bonding
The Periodic Table
1s2
2s22p6
4s23d104p6
5s24d105p6
2
8
818
18
3s23p6
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2
2+8
2+8+8
2+8+8+18
2+8+8+18+18
2+8+8+18+18+326s24f145d106p6
Noble Gas Configuration
8A
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CM1501 Week 1A & 1B – Structure & Bonding
The Periodic Table
Columns
1s2 2s1
1s2 2s22p6 3s1
1A
1s1
1s2 2s22p6 3s23p6 4s1
1s2 2s22p6 3s23p6 4s23d104p6 5s1
1s2 2s22p6 3s23p6 4s23d104p6 5s24d105p6 6s1
Vary the inner shell while keeping outer shell constant
2 8 8 18 18
2 8 8 18
2 8 8
2 8
2
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CM1501 Week 1A & 1B – Structure & Bonding
The Periodic Table
Rows
2 1s2 2s22p6
2 1s2
2s1 2s2 2s22p2 2s22p4 2s22p61s1 1s2
2s22p1 2s22p3 2s22p5
First row
Second rowVary the outer shell while
keeping inner shell constant
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CM1501 Week 1A & 1B – Structure & Bonding
• s orbitals: spherical, nucleus at center• p orbitals: dumbbell-shaped, nucleus at middle• d orbitals: cloverleaf-shaped, nucleus at center
The Periodic Table
1s orbital 2p orbital 3d orbitalNo electron density at the planar nodes
Shapes of Atomic Orbitals
http://winter.group.shef.ac.uk/orbitron/AOs/6s/index.html
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CM1501 Week 1A & 1B – Structure & Bonding
The Periodic Table
Shapes of Atomic Orbitals
X
Y
Z
http://winter.group.shef.ac.uk/orbitron/AOs/6s/index.html
• s orbitals: spherical, nucleus at center• p orbitals: dumbbell-shaped, nucleus at middle• d orbitals: cloverleaf-shaped, nucleus at center
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CM1501 Week 1A & 1B – Structure & Bonding
• Through bonding,
1) two atoms are joined in a stable arrangement.
2) atoms attain a complete outer shell of valence
electrons, a stable noble gas configuration.
• Ionic bonds: transfer of electrons from one element
to another.
• Covalent bonds: sharing of electrons between two
nuclei.
Bonding
Review2
2+8
2+8+8
2+8+8+18
2+8+8+18+18
2+8+8+18+18+32
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CM1501 Week 1A & 1B – Structure & Bonding
Bonding Forces
Ionic Bond
1s22s22p63s23p5
1s22s22p63s1
Change in electronic configuration
• Generally occurs when elements (e.g., Na) on the far left side of the periodic table combine with elements (e.g., Cl) on the far right side, ignoring noble gases.
2+8
2+8+8
2+8+8 (2+8+7)
2+8 (2+8+1)
Na
Cl
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CM1501 Week 1A & 1B – Structure & Bonding
• Hydrogen forms one covalent bond. Each has a filled valence shell of two electrons
Bonding in Molecular Hydrogen (H2)
Bonding Forces
Covalent bond
Lewis structure representation
• First row elements such as hydrogen can accommodate two electrons around it, making it like the noble gas helium.
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CM1501 Week 1A & 1B – Structure & Bonding
Bonding Structure
Noble gas configuration & Octet Rule
Examples: 1) Carbon has four valence electrons (2s22p2), forming four
bonds.
2) Nitrogen has five valence electrons (2s22p3) but formsonly three bonds.
3) Oxygen has six valence electrons (2s22p4) but forms twobonds.
• Second row elements can have no more than eight electrons around them. Atoms such as C, N, O, F with four or more valence electrons form enough bonds to give an octet.
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CM1501 Week 1A & 1B – Structure & Bonding
Elements in Groups 2A and 3A in the Second Row
Elements in the Third Row
Exceptions to the Octet Rule
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CM1501 Week 1A & 1B – Structure & Bonding
In a Lewis structure, a solid line indicates a two-electron covalent bond.
Bonding StructureLewis structures
Lewis structures are electron dot representations for molecules.Three general rules for drawing Lewis structures:
1. Draw only the valence electrons.2. Give each hydrogen two electrons3. Give second-row elements (C, N, O, & F) an octet of electrons, if possible.
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CM1501 Week 1A & 1B – Structure & Bonding
Lewis structures
Bonding Structure
Lewis structures are electron dot representations for molecules.Three general rules for drawing Lewis structures:
1. Draw only the valence electrons.2. Give each hydrogen two electrons3. Give second-row elements (C, N, O, & F) an octet of electrons, if possible.
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CM1501 Week 1A & 1B – Structure & Bonding
• Formal charge is the charge assigned to individual atoms in a Lewis structure.
• Formal charge is used to determine how the number of electrons around a particular atom compares to its number of valence electrons.
• The number of electrons “owned” by an atom is determined by its number of bonds and lone pairs.
• An atom “owns” all of its unshared electrons and half of its shared electrons.
Formal Charge
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CM1501 Week 1A & 1B – Structure & Bonding
The number of electrons “owned” by different atoms is indicated in the following examples:
Example 1: neutral
Example 2: neutral
Example 3: anion
Formal Charge
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CM1501 Week 1A & 1B – Structure & Bonding
Formal Charge
Formal charge observed with common bonding patters
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CM1501 Week 1A & 1B – Structure & Bonding
More than one arrangement of atoms is possible for a given molecular formula.
The above two are valid Lewis structures and both exist. These two compounds are called isomers.
Ethanol and dimethyl ether are constitutional isomers.
Isomers
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CM1501 Week 1A & 1B – Structure & Bonding
Some molecules cannot be adequately represented by a single Lewis structure.
The hybrid is a weighted average of the contributing resonance structures.
Resonance structures are two Lewis structures having the same placement of atoms but a different arrangement of electrons
Neither resonance structure is an accurate representation for the true structure, which is a composite of both resonance forms and is called a resonance hybrid.
Electron delocalization adds stability.
Resonance Structures
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CM1501 Week 1A & 1B – Structure & Bonding
1. Resonance structures are not real. An individual resonance structure does not accurately represent the structure of a molecule or ion. Only the hybrid does.
2. Resonance structures are not in equilibrium with each other. There is no movement of electrons from one form to another.
3. Resonance structures are not isomers. Two isomers differ in the arrangement of both atoms and electrons, whereas resonance structures differ only in the arrangement of electrons.
Basic Principles
Resonance Structures
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CM1501 Week 1A & 1B – Structure & Bonding
A “better” resonance structure is one that has 1) more bonds, 2) fewer charges, and 3) negative charges preferentially localized on more electronnegative elements.
Resonance Structures
Resonance Hybrids
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CM1501 Week 1A & 1B – Structure & Bonding
Drawing Resonance Structures
Rule [1]: Two resonance structures differ in the position of multiple bonds and nonbonded electrons. The placement of atoms and other single bonds always stays the same.
Rule [2]: Two resonance structures must have the same number of unpaired electrons.
Resonance Structures
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CM1501 Week 1A & 1B – Structure & Bonding
Rule [3]: Resonance structures must be valid Lewis structures: hydrogen must have two electrons and no second-row element can have more than eight electrons.
Drawing Resonance Structures
Resonance Structures
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CM1501 Week 1A & 1B – Structure & Bonding
• Shows the movement of an electron pair: the tail of the arrow always begins at the electron pair, either in a bond or lone pair. The head points to where the electron pair “moves.”
Example 1:
Example 2:
Resonance StructuresCurved Arrow Notation
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CM1501 Week 1A & 1B – Structure & Bonding
A lone pair is located on an atom directly bonded to a double bond
Drawing Resonance Structures
Resonance Structures
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CM1501 Week 1A & 1B – Structure & Bonding In the above examples,
Resonance Structures
An atom bearing a (+) charge is bonded either to a double bond or an atom with a lone pair.
Drawing Resonance Structures
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CM1501 Week 1A & 1B – Structure & Bonding
Two variables define a molecule’s structure: bond length and bond angle.
• Bond length decreases across a row of the periodic table as the size of the atom decreases.
• Bond length increases down a column of the periodic table as the size of an atom increases.
Molecular Dimensionality
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CM1501 Week 1A & 1B – Structure & Bonding
Bond angle determines the shape around any atom bonded to two other atoms.
• The number of groups surrounding a particular atom determines its geometry. A group is either an atom or a lone pair of electrons.
• The most stable arrangement keeps these groups as far away from each other as possible.
Molecular Dimensionality
Bond angle
Predicting Geometry Based on Counting Groups Around the Central Atom
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CM1501 Week 1A & 1B – Structure & Bonding
Two groups around an atom—
Molecular Dimensionality
Bond angle
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CM1501 Week 1A & 1B – Structure & Bonding
Three groups around an atom—
Molecular Dimensionality
Bond angle
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CM1501 Week 1A & 1B – Structure & Bonding
Four groups around an atom—
Molecular Dimensionality
Bond angle
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CM1501 Week 1A & 1B – Structure & Bonding
Drawing Three Dimensional Structures
• A solid line is used for a bond in the plane.
• A wedge is used for a bond in front of the plane.
• A dashed line is used for a bond behind the plane.
Molecular Dimensionality
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CM1501 Week 1A & 1B – Structure & Bonding
The molecule can be turned/rotated in many different ways, generating many equivalent representations. All of the followingare acceptable drawings for CH4.
Molecular DimensionalityDrawing Three Dimensional Structures
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CM1501 Week 1A & 1B – Structure & Bonding
Note that wedges and dashes are used for groups that are really aligned one behind another. It does not matter in the following two drawings whether the wedge or dash is skewed to the left or right, because the two H atoms are really aligned.
Molecular DimensionalityDrawing Three Dimensional Structures
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CM1501 Week 1A & 1B – Structure & Bonding
In water (H2O), two of the four groups attached to the central O atom are lone pairs. The two H atoms and two lone pairs around O point to the corners of a tetrahedron. The H-O-H bond angle of 105° is close to the theoretical tetrahedral bond angle of 109.5°. Water has a bent shape, because the two groups around oxygen are lone pairs of electrons.
Molecular Dimensionality
A Nonbonded Pair of Electrons is Counted as a “Group”
Drawing Three Dimensional Structures
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CM1501 Week 1A & 1B – Structure & Bonding
In ammonia (NH3), one of the four groups attached to the central N atom is a lone pair. The three H atoms and the lone pair point to the corners of a tetrahedron. The H-N-H bond angle of 107° is close to the theoretical tetrahedral bond angle of 109.5°. This shape is referred to as a trigonal pyramid.
Molecular DimensionalityDrawing Three Dimensional Structures
A Nonbonded Pair of Electrons is Counted as a “Group”
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CM1501 Week 1A & 1B – Structure & Bonding
Methane (CH4)
Ammonia (NH3)
Water (H2O)
In both NH3 and H2O, the bond angle is smaller than the theoretical tetrahedral bond angle because of repulsion of the lone pairs of electrons. The bonded atoms are compressed into a smaller space with a smaller bond angle.
Molecular Dimensionality
109o
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CM1501 Week 1A & 1B – Structure & Bonding
• Drawing every bond in organic molecule can become tedious.• Several shorthand methods have been developed to write
structures.• Condensed structures typically don’t have C-H or C-C single
bonds shown.
Molecular DimensionalityDrawing Organic Molecules—Condensed Structures
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CM1501 Week 1A & 1B – Structure & Bonding
Drawing Organic Molecules—Condensed Structures
• All atoms are drawn in with two-electron bond lines omitted.• Atoms are usually drawn next to the atoms to which they are
bonded.• Parentheses are used around identical groups bonded to the same
atom.• Lone pairs are omitted.
Molecular Dimensionality
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CM1501 Week 1A & 1B – Structure & Bonding
Skeletal structures
• Assume there is a carbon atom at the junction of any two lines or at the end of any line.
• Assume there are enough hydrogens around each carbon to make it tetravalent.
• Draw in all heteroatoms and hydrogens directly bonded to them.
Condensed Structures
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CM1501 Week 1A & 1B – Structure & Bonding
• A charge on a carbon atom takes the place of one hydrogen atom.
• Negatively charged carbon atoms have one lone pair and positively charged carbon atoms have none.
Condensed StructuresSkeletal structures
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CM1501 Week 1A & 1B – Structure & Bonding
When the 1s orbital of one H atom overlaps with the 1s orbital of another H atom, a sigma () bond that concentrates electron density between the two nuclei is formed.
This bond is cylindrically symmetrical because the electrons forming the bond are distributed symmetrically about an imaginary line connecting the two nuclei.
Hydrogen
Orbitals and Bonding
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CM1501 Week 1A & 1B – Structure & Bonding
Carbon has four valence electrons; two in the 2s orbital and one each in 2p orbitals.
Carbon forms four identical bonds in methane
Methane
Orbitals and Bonding
Methane (CH4)
Ground state
Excitedstate
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CM1501 Week 1A & 1B – Structure & Bonding
The mixing of a spherical 2s orbital and three dumbbell shaped 2p orbitals together produces four hybrid orbitals, each having one large lobe and one small lobe.
The four hybrid orbitals are oriented towards the corners of a tetrahedron, and form four equivalent bonds.
sp3 Hybrid Orbitals
Orbitals and Bonding
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CM1501 Week 1A & 1B – Structure & Bonding
Bonding Using sp3 Hybrid Orbitals
Each bond in CH4 is formed by overlap of an sp3 hybrid orbital of carbon with a 1s orbital of hydrogen. These four bonds point to the corners of a tetrahedron.
Orbitals and Bondingsp3 Hybrid Orbitals
4+
H (1s)C (sp3)
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CM1501 Week 1A & 1B – Structure & Bonding
• One 2s orbital and two 2p orbitals form three sp2 hybrid orbitals.
• One 2s orbital and one 2p orbital form two sp hybrid orbitals.
sp2 & sp Hybrid Orbitals
Orbitals and Bonding
sp3
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CM1501 Week 1A & 1B – Structure & Bonding
Determining Hybridization Patterns
To determine the hybridization of an atom in a molecule, we count the number of groups around the atom. The number of groups (atoms and nonbonded electron pairs) corresponds to the number of atomic orbitals that must be hybridized to form the hybrid orbitals.
Orbitals and Bonding
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CM1501 Week 1A & 1B – Structure & Bonding
Hybrid orbitals of NH3 and H2O
Orbitals and Bonding
2s22p5
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CM1501 Week 1A & 1B – Structure & Bonding
The bonds between B and F are the result of sp2 hybrid orbital overlapThis leaves the B atom and each of the F atoms with a p orbital not used in the bond formation. The filled F orbital and unfilled B orbital give rise to localized interactions
Orbitals and BondingHybridization in BF3
B: sp2 + one empty 2p orbital
F: sp2 + one filled 2p orbital
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CM1501 Week 1A & 1B – Structure & Bonding
Orbitals and Bonding
B: sp2 + one empty 2p orbital
F: sp2 + one filled 2p orbital
sp2
filled 2p empty 2p
B F
F
F
F B+3
+
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CM1501 Week 1A & 1B – Structure & Bonding
B F
F
F
Orbitals and Bonding
The presence of the resonance contributors in the bottom line account for the partial double bond character in BF3
Resonance Structures for BF3
B: sp2 + one empty 2p orbital
F: sp2 + one filled 2p orbital
CM1501 Lecture 1 – Structure & Bonding
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CM1501 Week 1A & 1B – Structure & Bonding
Orbitals and BondingResonance Structures for BF3
CM1501 Lecture 1 – Structure & Bonding
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CM1501 Week 1A & 1B – Structure & Bonding
Orbitals and Bonding
Each carbon is tetrahedral. Each carbon is sp3 hybridized
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CM1501 Week 1A & 1B – Structure & Bonding
Each carbon is trigonal and planar. Each carbon is sp2 hybridized
Orbitals and Bonding
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CM1501 Week 1A & 1B – Structure & Bonding
Each carbon is trigonal and planar. Each carbon is sp2 hybridized
Orbitals and Bonding
Unlike the C—C bond in ethane, rotation about the C—C double bond in ethylene is restricted as it involves the breaking of bond .
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CM1501 Week 1A & 1B – Structure & Bonding
Each carbon is diagonal and linear.
Each carbon is sphybridized
Two σ bonds and two bonds
Orbitals and Bonding
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CM1501 Week 1A & 1B – Structure & Bonding
Orbitals and Bonding
Each carbon is diagonal and linear.
Each carbon is sphybridized
Two σ bonds and two bonds
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CM1501 Week 1A & 1B – Structure & Bonding
• As the number of electrons between two nuclei increases, bonds become shorter and stronger.
Orbitals and Bonding
Bond Length and Bond Strength
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CM1501 Week 1A & 1B – Structure & Bonding
• The length and strength of C—H bonds vary depending on the hybridization of the carbon atom.
Orbitals and Bonding
Bond Length and Bond Strength
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CM1501 Week 1A & 1B – Structure & Bonding
Orbitals and Bonding
Bond Length and Bond Strength
Although sp3, sp2 and sp hybrid orbitals are similar in shape, they are different in size
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CM1501 Week 1A & 1B – Structure & Bonding
Electronegativity is a measure of an atom’s attraction for electrons in a bond.
Electronegativity values for some common elements
Electronegativity and Bond Polarity
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CM1501 Week 1A & 1B – Structure & Bonding
Periodic Electronegativity Values
Electronegativity and Bond Polarity
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CM1501 Week 1A & 1B – Structure & Bonding
Electronegativity values are used as a guideline to indicate whether the electrons in a bond are equally shared or unequally shared between two atoms. When electrons are equally shared, the bond is nonpolar. When differences in electronegativity result in unequal sharing of electrons, the bond is polar, and is said to have a “separation of charge” or a “dipole”.
Electronegativity and Bond Polarity
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CM1501 Week 1A & 1B – Structure & Bonding
Bonding between atoms of different electronegativity values results in unequal sharing of electrons.
Example: In the C-O bond, the electrons are pulled away from C (2.5) toward O (3.4), the element of higher electronegativity. The bond is polar, or polar covalent. The bond is said to have dipole; that is, separation of charge.
The direction of polarity in a bond is indicated by an arrow with the head of the arrow pointing towards the more electronegative element. The tail of the arrow, with a perpendicular line drawn through it, is drawn at the less electronegative element.
+ means the indicated atom is electron deficient.
- means the indicated atom is electron rich.
Electronegativity and Bond Polarity
E = 2.5 E = 3.4
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CM1501 Week 1A & 1B – Structure & Bonding
Use the following two-step procedure to determine if a molecule has a net dipole:
1. Use electronegativity differences to identify all of the polar bonds and the directions of the bond dipoles.
2. Determine the geometry around individual atoms by counting groups, and decide if individual dipoles cancel or reinforce each other in space.
Electrostatic potential plot of CH3Cl
Polarity of Molecules
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CM1501 Week 1A & 1B – Structure & Bonding
A polar molecule has either one polar bond, or two or more bond dipoles that reinforce each other. An example is water:
A nonpolar molecule has either no polar bonds, or two or more bond dipoles that cancel. An example is carbon dioxide:
Polarity of Molecules