5.111SC | Fall 2014 | Undergraduate

Principles of Chemical Science

Unit II: Chemical Bonding & Structure

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With the knowledge of atomic electronic configurations and ionization energies from Unit I, Unit II focuses on how (and why) atoms come together to form bonds and how (and why) certain molecular structures are formed as a result of bonding interactions. The unit starts with the periodic table where all the elements are introduced. Viewers are asked to consider why elements on one side of the table react by losing electrons whereas elements on the other side have the tendency to gain electrons, leading to the description of properties known as electron affinity and electronegativity. Viewers will be introduced to ionic, covalent, and polar covalent bonds, and to a theory that can predict bond strength (molecular orbital theory). Viewers will also learn about molecular structure, and theories that predict which arrangement of atoms and electrons is likely to yield the most stable molecule (Lewis structures), and which geometry is most likely to be observed (VSEPR and valence bond theory/hybridization). By the end of unit II, viewers should be able to identify periodic table trends, draw Lewis structures, and use molecular orbital theory to explain why it takes extremely high temperatures to break the nitrogen-nitrogen bond of dinitrogen. They should be able to use VSEPR theory to explain why the greenhouse gas carbon dioxide is linear, identify which organic molecule is likely to have a tetrahedral center, and explain to their parents or kids which vitamins are polar and thus safe to take in higher doses. 

Image excerpted from Lecture 8 Notes Lecture 8: The Periodic Table and Periodic Trends

Image excerpted from Lecture 9 Notes Lecture 9: Periodic Table; Ionic and Covalent Bonds

Image excerpted from Lecture 10 Notes Lecture 10: Introduction to Lewis Structures

Image excerpted from Lecture 11 Notes Lecture 11: Lewis Structures: Breakdown of the Octet Rule

Image excerpted from Lecture 12 Notes Lecture 12: The Shapes of Molecules: VSEPR Theory

Image excerpted from Lecture 13 Notes Lecture 13: Molecular Orbital Theory

Image excerpted from Lecture 14 Notes Lecture 14: Valence Bond Theory and Hybridization

Looking for something specific in this course? The Resource Index compiles links to most course resources in a single page.

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Topics

Image excerpted from Lecture 10 Notes 

  1. Lewis Structures
  2. Formal Charge
  3. Resonance Structures

Lecture Video

Lewis structures are simplistic views of molecular structure. They are based on the idea that the key to covalent bonding is electron sharing and having each atom achieve a noble gas electron configuration. Lewis structures correctly predict electron configurations around atoms in molecules about 90% of the time. They are not perfect, but writing a Lewis structure is a lot easier than solving the Schrödinger equation, so we recommend that you watch this lecture.

Lecture Notes

Notes for Lecture 10 (PDF)

Clicker Questions

Lecture 10 Clicker Questions (PDF)

Textbook Reading

TOPICS 5th EDITION 4th EDITION
Lewis Structures Section 2.5–2.8 Section 2.5–2.8

Problems and Solutions

Problems for Lecture 10 (PDF)

Solutions for Lecture 10 (PDF)

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Topics

Image excerpted from Lecture 11 Notes 

  1. Breakdown of the Octet Rule
    1. Odd Number of Valence Electrons
    2. Octet Deficient Molecules
    3. Valence Shell Expansion

Lecture Video

Radicals, expanded octets, and more, in this lecture about Lewis structures.

Lecture Notes

Notes for Lecture 11 (PDF)

Clicker Questions

Lecture 11 Clicker Questions (PDF)

Textbook Reading

TOPICS 5th EDITION 4th EDITION
Radicals and Biradicals Section 2.9 Section 2.9
Expanded Valence Shells Section 2.10 Section 2.10
The Unusual Structures of Some Group 13 / III Compounds Section 2.11 Section 2.11
Correcting the Covalent Model: Electronegativity Section 2.12 Section 2.12

Problems and Solutions

Problems for Lecture 11 (PDF)

Solutions for Lecture 11 (PDF)

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Topics

Image excerpted from Lecture 12 Notes 

  1. The Shapes of Molecules: VSEPR Theory
    1. Molecules without Lone Pairs
    2. Molecules with Lone Pairs

Lecture Video

Valence shell electron pair repulsion or VSEPR theory can be used to predict molecular geometry. The theory is based on Lewis structures and the simple idea that that the preferred geometry around a central atom is the one that minimizes electron repulsion. Chemist Stefanie Sydlik tells us how she uses VSEPR theory to design sensors that are capable of detecting landmines.

Lecture Notes

Notes for Lecture 12 (PDF)

Clicker Questions

Lecture 12 Clicker Questions (PDF)

Textbook Reading

TOPICS 5th EDITION 4th EDITION
The Basic VSEPR Model Section 3.1 Section 3.1
Molecules with Lone Pairs on the Central Atom Section 3.2 Section 3.2

Detecting Explosives To Save Lives In War Zone

Stefanie Sydlik explains how her research on designing sensors for explosives depends on the principles of VSEPR (valence shell electron pair repulsion) theory. Stefanie’s sensor design amplifies small-scale changes in bond angles following interaction with a target molecule, and she hopes that her work will lead to better detectors for landmines and improvised explosive devices.

Stefanie Sydlik’s Personal Story

Stefanie Sydlik describes how an exciting “Take Your Daughter to Work Day” convinced her to become a chemist. She considers chemistry to be a bridge between biology and physics that can help explain observations made in everyday life.

Problems and Solutions

Problems for Lecture 12 (PDF)

Solutions for Lecture 12 (PDF)

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Topics

Image excerpted from Lecture 13 Notes 

  1. Molecular Orbital Theory
    1. Homonuclear Molecules with MOs Originating from s Orbitals
    2. Homonuclear Molecules with MOs Originating from s and p Orbitals
    3. Heteronuclear Diatomic Molecules

Lecture Video

Why do some atoms readily form bonds with each other and other atoms don’t? Using molecular orbital theory, we can rationalize why molecular hydrogen (H2) is an abundant molecule whereas molecular helium (He2) is not. If you want to power your starship with dilithium (Li2) crystals, you should watch this lecture.

Lecture Notes

Notes for Lecture 13 (PDF)

Clicker Questions

Lecture 13 Clicker Questions (PDF)

Textbook Reading

TOPICS 5th EDITION 4th EDITION
The Limitations of Lewis’s Theory Section 3.8 Section 3.8
Molecular Orbitals Section 3.9–3.11 Section 3.9–3.11

Problems and Solutions

Problems for Lecture 13 (PDF)

Solutions for Lecture 13 (PDF)

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Topics

Image excerpted from Lecture 14 Notes 

  1. Valence Bond Theory and Hybridization
    1. Sigma and pi Bonds
    2. Hybridization of Atomic Orbitals
      1. sp3 Hybridization
      2. sp2 Hybridization
      3. sp Hybridization

Lecture Video

Valence bond theory and hybridization can be used to explain and/or predict the geometry of any atom in a molecule. In particular, the concept of hybridization is important for understanding the geometry of organic molecules.

Lecture Notes

Notes for Lecture 14 (PDF)

Clicker Questions

Lecture 14 Clicker Questions (PDF)

Textbook Reading

TOPICS 5th EDITION 4th EDITION
Valence Bond Theory Sections 3.4, 3.5, 3.6, and 3.7 Sections 3.4, 3.5, 3.6, and 3.7

Problems and Solutions

Problems for Lecture 14 (PDF)

Solutions for Lecture 14 (PDF)

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Topics

Image excerpted from Lecture 8 Notes 

  1. Ionization Energy and Photoelectron Spectroscopy
  2. Electron Affinity

Lecture Video

The periodic table is to chemistry like the laws of motion are to physics. In this lecture, we discover the secrets of the periodic table and meet the elements.

Lecture Notes

Notes for Lecture 8 (PDF)

Clicker Questions

Lecture 8 Clicker Questions (PDF)

Textbook Reading

TOPICS 5th EDITION 4th EDITION
Electronic Structure and the Periodic Table Section 1.14 Section 1.14
Atomic Radius Section 1.15 Section 1.15
Ionic Radius Section 1.16 Section 1.16
Ionization Energy Section 1.17 Section 1.17
Electron Affinity Section 1.18 Section 1.18
Diagonal Relationships Section 1.20 Section 1.20

Problems and Solutions

Problems for Lecture 8 (PDF)

Solutions for Lecture 8 (PDF)

Acknowledgement

Excerpt of “Meet the Elements” by They Might be Giants, courtesy of Idlewild / Disney Sound, used with permission. From Here Comes Science, 2009.

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Topics

Image excerpted from Lecture 9 Notes 

  1. Periodic Table (continued)
    1. Electronegativity
    2. Atomic and Ionic Radii and Isoelectronic Atoms
  2. Bonding
    1. Ionic Bonds
    2. Covalent Bonding
    3. Polar Covalent Bonds

Lecture Video

In this lecture, we complete the discussion of the periodic table and start to consider the types of bonds that are formed between elements. Chemist Kateryna Kozyrytska tells us about why the concept of electronegativity is important in the design of antibiotics.

Lecture Notes

Notes for Lecture 9 (PDF)

Clicker Questions

Lecture 9 Clicker Questions (PDF)

Textbook Reading

TOPICS 5th EDITION 4th EDITION
Ionic Bonds Sections 2.1–2.3 Sections 2.1–2.3
Covalent Bonds Sections 2.14–2.16 Sections 2.14–2.16
Lewis Structures Section 2.5–2.6 Section 2.5–2.6

Applying the Special Properties of Halogens in Drug Design

Bacteria can develop resistance to antibiotics, creating a need for current and future scientists to develop new types on antibiotics. Kateryna Kozyrytska discusses her research on proteins that catalyze a carbon-chlorine bond-forming reaction, and she describes how taking advantage of chlorine’s electronegativity may lead to new medications to fight bacteria and the other “bugs” that make us sick.

Kateryna Kozyrytska’s Personal Story

Kateryna Kozyrytska, a female biochemist born in Ukraine, describes how as a scientist she doesn’t have to choose between career and home-life like some of her peers back home, that there are examples, even at MIT, of women who have both.

Problems and Solutions

Problems for Lecture 9 (PDF)

Solutions for Lecture 9 (PDF)

Acknowledgement

Dogs Teaching Chemistry — Chemical Bonds” courtesy of Lauren Girard. Used with permission.

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