1. structure and bonding a review of needed material
TRANSCRIPT
1. Structure and Bonding
A Review of Needed Material
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Organic Chemistry
“Organic” – until mid 1800’s referred to compounds from living sources (mineral sources were “inorganic”)
Wöhler in 1828 showed that urea, an organic compound, could be made from a inorganic materials
Organic compounds are those based on covalently bonded carbon and study of their structures and reactions.
NH4Cl AgNCO H2N-C-NH2
OAgCl+ heat +
Ammoniumchloride
Silvercyanate
Urea Silverchloride
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Atomic Structure
Structure of an atom Nucleus = assigned a positive charged, very dense,
protons and neutrons in it and small (10-15 m), deflects an alpha particle shot at it.
Electrons = therefore are negatively charged, occupy allowed energies (sometimes called an electron cloud) (10-10 m across) around nucleus … and are not “orbiting” the nucleus … Ahhhhh see page 4!
Diameter is about 2 10-10 m (200 picometers (pm)) [the unit angstrom (Å) is 10-10 m = 100 pm]
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Isotopes
Isotopes are atoms of the same element that have different numbers of neutrons and therefore different mass numbers
Nuclear “spin” occurs when an odd number of nuclear particles are present.
The spin has a specific energy when placed in a magnetic field.
This energy is characteristic of the isotope and its environment … and can be detected, characterized, and used to determine which atoms are bonded to each other in a pure substance! NMR - Yaaahooo
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Atomic Structure: Orbitals
Quantum mechanics: describes electron energies by a wave equation A Wave function, , is a solution of wave equation A plot of 2 describes probable electron density The Shapes that come from all this math are
called orbitals ( 2 ). We pick the solutions that work and through the rest out.
We can mathematically combine these solutions to make other orbitals at our whim – again, we use the ones that work and leave the rest out:
HYBRID ORBITALS!
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It’s the Filled Orbitals – Stupid! Orbitals have an energy order to them … I hate the word “SHELL” Each primary quantum number denotes increasing energy of the
electrons within them and contain different numbers and kinds of orbitals
Each orbital can be occupied by two electrons n =1 contains one s orbital, denoted 1s, holds only two electrons n = 2 contains one s orbital (2s) and three p orbitals (2p), eight
electrons n = 3 contains an s orbital (3s), three p orbitals (3p), and five d orbitals
(3d), 18 electrons
Eliminate your idea of “filled shells” because n = 3 shell is very happy not being filled and only having 8 electrons. It is the filled orbitals that cause stability. Filled s and p orbitals are the ones we are most interested in with organic chemistry.
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Shapes of Atomic Orbitals
Four different kinds of orbitals are useful to discuss s, p, d, and f s and p orbitals most important in organic chemistry
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Chemical Bonding Theory
Observation: Carbon makes four bonds and has yet to be observed to ever have 5 bonds that are isolable.
Observation: 2-chlorobutane has two isomers
Explanation: Carbons with 4 bonds = tetrahedral
Note that a wedge indicates a bond is coming forward
Note that a dashed line indicates a bond is behind the page
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Chemical Bonds
Atoms form bonds because the compound that results is more stable than the separate atoms.
Bond Energy =
Bond Length
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Valence Bond Theory
Valence electrons are what make bonds. …
Lewis structures show valence electrons of an atom as dots
First bond cylindrically symmetrical, sigma () bond
Second and third bonds … called pi () bonds …
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Number of Covalent Bonds
Atoms with one, two, or three valence electrons form one, two, or three bonds and the empty p orbital
does not bond directly but is available to accept electron density – Lewis Acid!
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Number of Covalent Bonds
Atoms with four or more valence electrons form as many bonds as they need electrons to fill the s
and p orbitals = octet rule
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Valence Electrons of Boron
Boron has three valence electrons (2s2 2p1), forming three bonds (BF3)
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Valence Electrons of Carbon
Carbon has four valence electrons (2s2 2p2), forming four bonds (CH4)
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Valence of Nitrogen
Nitrogen has five valence electrons (2s2 2p3) but forms only three bonds (NH3)
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Valence Electrons of Oxygen
Oxygen has six valence electrons (2s2 2p4) but forms two bonds (H2O)
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Hybrid orbitals – Reorganization of orbital energies! In CH4, all C–H bonds are identical (tetrahedral) Each C–H bond has a strength of 438 kJ/mol and bond
length of 110 pm Bond angle: each H–C–H is 109.5°, the tetrahedral
angle.
Explanation: sp3 hybrid orbitals: s orbital and three p orbitals combine to form four equivalent orbitals (sppp = sp3), Pauling (1931) arranged in a tetrahedral array.
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Pictures – hybrid orbitals
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Bonding Ethane
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Bonding Ethene
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Bonding in Ethyne
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What about lone pairs?
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Molecular Orbital Theory
Helps us render the idea that the electrons are lowering in energy when bonds form. Best in 2 electron scenerios!
Bonding
Anti-bonding
But really … I have never had to use these ideas to remember or derive anything in all 10+ organic chemistry classes I have taken or with any of the organic synthesis I have accomplished.2 patents32 anticancer compounds synthesized4 new synthetic pathways7 novel reactions yielding >93% yield from others work
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What works!
• Thermodynamics, • Bond Energies - Will it even work• Equilibrium – Can you get enough of it
• Kinetics• Is the energy barrier to high?• Which of the “X” possible reactions will win?
• Polarity in molecules• Who likes whom?• Consonant vs. Dissonant synthesis
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Summary Organic chemistry – chemistry of carbon compounds
Atom: positively charged nucleus surrounded by negatively charged electrons
Electronic structure of an atom described by wave equation Electrons occupy orbitals around the nucleus with specific energies. Different orbitals have different allowed energies and different shapes
s orbitals are spherical, p orbitals are dumbbell-shaped
Covalent bonds - electron pair shared between two atoms are lower in energy
Valence bond theory – Valence electrons to the bonding
Sigma () bonds - Circular cross-section and are formed by head-on interaction
Pi () bonds – “dumbbell” shape from sideways interaction of p orbitals
Atoms use hybrid orbitals to form bonds in organic molecules. tetrahedral geometry has four sp3 hybrid orbitals planar geometry uses three equivalent sp2 hybrid orbitals and one unhybridized p orbital linear uses two equivalent sp hybrid orbitals with two unhybridized p orbitals