MCB124lecture2

MCB124lecture2 - What do we mean by Structure? - Need to...

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MCB 124 What do we mean by Structure? - Need to define a labeling scheme that allows us to uniquely define a particular molecule, protein, metal etc - Usually aim to find the smallest unique building block of the structure to define it - Basic principle of all the sciences is that if you can define the structure in this way, you can predict function - Used to design everything from the fastest computers to the newest drugs Started with physics, now need chemistry!
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MCB 124 There are four major types of non-covalent bonds: (1) Charge-charge interactions (ionic bonds) (2) Hydrogen bonds (3) Van der Waals forces (4) Hydrophobic interactions And there is the covalent bond: (5) Covalent bonds Chemical Bonds
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MCB 124 Trends in Atomic Sizes
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MCB 124 The Concept of Electronegativity Proposed by Nobel Laureate Linus Pauling (1901-1994) Proposed by Nobel Laureate Linus Pauling (1901-1994) Helps determine what types of bonding will take place between two atoms and the forces that occur between molecules
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MCB 124 Electronegativity Bonds between atoms with a large electronegativity difference (greater than or equal to 1.7) are usually considered to be ionic , while values between 1.7 and 0.4 are considered polar covalent . Values below 0.4 are considered non-polar covalent bonds , and electronegativity differences of 0 indicate a completely non-polar covalent bond.
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MCB 124 Ionic Bonding • Electrostatic interactions between two charged ions • Can be the strongest type of noncovalent forces • Can extend over greater distances than other forces • Are non-directional forces • Charge repulsion occurs between similarly charged ions
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MCB 124 Force vs. Separation Distance Attraction comes from the electrostatic interaction, repulsion comes from overlap of the electron orbitals
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MCB 124 Energy vs. Separation Distance Separation at the energy minimum corresponds to the equilibrium bond-length
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MCB 124 Essentially complete electron transfer from an element of low ionization energy (metal) to an element of high affinity for electrons (nonmetal) Therefore, ionic compounds exist primarily between metals at left of periodic table (Groups 1A and 2A and transition metals) and nonmetals at right (O and halogens). Structures that form depend on the sizes of the ions involved – face- centered cubic, hexagonal etc Ionic Bonding leading to Crystal Structures
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MCB 124 If bonds in the molecule are polar, some atoms will have partial electrostatic charges, which attract if opposite and repel otherwise. E is the Binding Energy Q i and Q j are the partial atomic charges for i and j, r ij is the separation distance between Q and Q j ε is the dielectric constant of the solute k is a units constant (k=2086 kcal/mol) Electrostatics between Molecules
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MCB 124 Molecules that have HF, OH or NH groups have particularly strong intermolecular attractions – unusually high melting and boiling points – unusually high solubility in water this kind of attraction is called a Hydrogen Bond Hydrogen Bonds
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MCB 124 How do we get Hydrogen Bonds?
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MCB124lecture2 - What do we mean by Structure? - Need to...

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