5.1 Biological Activity and Molecular Shape

Molecular recognition allows biomolecular structures to recognize and react when a particular molecule with a specific shape binds to a part of the structure known as an active site.

Lewis structures account for the bonding in molecules and polyatomic ions - they show what atoms are connected but they don’t show how the atoms are oriented in three dimensions or the overall shape.

Bond angle: the angle in degrees defined by lines joining the centers of two atoms to a third atom to which they are chemically bonded.

5.2 Valence-Shell Electron-Pair Repulsion Theory

VESPR is based on the principle that electrons have negative charges and repel each other and applies that idea by assuming that valence electrons are arranged around central atoms to minimize repulsions.

Electron-pair geometry: relative positions in 3-D space of all bonding and lone pairs of valence electrons

Molecular geometry: relative positions of atoms in a molecule

If no lone pairs are present, the electron-pair geometry is the same as the molecular geometry.

Central Atoms with No Lone Pairs

Steric Number (SN): is the sum of the number of atoms bonded to that atom and the number of lone pairs on it

• if the central atom has no lone pairs, the steric number is equivalent to the number of atoms bonded to the central atom

Linear pair: SN=2, three atoms in a straight line, angle between two bonds is 180

Trigonal planar: SN=3, three bonding atoms are as far apart as possible, bond angle is 120

Tetrahedral: SN=4, four bonding pairs form angles of 109.5

Trigonal Bipyramidal: SN=5, bond angles between equatorial are 120, angle between equatorial and axial bond is 90 and the bond between the two axial is 180

Octahedral: SN=6, two pairs in each set are 180 to each other and 90 to the other two pairs.

Central Atoms with Lone Pairs

Angular or Bent: SN=3 (two bonds, one lone pair) with a bond angle of 117

• repulsion between lone pairs and bonding pairs is greater than repulsion between bonding pairs

• repulsion caused by lone pair is greater than repulsion caused by double bond

• repulsion caused by a double bond is greater than repulsion caused by a single bond

• two lone pairs of electrons on a central atom exert a greater repulsive force on the atom’s bonding pairs than does one lone pair

Trigonal Pyramidal: SN=4 (3 bonds, one lone pair) with an angle of 107

Seesaw: SN=5 (4 bonds, one lone pair) has an angle of <90, <120

T-shaped: SN=5 (3 bonds, 2 lone pairs) has an angle of <90

Linear: SN=5 (2 bonds, 3 lone pairs) has an angle of <180

Square Pyramidal: SN=6 (5 bonds, 1 lone pair) has an angle of <90

Square Planar: SN=6 (4 bonds, 2 lone pairs) has an angle of 90

5.3 Polar Bonds and Polar Molecules

Bond Dipole: separation of charge caused by the electronegativity difference between two atoms

Permanent Dipole: the permanent separation of charge in a molecule resulting from unequal distributions of bonding and/or lone pairs

• the more polar a molecule, the more strongly it aligns with an electric field

5.4 Valence Bond Theory and Hybrid Orbitals

Valence bond theory: evolved in 1920s when Pauling merged quantum mechanics with Lewis’ model; states that a chemical bond forms when the atomic orbitals of two atoms overlap and are then attracted to the nuclei of both bonded atoms, lowering potential energy and greater stability.

Sigma Bond: a covalent bond in which the highest electron density resides between two atoms along the internuclear axis

Pi Bond: covalent bond in which electron densities are highest above and below the internuclear axis; one bond formed through two points of contact

Hybridization: mixing of atomic orbitals to generate new sets of orbitals that may form sigma bonds with other atoms

• repulsion is minimized when distance is maximized

5.5 Molecules with Multiple “Central” Atoms

Molecular Recognition: process by which molecules interact with receptors or active sites in your tissues, usually does not involve forming covalent bonds

Conjugation: alternating single and multiple bonds in molecular compounds in which adjacent atoms have unhybridized p orbitals

Intercalation: when polycyclic aromatic hydrocarbons (PAH) bind to cellular DNA

5.6 Chirality and Molecular Recognition

Isomers: compounds with the same chemical formula but different molecular structures

• stereoisomers: identical lewis structures but three dimensional bonds/orientations are not the same

• enantiomers: same composition, bonds but different three-dimensional shapes; nonsuperimposable mirror images

• diasteromers: stereoisomers that are not enantiomers

• optical isomers: stereoisomers that can rotate plane polarized light (electric fields oscillating in one plane) are optically active

Chirality: also known as stereocenter, contains 1+ chiral atoms, determined by the presence of any sp3 carbon groups bonded to four different atoms or groups of atoms. will be superimposable on its mirror image

Racemic Mixture: 50:50 mixture of two enatiomers

5.7 Molecular Orbital Theory

Molecular Orbital Theory: bonding theory based on the mixing of atomic orbitals of similar shapes and energies to form molecular orbitals that belong to the molecule as a whole; total number of molecular orbitals must match the number of atomic orbitals involved in forming them

• molecular orbitals are wave functions that represent discrete energy states inside molecules

  • lowest energy orbitals fill first

  • electrons can undergo absorption and emission

• bonding orbitals: lobes of high electron density that lie between bonded pairs of atoms, lower energies than the atomic orbitals that combined to form them; closer in energy to atomic orbitals of more electronegative atom

• antibonding orbitals: lobes of high electron density not located between bonding atoms, higher energies than the atomic orbitals that combined to form them; closer in energy to atomic orbitals of less electronegative atom

Sigma molecular orbital: oval shaped and spans two atomic center, two electrons create a single σ bond

• the higher energy antibonding molecular orbital is designated σ *

Pi molecular orbital: mixing of molecular orbitals oriented above/below or front/behind internuclear axis

• high-energy is designated π*,* electrons occupying π* detract from π bond formation

Bond order: .5(number of bonding electrons - number of antibonding electrons)

Diamagnetic: substances are repelled slightly by a magnetic field

Paramagnetic: substance is attracted by a magnetic field, increases as amount of unpaired electrons increases