• Nomenclature
  1. identify the longest carbon chain containing the highest-order functional group
  2. number the chain
  3. name the substituents
  4. assign a number to each substituent
• Naming substituents and functional groups

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• isomers of this type are the least similar of isomers
  • only share molecular formula and weight
  • don't share connectivity
  • vary in physical and chemical properties

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• subdivision of stereoisomers
  • share same connectivity, but differ in how these atoms are arranged in space
• conformational are most similar of all isomers and are in fact the same molecule aside from natural rotation about single (σ) bonds
• described best using newman projections which show angles of atoms and groups in relevance to each other
• best thought of in terms of straight-chain and cyclic conformations
  • straight-chain: staggered/anti, gauche, (totally) eclipsed
  • cyclic: referred to be conformational shapes; chair, envelope, boat, puckered, etc.

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• way of thinking about conformational isomers as applied to straight chains (as opposed to cyclic molecules)
• looks at angles separating different atoms/functional groups from one another
  • staggered - no overlap of atoms along line of sight
    • anti - particular type of staggered conformation in which largest functional groups are 180° from one another; most stable
    • gauche - particular type of staggered conformation in which largest functional groups are w/in 60° of one another; less stable
  • eclipsed - conformation in which groups or atoms are overlapping
    • eclipsed - largest groups are 120° apart (but are overlapping w/ other groups/atoms)
    • totally eclipsed - largest groups are 0° apart (totally overlapping); least stable

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• conformational interconversion barriers are small and easily overcome at room temperature

• way of thinking about conformational isomers as applied to cyclic molecules (as opposed to straight-chain)
• described by particular terms relating to overall shape
• stability of conformation is based on ring strain(based on three types of strain)
  • angle strain - when bond angles deviate from ideal values through compression or stretching
  • torsional strain - when cyclic molecules must assume conformations that have eclipsed or gauche interactions
  • non-bonded strain (van der Waals repulsion) - non-adjacent atoms or groups compete for same space
• cycloalkanes attempt to adopt non-planar conformations to alleviate strain
• cyclohexane's most stable form is known as the chair conformation
  • atoms surrounding main ring are referred to by their orientation with the plane of the ring
    • axial groups/atoms are perpendicular to plane of ring and stick up or down
    • equatorial groups/atoms are parallel to plane of ring and stick out
  • bulkiest groups surrounding cyclohexane favor the equatorial position to reduce flagpole interactions arising from van der waals repulsion
  • chair flip - when cyclohexane goes from one chair form to another
    • must pass through half-chair conformation (high energy)
    • at end of flip, all axial groups become equatorial and vice versa

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• subdivision of stereoisomers (other being conformational)
• these isomers are less similar as they must undergo a break and reformation in covalent bonds to change from one form to another
• determined based on their ability to be superimposed over one another and whether or not they are mirror images
  • enantiomers - non-superimposable mirror images
  • diastereomers - non-superimposable isomers that are not mirror images

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• optical isomers are molecules in which spatial arrangement of groups affects the rotation of plane-polarized light passing through
• rely on chirality
  • if mirror image of molecule/center cannot be superimposed on original molecule, then it is chiral
  • only chiral molecules can be considered optically active
• mixtures of chiral molecules of opposite types (enantiomers) in equal ratios create optically inactive mixture termed racemic
  • (+) - compound that rotates plane of polarized light to right - dextrorotatory (d-)
  • (-) - compound that rotates plane of polarized light to left - levorotatory (l-)
  • can only be determined experimentally and not by looking at the molecule's structure

• subset of configurational isomers that are nonsuperimposable mirror images of one another
• must have opposite configurations at every chiral center
• have identical chemical and physical properties
  • only differ in optical activity and reactions in chiral environments
    • optical activity
      • (+) vs. (-) designation
    • reactions in chiral environments
      • if racemic mixture reacted w/ (+), (+,+) and (-,+) are formed
      • if racemic mixture reacted w/ (-), (-,-) and (+,-) are formed

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• subset of configurational isomers that are non-superimposable and non-mirror images of each other
• can only occur if molecule has two or more chiral centers
  • for any molecule w/ n chiral centers, 2ⁿ possible diastereomers(and stereoisomers) exist
• have different chemical and physical properties
  • can behave in chemically similar ways due to presence of same functional groups
  • consistently different in physical properties due to differing spatial arrangements
• diastereomers are optically active, but knowing the way that one diastereomer rotates polarized light, gives no indication as to how another might
• by pulling individual enantiomers from pairs and comparing them to enantiomers from other pairs, we can identify diastereomers
  • I and II are not diastereomers of one another, but I and III or I and IV are

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• a molecule containing one or more chiral centers that is not optically active due to the presence of an internal plane of symmetry
• molecular equivalents of racemic mixtures - chiral centers cancel out

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• configuration of stereoisomer - spatial arrangement of atoms or groups in molecules
• relative configuration - configuration of chiral molecule in relation to another chiral molecule
  • often through chemical conversion
  • used to determine whether molecules are enantiomers, diastereomers or same molecule
  • require comparison of molecules
• absolute confirmation - describes exact spatial arrangement of atoms or groups independent of other molecules
  • can be described using E/Z, cis/trans, and R/S

• Cis/Trans system
  • used to describe geometric isomers that are a particular types of diastereomers
  • substituents must differ in position around immovable bond
  • really only applies to double bonds or cyclic molecules w/ one substituent on each side of the bond
  • indicates different molecules that cannot interconvert w/out breaking of a pi bond
  • cis - same side
  • trans - opposite sides

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• E/Z system
  • similarly used to describe geometric isomers, but can include molecules w/ more than one substituent on either side of the immovable bond
  • E (entgegen or opposite) - two highest-priority substituents are on opposite sides of bond
  • Z (zusammen or together) - two highest-priority substituents on same side of bond

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• used for chiral centers in molecules
• R (rectus - right) and S (sinister - left)
• To determine
  1. assign priority to groups surrounding center
  2. arrange molecule in space with lowest priority group facing back
  3. connect 1→2, 2→3, and 3→1 using arrows to create circle
  4. determine directionality of circle (clockwise or counterclockwise)
     • Clockwise means that center must receive R  designation
     • Counterclockwise means that center must receive S designation
  5. Name molecule by putting (R) and (S) in parentheses and separating from rest of name by hyphen
     • (R,S)-1,3-etc.

• formed when two atomic orbitals combined
• obtained mathematically by adding or subtracting the wave functions of the atomic orbitals
  • if signs of wave functions are same, lower-energy bonding orbital produced
  • if signs of wave functions are opposite, high-energy antibonding orbital produced

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• when formed by head-to-head or tail-to-tail overlap, resulting bond is called σ bond (single bond)
• when two p-orbitals line up in parallel, their electron clouds can overlap to form π bond
  • are extremely weak bonds(in comparison to σ) and don't form unless σ bond is present
  •  1 π bond w/ a σ creates double bond
  • 2 π bonds w/ a σ create triple bond

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• accounts for why a molecules like methane which takes 2 electrons from 2s orbital, one from the p_x-orbital, and one from the p_y-orbital (different energies) still forms 4 equivalent bonds
• these orbitals are formed by mixing different types of orbitals to produce a new orbital with hybrid s and p character
• sp³
  • tetrahedral geometry
  • no unhybridized p-orbitals to form π bonds
  • accomplished by promoting one 2s electron into 2p_z-orbital to produce four valence orbitals containing one electron each
  • 25% s character and 75% p character

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• sp²
  • trigonal planar geometry
  • one unhybridized p-orbital can be used to form one π bond
  • one s-orbital is mixed w/ two p-orbitals and 3 sp² orbitals are formed
  • bonds are 120° apart
  • 33% s and 67% p character
• sp
  • linear geometry
  • two unhybridized p-orbitals can be used to form two π bonds
  • one s-orbital is mixed w/ one p-orbital to form two sp orbitaals
  • 50% s and 50% p character
  • oriented 180° apart
  • can be triple bond or two single bonds

• delocalization of electrons that occurs in molecules w/ conjugated bonds
  • imparts increased stability
  • can also give a bond partial double-bond character like in proteins (making it immovable)
• conjugation - alternating single and double/triple bonds
  • allows for alignment of a number of unhybridized p-orbitals along backbone of molecule
  • π electrons can delocalize throughout this p-orbital system
• actual structures of molecules with resonance forms is something between all possible resonance forms
  • some forms are favored based on stability giving molecules more character of one form
    • lack of formal charges
    • formation of full octets on highly electronegative atoms (O or N)
    • stabilization of + and - charges through induction and aromaticity