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Fall 2022 > Chemistry Chapter 5 - Organic Molecules > Flashcards

Chemistry Chapter 5 - Organic Molecules Flashcards

1
Q

What is a functional group?

A

an atom or a group of atoms within a molecule that have a specific structure and/or sequence of atoms

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2
Q

What is a base of hydrocarbons?

A

carbon and hydrogen only

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3
Q

What is the functional group C-Z single bond in a compound?

A

carbon single bonded to Z (any element)

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4
Q

What are the three classes of functional groups?

A
  1. hydrocarbons
  2. C-Z
  3. C=O
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5
Q

What is spectroscopy?

A

use electromagnetic radiation for chemical analysis

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6
Q

During IR spectroscopy, what does the wavelength of IR light absorbed by a molecule depend on?

A

the functional groups present in the molecule and the structure of the molecule

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7
Q

What is wavenumber? What is it measured in?

A

reciprocal of the wavelength measured in cm^-1

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8
Q

Why is wavenumber used?

A

energy in joules are usually very small, frequency in hertz are usually very large
wavenumber are manageable (E=hv = hc/ƛ)

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9
Q

What is the relationship between wavenumber and energy?

A

directly proportional

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10
Q

What happens to a molecule when it absorbs IR light of the proper wavelength/wavenumber?

A

bonds experience VIBRATIONAL EXCITATION from ground state to excited state
–> e- do NOT get promoted to a higher orbital

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11
Q

What is the difference between IR and UV-vis spectroscopy?

A

IR - bonds are excited by IR light/wavelength

UV-vis - electrons are excited by UV/vis light/wavelength

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12
Q

What are the two main types of molecular vibration?

A

stretching and bending

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13
Q

How are bonds vibrationally excited?

A
  • bonds within molecules are constantly vibrating at SPECIFIC FREQUENCIES about their equilibrium point at room temperature which correspond to DISCRETE ENERGY LEVELS
    –> the specific frequency depend on type of bond
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14
Q

How do different vibrational modes compare?

A

different modes of vibration vibrate with different wavenumber = different energy

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15
Q

What is the energy range for IR light?

A

5-50 kJ mol-1

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16
Q

What are the types of stretching vibrations?

A

symmetric - all atoms connected to central atom stretch and compress at the same time

asymmetric - atoms connected to central atom stretch and compress differently

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17
Q

What are the types of bending vibrations?

A

scissoring

rocking

wagging

twisting

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18
Q

What condition must the bond of a molecule be under to absorb energy from IR light?

A

frequency of IR light radiating on molecule = frequency of bond vibration = bond(s) absorb energy = increased vibration

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19
Q

Why must the frequency of IR light radiated on a molecule be equal to the frequency of bond vibration for IR spectroscopy?

A

different types of bonds have different IR absorption frequencies, so the wavelength absorbed by a molecule gives information on the molecular structure

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20
Q

What does an IR spectrometer measure?

A
  • amount of IR light ABSORBED by sample at each WAVENUMBER between approx. 4000-500cm^-1
  • plots % transmittances as a function of wavenumber
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21
Q

What do absorption and transmission mean?

A

absorption is peaks of LOW transmission

100% absorption = no light transmission
100% transmission = no light absorption

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22
Q

What is the fingerprint region?

A

1500-500cm^-1
– complex but usually unique region for any compound

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23
Q

What is the functional group region?

A

region of IR spectrum from 4000-1500 cm^-1
– functional groups can be identified

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24
Q

How are functional groups determined from a transmittance vs wavenumber IR spectrum graph?

A

characteristic absorption peaks/transmittance dips)

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25
Q

What is the frequency of vibration for a classical harmonic oscillator given by? What does the harmonic oscillator represent?

A

v=1/2π x √k/µ
– k = force constant proportional to strength/stiffness of bond
–µ = reduced mass of the molecule (kg)
–harmonic oscillator is the molecular bond

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26
Q

What is a harmonic oscillator?

A

a system (bond) that when displaced from its EQUILIBRIUM position, experiences a restoring force proportional to the extension or compression

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27
Q

What does µ equal to?

A

m1m2/m1 + m2

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28
Q

What is the relationship between k and frequency?

A

stronger bond = higher k = higher frequency

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29
Q

What is the relationship between bond strength and vibrational frequency?

A

directly proportional – strong bonds = vibrates at higher frequencies = higher wavenumber

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30
Q

How do the number/type of bonds compare in strength?

A

bonds to hydrogen > triple bond > double bond > single bond

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31
Q

Why are bonds to hydrogen the strongest type of bond?

A

hydrogen are the lightest atom = higher frequency

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32
Q

Why do triple bonds have higher wavenumber than double and single?

A

triple bonds are stronger bonds = higher frequency

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33
Q

What type of bonds are in the fingerprint region?

A

single bonds

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34
Q

How does hybridization affect bond strength?

A

bonds are stronger in the order sp3 < sp2 < sp
–> more s character = stronger bond

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35
Q

Why are bonds with more s character stronger bonds?

A

s orbitals are closer to nucleus = more e- attraction to nucleus = bond shortens = bond stronger = more energy to bond = higher wavenumber = higher frequency

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36
Q

How does mass affect frequency of vibration?

A

higher mass = slower movement = low frequency

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37
Q

What do samples of IR spectra tell us?

A

What functional groups are present AND which as NOT present

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38
Q

What do peaks in an alkane show?

A

organic compounds that contain saturated alkyl groups

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39
Q

What is a terminal alkyne? What is an internal alkyne?

A

terminal - end of molecule
internal - middle of molecule – cannot have H bonded to it

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40
Q

Why is it difficult to notice C=C of alkenes?

A

their intensity is determined by the groups attached

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41
Q

What is a sp3 C-H stretch characterized by?

A

large double peak

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42
Q

What is the structure of aromatics?

A

benzene ring

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43
Q

What does an aromatic sp2 C-H stretch look like?

A

peak just after 3000

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44
Q

What functional group do alcohols have?

A

hydroxyl (R-OH), where R is any alkyl carbon

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45
Q

How are OH characterized in IR spectra?

A

broad peaks

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46
Q

What is the absorption frequency of C-O bonds?

A

1100 cm^-1

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47
Q

What is the absorption frequency of C-C?

A

1200 cm^-1

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48
Q

What are the absorption frequencies of sp C-H, sp2 C-H, and sp3 C-H?

A

sp C-H –> 3300cm^-1

sp2 C-H –> 3100cm^-1

sp3 C-H –> 2900cm^-1

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49
Q

What is the general formula for the amine functional group?

A

R-NH2, R2NH, or R3N

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50
Q

What does the number of N-H absorption bands depend on?

A

number of H atoms connected to N

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51
Q

What is a primary amine?

A

one carbon connected to N (2 N-H)

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52
Q

What is a secondary amine?

A

two carbons connected to N (1 N-H)

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53
Q

What is a tertiary amine?

A

three carbons connected to N (no N-H)

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54
Q

What is a carbonyl group?

A

compound containing C=O

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55
Q

What does a carbonyl group look like on IR spectra?

A

sharp, strong peak – location depends on type of group

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56
Q

How can you differentiate a ketone and an aldehyde since they are both carbonyl groups in the same relative location on IR spectra?

A

aldehyde has C-H stretches in the 2700-2900 cm^-1 region

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57
Q

What are characteristics of carboxylic acids?

A

strong C=O stretch and broad O-H

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58
Q

How can esters and carboxylic acids be distinguished?

A

both have similar C=O stretches in the same location of IR spectra but carboxylic acids also have broad O-H

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59
Q

What is the difference in the shape of OH peaks of alcohols and carboxylic acids?

A

carboxylic acids are much broader than alcohol

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60
Q

How does the number of one type of bond relate to absorption/transmission?

A

more of one type of bond = larger transmission dips/absorption peaks

61
Q

What are alkanes?

A

straight or branched-chained compounds with C and H atoms and only SINGLE carbon-carbon bonds

62
Q

What is the formula for ACYCLIC alkanes?

A

CnH2n+2

63
Q

What is the compound formed for acyclic alkanes when n=1?

A

CH4 - METHANE

64
Q

What is a homologous series?

A

structurally related compounds that form new substances by adding the same atom(s)

65
Q

How is methane the start of a homologous series?

A

CH4 + any number of CH2

66
Q

How does the size of a molecule in a homologous series alter boiling point/state at room temperature?

A

larger molecule = more SA = more dispersion forces = more difficult to break bonds = higher boiling point

–> methane, ethane, propane are gases at room temperature
–> butane, pentane, hexane are liquids at room temperature

67
Q

What is a CONSTITUTIONAL ISOMER?

A

bonding sequence differences for compounds with the SAME MOLECULAR FORMULA

68
Q

Why is it important to consider constitutional isomer?

A
  • the possibilities for bonding sequences increases rapidly with molecular size (more atoms)
    –> molecular diversity
  • chemical and physical properties vary for constitutional isomers
69
Q

How can you draw constitutional isomers?

A
  • draw the longest carbon chain and shorten the chain by one carbon each type
    –> notice if the new drawing is a reflection/rotation or a new molecule
    –> 2D
70
Q

What are the three types of 3D depictions of alkanes?

A
  1. Dot-line-wedge
  2. Sawhorse projections
  3. Newman’s projections
71
Q

What is the dot-line-wedge formula for alkanes?

A

lines - bonds in the plane of the paper
dotted line - bond behind paper
wedge - bonds in from of the plane of paper

72
Q

What is the SAWHORSE projection?

A
  • in shape of sawhorse using only lines
  • useful for simple molecules only
73
Q

What is a NEWMAN PROJECTION?

A

molecule viewed along C-C bond axis
- bonds drawn in from of and along the edge of a circle
- usually used for conformations

74
Q

What are CONFORMATIONS?

A

NON-PERMANENT spatial arrangements of atoms on a molecule produced by ROTATIONS about SINGLE BONDS

75
Q

What are the two key conformations of alkanes?

A
  1. ECLIPSED - C-H bonds are aligned
  2. STAGGERED - C-H bond in from bisect that H-C-H bond angles in back
76
Q

How does the spatial (steric) repulsion compare for staggered and eclipsed conformations?

A

Staggered » minimized steric repulsion = lower energy conformation = more stable

Eclipsed » increased steric repulsion = more energy conformation = less stable

77
Q

What is the relative energy difference between staggered and eclipsed conformations? What dues this mean?

A

Energy difference is present but small – conformation s interconvert at a very fast rate; the conformations can’t be isolated in pure form

78
Q

Why does staggered have more stability? Why does have eclipsed less stability?

A

Eclipsed = C-H bonds are shorter so atoms are closer together

Staggered = C-H bonds are shorter so the atoms are farther apart

79
Q

How do eclipsed and staggered conformations compare in energy with larger molecules bonded to the carbon?

A

Highest energy/most repulsion: eclipsed with large molecules on the same axis

2nd highest energy: staggered with large molecules on close axis –GAUCHE CONFORMER

3rd: eclipsed large molecule is on different axes

4th: staggered with large molecule on perpendicular axis - ANTI CONFORMER

80
Q

What is the dihedral angle?

A

Angle between two molecules that are the same on opposite carbons

81
Q

What are cycloalkanes?

A

Hydrocarbons containing a ring of carbonatoms connected by single C-C-c bonds

82
Q

What is the general formula for all cycloalkanes that have one ring?

A

CnH2n (not CnH2+2 because two H’s must be removed to close the ring)

83
Q

What occurs in rotations of cycloalkanes?

A

Rotations around single bonds is hindered due to cycle structure but conformation changes still occur.

84
Q

How are 4 and 5 carbon cycloalkanes structured?

A

nearly in one plane with the substituents above and below this plane

85
Q

What does it mean for a ring to pucker? Why does this occur?

A

4/5 carbon cycloalkanes bend slightly out of plane to reduce eclipsed interactions

86
Q

Wear are the bonds like in cyclopropane? (angle and nature)

A

C3H6 – 60 degrees and highly strained
–> all C-H are eclipsed

87
Q

What are the bonds like in cyclobutane?

A

C4H8 – about 90 degrees
–> has puckering to reduce repulsion between adjacent eclipsed C-H bonds

88
Q

What are the bonds like in cyclopentane?

A

C5H10 – about 109.5 degrees (pentagon has 108)
–> has puckering to reduce repulsion between adjacent eclipsed C-H bonds

89
Q

What is the hybridization of carbons In a cycloalkane?

A

sp3 (4 single bonds)

90
Q

What are the conformations of cyclohexane? What is the molecular geometry of the carbon atoms?What causes the conformations?

A

boat and chair conformation where all carbons have normal tetrahedral geometry (109.5 approx)
–> caused by bond rotation

91
Q

What does the boat conformation look like?

A

CYCLOHEXANE
-pair of two adjacent lowered carbons are eclipsed
- other two carbons undergo flagpole interactions

92
Q

What does the flagpole interaction in boat conformation cause? How many C-H bonds are each of the alkane conformation types?

A

flagpole interactions cause steric hinderance – atoms bump into each other = repulsion = higher energy = less stability = UNFAVOURABLE

2 ECLIPSED
4 STAGGERED
–> <0.1% boat conformation in a conformation equilibrium mixture

93
Q

What are the alkane conformations in the chair conformation of cyclohexane?

A

all C-H bonds are staggered = no flagpole interactions

94
Q

Where are the positions of substituents of carbons in cyclohexane? How many of each?

A

6 axial and 6 equatorial (one of each type on each carbon)

95
Q

Which constituent position in more favourable? Why? What does this mean of large molecules?

A

equatorial b/c there is more space – preference for large molecules for less steric hinderance

96
Q

How do substituents ensure that there is 109.5 degrees (approx) between them?

A

if equatorial is down, axial will be slightly up on the same carbon

if equatorial is up, axial will be slightly down on the same carbon

FOR ADJACENT CARBONS: one carbon up means next carbon down; one carbon slightly up means next carbon slightly down

97
Q

What happens to the substituents during a ring flip for a cyclohexane in chair conformation?

A

equatorial becomes axial and vice versa –> substituents that are above the ring stays up and the substituents that are below the ring stays below

98
Q

How do large molecules impact ring flips?

A

large molecules prefer equatorial position for chair conformations are interconverting = one char conformation will be more stable than the other

99
Q

Why are large molecules unfavourable in axial positions?

A

two carbons in the same direction have significant repulsion

100
Q

What is the difference between conformations and constitutional isomerism?

A

conformations: same substance, interconvert through bond rotations, same connectivity, same bonding sequence

constitutional isomerism: different substance, not rotation, different connectivity, different bonding sequenct

– constitutional isomers may have their own conformations

101
Q

Can cycloalkanes have constitutional isomers?

A

YES – atoms/molecules bonded to the ring can be on different carbons to make different substances, connectivity, and bonding sequences

102
Q

What is STEREOISOMERISM?

A

SAME: formula, bonding sequence, constitutional isomer, connectivity

DIFFERENT: spatial arrangements

103
Q

When does stereoisomerism occur for cycloalkanes?

A

when the cycloalkane ring has two or more NON-HYDROGEN substituents on DIFFERENT CARBONS

– these substituents can occupy TWO different positions relative to the (approx) ring plane

104
Q

What are the two positions of stereoisomers in cycloalkanes? What do they mean?

A

Cis isomer - two substituents on the same side of the ring plane (both above or both below)
Trans isomer - two substituents on opposite sides of the ring plane (one above and one below)

105
Q

Are stereoisomers interconverting? Why?

A

NO! the substituents are oriented in space differently and cannot interconvert by single bond rotations

–> each stereoisomer can have their own conformations which are interconverting

106
Q

What are ALKENES?

A

hydrocarbons with one or more DOUBLE BOND

107
Q

What is the general form of homologous alkenes with one C=C bond?

A

CnH2n

108
Q

What are ALKYNES?

A

hydrocarbons with one or more TRIPLE BOND

109
Q

What Is the general form of homologous alkynes with one C≡C?

A

CnH2n-2

110
Q

What does it mean for a hydrocarbon to be saturated/unsaturated? What is an example of an unsaturated hydrocarbon?

A

saturated - maximum number of possible hydrogens
unsaturated - less that the max number of hydrogen
–> alkenes and alkynes

111
Q

How is a unit of unsaturation measured? What will result from this?

A

2 hydrogens removed = 1 unit of unsaturation
each unit may create a π bond or a ring

2 units: ring with a double bond, 2 double bonds, 1 triple bond

112
Q

What is the hybridization of the carbon in a C=C?

A

sp2 - trigonal planar (bonded to three atoms) bond angle 120

113
Q

Why is the C=C planar?

A

each of the carbons are sp2 with three obtains form sigma bonds and the last orbital overlaps with the other carbons orbital (π)

114
Q

What is the hybridization of the carbons in a C≡C?

A

sp - linear (bonded to two atoms) bond able 180

115
Q

Why is C≡C planar?

A

each of the carbons have sigma bonds (2) and the remaining p orbitals overall with the other carbon resulting in two pi bonds

116
Q

What is the consequence of C=C bond’s inability to rotate?

A

geometric isomerism - cis-trans isomerism

117
Q

What is cis isomerism in an alkene? What is trans isomerism in an alkene?

A

two identical substituents on the same side

two identical substituents on opposite sides (diagonal)

118
Q

Why can’t there me trans arrangement in small rings?

A

7C or less – trans arrangement is strained, but cis geometry is possible

119
Q

How can you determine how many cis-trans isomers a molecule with C=C has (alkene)?

A

2^n where n is there number of π bonds
–> the actual number may be less because the C is bonded to the same substituents on all sides

120
Q

What is retinal?

A

form of vitamin a found in the bonds linked to vision
– contains 4 C=C bonds in trans configuration

121
Q

Can cis and trans isomers interconvert? What does that mean for retinal?

A

NO!
–>enzyme required to break pi bond in trans retinal
–> rotate part of the molecule about the resulting C-C bond
–> restore the pi bond to create cis-retinal

122
Q

Why is the E-Z system used? How is it used?

A

describe geometric (cis-trans) isomers without ambiguity
–> uses priority rules: if the substituents with the higher priorities are found on the same side of the double bond it is Z; if the substituents with the higher priorities are found on opposite sides of the double bond it is E

123
Q

What are the 3 rules of E-Z Nomenclature?

A
  1. Look at the atom bonded DIRECTLY to alkene C. HIGHER ATOMIC # = HIGHER PRIORITY

if there is a tie

  1. Look at the atoms bonded DIRECTLY to the ATOMS that is tied in either side and write a list of what they are bonded to;
    HIGER ATOMIC # = HIGHER PRIORITY
  2. Phantom Rule: DOUBLE/TRIPLE bonded atoms are given single bond equilvilencies (double bond = two single bonds and triple bond = three single bonds) –when writing the list of atoms bonded to it, include the atom with the number assigned to its bond (cancel out the same ones)
124
Q

Is E always trans?

A

Not always! Yes for simple molecules (one c=c double bond) but not for complex molecules (bk ex)
— small rings cannot be assigned cis/trans, but can still be assigned E/Z

125
Q

What is chirality?

A

Another type of stereoisomer
- chiral objects have NO plane off symmetry so their mirror images are NON-SUPERIMPOSABLE

126
Q

What is achirality?

A

Have a plane of symmetry cuts the object in half
—these half’s are mirror images
— SUPERIMPOSABLE

127
Q

What are enantiomer?

A

pair of molecules that have
- same molecular formula
- same bonding sequence
- non-superimposable mirror images of each
—STEREOISOMERS
- Chiral - CHXYZ (all 4 bonds to the C are different substituents)

128
Q

When is a molecule not an enantiomer?

A
  • achiral (molecule and mirror image are the same)
  • molecules have at least two of the same substituents
    —CH3X and CH2XY
129
Q

Can enantiomer interconvert?

A

Not an room temperature because they are different compounds

130
Q

Do enantiomer have the same physical and chemical properties?

A

Yes besides:
- different behaviour on plane-polarized light
- react differently with other chiral compounds

131
Q

What is a stereocentre/chiral centre?

A

Atom bonded to 4 different groups in a TETRAHEDRAL geometry
— ex. Carbon bonded to 4 different substituents

132
Q

When is a carbon atom in a RING a CHIRAL centre?

A
  1. Has 2 different substituents OUTSIDE the ring
  2. Path around the ring is traced from that carbon in one direction is DIFFERENT from the path traced in the other direction
133
Q

What is a FISCHER PROJECTION?

A
  • representations of 3D structure of molecules with chiral centres shown with 90 degrees (but true bond angles are 109.5)
    — vertical = behind page plane
    — horizontal = out of page
134
Q

What is R/S DESIGNATION?

A
  • Used to specify the 3D configuration of stereocentres (identify which enantiomer from the pair)
135
Q

What are the R/S designation rules?

A

Same as E/Z (assign priorities to the 4 substituents on chiral carbon)

  1. Lowest (4) behind plane (H)
  2. Determine the 1-2-3 direction
  3. R - CLOCKWISE S-COUNTERCLOCKWISE
136
Q

Why are biologically active molecules in living organisms found in only on stereoisomer form?

A

In vivo synthesis is is catalyze by CHIRAL PROTEINS -ENZYMES

137
Q

Why are chiral proteins/enzymes needed?

A

Physiological receptors’s active sites only interact with one particular enantiomer

138
Q

Why must drugs be sold in the enantiomerically pure form?

A

Inactive enantiomeric form of a drug can interact with the body in a harmful way

139
Q

What is THALIDOMIDE?

A
  • drug sold to pregnant women with one stereocenter and a mixture of S and R forms
  • S = anti nausea
  • R = birth defects
140
Q

How can the number of maximum stereoisomers of a molecule be calculated?

A

2^n where n is the number of chiral centres
— maximum is not always attained

141
Q

What is the L-series sugars?

A

8 stereoisomers of the D series sugars

142
Q

Can there me cis-trans and R,S stereoisomerism simultaneously?

A

Yes (pg78)
- chiral centres cause R,S
- double bonds cause cis-trans
— in the same molecule

143
Q

What does it mean for a photon to be plane-polarized?

A

All wave oscillate in the SAME plane (normal sunlight is not plane polarized, but can be polarized by passing it through a polarizer-filter)

144
Q

How does a polarizer work?

A

Blocks all photons except those that oscillate in a certain plane

145
Q

What does a chiral compound do to a plane-polarized light?

A

Rotates the plane that the light propagates at

146
Q

Is the rotation of the plane of light different for each enantiomer?

A

Yes!
- rotors the plane of polarization in opposite directions but what equal magnitude
— this is why enantiomers are called OPTICAL ISOMERS

147
Q

Do achiral molecules rotate the plane of polarized light?

A

No

148
Q

How are the different rotations of polarized light distinguished?

A

plane or polarization is rotated by optical isomer to the RIGHT (+)

plane of polarization is rotated by optical isomer to the LEFT (-)

— as seen by an observer whom the light is approaching
— same angle for each, one is positive and one is negative

Fall 2022 (12 decks)

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