Chemistry Chapter 5 - Organic Molecules Flashcards
What is a functional group?
an atom or a group of atoms within a molecule that have a specific structure and/or sequence of atoms
What is a base of hydrocarbons?
carbon and hydrogen only
What is the functional group C-Z single bond in a compound?
carbon single bonded to Z (any element)
What are the three classes of functional groups?
- hydrocarbons
- C-Z
- C=O
What is spectroscopy?
use electromagnetic radiation for chemical analysis
During IR spectroscopy, what does the wavelength of IR light absorbed by a molecule depend on?
the functional groups present in the molecule and the structure of the molecule
What is wavenumber? What is it measured in?
reciprocal of the wavelength measured in cm^-1
Why is wavenumber used?
energy in joules are usually very small, frequency in hertz are usually very large
wavenumber are manageable (E=hv = hc/ƛ)
What is the relationship between wavenumber and energy?
directly proportional
What happens to a molecule when it absorbs IR light of the proper wavelength/wavenumber?
bonds experience VIBRATIONAL EXCITATION from ground state to excited state
–> e- do NOT get promoted to a higher orbital
What is the difference between IR and UV-vis spectroscopy?
IR - bonds are excited by IR light/wavelength
UV-vis - electrons are excited by UV/vis light/wavelength
What are the two main types of molecular vibration?
stretching and bending
How are bonds vibrationally excited?
- 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
How do different vibrational modes compare?
different modes of vibration vibrate with different wavenumber = different energy
What is the energy range for IR light?
5-50 kJ mol-1
What are the types of stretching vibrations?
symmetric - all atoms connected to central atom stretch and compress at the same time
asymmetric - atoms connected to central atom stretch and compress differently
What are the types of bending vibrations?
scissoring
rocking
wagging
twisting
What condition must the bond of a molecule be under to absorb energy from IR light?
frequency of IR light radiating on molecule = frequency of bond vibration = bond(s) absorb energy = increased vibration
Why must the frequency of IR light radiated on a molecule be equal to the frequency of bond vibration for IR spectroscopy?
different types of bonds have different IR absorption frequencies, so the wavelength absorbed by a molecule gives information on the molecular structure
What does an IR spectrometer measure?
- amount of IR light ABSORBED by sample at each WAVENUMBER between approx. 4000-500cm^-1
- plots % transmittances as a function of wavenumber
What do absorption and transmission mean?
absorption is peaks of LOW transmission
100% absorption = no light transmission
100% transmission = no light absorption
What is the fingerprint region?
1500-500cm^-1
– complex but usually unique region for any compound
What is the functional group region?
region of IR spectrum from 4000-1500 cm^-1
– functional groups can be identified
How are functional groups determined from a transmittance vs wavenumber IR spectrum graph?
characteristic absorption peaks/transmittance dips)
What is the frequency of vibration for a classical harmonic oscillator given by? What does the harmonic oscillator represent?
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
What is a harmonic oscillator?
a system (bond) that when displaced from its EQUILIBRIUM position, experiences a restoring force proportional to the extension or compression
What does µ equal to?
m1m2/m1 + m2
What is the relationship between k and frequency?
stronger bond = higher k = higher frequency
What is the relationship between bond strength and vibrational frequency?
directly proportional – strong bonds = vibrates at higher frequencies = higher wavenumber
How do the number/type of bonds compare in strength?
bonds to hydrogen > triple bond > double bond > single bond
Why are bonds to hydrogen the strongest type of bond?
hydrogen are the lightest atom = higher frequency
Why do triple bonds have higher wavenumber than double and single?
triple bonds are stronger bonds = higher frequency
What type of bonds are in the fingerprint region?
single bonds
How does hybridization affect bond strength?
bonds are stronger in the order sp3 < sp2 < sp
–> more s character = stronger bond
Why are bonds with more s character stronger bonds?
s orbitals are closer to nucleus = more e- attraction to nucleus = bond shortens = bond stronger = more energy to bond = higher wavenumber = higher frequency
How does mass affect frequency of vibration?
higher mass = slower movement = low frequency
What do samples of IR spectra tell us?
What functional groups are present AND which as NOT present
What do peaks in an alkane show?
organic compounds that contain saturated alkyl groups
What is a terminal alkyne? What is an internal alkyne?
terminal - end of molecule
internal - middle of molecule – cannot have H bonded to it
Why is it difficult to notice C=C of alkenes?
their intensity is determined by the groups attached
What is a sp3 C-H stretch characterized by?
large double peak
What is the structure of aromatics?
benzene ring
What does an aromatic sp2 C-H stretch look like?
peak just after 3000
What functional group do alcohols have?
hydroxyl (R-OH), where R is any alkyl carbon
How are OH characterized in IR spectra?
broad peaks
What is the absorption frequency of C-O bonds?
1100 cm^-1
What is the absorption frequency of C-C?
1200 cm^-1
What are the absorption frequencies of sp C-H, sp2 C-H, and sp3 C-H?
sp C-H –> 3300cm^-1
sp2 C-H –> 3100cm^-1
sp3 C-H –> 2900cm^-1
What is the general formula for the amine functional group?
R-NH2, R2NH, or R3N
What does the number of N-H absorption bands depend on?
number of H atoms connected to N
What is a primary amine?
one carbon connected to N (2 N-H)
What is a secondary amine?
two carbons connected to N (1 N-H)
What is a tertiary amine?
three carbons connected to N (no N-H)
What is a carbonyl group?
compound containing C=O
What does a carbonyl group look like on IR spectra?
sharp, strong peak – location depends on type of group
How can you differentiate a ketone and an aldehyde since they are both carbonyl groups in the same relative location on IR spectra?
aldehyde has C-H stretches in the 2700-2900 cm^-1 region
What are characteristics of carboxylic acids?
strong C=O stretch and broad O-H
How can esters and carboxylic acids be distinguished?
both have similar C=O stretches in the same location of IR spectra but carboxylic acids also have broad O-H
What is the difference in the shape of OH peaks of alcohols and carboxylic acids?
carboxylic acids are much broader than alcohol
How does the number of one type of bond relate to absorption/transmission?
more of one type of bond = larger transmission dips/absorption peaks
What are alkanes?
straight or branched-chained compounds with C and H atoms and only SINGLE carbon-carbon bonds
What is the formula for ACYCLIC alkanes?
CnH2n+2
What is the compound formed for acyclic alkanes when n=1?
CH4 - METHANE
What is a homologous series?
structurally related compounds that form new substances by adding the same atom(s)
How is methane the start of a homologous series?
CH4 + any number of CH2
How does the size of a molecule in a homologous series alter boiling point/state at room temperature?
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
What is a CONSTITUTIONAL ISOMER?
bonding sequence differences for compounds with the SAME MOLECULAR FORMULA
Why is it important to consider constitutional isomer?
- the possibilities for bonding sequences increases rapidly with molecular size (more atoms)
–> molecular diversity - chemical and physical properties vary for constitutional isomers
How can you draw constitutional isomers?
- 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
What are the three types of 3D depictions of alkanes?
- Dot-line-wedge
- Sawhorse projections
- Newman’s projections
What is the dot-line-wedge formula for alkanes?
lines - bonds in the plane of the paper
dotted line - bond behind paper
wedge - bonds in from of the plane of paper
What is the SAWHORSE projection?
- in shape of sawhorse using only lines
- useful for simple molecules only
What is a NEWMAN PROJECTION?
molecule viewed along C-C bond axis
- bonds drawn in from of and along the edge of a circle
- usually used for conformations
What are CONFORMATIONS?
NON-PERMANENT spatial arrangements of atoms on a molecule produced by ROTATIONS about SINGLE BONDS
What are the two key conformations of alkanes?
- ECLIPSED - C-H bonds are aligned
- STAGGERED - C-H bond in from bisect that H-C-H bond angles in back
How does the spatial (steric) repulsion compare for staggered and eclipsed conformations?
Staggered » minimized steric repulsion = lower energy conformation = more stable
Eclipsed » increased steric repulsion = more energy conformation = less stable
What is the relative energy difference between staggered and eclipsed conformations? What dues this mean?
Energy difference is present but small – conformation s interconvert at a very fast rate; the conformations can’t be isolated in pure form
Why does staggered have more stability? Why does have eclipsed less stability?
Eclipsed = C-H bonds are shorter so atoms are closer together
Staggered = C-H bonds are shorter so the atoms are farther apart
How do eclipsed and staggered conformations compare in energy with larger molecules bonded to the carbon?
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
What is the dihedral angle?
Angle between two molecules that are the same on opposite carbons
What are cycloalkanes?
Hydrocarbons containing a ring of carbonatoms connected by single C-C-c bonds
What is the general formula for all cycloalkanes that have one ring?
CnH2n (not CnH2+2 because two H’s must be removed to close the ring)
What occurs in rotations of cycloalkanes?
Rotations around single bonds is hindered due to cycle structure but conformation changes still occur.
How are 4 and 5 carbon cycloalkanes structured?
nearly in one plane with the substituents above and below this plane
What does it mean for a ring to pucker? Why does this occur?
4/5 carbon cycloalkanes bend slightly out of plane to reduce eclipsed interactions
Wear are the bonds like in cyclopropane? (angle and nature)
C3H6 – 60 degrees and highly strained
–> all C-H are eclipsed
What are the bonds like in cyclobutane?
C4H8 – about 90 degrees
–> has puckering to reduce repulsion between adjacent eclipsed C-H bonds
What are the bonds like in cyclopentane?
C5H10 – about 109.5 degrees (pentagon has 108)
–> has puckering to reduce repulsion between adjacent eclipsed C-H bonds
What is the hybridization of carbons In a cycloalkane?
sp3 (4 single bonds)
What are the conformations of cyclohexane? What is the molecular geometry of the carbon atoms?What causes the conformations?
boat and chair conformation where all carbons have normal tetrahedral geometry (109.5 approx)
–> caused by bond rotation
What does the boat conformation look like?
CYCLOHEXANE
-pair of two adjacent lowered carbons are eclipsed
- other two carbons undergo flagpole interactions
What does the flagpole interaction in boat conformation cause? How many C-H bonds are each of the alkane conformation types?
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
What are the alkane conformations in the chair conformation of cyclohexane?
all C-H bonds are staggered = no flagpole interactions
Where are the positions of substituents of carbons in cyclohexane? How many of each?
6 axial and 6 equatorial (one of each type on each carbon)
Which constituent position in more favourable? Why? What does this mean of large molecules?
equatorial b/c there is more space – preference for large molecules for less steric hinderance
How do substituents ensure that there is 109.5 degrees (approx) between them?
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
What happens to the substituents during a ring flip for a cyclohexane in chair conformation?
equatorial becomes axial and vice versa –> substituents that are above the ring stays up and the substituents that are below the ring stays below
How do large molecules impact ring flips?
large molecules prefer equatorial position for chair conformations are interconverting = one char conformation will be more stable than the other
Why are large molecules unfavourable in axial positions?
two carbons in the same direction have significant repulsion
What is the difference between conformations and constitutional isomerism?
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
Can cycloalkanes have constitutional isomers?
YES – atoms/molecules bonded to the ring can be on different carbons to make different substances, connectivity, and bonding sequences
What is STEREOISOMERISM?
SAME: formula, bonding sequence, constitutional isomer, connectivity
DIFFERENT: spatial arrangements
When does stereoisomerism occur for cycloalkanes?
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
What are the two positions of stereoisomers in cycloalkanes? What do they mean?
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)
Are stereoisomers interconverting? Why?
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
What are ALKENES?
hydrocarbons with one or more DOUBLE BOND
What is the general form of homologous alkenes with one C=C bond?
CnH2n
What are ALKYNES?
hydrocarbons with one or more TRIPLE BOND
What Is the general form of homologous alkynes with one C≡C?
CnH2n-2
What does it mean for a hydrocarbon to be saturated/unsaturated? What is an example of an unsaturated hydrocarbon?
saturated - maximum number of possible hydrogens
unsaturated - less that the max number of hydrogen
–> alkenes and alkynes
How is a unit of unsaturation measured? What will result from this?
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
What is the hybridization of the carbon in a C=C?
sp2 - trigonal planar (bonded to three atoms) bond angle 120
Why is the C=C planar?
each of the carbons are sp2 with three obtains form sigma bonds and the last orbital overlaps with the other carbons orbital (π)
What is the hybridization of the carbons in a C≡C?
sp - linear (bonded to two atoms) bond able 180
Why is C≡C planar?
each of the carbons have sigma bonds (2) and the remaining p orbitals overall with the other carbon resulting in two pi bonds
What is the consequence of C=C bond’s inability to rotate?
geometric isomerism - cis-trans isomerism
What is cis isomerism in an alkene? What is trans isomerism in an alkene?
two identical substituents on the same side
two identical substituents on opposite sides (diagonal)
Why can’t there me trans arrangement in small rings?
7C or less – trans arrangement is strained, but cis geometry is possible
How can you determine how many cis-trans isomers a molecule with C=C has (alkene)?
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
What is retinal?
form of vitamin a found in the bonds linked to vision
– contains 4 C=C bonds in trans configuration
Can cis and trans isomers interconvert? What does that mean for retinal?
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
Why is the E-Z system used? How is it used?
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
What are the 3 rules of E-Z Nomenclature?
- Look at the atom bonded DIRECTLY to alkene C. HIGHER ATOMIC # = HIGHER PRIORITY
if there is a tie
- 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 - 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)
Is E always trans?
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
What is chirality?
Another type of stereoisomer
- chiral objects have NO plane off symmetry so their mirror images are NON-SUPERIMPOSABLE
What is achirality?
Have a plane of symmetry cuts the object in half
—these half’s are mirror images
— SUPERIMPOSABLE
What are enantiomer?
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)
When is a molecule not an enantiomer?
- achiral (molecule and mirror image are the same)
- molecules have at least two of the same substituents
—CH3X and CH2XY
Can enantiomer interconvert?
Not an room temperature because they are different compounds
Do enantiomer have the same physical and chemical properties?
Yes besides:
- different behaviour on plane-polarized light
- react differently with other chiral compounds
What is a stereocentre/chiral centre?
Atom bonded to 4 different groups in a TETRAHEDRAL geometry
— ex. Carbon bonded to 4 different substituents
When is a carbon atom in a RING a CHIRAL centre?
- Has 2 different substituents OUTSIDE the ring
- Path around the ring is traced from that carbon in one direction is DIFFERENT from the path traced in the other direction
What is a FISCHER PROJECTION?
- 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
What is R/S DESIGNATION?
- Used to specify the 3D configuration of stereocentres (identify which enantiomer from the pair)
What are the R/S designation rules?
Same as E/Z (assign priorities to the 4 substituents on chiral carbon)
- Lowest (4) behind plane (H)
- Determine the 1-2-3 direction
- R - CLOCKWISE S-COUNTERCLOCKWISE
Why are biologically active molecules in living organisms found in only on stereoisomer form?
In vivo synthesis is is catalyze by CHIRAL PROTEINS -ENZYMES
Why are chiral proteins/enzymes needed?
Physiological receptors’s active sites only interact with one particular enantiomer
Why must drugs be sold in the enantiomerically pure form?
Inactive enantiomeric form of a drug can interact with the body in a harmful way
What is THALIDOMIDE?
- drug sold to pregnant women with one stereocenter and a mixture of S and R forms
- S = anti nausea
- R = birth defects
How can the number of maximum stereoisomers of a molecule be calculated?
2^n where n is the number of chiral centres
— maximum is not always attained
What is the L-series sugars?
8 stereoisomers of the D series sugars
Can there me cis-trans and R,S stereoisomerism simultaneously?
Yes (pg78)
- chiral centres cause R,S
- double bonds cause cis-trans
— in the same molecule
What does it mean for a photon to be plane-polarized?
All wave oscillate in the SAME plane (normal sunlight is not plane polarized, but can be polarized by passing it through a polarizer-filter)
How does a polarizer work?
Blocks all photons except those that oscillate in a certain plane
What does a chiral compound do to a plane-polarized light?
Rotates the plane that the light propagates at
Is the rotation of the plane of light different for each enantiomer?
Yes!
- rotors the plane of polarization in opposite directions but what equal magnitude
— this is why enantiomers are called OPTICAL ISOMERS
Do achiral molecules rotate the plane of polarized light?
No
How are the different rotations of polarized light distinguished?
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
