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Enzymes & Metabolism > Organic Chemistry > Flashcards

Organic Chemistry Flashcards

1
Q

Nucleophile

A

an electronegative functional group which has an electron pair that can be used to form a covalent bond

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2
Q

Electrophile

A

an electron deficient functional group which accepts an electron pair to form a covalent bond
must have an empty orbital

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3
Q

Aromaticity and Hunkel’s Rule

A

to be aromatic a compound must be planar and cyclic and have 4n+2 delocalised pi electrons, where n is an integer

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4
Q

Hybridization

A

the mixing of atomic orbitals to make molecular orbitals

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5
Q

sp3 hybridization

A

4 identical hybrid orbitals
tetrahedral
can have lone pair not involved in bonding available to hydrogen bond

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6
Q

sp2 hybridization

A

3 identical hybrid orbitals
trigonal planar
p orbital not involved in bonding is at right angles to the plane and can for m a double bond
partial double bonds and resonance require this

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7
Q

Tautomers

A

structural isomers differing in position of a hydrogen and a double bond
eg. keto to enol or imine to enamine

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8
Q

Hydroxyl Group

A
  • sp3 hybridisation
  • 2 lone pairs
  • electronegative
  • H bonding
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9
Q

Ether

A
  • sp3 hybridization
  • lone pairs but poor nucleophile
  • unreactive
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10
Q

Carboxylic Acid

A
  • sp2 hybridisation of oxygen promotes delocalisation of lone pair
  • forms carboxylate ion which acts as a base
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11
Q

Ester

A
  • sp3 hybridization of oxygen promotes delocalisation of lone pair
  • reduces electrophilicity of carbonyl carbon and the nucleophilicity of the alpha carbon
  • less reactive than carbonyl compounds
  • less acidic because the ester O pushes its electrons into the system, competing with the carbonyl electrons
  • partial double bond character and planar
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12
Q

Carbonyl compounds (ketons/aldehydes)

A
  • sp2 hybridization of oxygen promotes delocalisation of lone pair
  • reactive electrophilic carbon
  • acidic alpha carbon that acts as a nucleophile when deprotonated
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13
Q

Enolate ion

A
  • H removal from alpha carbon by a base from a carbonyl compound
  • stabilised by delocalisation of charge over the system
  • removal changes hybridisation to sp2 so that pi orbital overlap can occur to form a double bond
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14
Q

Aldehydes

A

More reactive than ketones

  • less steric hindrance as it lacks the R group
  • inductive effect in which the alpha carbon shares some of its electron cloud with the carbonyl carbon, partially quenching the partial positive charge
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15
Q

Amine

A
  • sp3 hybridization
  • one lone pair
  • electronegative
  • can be a base and a nucleophile only if deprotonated
  • when protonated can donate a proton (acid)
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16
Q

Amide

A
  • sp3 hybridization of N promotes delocalisation of lone pair and reduces electrophilicity of carbonyl carbon, ie. reactivity reduced
  • N is not basic or a nucleophile
  • planar molecule
17
Q

Imine

A
  • similar to carbonyl compounds
  • N protonated at physiological pH so it is strongly polarised
  • carbon highly electrophilic
18
Q

Schiff Base

A
  • protonation of imine causes N to pull more electrons towards it because of its positive charge
  • p orbital sharing to form double bond between N and C
19
Q

Thiol

A
  • sulfur equivalent of hydroxyl
  • more nucleophilic because its lone pairs are in level 3 and highly polarisable
  • orbitals are too big for effective overlap with hydrogen so no hydrogen bonding
  • not basic
  • good leaving group
20
Q

Thioester

A
  • sp3 hybridization as it couldn’t effectively overlap with 2p orbitals if sp2 hybridized
  • no electron sharing with carbonyl
  • similar reactivity to aldehydes
  • no resonance
  • alpha carbon is nucleophilic as S doesn’t interfere with enolate anion formation
  • good leaving group as it is highly polarisable
21
Q

Nucleophilic Substitution (Sn1)

A
  • two step mechanism
  • nucleophilic attack from either side of the plane to form racemic mixture
  • carbocation intermediate formed as X removes electrons
22
Q

Nucleophilic Substitution (Sn2)

A
  • one step mechanism (concerted)
  • forms transition state where both groups are attached via stretched p orbitals
  • TS is sp2-like in the same plane as its substituents
  • inversion of stereochemistry
23
Q

Elimination

A
  • loss of a leaving group from a tetrahedral carbon together with a hydrogen from the adjacent carbon to form a C-C double bond
  • need a base
  • base pulls off hydrogen and leaving group leaves
  • pi bond formed from p orbital overlap
  • p orbitals form as groups leave
  • change to sp2 hybridization in both carbons
24
Q

E2

A
  • single step mechanism
  • B attacks hydrogen
  • electron flow back into C-C bond
  • X pulls off electrons and leaves
  • formation of sp2 like TS
25
Q

E1

A
  • two step mechanism
  • X leaves first and pulls off electrons
  • carbocation intermediate with empty p orbital forms
  • base attacks hydrogen and electrons flow into C-C bond
26
Q

Electrophilic Addition to C-C double bond

A
  • pi cloud of the double bond acts as the nucleophile
  • protons are electrophiles
  • addition of a proton (from water) to the double bond gives carbocation intermediate that reacts with nucleophile (water) to give product
27
Q

Nucleophilic Addition

A
  • carbonyl compounds without a leaving group
  • nucleophilic attack at electrophilic carbonyl carbon (sp2 hybridized)
  • as the bond forms between the carbonyl carbon and the nucleophile, the carbon and oxygen of the carbonyl group begin to change their hybridisation to sp3
  • this provides the orbitals needed for bonding to the nucleophile and for the pi electrons to finish as a lone pair on the oxygen
  • base pulls hydrogen off hydroxyl group
  • attack on carbon and flow of electrons onto oxygen
  • tetrahedral intermediate that is protonated to give the product
  • protonation via attack on acid and breakage of acid hydrogen bond
28
Q

Imine formation

A
  • nucleophilic addition

- addition of amine to aldehyde (or ketone) followed by loss of oxygen as water

29
Q

Hemiacetal Formation

A
  • alcohol and aldehyde
  • nucleophilic addition mechanism
  • this then reacts with a second alcohol to form an acetal via a glycosidic linkage
  • see notes for mechanism*
30
Q

Schiff Base (Imine) Formation

A
  • amine + aldehyde
    eg. lysine side chain and PLP
  • nucleophilic attack of N of amine on the carbonyl carbon
  • electron flow back onto oxygen
  • NH electron flow into N-C bond to make it a double bond and hydroxyl is protonated and leaves as water (is pushed off)
  • unstable tetrehedral intermediate
31
Q

Nucleophilic Substitution

A
  • carbonyl compounds with leaving groups
  • mechanism the same as addition up to the formation of the tetrahedral intermediate
  • base deprotonates water and nucleophilic attack on carbonyl carbon
  • electrons flow back onto oxygen
  • oxonium ion intermediate
  • because there is a leaving group, electrons can flow back to reform the carbonyl pi cloud and the leaving group departs
  • sp2 collapsed product
32
Q

Aldol Reactions

A
  • nucleophilic attack of an enolate anion on a second carbonyl
  • alpha carbon of second carbonyl is the nucleophile
33
Q

Aldol Addition

A
  • electrophile doesn’t have a leaving group
  • carbanion attack on carbonyl carbon
  • electrons flow onto oxygen, which is protonated by an acid
  • product: B hydroxy carbonyl
34
Q

Aldo Substitution

A
  • electrophile has leaving group
  • carbanion attack on carbonyl carbon
  • electron flow onto oxygen
  • formation of negative oxygen intermediate
  • electrons flow back into C-O bond and leaving group leaves
  • product: B keto carbonyl compound

Enzymes & Metabolism (12 decks)

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