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Medicinal Chemistry > Molecular Shape & Reactivity > Flashcards

Molecular Shape & Reactivity Flashcards

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1
Q

What is drug structure controlled by?

A

Structure + orientation of functional groups

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2
Q

What is functional group structure controlled by?

A

Electronic arrangement
= individual atoms
= valency
= hybridisation

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3
Q

Describe ethane

A 
C2H6
2 carbons = both tetrahedral 
C-H  formed by overlap sp3 C + H s orbital
C-C formed by overlap of 2 C sp3 
109.5 degrees
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4
Q

How can ring structures be simply made?

A

By having 2 sp3-sp3 C-C bonds

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5
Q

Describe bonds in ethene

C2H4

A

Each C has 4 bonds
Hybridisation of s with 2x 2p = 1 p orbital left non-hybridised
120 degrees

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6
Q

What is e- repulsion minimised by in ethene?

A

3x sp2 orbitals

point corners of equilateral triangle

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7
Q

Where is the unhybridised p orbital?

A

Perpendicular to plane

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8
Q

How is the double bond formed in ethene?

A 
1st = overlap of sp2 from each C = sigma bond
2nd = side to side overlap of unhybridised p orbital = pi bond
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9
Q

Describe the bonds in ethyne

C2H2

A

Triple bond

Hybridisation of only 2 orbitals (sp) = 2 p orbitals left (2p)

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10
Q

Describe sp orbitals in ethyne

C2H2

A

2 side to side overlap = 2 pi bonds

C form 1 sigma bond

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11
Q

Describe bonding in methyl cation

A

C positively charged
Bonded to 3x H
sp2 hybridisation
Non-hybridised p remains empty + perpendicular to plane

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12
Q

Describe bonding in methyl radical

A

C bonded to 3x H

sp2 hybridised

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13
Q

What is the difference between methyl cation and methyl radical?

A

Radical has one more e- that resides in non-hybridised p orbital

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14
Q

Describe bonding in methyl anion

A

C bonded to 3x H
3 bonding pairs + 1 L.P
Negatively charged C = sp3
L.P resides in sp3

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15
Q

How are the 3 bonds formed in methyl anion?

A

sp3-s overlap

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16
Q

What does nitrogen hybridise to form?

A

4x sp3 orbitals

1 = occupied by 2x non-bonding e-

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17
Q

How are N-H formed?

A

sp3-s overlap

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18
Q

Describe bonding in amines

A

N has same geometry as in NH3

C-N bonds formed by sp3-sp3 overlap

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19
Q

What can Hs be replaced by in amines?

A

1 alkyl or aryl group = primary amine
2 alkyl or aryl group = secondary amine
3 alkyl or aryl group = tertiary amine

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20
Q

Why can H2O + NH3 act as bases (nucleophiles)?

A

Use L.P to bond H+

Formal charge of +1

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21
Q

What is the bond angle of N-H?

A

109.5 degrees

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22
Q

How are O-H bonds formed?

A

sp3-s orbital overlap

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23
Q

How are C-O bonds formed?

A

sp3-sp3 orbital overlap

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24
Q

How are S-H bonds formed?

A

sp3-s orbital overlap

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25
Q

How are S-C bonds formed?

A

sp3-sp3 orbital overlap

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26
Q

What can O + N form?

A

Double bonds

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27
Q

What can N form?

A

Triple bonds

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28
Q

What does phosphorus use for bonding?

A

3rd shell e-

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29
Q

Why does phosphorus use 3rd shell e- for bonding?

A

Smaller energy gap between the occupied 3p orbitals + vacant 3d orbitals

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30
Q

Where is the bond formed in HF?

A

Between H 1s orbital + F 2sp3 orbital

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31
Q

Where is the bond formed in HCl?

A

Between H 1s + Cl 3sp3

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32
Q

What happens to e- density in region of s-sp3 overlap as size of hydrogen halide increases?

A

Decreases

= H-X bond becomes weaker

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33
Q

What happens to hydrogen halide bond strength down the group?

A

Decreases

34
Q

How is the C-X bond formed in alkyl halides?

A

sp3-sp3 orbital overlap

35
Q

What happens as size of halogen increased in alkyl halides?

A

sp3 orbital from higher shell used in bond decreased in e- density
= longer + weaker

36
Q

What is electronegativity?

A

Tendency of an atom to pull bonding e- towards itself

37
Q

What is a polar covalent bond?

A

Covalent bond in which e- distribution between atom is unsymmetrical

38
Q

Describe inductive effect

A

Atom’s ability to polarise a bond

e- -attracting or e- -withdrawing effect transmitted through S bonds

39
Q

What do electronegative elements have?

A

e- -withdrawing inductive effect

40
Q

What is dipole moment a measure of?

A

Net polarity of a molecule

41
Q

What are covalent compounds composed of?

A

Discrete molecules

42
Q

What are the 4 main type of interactions?

A

Van der Waals
Dipole-dipole interactions
Hydrogen bonding
Ion-ion

43
Q

Describe Van Der Waals

A

Weak interactions caused by momentary change in e- density

Present in non-polar compounds

44
Q

What determines the strength of Van Der Waals?

A

SA of molecule

45
Q

What is polarizability?

A

Measure of how e- cloud around an atom responds to changes in its electronic environment

46
Q

What are dipole-dipole interactions?

A

Attractive forces between the permanent dipoles of 2 polar molecules

47
Q

Describe H bonding

A

Most important

Short range, directional, inter or intramolecular no-bonded interaction

48
Q

Describe how H bonding works

A

Non-bonded interaction between H atom bonded to electronegative atom + another electronegative atom

49
Q

What is the e- deficient H called?

A

Hydrogen bond donor

50
Q

What is the e- rich H called?

A

Hydrogen bond acceptor

51
Q

What is H bonding important for?

A

Drug molecule - receptor interactions

52
Q

What are the conformational strains for alkanes?

Ethane

A

Staggered

Eclipsed

53
Q

What is the torsional strain?

Alkanes

A

Repulsion felt by bonding e- as they pass close to bonding e- of an adjacent substituent

54
Q

What is conformational analysis?

Alkanes

A

Investigation of a compound’s conformations + their relative stabilities

55
Q

Describe conformation of butane

A

Rotation can occur around all 3 bonds
Staggered conformers of equal energy
Eclipsed conformers of equal, BUT higher energy

56
Q

What does rotation around the C2-C3 bond of butane give?

A 
6 important conformations 
Staggered gauche
Eclipsed
Staggered anti
Eclipsed
Staggered gauche
Eclipsed
57
Q

What is gauche conformation compared to anti?

A

Less stable due to repulsive Van Der Waals between 2 CH3

58
Q

Describe conformation of cycloalkanes

A

Molecules not static = rotation around each C-C continuous
= many interconverting conformers can exist at any 1 time
=separation of conformers not possible

59
Q

Why is separation of conformers not possible in cycloalkanes?

A

Due to paid speed of inter-conversion

60
Q

What is the relative no. of molecules in a particular conformation of cycloalkanes dependent on?

A

Conformer stability with majority in staggered conformations

61
Q

What is the difference with cycloalkane formation?

A

Ring rotation is limited = molecules twist + bend to minimise source of strain

62
Q

What are the different sources of strain?

A

Angle strain
Torsional strain
Steric strain

63
Q

What is angle strain?

A

Deviation from ideal tetrahedral bond angle

64
Q

What is torsional strain?

A

Repulsion of proximate bonding e-

65
Q

What is steric strain?

A

Where atoms/groups approach too closely

66
Q

Describe conformations of cyclopropane

A

Torsional strain = C-H bonds eclipsed

Angle strain = orbitals overlap at slight angle

67
Q

What does the conformations do to cyclopropane?

A

Weaker + more reactive than typical alkane bonds

68
Q

Describe conformations of cyclobutane

A

Torsional strain= 1 C lies 25 degrees above plane of other 3

69
Q

Is the angle strain of cyclobutane less or more than cyclopropane?

A

MORE

= larger number of ring H

70
Q

Describe conformations of cyclopentane

A

Twists to non-planar conformation
= C-C 108 degrees
= C5 out of plane

71
Q

Is the angle strain of cyclopentane less or more than cyclobutane + cyclopropane?

A

LESS

72
Q

What would the planar cyclopentane exhibit?

A

Minimal angle strain

Large torsional strain = H eclipsed

73
Q

Describe conformations of cyclohexane

A

No angular strain = C-C-C 111.5, close to 109.5

No torsional strain = neighbouring C-H staggered

74
Q

What conformation does cyclohexane adopt?

A

Chair conformation/ boat conformation

75
Q

What can happen to chair conformations?

A

Interconvert = exchanging axial + equatorial positions

76
Q

Describe monosubstituted cyclohexane conformations

A

2 chair conformations not equal stability

Bulkier substituent = greater preference for equatorial substitution

77
Q

Why is there an energy difference between axial + equatorial conformations?

A

Steric strain caused by 1,3-diaxial interactions

78
Q

Describe disubstituted cyclohexane conformations

A

1,2-dimethylcyclohexane
Trans-isomer
2 methyl groups on opposite faces
Exist in diequatorial conformation

79
Q

What are all substituents in glucose?

A

Equatorial

80
Q

What are all substituents in mannose?

A

1 OH group axial

= mannose more strained

Medicinal Chemistry (19 decks)

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