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Organic y3 term 2 > Topic 1- intro to supramolecular chemistry > Flashcards

Topic 1- intro to supramolecular chemistry Flashcards

1
Q

What is supramolecular chemistry?

A

The study of molecules that interact non covalently with each other via intermolecular forces

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2
Q

Two main themes of supramolecular chemistry

A

host guest chemistry and self assembly

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3
Q

what is host guest chemistry

A

the selective recognition and binding of one chemical entity to another

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4
Q

what is self assembly?

A

the spontaneous association of multiple small mollecules into larger and more complex structures.

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5
Q

is self assembly a spontaneous process?

A

yes

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6
Q

what can hosts also be called?

A

ligands
receptors
enzymes

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7
Q

what can guests also be called?

A

metal ions
substrates
drugs

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8
Q

what can complexes also be called?

A

assembly, supermolecule, structure, architecture

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8
Q

what is the association constant and what does it tell us?

A

Ka
tells us the strength of the reaction between the host and guest
how reversible the reaction is

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9
Q

What other words can we use to describe binding?

A

non covalent interactions
association
complexation
coordination
recognition

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10
Q

Why is complementarity important?

A

It maximises the strength of non covalent interactions

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11
Q

what are the three ways in which a structure can be complementary?

A

size
shape
electronics

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12
Q

Why is preorganisation important?

A

Shapes are preorganised to cause strong interactions between hosts and guests.
If a host is not preorganised, it has to undergo conformational changes to become complementray to the guest which has an energy cost.
these conformational chnages are minimal if the complex is preorganised.

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12
Q

what is the chelate effect?

A

guest binding is stabilised (more favoured) by the presence of multiple binding sites on the host.

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13
Q

How does entropy contribute to the chelate effect?

A

multidentate ligand binding results in an overall greater number of displaced individual water molecules compared with a monodentate ligand.

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14
Q

how does enthaply contribute to the chelate effect?

A

Having groups such as amino groups covalently held together means they are preorganised. This means no energy is spent reorganising . Also the replusion between two lone nh3 groups would be larger than them covalently together so coordination is favoured.

covalent bridges between amino groups also increases their basicities compared with nh3. (inductive effects) further increasing their donor capabilities.

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15
Q

What is the macrocyclic effect?

A

Similar to chelate effect in that multidentate ligands are more stable. A macrocyle goes the whole way round a molecule. Makes up most donor sites on one ligand.

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16
Q

are macrocycles more or less flexible than acyclic analogues?

A

less, they lose fewer degrees of freedom on complexation

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17
Q

Are macrocycles more or less heavily solvated then acyclic analogues? What effect does this have on enthalpy?

A

often less heavily solvated
coordination is enthapically favoured as less energy is needed for ligand desolvation before binding can take place.

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18
Q

What is a cryptand ligand?

A

A macrocyle with a third strap which contains chelating atoms.
this completely encloses the metal cation in a three dimensional cage.

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19
Q

order of strength of guest complexation of macrocycles, chelates cryptates, monodentate ??

A

monodentate< chelate< macrocyclic< cryptate

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20
Q

order of rates of guest complexation of macrocycles, chelates cryptates, monodentate ??

A

monodentate< chelate< macrocyclic< cryptate

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21
Q

Thermodynamics of chelate effect : (bullet points)

how does entropy effect chelate effect?

A

solvent displacement-
increasing disorder is entropically favoured

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22
Q

Thermodynamics of chelate effect : (bullet points)

how does enthalpy effect chelate effect?

A

overcome repulsions

inductive effects increase basicity (donor capabilities)

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23
Q

why is a cyclam ligand better than a 2,3,2-tet ligand?

A

cyclam is a macrocyle. it is super preorganised which means there is a lesser enthalpic cost as it doesnt have to preorganise.

they have the same amount of donor atoms

2,3,2-tet is a chelating ligand, it is not a macrocycle. it has a small degree of flexibility and id therefore subject to a small enthalpic cost of preorganisation. Also is likely more solvated than the macrocyle, meaning more energy is needed for desolvation.

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24
Q

What factors must always be considered when rationalising the rates of monodentate, bidentate, chelate, macrocyclic and cryptate ligands?

A

How many donor atoms?

what type of ligand is it ? bidentate… macrocycle ….etc? how does this effect rates?

Sterics - is it too bulky or too small?

Size of bridge between donor atoms- link to sterics

entropy

Character of donor atoms.

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25
Q

6 common types of non covalent interactions:

A

1) electrostatics
2) hydrogen bonding
3) aromatic stacking
4) halogen bonding
5) van de waals forces
6) the hydrophobic effect

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25
Q

What three types of electrostatic interactions are there?

A

Ion-ion
Ion-dipole
dipole-dipole

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26
Q

An ion ion interaction is also known as ….

A

coulombic attraction

+ ////// -

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27
Q

Ion ion interaction is the ……. type of electrostatic interaction ?

A

strongest

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28
Q

ion dipole interactions often occur through a dipole on what atom ? what type of bonding does this resemble?

A

H

resembles hydrogen bonding

  • ////// Hd+——Cld-
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29
Q

dipole dipole interactions are the …… type of electrostatic interaction ?

A

weakest

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30
Q

schematic for a dipole dipole interaction?

A

H——Cl ///// H—-Cl
d+ d-//////d+ d-

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31
Q

order of strength of electrostatic interactions?

A

dipole dipole< ion dipole< ion ion

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32
Q

Aromatic stacking interactions are also known as ..?

A

Pi pi aromatic stacking interactions

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33
Q

three types of aromatic stacking interactions :

A

Face to face
offset parallel
edge to face

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34
Q

which is the most common type of aromatic stacking interaction?

A

Face to face

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35
Q

How does face to face stacking work?

A

pi orbs on the aromatic ring interact with eachother . The rings stack on top of eachother , face to face .

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36
Q

what effect may other substituents on an aromatic ring have on face to face aromatic stacking?

A

they may strengthen or weaken interactions based on their ew or ed abilities.

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37
Q

how does offset parallel stacking work?

A

a H from one aromatic group H bonds to the pi density from the aromatic ring.

an H from the other aromatic ring bonds in the same manner to the other.

eg

ring pi system —-H
/// ///
H——-ring pi system

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38
Q

how does edge to face stacking work?

A

a H from one aromatic group H bonds to the pi density from the aromatic ring.

ring—H////////ring pi system

c—H //// pi system

39
Q

Hydrogen bonding occurs when…

A

a H atom is bonded to an atom more electronegative than itself, the resulting H atom is able to interact with anions or lone pairs on electron rich atoms.

40
Q

Strength of hydrogen bonds is dependent on what?

A

Directionality of the bond.
greatest at 180 (linear)

41
Q

Hydrogen bonds have the greatest strength at what bond angle?

A

180
linear

42
Q

How are hydrogen bonds most often seen to bind a guest?

A

Often a large number of convergent hydrogen bond interactions are used to strongly bind a guest.

eg

      H

H Cl- H

H        H

all H are H bonding with the Cl- ion.

43
Q

How do van de waals forces occur?

A

Attractive interactions between instantaneous diploes which form in electron clouds of molecules.

44
Q

What strength to vdw forces have?

A

very weak . they are very general in nature and occur between every pair of interacting molecules.

45
Q

Are VdW forces common?

A

yes they occur between every pair of interacting molecules but they are very weak.

46
Q

When does Halogen bonding occur?

A

When an electron defficient heavy halogen atom (BR/I) is bonded to an electron withdrawing group (E) and interacts with a lewis base (LB), which can be an electron rich atom or anion.

E-X ———:LB

<———–+—-
dipole formed away from halogen

47
Q

What halogens can halogen bonding occur with? why?

A

heavy ones such as I or Br

down the group the atoms are larger and more diffuse, electron density is more easily withdrawn from them.

48
Q

What shape can a halogen bond take?

A

ONLY 180 degrees
STRICT LINEARITY

technically can be >170

49
Q

How does halogen bonding occur in terms of dipoles and orbitals?

A

E-X ———:LB

<———–+—-
dipole formed away from halogen

d+ on halogen makes a larger sigma* orbital on X.
This interacts better with the lewis base.

50
Q

What form can the lewis base be in halogen bonding?

A

Lewis base or an anion

51
Q

What form can the EWG be for halogen bonding?

A

Any EWG
common ones are F3C- or sp2 C atoms

52
Q

Why is the hydrophobic effect important in this course specifically?

A

most things we stufy will be aqueous so we have to consider interactions with water.

53
Q

How does the strength of halogen bonding compare to hydrogen bonding?

A

similar strengths (10 to 200 KJ/mol)

54
Q

How does the hydrophobic effect work?

A

Guest is likely to have a hydrophobic cavity which is filled with water as its in solution.
This cannot H bond with the water as its not very polar and the water molecules are.

The hydrophobic effect is the driving force for the association of hydrophobic molecules in aqueous solution.

on associating a hydrophobic guest molecule, the hydrophobic host can offer favourable interactions which were not possible with the water.

55
Q

Effect of enthalpy on the hydrophobic effect?

A

Delta H is favourable
Water molecules are polar and are not able to bond to the apolar hydrophobic Host cavity. This causes unfavourable interactions.
Once the water is outside the cavity and in solution, it can form more favourable interactions with solution or the outside of the cavity.
There are more favourable H bonds possible in solution than in the cavity therefore delta H is favoured.

56
Q

effect of entropy on the hydrophobic effect?

A

Delta S is favourable due to the ejection of disordered water.

these water molecules were ordered within the host cavity but have now been ejected to solution and are disordered.

57
Q

Solvent effects:

During host guest binding, …….. of the host and guest will occur

A

desolvation

58
Q

solvent effects:

is desolvation of the host and guest enthalpically favoured?

A

yes and no.

no- There are energetic demands required to break bonds with the solvent.

yes- there is a new favourable interaction between the host and guest.

overall the bookelt says its disfavoured but ultimately it depends on delta G.

59
Q

solvent effects:

is desolvation of the host and guest entropically favoured?

A

yes and no

yes- desolvation liberates solvent molecules so there is an increase in free solvent.

no- there is ordering of the host and guest together

booklet says generally delta S is favourable but ultimately it depends on delta G

60
Q

What is a “competitive solvent”?

A

A solvent that can disrupt a complex formation and compete with the guest for binding to the host.

61
Q

What key properties can we use to determine how competitive a solvent is?

A

1)Size and shape- smaller molecules are able to penetrate the binding cavity more effectively. more competition for binding.
2) Polarity/ dielectric constant- solvated molecules have to be able to orientate their d- end towards the host . How much can the polarity influence the electrostatic interactions?
3) H bonding ability- H20 is a competitive solvent as it H bonds well to many things.
Dmso is less competitive.
4) Donor acceptor numbers, ability to accept or donate electron pairs

62
Q

Why is H2O a competitive solvent?

A

H2O H bonds well to many things, both Hs are able to act as H bond donating groups as they have a slight d+ and the O can act as a H bond accepting group due to its two lone pairs.

63
Q

What is a good example of a less competitive solvent than H2O?

A

DMSO

The O is a good H bond acceptor so can interact to form H bonds but the methyl groups are weak H bond donors and will not interact nearly as strongly as the Hs on water will.

64
Q

In the lab:

How does a flouresence spectrum tell us if there has been a host guest interaction?

example of a fullerene in a macrocycle.

A

As we add the guest, emission intensity decreases.
The change tells us that there has been an electric interaction between host and guest.

65
Q

In the lab:

How does a UV-VIS spectrum tell us if there has been a host guest interaction?

example of a fullerene in a macrocycle.

A

UV-VIS studies pi—> pi* interactions.
we can tell that there has been an interaction by the change in energy of pi–>pi*. (change in UV-VIS spectrum from just the macrocycle).

Aromatic stacking involves pi orbitals therefrore we can tell the fullerence has interacted with the macrocycle as there is evidence of these interactions.

66
Q

In the lab:

How does a NMR spectrum tell us if there has been a host guest interaction?

A

Shift in signal indicates an interaction between host+ guest.

In HNMR, some shifts are larger than others, showing that certain Hs that exhibit a large shit may be closer in space to the guest.

67
Q

In the lab:

How does a NMR spectrum tell us anything about the structure of a host guest interaction?

A

In HNMR, some shifts are larger than others, showing that certain Hs that exhibit a large shit may be closer in space to the guest.

As a result we can infer some information about the orientation and structure of the interaction.

68
Q

In the lab:

What does mass spectrometry tell us about host guest binding? How?

A

Tells us about the stoichiometry of binding.

we see a peak for mass of 1:1 host : guest for example. we dont see 1:2 for host:guest.
therefore we can tell the stoichiometry of the host guest complex.

69
Q

In the lab:

What type of ionisation methods are required for mass spec to see the host guest interaction?

A

mild ionisation methods. eg electrospray ionisation to ensure the host guest complex does not dissociate within the spectrometer before it reaches the detector.

70
Q

In the lab:

What is circular dichroism (CD) useful for?

A

Studying conformational changes of chiral molecules during host guest binding. eg DNA.

71
Q

In the lab:

What information can xray crystallography tell us about host guest complexes?

A

will reveal the STRUCTURE of a complex.
STOICHIOMETRY of binding
conformation / shape of binding site.
tells us what types of interactions hold the complex together.

72
Q

In the lab:

What is the drawback with xray crystallography for telling us about host guest complexes?

A

Crystallography only provides information of the complex in the solid state, which may not be identical to that in solution.

73
Q

In the lab:

How does electrochemistry allow us to get information about host guest complexes?

A

Detects how binding changes the redox potential.

74
Q

In the lab:

How does isothermal titration allow us to get information about host guest complexes?

A

detects how binding changes the temperature.

75
Q

Thermodynamics of host guest complexes:

We can tell the strength of host guest binding how?

A

Via the association constant Ka

76
Q

Thermodynamics of host guest complexes:

Equation for host guest binding.

A

H + G —-reversible arrow—- HG

Ka is ontop of the reversible arrow

77
Q

Thermodynamics of host guest complexes:

eqn for Ka:

A

[HG]
——— = Ka
[H] X[G]

all concs at equilibrium

78
Q

Thermodynamics of host guest complexes:

eqn for Kd:

A

kd= 1/ka

79
Q

Thermodynamics of host guest complexes:

What is Kd?

A

dissociation constant

80
Q

Thermodynamics of host guest complexes:

Ka units:

A

M^-1

81
Q

Thermodynamics of host guest complexes:

[H], [G] and [HG] units

A

M

82
Q

Thermodynamics of host guest complexes:

DELTAG units:

A

KJ/mol

83
Q

Thermodynamics of host guest complexes:

kd units:

A

M

84
Q

Thermodynamics of host guest complexes:

eqn for delta G (from Ka):

A

Delta G = - RTlnKa

85
Q

Thermodynamics of host guest complexes:

eqn for deltaG (from entropy and enthalpy)

A

deltaG= deltaH- TdeltaS

86
Q

Thermodynamics of host guest complexes:

On a equivalent of guest vs chemical shift plot, how can we tell which experiment has greatest binding.

A

The steepest curve will have the greatest binding and therefore strongest Ka.

87
Q

In the lab:

How does a NMR spectrum tell us about the thermodynamics of an interaction?

A

We can plot a graph in which equivalents of guest are plotted against chemical shift and the steepness of the curve is indicative of host guest binding affinity.
steeper curve = stronger binding. larger Ka.

88
Q

group these into competitive and non competitive solvents for the inside of a macrocycle complex with lots of H on the inside. (as in the lecture with cl anion in the middle) :

diethyl ether
n hexane
acetonitrile
water
methanol
dimethyl sulfoxide
dichloromethane

A

non competitive :
diethyl ether
n hexane
dichloromethane

competitive :
acetonitrile
water
methanol
dimethyl sulfoxide

note: It is often desirable to perform anion binding in competitive solvents such as water because we wish to manipulate anions (and other guests) under biological conditions for their application in medicine e.g. ion transport.

89
Q

How to order ligands in term of increasing preorganisation:

A

Classify ligands as chelates, macrocycles and cryptands.

Consider possible intramolecular hydrogen bonding as a way of increasing preorganisation

The side chains present additional degrees of freedom versus a macrocycle

90
Q

categorise DNA and RNA nucleotide base pairs by max number of H bond interactions possible between bases:

UA
AC
GC
GU
GT
AT

A

2 H bonds:
UA
AC
GU
GT
AT

3 H bonds:
GC

91
Q

What types of bond are DNA and RNA stabilised by?

A

DNA (and RNA) are stabilised by aromatic stacking interactions between the aromatic heterocycles of the base pairs and the potential for electrostatic interactions between negatively charged phosphate and counter cations in the sugar-phosphate backbone.
They are also subject to H bonds when forming pairs such as GC or AT

92
Q

Place the following types of non-covalent interactions in order of their dependence on directionality:

Electrostatic interactions
Hydrogen bonding
Halogen bonding
Aromatic stacking interactions

A

least directional

Electrostatic interactions

Aromatic stacking interactions

Hydrogen bonding

Halogen bonding

most directional

note: hydrophobic effect also has no directionality

93
Q

Place these non-covalent interactions in order of their typical strength

ion-dipole electrostatic interactions
aromatic stacking interactions
van der Waals forces
hydrogen bonding (no charges)
ion-ion electrostatic interactions

A

weakest :
van der Waals forces
aromatic stacking interactions
hydrogen bonding (no charges)
ion-dipole electrostatic interactions
ion-ion electrostatic interactions
strongest

94
Q

What would a graph of equivalents of host added vs chemical shift look like for a 1:2 ratio of host to guest binding vs a 1:1 ratio?

A

initial steep gradient of curve indicates strong binding, however it continues to increase (linearly) as more guest is added. This is indicative of 1:2 host-guest binding i.e. the binding of a second guest is weaker then the first. This is typical for the non-cooperative binding of guests of the same charge (e.g. cation/anion).

1:1 binding will also have an initial steep gradient of the curve but will plateau as more guest is added

95
Q

Ligands trien ans 2,3,2-tet are able to bind to transition metal cations, match each TM cation to the ligand with which it will form the strongest complex:

Co2+
Fe2+
Hg2+
pt2+
Pb2+
cu2+

A

trien: Hg2+ Pt2+ Pb2+
2,3,2-tet: Cu2+ Co2+ Fe2+

difference in bite size effects ring strain in the complex and bond length between M and L.
Larger ions prefer a bite size of a 5 membered chelate ring , larger distance between donor atoms, more room for ion. therefore prefer trien shape
smaller ions prefer a bite size of a 6 membered chelate ring, smaller distance between donor atoms so the cation will fit nicely, therefore preferring 2,3,2-tet shape.

96
Q

large metal cations favour what size membered ring bite angle?

A

5 membered rings
eg in trien

97
Q

small metal cations favour what size membered ring bite angle?

A

6 membered ring eg 2,3,2-tet

98
Q
A

Organic y3 term 2 (3 decks)

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