Structure of Metal-Organic Frameworks (MOFs)

Question 1

• If a square planar metal ion was combined with a linear ditopic monodentate linker like 4,4’-bipy, the pieces could assemble into a 2D square lattice
• However, this often does not work, as there are several factors that disfavour this
• Why?

Answer 1

• Entropy
• Flexibility
• Charge balance

Question 2

why does entropy mean an extended polymeric species doesn’t form?

Answer 2

• Entropy favours multiple different discrete species forming, (-)ve entropy change
• Therefore, for the overall assembly to be thermodynamically favourable, strong bonds
• Pd(II)-pyridin bond is only reasonably strong due to low ionic contribution as ligand isn’t charged

Question 3

Why does flexibility mean an extended polymeric species doen’t form?

Answer 3

• 4-4’-bipy ligand is fairly rigid and planar
• However, there is nots of flexibility in the M(II)-pyridine bonds
• This can lead to triangles and squares with discrete boxes
• An extended porous structure such as this would rapidly become irregular if these is flexibility
• (need to reduce flexibility)

Question 4

Why does charge balance mean an extended polymeric species doesn’t form?

Answer 4

• 4,4’-bipy ligand is neutral and Pd(II) is cationic
• For every metal centre there is a charge of +2 that needed balancing
• These can be balanced by non-coordinating anions that sit around the discrete structure
• However, in an extended structure they cannot just all be around the edge
• This can be overcome by putting the anions between the layers

Question 5

What is the issue with charge balance in the analogous 3D structure as a primitive cubic lattice, where there is an octehdral metal ion such as Fe(II) at each lattice point

Answer 5

There would now be no space between the layers and counteranions would have to be put in the voids in the middle
This is an issue however, because the voids within these structures allowing guest to bind are what make them useful to science, and having anions in them would remove this and porosity would be lost

Question 6

Define Coordination polymer

Answer 6

A coordination compound continuously extending in one, two or three dimensions through coordination bonds

Question 7

Define Coordination network

Answer 7

A coordination compound extending, through coordination bonds, in one dimension, but with cross-links between two or more individual chains, loops or spiro-links, or a coordination compound extending through coordination bonds in two or three dimersions

Question 8

Define Metal Organic Framework (MOFs)

Answer 8

is a coordination polymer (or alternatively coordination network) with an open framework containing potential voids

Question 9

What is the most widely used ligand for making MOFs is

Answer 9

Carboxylates
(different to discrete structures which was pyridines)

Question 10

What is the charge on carboxylates and what is the benefit of this?

Answer 10

• Carboxylates carry a charge of -1
• THis helps them form strong bonds to metal centres as there is an ionic contribution to the interaction as well as a covalent contribution

Question 11

What are the two ways a ditopic carboxulate ligand can bind?

Answer 11

• It is possible for the 2 donor atoms tto coordinate to the same metal in a bidentate fashion
• OR for each carboxylate to coordinate to two nearby metal ions. Both metal ions sit at the same site

Question 12

Why is it rarer for a carboxylate to coordinate in a bidentate fashion?

Answer 12

• This makes a 4-membered chelate ring which is strained
• With bidentate ligands at a single metal ion, we would rapidly run out of available coordination sites
• for example, a square lattice where each ditopic linker was bidentate would require 8 sites on the metal ion

Question 13

What is the benefit of the structure of the dicarboxylate for the MOF formation?

Answer 13

• Whilst strictly being monodentate to any individual metal ion, the carboxylate is bidentate to the node or cluster of metal ions at the corner of the framework
• This chelating nature makes the structure much more rigid and is crucial for MOF formation
• The carboxylate coordinates to 2 nearby metal ions. Both metal ions sit at the same node of the structure

Question 14

The simplest example of the dicarboxylate ligand is in a paddlewheel
Describe the structure of it?

Answer 14

• The centre of the paddlewheel has two metal ions
• Four carboxylate ligands span out from the centre of the paddlewheel at angles of 90 degrees to each other
• The two metal ions are close together and there is a metal-metal bond between them
• In this structure here the metal ions are Cu(II)

Question 15

What is the overall charge for each node

Answer 15

• 2 x Cu²⁺
• 4 x RCO₂⁻
• Overall charge for each node is zero

Question 16

Is the copper in the paddlewheel para- or diamagnetic

Answer 16

• Cu(II) has a d⁹ electron configuration meaning the material is paramagnetic
• This is observed at elevated temperatures
• At low temperatures however, the unpaired electron spind undergo antiferromagnetic exchange coupling making the overall node diamagnetic

Question 17

We have seen that Cu(II) often likes to be 5-coordinate or Jahn Teller distorted octehedral
How is a Jahn Teller distorted octehedral formed?

Answer 17

• Each copper makes one bond to another copper
• 4 bonds to carboxylates
• making 5 in total
• There is always a sixth ligand that coordinates on the top and bottom of the paddlewheel

Question 18

The sixth ligand is often the reaction solvent used in the synthesis of the material, they are diethylformamide
What are the consequences of the coordinated solvent on the overall structures of the material

Answer 18

• The copper paddlewheel is a square planar node and the benenedicarboxylate is a ditopic linker. Together these make a square lattice
• Corrdinated solvent molecules sit on the top and bottom of each paddlewheel in the layer
• Multiple layers staggered together in an alternating fashion. This allows the coordinated solvent molecules to protrude into the square cavity on the layer above and below

Question 19

• It is possible to remove the solvent under certain conditions
• However, even with the solvent removed, the top and bottom of the paddlewheel still need a sixth ligand to coordinate to the metal
• How this this overcome?

Answer 19

• This is now provided by one of the oxygen atoms on a carboxylate of the next layer
• The nearest copper metal centres of the adjacent layers are shown in gold
• The resultant structure is much more porous as no additional coordated solvent molecules are needed

Question 20

The addition of second ligand to coordinate to the sixth position of the padlewheels can hold the layers further apart
This ligand should be neutral (4,4’-bipy) given that we do not want to build up charge in the framwork
What overall structure is formed

Answer 20

• There are two interpenetrating versions of the same framework (one in red and other blue)
• This is analogous to the catenanes that can form in equilirbrium with molecular boxes
• The interpenetrating structure maximises other through space interactions such as π-π stacking + van der Waals interactions

Question 21

What is the difference between the way MOFs and discrete structures will interact with solvent

Answer 21

• MOFs are extended solid state materials
• By constrast, the discrete structures we have seen in previous units (boxes, cages, etc) are soluble
• In solution, solvent will fill only gaps in the structure

Question 22

Unless a vacuum is tightly sealed, things from nearby come to fill the vacuum. This is driven by entropy
How can we avoid MOFs becoming interpenetrated?

Answer 22

To avoid MOFs becoming interpenetrated, the ligands must be designed carefully for them not to do this
(However, if the ligands used to make MOFs leave lots of room for interpenetration, then any different frameworks can be interpenetrated

Question 23

When thinking about designing a connecting node to span 3D as opposed to the 2D of the paddlewheel
This can be achieved with a structed based on four Zn²⁺ ions
Wht is the geometry of this?

Answer 23

• An ocetahedral node would have six carboxylate ligands meeting, with 90° between each of the carboxylate ligands coming off

Question 24

On its own, at the node this would give 4x Zn²⁺ and 6x RCO₂⁻, leaving an overall charge of +2
How is this overcome?

Answer 24

• The 4 zinc(II) ions are arranged in a tetrahedron
• In the centre of the tetrahedron there is an oxgyen atom (formally O²⁻)
• This oxygen is four-coordinate and surrounded by a tetrahedron of four zinc(II) ions
• The zincs are to far apart now however so no Zinc-zinc bonding
• Overall charge is zero

Question 25

The geometry arond each zinc in this compound is?

Answer 25

* Each of the four zinc(II) ions is in a tetrahedral coordination environment provides by four oxygen atoms * Around any one zinc, three of the oxygens come from carboxyate ligands and the fourth comes from the central oxgyen * These four ZnO₄ tetrahedra share their central vertex

Question 26

What is the overall structure formed when these unit polymerise?

Answer 26

* The overall structure of the solid is based on a primitive cubic lattice * There are channels with a square cross section running in all three directions (x, y, z)

Question 27

What is a Isoreticular MOF?

Answer 27

* Larger versions of MOFs with the same structure can easily be made by constructing MOFs from longer ligands * Also known as IRMOFs

Question 28

As the ligand get longer, what happens to the properties of the MOF?

Answer 28

As the ligand gets longer, the potential cavity in the MOF gets larger and the structure more porous

Question 29

MOFs are often characterised by two different sphere sizes What are they?

Answer 29

* There is a larger size that represents the largest sphere that would fit within a void but be trapped from moving * There is also a smaller size that represents the largest sphere that could move freely though the pores in the structure

Question 30

* With many larger IRMOFs, a doubly interpenetrated structure can also be formed, depending on the conditions used for synthesis * Explain?

Answer 30

* Performing the synthesis at higher concentrations leads to the interpenetrated structure being formed * Performing the synthesis at hower concentrations leads to the non-interpenetrated structure being formed

Question 31

What can we disfavour the formation of interpenetrating structures?

Answer 31

Substituent groups can also be added to the dicarboxylate ligand to disfavour interpenetrating structures (These also, however, reduce the amount of free space in the structure)

Question 32

More generally, the subunits of a MOF are referred to as...

Answer 32

...secondary building units (SBUs) These consist of the metal nodes or clusters linked together by the multitopic bridging ligand

Question 33

The combination of metal-based SBUs and ligand(s) determines the...

Answer 33

... overall topology or net of the structure

Question 34

MOF-235: consists of a secondary building unit consructed from 3 Fe(III) ions. These three metal ions form a... A central oxgyen sits in the middle of the triangle (O²⁻). A carboxylate ligand bridges each edge on the top of the triangle and each edge on th bottom of the triangle. This gives the SBU a ..... shape

Answer 34

* Triangle linked by metal-metal bonds * Trigonal prismatic shape

Question 34

MOF-235: Each Fe(III) ion is in an overall octahedral environment, consisting of four bonds to carboxylate oxygens, one bond to the central oxgyen and one bond to a coordinated DMF solvent What is the charge on the node?

Answer 34

* 3 x Fe³⁺ * 6 x RCO₂⁻ * 1 x O²⁻ * = overall +1 charge * (Hence this structure must have one anion in the void for every node of the structure. In this case the anion is [FeCl₄]⁻

Question 35

MOF HKUST-1: what is the difference of the ligands on this MOF? And how does this affect the structure?

Answer 35

* The ligands linking these SBUs are now trotopic as it is a benzentricarboxylate * This means the paddlewheels are linked together in different ways * In particular, the paddlewheels no longer form layers and are not all orientated in the same direction

Question 36

What is the structure of the overall polymer formed from this unit?

Answer 36

* Octahedral units within this structure with alternating faces capped by the tricarboxylate ligand (four out of eight faces capped) * Now at each vertex of the octahedron are two metals of the copper paddlewheel SBU rather than just one