SAALIHA VIVA - METHOD

Question 1

Summarise method

Answer 1

• Structures were drawn in Conquest
• Three distances were defined: two intermolecular distances and one intramolecular distance
• Parameters were defined
• Searches were run
• ND vs XRD
• Data exported into Mercury and analysed

Question 2

How did the Frank Allen papers help select motifs for this experiment?

Answer 2

• FA developed a method for H-bonded motifs between 2 organic molecules
• Including the investigation of COOH and CONH2

From this I picked my motifs, aswell as developed my own methodology
- He used:

1. Intermolecular contact search
2. Generation of graph set descriptors: PLUTO vs Mercury

Question 3

Define Intermolecular H-bonds

Answer 3

• Intermolecular H-bonds occur between separate molecules in a substance.
• Therefore, the electron donor and electron acceptor should be present in two separate molecules

Question 4

Define Intramolecular bonds

Answer 4

Intramolecular bonds are those occurring within a single molecule.

Question 5

Define COOH

Answer 5

• Organic compound that contains a carboxyl group which is responsible for its acidic properties.
• The COOH contains an OH group which causes them to be strobgly associated with H bonding

Question 6

Define CONH2

Answer 6

• Amides are derived from carboxylic acids, which contain a -COOH group.
• Formed by the hydroxyl (-OH) part of the -COOH group being replaced by an amino group (-NH2).
• Therefore, amides contain a -CONH2 group
• Bond between the carbonyl carbon and the nitrogen of ammonia is the amide bond.

Question 7

Rationale for using COOH and CONH2

Answer 7

• Although H-bonds may be formed from a wide variety of structures, the CONH2 and COOH functional groups are among the most researched H-bonding patterns.
• A 1997 study carried out by Wash et al indicated that carboxylic acids proved to be particularly useful models for investigating H-bonding interactions.
• This was validated by the Frank Allen study

Question 8

Using 3D coordinates only

Answer 8

• 3D coordinates used when analysing crystal structures
• A way to describe the positions of atoms within the crystal lattice in a precise and quantitative way.
• Detailed picture of the arrangement of atoms
• This information can then be used to understand the physical and chemical properties of the material

Question 9

Only non-disordered structures

Answer 9

• Since a crystal is a spatial average of a pattern, disorder contradicts 3D periodicity.
• With disorder, an atom occupies more than one site so disorder structures were omitted
• Avoid any factors that would give a large deviation

Question 10

No errors

Answer 10

• Even small errors can lead to significant inaccuracies in the final results.
• This can be particularly problematic in crystal structure analysis, where the positions of individual atoms within the crystal lattice can have a significant impact on the properties of the material.
• We want to ensure our results are as accurate and reliable as possible, to aid the understanding of the material being studied.

Question 11

Not polymeric

Answer 11

Polymeric structures involve a repeating unit, these were excluded to obtain data from monomers.

Question 12

No ions

Answer 12

• Charged ions can be excluded in crystal structure analysis because they can be difficult to locate accurately using X-ray or neutron diffraction techniques.
• Therefore, many crystal structure analysis only consider the positions of neutral atoms within the crystal lattice.

Question 13

Only organics

Answer 13

• Organometallics contain heavy metal atoms that scatter X-rays and neutrons strongly, which can lead to significant errors in the analysis.
• They are also highly reactive, which can make it difficult to obtain high-quality single crystals suitable for diffraction analysis.
  o Therefore, researchers often focus on studying the crystal structures of organic compounds, which are typically easier to analyse using these techniques.

Question 14

Why was the R factor specified?

Answer 14

• Refinement of the R-factor allows us to enhance structure quality to compare the resulting quality of models calculated at different times and with different refinement strategies.
• Small organic molecules commonly refine to ≤0.05.

Question 15

Why was Mercury used?

Answer 15

Bond length entries derived from the CSD were imported and analysed using the Mercury tool which generated descriptive statistics. Mean, range, and SD.