SAALIHA VIVA - METHOD Flashcards
1
Q
Summarise method
A
- 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
2
Q
How did the Frank Allen papers help select motifs for this experiment?
A
- 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:
- Intermolecular contact search
- Generation of graph set descriptors: PLUTO vs Mercury
3
Q
Define Intermolecular H-bonds
A
- Intermolecular H-bonds occur between separate molecules in a substance.
- Therefore, the electron donor and electron acceptor should be present in two separate molecules
4
Q
Define Intramolecular bonds
A
Intramolecular bonds are those occurring within a single molecule.
5
Q
Define COOH
A
- 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
6
Q
Define CONH2
A
- 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.
7
Q
Rationale for using COOH and CONH2
A
- 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
8
Q
Using 3D coordinates only
A
- 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
9
Q
Only non-disordered structures
A
- 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
10
Q
No errors
A
- 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.
11
Q
Not polymeric
A
Polymeric structures involve a repeating unit, these were excluded to obtain data from monomers.
12
Q
No ions
A
- 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.
13
Q
Only organics
A
- 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.
14
Q
Why was the R factor specified?
A
- 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.
15
Q
Why was Mercury used?
A
Bond length entries derived from the CSD were imported and analysed using the Mercury tool which generated descriptive statistics. Mean, range, and SD.
