SAALIHA VIVA - DISCUSSION Flashcards
Define R factor
- Signifies a measure of agreement between the aplitudes of the structure factors.
- It is calculated during each cycle of least-square structure refinement to assess progress and incorporates the observed and calculated diffraction data
What is the least squares method?
- The R factor is calculated during each cycle of least-square structure refinement
- It’s a statistical method to fit a line to a set of data points.
- It’s a way of finding the line of best fit for a set of data points by minimizing the sum of the squares of the distances between the data points and the line.
What does the R factor equation mean?
Sum of absolute difference between observed (Fo) and calculated (Fc) over the sum of the observed
Is R-factor an indicator of accuracy or precision?
The R factor must always be treated with caution, as an indicator of precision and not accuracy.
- I used a low R-factor, this is not a good guide for the correctness of a structure
- So we can use a higher R-factor – this IS a good guide for incorrectness of a structure
- However, tendency to overrefine models
Why was standard deviation useful?
- SD being an indicator of how dispersed the data is compared to the mean
- The SD value for COOH were lower than for CONH2, this is significant considering there were more hits for CONH2
What does the lower SD value mean?
- ND has lower SD
- Lower SD = more concentrated around the mean = more concordant results = more accurate
CONH2 has greater H bond lengths
- CONH2 has a greater H-bond length than COOH
- The greater the bond length, the weaker the bond
- However, the properties of CONH2 = two donor and two acceptor atoms, outlining the increased capability of amides to form H-bonds
Why did I include experiment 3??
- Experiment 3 was carried out to provide a comparison of experiments 1 and 2.
- Admitedly, this experiment could have been developed on further. It was left on its own, and not much work was done it,
- by analysing both the intramolecular O-H and the N-H and analysing distance 2 (which was my hydrogen bond) in terms of N-H…O aswell.
- From this I could’ve compared the acceptor and the donor lengths.
- And compared it to experiment 1 and 2 individually.
- However table 6 + 7 which is the intramolecular O-H and N-H show little disparity between the expected for N-H…O and N-H, therefore it would not have provided that diff results
Why is there a lower number of hits for neutron diffraction?
- ND requires access to a suitable source available at a limited number of highly specialised centres
- More challenging than X-ray diffraction.
- Time-consuming and expensive
- Some materials are more difficult to study using ND than XRD, which can further limit the amount of available data.
Neutron radiation mentioned on pg 26. Is neutron diffraction and neutron radiation the same thing?
- No, they are different things.
- Neutron diffraction is a technique whereby a crystal structure is subjected to a high energy neutron in order to obtain a diffraction pattern, used to study the structure of materials at the atomic level.
- Whilst neutron radiation is a type of ionizing radiation that consists of neutrons that have been emitted from a radioactive source
- I meant it in the sense where the neutrons are being directed at the sample
How do you calculate a hydrogen bond?
The distance between the donor and acceptor atoms
H-bond exists when the distance between the donor and acceptor atoms is less than the total of the:
* acceptor atom’s atomic radius (1.5Å),
* the H atom’s atomic radius (1.2Å)
* and the length of the link between the donor atom and the H atom (1Å)
* So the total of this is 3.5
* So H bonds exist when the total is less than 3.5
* Any more than this = pure dipole to dipole interaction
What is a pure dipole to dipole interaction?
Type of intermolecular force that occurs between two polar molecules. In a polar molecule there is an uneven distribution of electrons = partial negative charge on one end of the molecule and a partial positive charge on the other end
What makes a good H bond?
A study carried out by Sigala et al showed that in general, H-bonds have a distance of 2.8Å. Therefore, I compared my values to this 2.8 value.
The X-ray bond lengths appear shorter, therefore the XRD model is shorter than the ND model, explain this concept
- My results showed that XRD models were shorter than ND models
- XRD technique assumes all atoms in the crystal are stationary.
- In reality, atoms are constantly vibrating due to thermal motion
- This can cause the XRD pattern to be broadened, leading to an apparent shortening of the bond length.
- Electron density around the atoms can be distorted by the presence of other atoms in the crystal, which can also affect the measured bond length.
- The electron distribution is displaced along the covalent X-H bond towards atom X. Atom X is the O, because O is more electron negative.
- O is more electron negative.
- O atom attracts the shared electrons in the covalent bonds more strongly than the hydrogen atoms do.
- electron distribution to be displaced towards the oxygen end of the molecule.
- Which causes the XRD bond lengths to appear shorter
Define electronegativity?
Electronegativity is a measure of an atom’s ability to attract electrons towards itself in a covalent bond.
What is IAM
- The independent atom model (IAM) is a simplified model of the electronic structure of a molecule that treats each atom in the molecule as if it were isolated from the others
- and atomic electron densities as spherical densities of independent atoms.
What is a limitation of IAM?
A limitation of IAM includes the fact that it does not recognise the aspherical nature of atomic electron densities, lone pairs, and other interactions. Because of this IAM fails to correctly describe the position of H atoms, which only have one valence electron
What is a study to overcome the limitation of IAM?
The Woińska et al study posed the question of whether it was feasible to accurately determine the location of H atoms and their related bond lengths from XRD to overcome the limitations of IAM. Using HAR.
Define HAR
- Hirshfeld atom refinement is a method for refining crystal structures using XRD data.
- The method involves calculating the Hirshfeld surfaces of the atoms in the crystal,
- By comparing the calculated Hirshfeld surfaces with the experimental X-ray diffraction data, researchers can refine the positions of the atoms in the crystal and obtain a more accurate picture of the crystal structure.
- This method has been shown to be particularly useful for studying hydrogen atoms, which are typically difficult to locate using traditional X-ray diffraction techniques.
What does page 30 para 1 mean? What is an electron density map?
An electron density map is a three-dimensional representation of the distribution of electrons in a molecule or crystal.
How do we infer the location of the neighbouring H atom using the O atom?
- To identify heavy atoms in a crystal, the electron density map is examined to identify regions of high electron density
- Heavy atoms scatter X-rays more strongly than light atoms, which results in higher electron density around the heavy atoms in the electron density map.
- Heavy atoms will have a higher electrostatic potential than light atoms, which can be used to identify their positions in the molecule.
What were the peaks notes in figure 10 and figure 16
It is suggested in a study by Lusi that these peaks represent the “free” H atoms.
How do you fix a position of an atom? Refer to Lusi experiment
- In molecular modeling, the position of a hydrogen atom can be fixed.
- This is often done when the position of the hydrogen atom is known with high certainty, such as when it is part of a functional group that has been well characterized experimentally.
- Most refining software programmes give crystallographers the option of fixing the X-H bond distance in the riding model to a value that minimises the R factor to a “known” value established using other methods.
