SAALIHA VIVA - INTRO Flashcards

1
Q

Define crystal structure and unit cell

A
  • A crystal structure is defined as the repeating arrangement of atoms throughout a crystal.
  • The unit cell is the smallest group of atoms that enables identical cells to be stacked on top of each other to completely fill a space
  • An entire crystal structure can be created by the repetition of cells in three dimensions
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2
Q

Define Laue spots

A
  • The Laue method is used extensively for the determination of the orientation of single crystals
  • Laue spots are bright spots formed when X-rays are diffracted by a crystal lattice
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3
Q

Amorphous vs crystalline structure

A
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4
Q

Define H bonds

A

Electrostatic interaction that occurs between molecules containing hydrogen and another electronegative atom such as O, N or a halogen

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5
Q

Importance of H bonding

A
  • Unique properties of H2O - high boiling point and surface temperature
  • Protein binding and DNA structure
  • Designing new material
  • Identifying polymorphs
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6
Q

Ritanovir

A

HIV treatment Ritonavir. Ritonavir is a polymorphic drug
- LHP method was used to identify the probability of H-bond formation to assess crystal stability based on H-bonding
- This can differentiate between a drug being effective or ineffective in industry
- H-bond geometry from the CSD

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7
Q

Explain salt-cocrystal continuum

A
  • Concept which describes the relationship between salts and cocrystals
  • The continuum refers to the fact that there is a range of possible combinations (between API and a coformer) of drug molecules that can form either a salt or a co-crystal.
  • The location of the H ion is what differentiates the two
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8
Q

Coformers

A

Conformational isomers
- stereoisomers produced by rotation about a single bond

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9
Q

What is the difference between a salt and a cocrystal?

A
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10
Q

Rationale for salt co-crystal continuum

A
  • Co-crystallisation is an important concept which has only recently gained widespread attention as a means of identifying the H atom position.
  • A study by Edwards et al describes the two states where the H-atom is either situated close to the proton donor (co-crystal) or close to the proton acceptor
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11
Q

Define bond length

A

Geometrical descriptor used throughout this report to analyse data, characterised by the distance between the centres of the two covalently bonded atoms.

Measured in Angstroms

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12
Q

Define covalent bond

A

A covalent bond is defined as the sharing of electrons whereby the electrons from two different atoms share the orbital, binding the two atoms together.

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13
Q

What does a higher bond order mean?

A

Means a shorter bond length due to the stronger pull between the two atoms

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14
Q

Define elastic scattering in terms of XRD

A
  • An incoming X-ray interacts with a crystal structure
  • X-ray’s energy is absorbed
  • And then scattered by the atom’s electrons
  • Then released as a new X-ray after impact.
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15
Q

How does the number of electrons effect how light is scattered?

A
  • Atoms in these crystals are arranged in a regular pattern and are each surrounded by a cloud of electrons
  • This allows them to diffract light.
  • Each atom can be thought of as a coherent point scatterer.
  • The number of electrons surrounding an atom determines how strongly it scatters light
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16
Q

What are the advantages of XRD

A
  • Can create 3D representation of the density of electrons within the crystal with the help of a computer programme by analysing the angles and intensities of these diffracted beams
  • X-ray sources are so accessible and reasonably priced, the X-ray diffractometer is the most frequently utilised diffraction technique in solid-state laboratories.
17
Q

H atoms and XRD

A
  • The more electrons an atom has, the greater it diffracts.
  • Because H only has one electron, it makes it difficult to determine the precise position of H atoms, especially in the presence of heavy atoms that dominate the diffraction pattern
18
Q

SCXRD vs PXRD

A
19
Q

How are single crystals formed?

A
  1. Slow diffusion – solution of compound of interest is place in a solvent that is less miscible with the original solvent. Overtime, solvent diffuses slowly into the solution = single crystals
  2. Sublimation – heat compound of interest, to a temp at which is vaporises. Cool vapor, condense on a cooler surface
20
Q

Define ND

A
  • Technique used to study the atomic structure of materials.
  • It involves directing a beam of neutrons at a sample, and then analyzing the way the neutrons scatter to determine the positions of atoms within the sample.
21
Q

The role of neutrons in ND

A
  • By subjecting materials to high-energy neutrons, some will be absorbed others will emerge in a new direction, known as scattered neutrons
  • With or without a change in energy
  • The rest will pass through the material unaffected.
  • Neutrons interact with nuclei and lose energy in the process.
22
Q

Why is ND preferred for locating the position of H atom?

A
  • In contrast to X-rays, neutrons interact with the atom’s nucleus rather than its electron shell, specifically with its spin
  • Scattering power is not effected by the fact that hydrogen only has one electron.
  • Therefore, provides accurate structural data on H atom locations
23
Q

Difference between XRD and ND

A
24
Q

Summarise Aims

A
  • Study the usefulness of the H atom in the CSD for common H-bonding patterns
  • COOH and CONH2 were investigated
  • 3 distances were defined for each motif following common H bonding synthons
  • Bond length entries derived from the CSD were imported and analysed
  • Subjected to both XRD and ND
  • Crystal structures were subjected to further refinement methods, by specifying the R factor ≤0.05, and powder vs single crystal diffraction, to identify which analytical tool would determine the H atom most accurately.