Jan 15 Flashcards
What wavelength is vis light?
400-700nm
Why need Xrays and mostly soft ones to see proteins?
CC bonds are about 1.5 A, need short wavelength to see atoms.
How do xrays diffract?
They interact with the electrons of atoms and diffract.
What is a unit cell?
It is a repeating unit of the crystal that goes on for forever.
What are nodes? Lattice?
Nodes are at the 8 corners of unit cells. Each node interacts with 8 unit cells. These nodes when connected form a lattice.
What is translational symmetry?
It is that there is repetition between unit cells in the x,y, and z planes.
What are atomic coordinates?
A node is picked as the origin 0,0,0. Then each atom has a x,y,z coordinate. If there is symmetry-related atoms in the same unit cell, only need 1 molecule and this symmetry to describe the entire crystal.
What is contouring?
From electron density, any density below certain threshold not included. Anything above is included. From this shape can develop the molecule from it. This model is fitted into the electron density
Why is centre of Xray diffraction pattern blank?
Because have beam stop to stop undiffracted x rays from the direct beam hitting the detector.
What is the correlation between array of spheres and diffraction pattern/
The lattice spacing is inversed in diffraction pattern (shorter distances in real space are longer in pattern)
Benzene has 6 fold symmetry in real space, does its diffraction pattern have 6 fold symmetry?
No pattern has 2 fold symmetry
How do you see unrecorded reflections, how give coordinates?
Get diffraction pattern, but some beams not in state to be constructive interference on the film, so are unrecorded. To see these, need to rotate the crystal. These unrecorded reflections in reciprocal space have h,k,l coordinates. The center of the film is usually the origin
What does a FT do?
Fourier transform combines all structure factors from pattern. You get the electron density at x,y,z
Each diffracted xray is _________ of the contributions from all atoms in the unit cell
the sum
How are structure factors written?
They are vectors, you put Fa, Fb etc. and do it for any symmetrically related atoms in the same unit cell with a’, b’ etc.
What is a structure factor?
It is a wave (fourier sum) created from adding all the waves from individual atoms.
