Shelx and Hydrogen Atoms

1
Shelx and Hydrogen Atoms

• How and why

2
Riding Hydrogen Atoms

• The default treatment is to calculate idealized
  positions for the hydrogen atoms and constrain
  them so they are at a set X-H distance.
• This is referred to as riding atoms because they
  ride with the atom they are attached to.
• The default is to fix the hydrogen adp to some
  multiple of the ridden atoms adp

3
HFIX cards

• The general format of the HIX card for adding
  hydrogen is
• HFIX mn U d atom name(s)
• Where mn is the code (see next)
• U is the adp to use (usually not entered)
• d is the bond distance (usually not entered)
• Atom names are the atoms to be ridden
• HFIX cards create AFIX cards in future cycles

4
Local Default Codes

• The first m describes the atom geometry and n
  defines the type of refinement.
• For everything but methyl and OH groups the value
  of n is 3 (ride with fixed distance)
• For SP3 carbon with 1 hydrogen mn13
• For SP3 carbon with 2 hydrogens mn23
• For SP2 atom with 1 hydrogen mn43
• For SP2 atom with 2 hydrogen mn93
• For SP carbon mn163

5
Methyl and OH Groups

• Calculate the best positions from the Fourier map
• Allow rotation around the single bond
• For methyl mn137
• For OH mn147
• If these do not refine change to 133 and 143
• mn 137 and 147 add a parameter for the torsion
  angle

6
Non HFIX Hydrogens

• Not all hydrogens can be added using HFIX cards
• Any hydrogen on a nitrogen or phosphorus
• H atoms on water
• The H atom on a carboxyl group
• These must be found from the difference Fourier
  map and should be refined!

7
Some Caveats

• If hydrogen distances and angles are important do
  NOT use HFIX cards!
• Can remove the fixed part of OH (147) cards by
  freeing the OH in the REFINE gui
• Never use HIFX if you are not sure what is going
  on. For incorrectly characterized organics it is
  best to refine the hydrogens.
• Never use HFIX for metal hydrides!

8
Automatic HFIX generation

• The programs XHYDRO or PLATON can be use.
• This is best done from the REFINE gui.
• Note it is best to check that hydrogens are
  correct before going on
• Problem areas
• 1. Carbons near symmetry
• 2. Carbons next to carbonyl groups