Shelx and Hydrogen Atoms How and why
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 atom’s adp
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
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 mn=13 • For SP3 carbon with 2 hydrogens mn=23 • For SP2 atom with 1 hydrogen mn=43 • For SP2 atom with 2 hydrogen mn=93 • For SP carbon mn=163
Methyl and OH Groups • Calculate the best positions from the Fourier map • Allow rotation around the single bond • For methyl mn=137 • For OH mn=147 • If these do not refine change to 133 and 143 • mn 137 and 147 add a parameter for the torsion angle
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!
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!
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