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Shelx and Hydrogen Atoms

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.

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Shelx and Hydrogen Atoms

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  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 atom’s 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 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

  5. 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

  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

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