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Problem Set

Problem Set. Problem 1—These are NOT orthogonal coordinates. Generally d=(a 2 x 2 +b 2 y 2 +c 2 z 2 +2abxycos g +2acxzcos b +2bcyzcos a ) 1/2 Similar formula for cross product. Problem Set. Problem 1 continued

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Problem Set

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  1. Problem Set Problem 1—These are NOT orthogonal coordinates. Generally d=(a2x2+b2y2+c2z2+2abxycosg +2acxzcosb+2bcyzcosa)1/2 Similar formula for cross product

  2. Problem Set Problem 1 continued When doing trig functions on a computer make sure you know units. Most programs use radians not degrees! To convert degrees to radians multiply by p/180.

  3. Problem Set

  4. Problem Set

  5. What to do when Sir Fails • Did the right .sca file get formatted edit xl.hkl move to bottom are there enough reflections? yes—not problem no—run dform changing the .sca file then cp shelx.hkl xl.hkl

  6. Did you swap cell axes? • no—go to next step • yes—make sure xl.hkl and shelx.hkl are • different • diff xl.hkl shelx.hkl • if the same (no output) then • xprep xl

  7. Is space group part of a centric/accentric • pair? • If the centric space group was used change to • the accentric one. • Note for some orthorhombic space groups • (i.e. Pnma Pna21) you must rotate the cell • axes. Copy shelx.hkl to xl.hkl and then run • xprep and select space group

  8. Is Space Group Correct? • Run absen • Is the cell the same as xprep? • Look at absen output carefully and see if it • has determined the space group • correctly. • If neither xprep or absen can determine the • space group probable twin--PUNT

  9. Check cell contents and Z • Does the Z value make sense? • Using the “rule of twenty” does the volume • agree with the formula and Z? • May require some chemical analysis before • it will solve

  10. Check heavy metal count! • Does it not have a heavy atom when one • is expected • Does it have one when none is expected • Run a Patterson Map • If the above checks fail either the crystal is • no good (twinned, cracked, etc.) or the data • is no good! PUNT

  11. Heavy Metal Techniques • Direct Methods works in reciprocal space using normalized structure factors. • Heavy Atoms works in real space. • Patterson Map uses Fo with no phases. • Produces a map with intensity at the end of each atomic vector from origin. • Height of the peak is proportional to the product of the number of e in each atom

  12. Patterson • Large peak at 0,0,0 –vector from each atom to itself. • All vectors observed not just bonding vectors. • All Patterson maps are centric because there is vector a-b and b-a.

  13. Harker Vectors • Symmetry creates vectors between the same atom • Take case of P-1 Atom at x,y,z and symmetry creates –x,-y,-z The vector between these two is (x-(-x)),(y-(-y)),(z-(-z)) or 2x,2y,2z This vector is called a Harker vector and if the atom has a high atomic number is very large.

  14. Program Dirdif • Direct methods on partial solutions • Written by Paul Buerskens at the University of Nimegen in the Netherlands • Very formula sensitive • Three results 1. r-factor very large –no solution 2. r-factor reasonable (<15%)—solution 3. r-factor in between—probable solution with misassigned atoms.

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