11/18/2013 SHELX. History SHELXS. .ins File for SHELXS TITL. .ins File Organization

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SHELX George Sheldrick British 1976 It is surprising that SHELX has been able to maintain a dominant position in small-molecule structure determination for the last 30 years, even though computers

1 SHELX George Sheldrick British 1976 It is surprising that SHELX has been able to maintain a dominant position in small-molecule structure determination for the last 30 years, even though computers have changed out of all recognition in this time. History SHELX is a set of programs for crystal structure determination from single-crystal diffraction data, first written in late 1960's FORTRAN development enabled it to be widely distributed in 1976 as SHELX-76 SHELXS-86 update of structure solution because of major advances in direct methods SHELXL-93 achieved a revision of least-squares part SHELX-97-2 is the current version in Oscail SHELX-97 is divided into: SHELXS solution Patterson and direct methods SHELXL refinement Fourier synthesis and Least-squares SHELXS before running SHELXS, two files are required: name.ins name.hkl instructions, crystal and atom data etc. reflection data with format (3I4,2F8.2) 5 pieces of data: h, k, l, I (or F), I (or F ) 4 spaces (each) allotted for h, k, l (including ) - right justified 8 spaces (each) allotted for I (F) and I ( F ) (including.), 2 places past decimal point - right justified TITL Au(DPK)Cl2 Cl in P2(1)/n CELL ZERR LATT 1 SYMM.5-X,.5+Y,.5-Z SFAC C H N O CL AU UNIT HKLF 4.ins File for SHELXS 12 h k l F F.ins File Organization all instructions start with a four (or less) letter word; numbers and other information follow in free format, separated by spaces TITL, CELL, ZERR, LATT, SYMM, SFAC and UNIT must be given in that order; all remaining instructions, atoms come between UNIT and last instruction, HKLF program generates defaults [#] based on available information continuation given by '=' at end of a line; instruction continues on next line, starting with at least one space TITL [ ] TITL title of up to 76 characters; appears at suitable places in output title should include chemical formula and space group; update these if UNIT or SYMM instructions are changed later TITL Au(DPK)Cl2 Cl in P2(1)/n AU =

2 CELL ZERR CELL a b c x-ray wavelength and unit-cell dimensions in Å and degrees ZERR Z esd(a) esd(b) esd(c) esd( ) esd( ) esd( ) Z value (formula units per cell) followed by the estimated errors in unit-cell parameters CELL ZERR LATT SYMM symmetry operation SYMM coordinates of general positions LATT N[1] lattice type: 1 = P, 2 = I, 3 = R, 4 = F, 5 = A, 6 = B, 7 = C N if structure is non-centrosymmetric LATT 1 x, y, z assumed: not given if structure is centric, origin must lie on 1 so positions generated by changing signs are assumed and not given operators using decimals or fractions, separated by commas: 1/2-X,1/2+Y,-Z 0.5-X,0.5+Y,-Z one SYMM for each general position specified SYMM 0.5-X, 0.5+Y, 0.5-Z SFAC UNIT SFAC elements element symbols define order of scattering factors used; first 94 elements of periodic table allowed (all caps) also uses information to determine absorption coefficients first two SFAC types are C and H, (if present) in that order SFAC C H N O CL AU UNIT n1 n2... total number of each atom type in unit cell, in SFAC order # of each type of atom in the molecule multiplied by Z UNIT

Program and File Organization SHELXS a brief summary of the progress of the structure solution appears on screen, and a full listing is written to name.

ins file, followed by potential atoms two types of solution performed with SHELXS; structure of.ins very similar for both (.hkl file always same) Direct Methods: Patterson: TITL... TITL... CELL... CELL... ZERR.

minimum allowed length for HA to HA vector effective resolution in Å number of unique peaks to be found by searching the superposition function.

3 Program and File Organization SHELXS a brief summary of the progress of the structure solution appears on screen, and a full listing is written to name.lst, which can be printed or examined as a text file after structure solution, name.res is written; this contains crystal data etc. as in the name.ins file, followed by potential atoms two types of solution performed with SHELXS; structure of.ins very similar for both (.hkl file always same) Direct Methods: Patterson: TITL... TITL... CELL... CELL... ZERR... ZERR... LATT... LATT... SYMM... SYMM... SFAC... SFAC... UNIT... UNIT... TREF PATT HKLF HKLF PATT PATT nv[#] dmin[#] resl[#] Nsup[#] Zmin[#] maxat[#] patterson superposition procedure nv: dmin: resl: Nsup: Zmin: maxat: number of superposition vectors to be tried minimum allowed length for HA to HA vector effective resolution in Å number of unique peaks to be found by searching the superposition function. minimum atomic number to be included maximum number of potential atoms to be included generally use defaults PATT nv 1 dmin 1.80 resl 0.77 Nsup 114 Zmin 7.00 maxat 8 PATT TREF TREF np[100] ne[#] kapscal[#] ntan[#] wn[#] a large number of parameters which can be varied, but based on experience of many thousand structures can usually be relied on to choose sensible default values np: number of direct methods attempts ne: reflections are employed kapscal: multiplies products of the three E-values used in triplet phase relations; fudge factor ntan: wn: number of cycles of tangent formula refinement parameter used to calculate combined figure of merit TREF np 256. ne 262 kapscal ntan 2 wn TREF 3

4 MORE OMIT MORE verbosity [1] sets the amount of.lst output verbosity is in the range: 0 (least) to 3 (most verbose) OMIT s [4] 2 (lim) [180] thresholds for flagging reflections (F) as 'unobserved' SHELXL Fourier, Peak Search, Lineprinter Plot refinement of crystal structures, primarily for small molecules very general and valid for all space groups special position constraints are generated automatically can handle twinning, complex disorder, absolute structure determination,.cif and.pdb output, and provides a large variety of restraints and constraints for control of difficult refinements starts with the same TITL to UNIT instructions as SHELXS and ends with HKLF FMAP code[2] axis[#] nl[53] unique unit of the cell for performing Fourier calculation is set automatically unless specified by user using FMAP and GRID; program chooses a 53 x 53 x nl or 103 x 103 x nl grid depending on resolution of data. axis 1, 2 or 3 defines direction to layers code = 2: difference e density synthesis ( F o F c and c ) code = 3: e density synthesis ( F o and c ) FMAP 3 Fourier, Peak Search, Lineprinter Plot Atom List atomname sfac x y z sof [11] U [0.05] or U11 U22 U33 U23 U13 U12 PLAN npeaks[20] if npeaks is positive, a Fourier peak list is printed and written to.res file; if negative, molecule assembly and lineprinter plots are also performed PLAN -20 atom instructions begin with an atom name (up to 4 characters that do not correspond to any SHELXL command, a scattering factor number (refers to list defined by SFAC), x, y, and z in fractional coordinates, a site occupation factor sof, and an isotropic U or six anisotropic U i j components to fix any parameter, add 10 AU =

5 mn d[#] applies constraints and/or generates idealized coordinates for all atoms; digits mn control two separate operations m geometrical operations performed before first L.S. cycle n sets up constraints applied throughout refinement. d bond lengths in the idealized groups. instruction followed by required number of H or other atoms end with 0 m = 0 no action. 1 idealized tertiary C-H with all X-C-H angles equal must have three bonds to immediately preceding atom 2 idealized secondary CH 2 with all X-C-H and Y-C-H angles equal, and H-C-H determined by X-C-Y 3 idealized CH 3 group with tetrahedral angles; group is staggered wrt shortest bond to atom which -CH 3 attached 4 aromatic C-H or amide N-H 5 next five non-hydrogen atoms fit to regular pentagon 6 next six non-hydrogen atoms fit to regular hexagon 8 idealized OH group, with X-O-H angle tetrahedral 9 idealized terminal X=CH 2 or X=NH idealized pentamethylcyclopentadienyl (Cp*); followed by 5 ring C and 5 methyl C in cyclic order 11 idealized naphthalene group with equal bonds 13 idealized CH 3 group with tetrahedral angles; if coordinates of first H are non-zero, define torsion angle of methyl group 14 idealized OH group; X-O-H angle tetrahedral; if coordinates of H atom are non-zero, used to define torsion angle 16 acetylenic C-H, with X-C-H linear n = 0 no action. 1 coordinates, sof and U or Uij are fixed. 2 sof and U (or Uij) are fixed, but coordinates free to refine 3 coordinates, but not sof or U (or Uij) 'ride' on coordinates of previous atom with n not equal to 3 4 same as n = 3 except that X-H distance is free to refine 5 next atom(s) are 'dependent' atoms in a rigid group 6 next atom is the 'pivot atom' of a NEW rigid group, i.e. other atoms in the rigid group rotate about this atom HFIX OW = HO HO HFIX mn U [#] d[#] atomnames generates instructions and dummy H atoms must precede referenced atoms if U is 1.5 (or 1.2), isotropic temperature factor is 1.5 (1.2) x the atom it is attached to. 1.5 x U iso of last atom HFIX C2 > C6 calculates H s for a benzene, makes H atom instruction (surrounded by ), fixes temperature factor at 1.2x atom it is attached to and set it to ride on that atom during refinement 5

6 Least-Squares Refinement FVAR L.S. nls[0] nls cycles of full-matrix least-squares refinement are performed, followed by a structure factor calculation L.S. 10 FVAR osf[1] free variables osf overall scale factor estimate free variables are factors used to make constraints on some retrained parameters FVAR C1A C1B ANIS ANIS n next n isotropic non-hydrogen atoms are made anisotropic BOND atomnames outputs bond lengths for all bonds (defined in connectivity list) that involve two atoms named on same BOND instruction; angles are output for all pairs of such bonds involving a common atom no parameters outputs bond lengths/angles for all bonds in table BOND $H includes all bonds to H BOND set automatically by ACTA, and bond lengths and angles are written to.cif file CONF atomnames named atoms define a chain of at least four atoms; generates a list of torsion angles with esd's for all torsion angles defined by this chain MPLA na atomnames L.S. plane calculated through first na named atoms, and equation of plane and deviations of all named atoms from plane are listed with esd s; angle to previous L.S. plane (if any) is also given na must be at least 3 MPLA 4 N1 N3 N4 N6 AU1 CL1 6

7 HTAB dh[2.0] gives an analysis of H-bonding over all polar H s in structure; H-bonds printed for: HA < r(a)+dh and <DHA > 110º check output since algorithms are not infallible HTAB D-atom A-atom gives esd and CIF output; rogram decides which of H atoms (if any) makes the most suitable H-bond only A-atom may specify a symmetry operation (_$n) ACTA 2thetafull[#] name.cif created; automatically sets BOND, FMAP 2, and PLAN, so may not be used with other FMAP a warning given if cell contents on UNIT are not consistent with atom list, because they are used to calculate density etc 2thetafull used to specify value of 2 for which program calculates completeness of data for.cif as required by Acta Crystallographica; if no value given, program uses maximum value of 2 for reflection data WPDB writes refined coordinates to a.pdb file (without H s) OSCAIL also does this through FORMATS, INS >>>> PDB (can also convert PDB >>>> INS) EQIV $n symmetry operation defines symmetry operation $n for referencing symmetry equivalent atoms on any instruction which allows atom names, by appending '_$n' (where n is an integer between 1 and 511 inclusive) to atom name such a symmetry operation must be defined before it is used; it does not have to be an allowed operation of the space group, but the same notation is used as on SYMM instruction EQIV $1 -x, 1-y, -z BIND atom1 atom2 specified 'bond' (may be any length) is added to connectivity list if it is not there already; only one of the two atoms may be an equivalent atom (i.e. have extension _$n) BIND HO1 CL1_$1 FREE atom1 atom2 specified 'bond' is deleted from connectivity list (if present); only one of the two atoms may be an equivalent atom (i.e. have extension _$n) 7

8 DFIX d s[0.02] atom pairs distance between first and second named atom, third and fourth, etc. (if present) is restrained to a target value d with esd s d may refer to a 'free variable', otherwise considered fixed; value may lie between 0 and 15.res File TITL Cu(4-ClTAAB)(BF4)2 in C2/c CELL ZERR LATT 7 SYMM -X, Y,.5-Z SFAC C H B N F CL CU UNIT FMAP 2 PLAN -25 WGHT FVAR CU CL CL HKLF 3 REM Cu(4-ClTAAB)(BF4)2 in C2/c REM R1 = for 2266 Fo > 4sig(Fo) and for all 3753 data REM 11 parameters refined using 0 restraints END WGHT REM Highest difference peak , deepest hole , 1-sigma level res File Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q cutaab12 started at 16:51:46 on 5-Apr for use of this program please cite G.M. Sheldrick, SHELXL-97, University of Gottingen TITL Cu(4-ClTAAB)(BF4)2 in C2/c CELL ZERR LATT 7 SYMM -X, Y,.5-Z SFAC C H B N F CL CU UNIT V = F(000) = Mu = 1.07 mm-1 Cell Wt = Rho = FMAP 3 PLAN -30 WGHT FVAR CU CL CL HKLF 3 Covalent radii and connectivity table for Cu(4-ClTAAB)(BF4)2 in C2/c C H B N F CL CU Cu - no bonds found Cl1 - no bonds found Cl2 - no bonds found 3753 Reflections read, of which 0 rejected -17 =< h =< 17, 0 =< k =< 23, 0 =< l =< 17, Max. 2-theta = Systematic absence violations 0 Inconsistent equivalents 3753 Unique reflections, of which 0 suppressed R(int) = R(sigma) = Friedel opposites merged Maximum memory for data reduction = 474 / Special position constraints for Cu x = z = sof = Input constraints retained (at least in part) for sof ** Cell contents from UNIT instruction and atom list do not agree ** Unit-cell contents from UNIT instruction and atom list resp. C H B N F CL CU Cu(4-ClTAAB)(BF4)2 in C2/c ATOM x y z sof U11 U22 U33 U23 U13 U12 Ueq Cu Cl Cl Final Structure Factor Calculation for Cu(4-ClTAAB)(BF4)2 in C2/c 8

9 Total number of l.s. parameters = 11 Maximum vector length = 511 wr2 = before cycle 1 for 3753 data and 0 / 11 parameters GooF = S = 8.141; Restrained GooF = for 0 restraints Weight = 1 / [ sigma^2(fo^2) + ( * P )^ * P ] where P = ( Max ( Fo^2, 0 ) + 2 * Fc^2 ) / 3 R1 = for 2266 Fo > 4sig(Fo) and for all 3753 data wr2 = , GooF = S = 8.141, Restrained GooF = for all data Occupancy sum of asymmetric unit = 2.50 for non-hydrogen and 0.00 for hydrogen atoms Analysis of variance for reflections employed in refinement K = Mean[Fo^2] / Mean[Fc^2] for group Resolution(A) Number in group GooF K R Recommended weighting scheme: WGHT Note that in most cases convergence will be faster if fixed weights (e.g. the default WGHT 0.1) are retained until the refinement is virtually complete, and only then should the above recommended values be used. Most Disagreeable Reflections (* if suppressed or used for Rfree) Fc/Fc(max) Number in group GooF K h k l Fo^2 Fc^2 Delta(F^2)/esd Fc/Fc(max) Resolution(A) HKLF HKLF n[0] s[1] r11...r33[ ] n = 3: h k l F o F BN [1] (if batch # absent or 0, set to 1). n = 4: h k l F o2 F2 BN [1] indices can be transformed using 3 x 3 matrix r 11...r 33 : HKLF 3 h is r 11 * h + r 12 * k + r 13 * l k is r 21 * h + r 22 * k + r 23 * l l is r 31 * h + r 32 * k + r 33 * l HKLF instruction must come last 9

SHELXL Instruction Summary

SHELXL Instruction Summary This file lists the instructions that may be used in the. ins file for SHELXL-97. Defaults are given in square brackets; '#' indicates that the program will generate a suitable