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The XD Program System and Calculation of Properties

Jyväskylä Summer School on Charge Density August 2007. The XD Program System and Calculation of Properties. Louis J Farrugia. Jyväskylä Summer School on Charge Density August 2007. The XD Program System.

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The XD Program System and Calculation of Properties

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  1. Jyväskylä Summer School on Charge Density August 2007 The XD Program System andCalculation of Properties Louis J Farrugia

  2. Jyväskylä Summer School on Charge Density August 2007 The XD Program System The XD program system is a comprehensive computer program package for multipole refinement, topological analysis of charge densities and evaluation of intermolecular energies from experimental or theoretical structure factors. XD uses THREE primary input files : XD.INP/XD.RES - contains the refined parameters XD.HKL - the reflection data as F or F2 with sigma's and optional dir cosines XD.MAS - contains all the program instructions A. Volkov, P. Macchi, L. J. Farrugia, C. Gatti, P. R. Mallinson, T. Richter, T. Koritsanszky (2006).

  3. Jyväskylä Summer School on Charge Density August 2007 The XD Program System

  4. Jyväskylä Summer School on Charge Density August 2007 The XD Program System

  5. Jyväskylä Summer School on Charge Density August 2007 The XD Program System

  6. Jyväskylä Summer School on Charge Density August 2007 The XDINI Program The XDINI program provides a link between "standard" refinement programs like SHELXL or the standard crystallographic file format (CIF) and the XD program system. XDINI reads either SHELX.INS & SHELX.HKL (or XD.CIF & XD.FCF) and writes default versions of XD.INP, XD.MAS, XD.HKL. It needs to know (a) format you are using (b) ID name (XD) (c) the database you wish to use. Command line XDINI <name> <format> <databank code> XDINI xd shelx SCM

  7. Jyväskylä Summer School on Charge Density August 2007 Choice of the Databank xd.bnk_RHF_CR: (BANK CR) CHFW Non relativistic wave functions (H-Kr, including ions) Clementi, E. & Roetti, C. (1974). At. Data Nucl. Data Tables, 14, 177-478 RDSD E. Clementi and D. L. Raimondi, J. Chem. Phys. 38, 2686-2689 (1963). Analytical Fit : International Tables for Crystallography xd.bnk_RHF_BBB: (BANK BBB) CHFW Non relativistic wave functions (H-Xe) C. F. Bunge, J. A. Barrientos, A. V. Bunge At. Data Nucl. Data Tables, 53, 113-162 (1993). RDSD E. Clementi and D. L. Raimondi, J. Chem. Phys. 38, 2686-2689 (1963). Analytical Fit : International Tables for Crystallography xd.bnk_RDF_SCM: (BANK SCM) CHFW Relativistic wave functions (H-Xe, including ions) Z. Su and P. Coppens Acta Cryst., A54, 646 (1998): P. Macchi and P. Coppens Acta Cryst., A57, 656 (2001). RDSD E. Clementi and D. L. Raimondi, J. Chem. Phys. 38, 2686-2689 (1963). Analytical Fit : Su, Z.; Coppens, P. Acta Cryst1997,A53, 749, Macchi, P.; Coppens, P. Acta Cryst., 2001, A57, 656 xd.bnk_PBE-QZ4P-ZORA: (BANK VM) CHFW Relativistic wave functions (H-Cf) unpublished RDSD E. Clementi and D. L. Raimondi, J. Chem. Phys. 38, 2686-2689 (1963). Analytical Fit : Macchi, P.; Volkov, A. unpublished

  8. Jyväskylä Summer School on Charge Density August 2007 The XD.INP Parameter File !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! <<< X D PARAMETER FILE >>> $Revision: 5.39 (Jun 5 2007)$ 24-Jun-06! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! XDPARFILE VERSION 2 XD MODEL 0 0 0 0 LIMITS nat 2000 ntx 31 lmx 4 nzz 30 nto 0 nsc 20 ntb 20 nov 2500 USAGE 20 0 0 4 0 1 0 0 4 0 0 0 0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000E+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 O(1) 3 2 13 1 6 2 1 1 0 0 0 0.202009 0.200013 0.479127 1.0000 0.025050 0.012910 0.009490 -0.010960 0.000890 -0.000330 6.0000 0.0000 O(2) 3 2 6 2 13 2 1 1 0 0 0 -0.004865 0.031916 0.359431 1.0000 0.023710 0.015640 0.007150 -0.007000 -0.000440 -0.001250 6.0000 0.0000 . . . H(7) 3 2 5 20 19 1 4 4 0 0 0 0.930190 0.964298 0.213487 1.0000 0.024890 0.000000 0.000000 0.000000 0.000000 0.000000 1.0000 0.0000 1 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 2 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 3 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 4 1.200000 1.200000 1.200000 1.200000 1.200000 1.200000 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.117148E+01

  9. Jyväskylä Summer School on Charge Density August 2007 The XD.INP Parameter File <name> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! <<< X D PARAMETER FILE >>> $Revision: 5.39 (Jun 5 2007)$ 24-Jun-06! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! XDPARFILE VERSION 2 XD MODEL 0 0 0 0 LIMITS nat 2000 ntx 31 lmx 4 nzz 30 nto 0 nsc 20 ntb 20 nov 2500 USAGE 20 0 0 4 0 1 0 0 4 0 0 0 0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000E+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 O(1) 3 2 13 1 6 2 1 1 0 0 0 0.202009 0.200013 0.479127 1.0000 0.025050 0.012910 0.009490 -0.010960 0.000890 -0.000330 6.0000 0.0000 O(2) 3 2 6 2 13 2 1 1 0 0 0 -0.004865 0.031916 0.359431 1.0000 0.023710 0.015640 0.007150 -0.007000 -0.000440 -0.001250 6.0000 0.0000 . . . H(7) 3 2 5 20 19 1 4 4 0 0 0 0.930190 0.964298 0.213487 1.0000 0.024890 0.000000 0.000000 0.000000 0.000000 0.000000 1.0000 0.0000 1 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 2 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 3 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 4 1.200000 1.200000 1.200000 1.200000 1.200000 1.200000 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.117148E+01

  10. Jyväskylä Summer School on Charge Density August 2007 The XD.INP Parameter File number of atoms !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! <<< X D PARAMETER FILE >>> $Revision: 5.39 (Jun 5 2007)$ 24-Jun-06! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! XDPARFILE VERSION 2 XD MODEL 0 0 0 0 LIMITS nat 2000 ntx 31 lmx 4 nzz 30 nto 0 nsc 20 ntb 20 nov 2500 USAGE 20 0 0 4 0 1 0 0 4 0 0 0 0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000E+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 O(1) 3 2 13 1 6 2 1 1 0 0 0 0.202009 0.200013 0.479127 1.0000 0.025050 0.012910 0.009490 -0.010960 0.000890 -0.000330 6.0000 0.0000 O(2) 3 2 6 2 13 2 1 1 0 0 0 -0.004865 0.031916 0.359431 1.0000 0.023710 0.015640 0.007150 -0.007000 -0.000440 -0.001250 6.0000 0.0000 . . . H(7) 3 2 5 20 19 1 4 4 0 0 0 0.930190 0.964298 0.213487 1.0000 0.024890 0.000000 0.000000 0.000000 0.000000 0.000000 1.0000 0.0000 1 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 2 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 3 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 4 1.200000 1.200000 1.200000 1.200000 1.200000 1.200000 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.117148E+01

  11. Jyväskylä Summer School on Charge Density August 2007 The XD.INP Parameter File Parameters for atom O(1) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! <<< X D PARAMETER FILE >>> $Revision: 5.39 (Jun 5 2007)$ 24-Jun-06! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! XDPARFILE VERSION 2 XD MODEL 0 0 0 0 LIMITS nat 2000 ntx 31 lmx 4 nzz 30 nto 0 nsc 20 ntb 20 nov 2500 USAGE 20 0 0 4 0 1 0 0 4 0 0 0 0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000E+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 O(1) 3 2 13 1 6 2 1 1 0 0 0 0.202009 0.200013 0.479127 1.0000 0.025050 0.012910 0.009490 -0.010960 0.000890 -0.000330 6.0000 0.0000 O(2) 3 2 6 2 13 2 1 1 0 0 0 -0.004865 0.031916 0.359431 1.0000 0.023710 0.015640 0.007150 -0.007000 -0.000440 -0.001250 6.0000 0.0000 . . . H(7) 3 2 5 20 19 1 4 4 0 0 0 0.930190 0.964298 0.213487 1.0000 0.024890 0.000000 0.000000 0.000000 0.000000 0.000000 1.0000 0.0000 1 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 2 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 3 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 4 1.200000 1.200000 1.200000 1.200000 1.200000 1.200000 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.117148E+01

  12. Jyväskylä Summer School on Charge Density August 2007 The XD.INP Parameter File !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! <<< X D PARAMETER FILE >>> $Revision: 5.39 (Jun 5 2007)$ 24-Jun-06! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! XDPARFILE VERSION 2 XD MODEL 0 0 0 0 LIMITS nat 2000 ntx 31 lmx 4 nzz 30 nto 0 nsc 20 ntb 20 nov 2500 USAGE 20 0 0 4 0 1 0 0 4 0 0 0 0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000E+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 O(1) 3 2 13 1 6 2 1 1 0 0 0 0.202009 0.200013 0.479127 1.0000 0.025050 0.012910 0.009490 -0.010960 0.000890 -0.000330 6.0000 0.0000 O(2) 3 2 6 2 13 2 1 1 0 0 0 -0.004865 0.031916 0.359431 1.0000 0.023710 0.015640 0.007150 -0.007000 -0.000440 -0.001250 6.0000 0.0000 . . . H(7) 3 2 5 20 19 1 4 4 0 0 0 0.930190 0.964298 0.213487 1.0000 0.024890 0.000000 0.000000 0.000000 0.000000 0.000000 1.0000 0.0000 1 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 2 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 3 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 4 1.200000 1.200000 1.200000 1.200000 1.200000 1.200000 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.117148E+01 positional parameters

  13. Jyväskylä Summer School on Charge Density August 2007 The XD.INP Parameter File !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! <<< X D PARAMETER FILE >>> $Revision: 5.39 (Jun 5 2007)$ 24-Jun-06! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! XDPARFILE VERSION 2 XD MODEL 0 0 0 0 LIMITS nat 2000 ntx 31 lmx 4 nzz 30 nto 0 nsc 20 ntb 20 nov 2500 USAGE 20 0 0 4 0 1 0 0 4 0 0 0 0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000E+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 O(1) 3 2 13 1 6 2 1 1 0 0 0 0.202009 0.200013 0.479127 1.0000 0.025050 0.012910 0.009490 -0.010960 0.000890 -0.000330 6.0000 0.0000 O(2) 3 2 6 2 13 2 1 1 0 0 0 -0.004865 0.031916 0.359431 1.0000 0.023710 0.015640 0.007150 -0.007000 -0.000440 -0.001250 6.0000 0.0000 . . . H(7) 3 2 5 20 19 1 4 4 0 0 0 0.930190 0.964298 0.213487 1.0000 0.024890 0.000000 0.000000 0.000000 0.000000 0.000000 1.0000 0.0000 1 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 2 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 3 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 4 1.200000 1.200000 1.200000 1.200000 1.200000 1.200000 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.117148E+01 Occupancy - not refinable !

  14. Jyväskylä Summer School on Charge Density August 2007 The XD.INP Parameter File !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! <<< X D PARAMETER FILE >>> $Revision: 5.39 (Jun 5 2007)$ 24-Jun-06! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! XDPARFILE VERSION 2 XD MODEL 0 0 0 0 LIMITS nat 2000 ntx 31 lmx 4 nzz 30 nto 0 nsc 20 ntb 20 nov 2500 USAGE 20 0 0 4 0 1 0 0 4 0 0 0 0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000E+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 O(1) 3 2 13 1 6 2 1 1 0 0 0 0.202009 0.200013 0.479127 1.0000 0.025050 0.012910 0.009490 -0.010960 0.000890 -0.000330 6.0000 0.0000 O(2) 3 2 6 2 13 2 1 1 0 0 0 -0.004865 0.031916 0.359431 1.0000 0.023710 0.015640 0.007150 -0.007000 -0.000440 -0.001250 6.0000 0.0000 . . . H(7) 3 2 5 20 19 1 4 4 0 0 0 0.930190 0.964298 0.213487 1.0000 0.024890 0.000000 0.000000 0.000000 0.000000 0.000000 1.0000 0.0000 1 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 2 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 3 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 4 1.200000 1.200000 1.200000 1.200000 1.200000 1.200000 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.117148E+01 anisotropic thermal parameters U11 U22 U33 U12 U13 U23

  15. Jyväskylä Summer School on Charge Density August 2007 The XD.INP Parameter File !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! <<< X D PARAMETER FILE >>> $Revision: 5.39 (Jun 5 2007)$ 24-Jun-06! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! XDPARFILE VERSION 2 XD MODEL 0 0 0 0 LIMITS nat 2000 ntx 31 lmx 4 nzz 30 nto 0 nsc 20 ntb 20 nov 2500 USAGE 20 0 0 4 0 1 0 0 4 0 0 0 0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000E+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 O(1) 3 2 13 1 6 2 1 1 0 0 0 0.202009 0.200013 0.479127 1.0000 0.025050 0.012910 0.009490 -0.010960 0.000890 -0.000330 6.0000 0.0000 O(2) 3 2 6 2 13 2 1 1 0 0 0 -0.004865 0.031916 0.359431 1.0000 0.023710 0.015640 0.007150 -0.007000 -0.000440 -0.001250 6.0000 0.0000 . . . H(7) 3 2 5 20 19 1 4 4 0 0 0 0.930190 0.964298 0.213487 1.0000 0.024890 0.000000 0.000000 0.000000 0.000000 0.000000 1.0000 0.0000 1 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 2 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 3 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 4 1.200000 1.200000 1.200000 1.200000 1.200000 1.200000 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.117148E+01 multipole parameters - currently only Pv and P00 are present

  16. Jyväskylä Summer School on Charge Density August 2007 The XD.INP Parameter File !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! <<< X D PARAMETER FILE >>> $Revision: 5.39 (Jun 5 2007)$ 24-Jun-06! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! XDPARFILE VERSION 2 XD MODEL 0 0 0 0 LIMITS nat 2000 ntx 31 lmx 4 nzz 30 nto 0 nsc 20 ntb 20 nov 2500 USAGE 20 0 0 4 0 1 0 0 4 0 0 0 0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000E+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 O(1) 3 2 13 1 6 2 1 1 0 0 0 0.202009 0.200013 0.479127 1.0000 0.025050 0.012910 0.009490 -0.010960 0.000890 -0.000330 6.0000 0.0000 O(2) 3 2 6 2 13 2 1 1 0 0 0 -0.004865 0.031916 0.359431 1.0000 0.023710 0.015640 0.007150 -0.007000 -0.000440 -0.001250 6.0000 0.0000 . . . H(7) 3 2 5 20 19 1 4 4 0 0 0 0.930190 0.964298 0.213487 1.0000 0.024890 0.000000 0.000000 0.000000 0.000000 0.000000 1.0000 0.0000 1 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 2 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 3 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 4 1.200000 1.200000 1.200000 1.200000 1.200000 1.200000 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.117148E+01 Kappa parameters

  17. Jyväskylä Summer School on Charge Density August 2007 The XD.INP Parameter File !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! <<< X D PARAMETER FILE >>> $Revision: 5.39 (Jun 5 2007)$ 24-Jun-06! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! XDPARFILE VERSION 2 XD MODEL 0 0 0 0 LIMITS nat 2000 ntx 31 lmx 4 nzz 30 nto 0 nsc 20 ntb 20 nov 2500 USAGE 20 0 0 4 0 1 0 0 4 0 0 0 0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000E+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 O(1) 3 2 13 1 6 2 1 1 0 0 0 0.202009 0.200013 0.479127 1.0000 0.025050 0.012910 0.009490 -0.010960 0.000890 -0.000330 6.0000 0.0000 O(2) 3 2 6 2 13 2 1 1 0 0 0 -0.004865 0.031916 0.359431 1.0000 0.023710 0.015640 0.007150 -0.007000 -0.000440 -0.001250 6.0000 0.0000 . . . H(7) 3 2 5 20 19 1 4 4 0 0 0 0.930190 0.964298 0.213487 1.0000 0.024890 0.000000 0.000000 0.000000 0.000000 0.000000 1.0000 0.0000 1 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 2 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 3 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 4 1.200000 1.200000 1.200000 1.200000 1.200000 1.200000 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.117148E+01 Extinction parameters

  18. Jyväskylä Summer School on Charge Density August 2007 The XD.INP Parameter File !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! <<< X D PARAMETER FILE >>> $Revision: 5.39 (Jun 5 2007)$ 24-Jun-06! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! XDPARFILE VERSION 2 XD MODEL 0 0 0 0 LIMITS nat 2000 ntx 31 lmx 4 nzz 30 nto 0 nsc 20 ntb 20 nov 2500 USAGE 20 0 0 4 0 1 0 0 4 0 0 0 0 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000E+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 O(1) 3 2 13 1 6 2 1 1 0 0 0 0.202009 0.200013 0.479127 1.0000 0.025050 0.012910 0.009490 -0.010960 0.000890 -0.000330 6.0000 0.0000 O(2) 3 2 6 2 13 2 1 1 0 0 0 -0.004865 0.031916 0.359431 1.0000 0.023710 0.015640 0.007150 -0.007000 -0.000440 -0.001250 6.0000 0.0000 . . . H(7) 3 2 5 20 19 1 4 4 0 0 0 0.930190 0.964298 0.213487 1.0000 0.024890 0.000000 0.000000 0.000000 0.000000 0.000000 1.0000 0.0000 1 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 2 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 3 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 4 1.200000 1.200000 1.200000 1.200000 1.200000 1.200000 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.117148E+01 Overall scale factor

  19. Jyväskylä Summer School on Charge Density August 2007 The XD.HKL Reflection File XD F^2 NDAT 6 -5 -7 1 1 5.300 0.790 -5 -7 2 1 74.050 2.480 -5 -7 3 1 2.740 1.540 -5 -7 4 1 11.410 10.700 -5 -6 1 1 21.890 1.880 -5 -6 2 1 0.540 1.210 -5 -6 3 1 5.140 0.860 -5 -6 4 1 3.090 1.030 -5 -6 5 1 94.190 2.830 -5 -6 6 1 17.450 13.830 -5 -5 1 1 2.680 1.130 . . . Data may be presented either as F or F2 (NOTE in current version the sigma cutoff is applied BEFORE conversion) Several batch scale factors can be refined Phases may optionally be present (phase angle in radians, NDAT = -7)

  20. Jyväskylä Summer School on Charge Density August 2007 The XD.MAS Control File !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! <<< X D MASTER FILE >>> $Revision: 5.39 (Jun 5 2007)$ 24-Jun-06! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! TITLE XD CELL 3.6782 7.5991 12.4999 85.662 88.029 84.225 WAVE 0.71073 CELLSD 0.0003 0.0005 0.0008 0.003 0.003 0.002 LATT C P SYMM 1/2+X,1/2-Y,1/2+z BANK SCM !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! MODULE *XDLSM SELECT model 0 2 1 0 based_on F test verbose 1 SELECT cycle -1 dampk 1. cmin 0.6 cmax 1. eigcut 1.d-09 convcrit 0.0 SAVE deriv lsqmat *cormat SOLVE *inv diag *cond !------------------------------------------------------------------------------ SCAT CORE SPHV DEFV 1S 2S 3S 4S 2P 3P 4P 3D 4D 4F 5S 5P 6S 6P 5D 7S 6D 5F DELF' DELF'' NSCTL O CHFW CHFW CSZD 2 -2 0 0 -4 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0110 0.0060 0.580 N CHFW CHFW CSZD 2 -2 0 0 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0060 0.0030 0.936 C CHFW CHFW CSZD 2 -2 0 0 -2 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0030 0.0020 0.665 H CHFW CHFW CSZD -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 -0.374 END SCAT . . END XDLSM Divided into sections - one main section and eight other sections giving commands for the main program modules.

  21. Jyväskylä Summer School on Charge Density August 2007 The XD.MAS Control File !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! <<< X D MASTER FILE >>> $Revision: 5.39 (Jun 5 2007)$ 24-Jun-06! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! TITLE XD CELL 3.6782 7.5991 12.4999 85.662 88.029 84.225 WAVE 0.71073 CELLSD 0.0003 0.0005 0.0008 0.003 0.003 0.002 LATT C P SYMM 1/2+X,1/2-Y,1/2+z BANK SCM !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! MODULE *XDLSM SELECT model 0 2 1 0 based_on F test verbose 1 SELECT cycle -1 dampk 1. cmin 0.6 cmax 1. eigcut 1.d-09 convcrit 0.0 SAVE deriv lsqmat *cormat SOLVE *inv diag *cond !------------------------------------------------------------------------------ SCAT CORE SPHV DEFV 1S 2S 3S 4S 2P 3P 4P 3D 4D 4F 5S 5P 6S 6P 5D 7S 6D 5F DELF' DELF'' NSCTL O CHFW CHFW CSZD 2 -2 0 0 -4 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0110 0.0060 0.580 N CHFW CHFW CSZD 2 -2 0 0 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0060 0.0030 0.936 C CHFW CHFW CSZD 2 -2 0 0 -2 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0030 0.0020 0.665 H CHFW CHFW CSZD -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 -0.374 END SCAT . . END XDLSM Everything between MODULE *XDLSM and END XDLSM refers to commands and/or information for the refinement program XDLSM. The *XDLSM indicates that this module is activated - a common usage in XD

  22. Jyväskylä Summer School on Charge Density August 2007 The XDLSM Commands MODULE *XDLSM SELECT model 0 2 1 0 based_on F test verbose 1 SELECT cycle -1 dampk 1. cmin 0.6 cmax 1. eigcut 1.d-09 convcrit 0.0 SAVE deriv lsqmat *cormat SOLVE *inv diag *cond !------------------------------------------------------------------------------ SCAT CORE SPHV DEFV 1S 2S 3S 4S 2P 3P 4P 3D 4D 4F 5S 5P 6S 6P 5D 7S 6D 5F DELF' DELF'' NSCTL O CHFW CHFW CSZD 2 -2 0 0 -4 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0110 0.0060 0.580 N CHFW CHFW CSZD 2 -2 0 0 -3 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0060 0.0030 0.936 C CHFW CHFW CSZD 2 -2 0 0 -2 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0030 0.0020 0.665 H CHFW CHFW CSZD -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 -0.374 END SCAT . . END XDLSM XDLSM is a standard full-matrix least-squares refinement program, which can refine on F or F2 (based_on F/F^2). Few sophisticated features. Convergence criterion - refinement stops when I/sig(I) < convcrit The SCAT table defines the scattering model used for each atomic type. The numbers define the occupations of the HF orbitals - negative numbers mean that those electrons are defined as the valence electrons, otherwise they are assumed to be core. More than one entry for a particular element is allowed. In general, the SCAT table written by the import program XDINI will be satisfactory for an initial model.

  23. Jyväskylä Summer School on Charge Density August 2007 The ATOM Table ATOM ATOM0 AX1 ATOM1 ATOM2 AX2 R/L TP TBL KAP LMX SITESYM CHEMCON O(1) C(1) X O(1) N(1) Y R 2 1 1 4 m N(1) C(1) Z N(1) O(1) Y R 2 2 2 4 mm2 C(1) N(1) X C(1) O(1) Y R 2 3 3 4 m H(1) N(1) Z H(1) C(1) Y R 1 4 4 1 cyl H(2) N(1) Z H(2) C(1) Y R 1 4 4 1 cyl H(3) C(1) Z H(3) O(1) Y R 1 4 4 1 cyl DUM0 0.0000 0.0000 0.0000 END ATOM The ATOM table defines the local coordinate system used for each atom, as well as identifying the scattering type and Kappa set for that atom. Limits on the multipole expansion, thermal motion description and chemical constraints are also applied here. In general, the ATOM table written by the import program XDINI will be NOT satisfactory for an initial model.

  24. Jyväskylä Summer School on Charge Density August 2007 The ATOM Table ATOM ATOM0 AX1 ATOM1 ATOM2 AX2 R/L TP TBL KAP LMX SITESYM CHEMCON O(1) C(1) X O(1) N(1) Y R 2 1 1 4 m N(1) C(1) Z N(1) O(1) Y R 2 2 2 4 mm2 C(1) N(1) X C(1) O(1) Y R 2 3 3 4 m H(1) N(1) Z H(1) C(1) Y R 1 4 4 1 cyl H(2) N(1) Z H(2) C(1) Y R 1 4 4 1 cyl H(3) C(1) Z H(3) O(1) Y R 1 4 4 1 cyl DUM0 0.0000 0.0000 0.0000 END ATOM C atom m O atom m N atom mm2 H atom cyl Formamide HC(=O)NH2

  25. Jyväskylä Summer School on Charge Density August 2007 The KEY Table KEY xyz --U2-- ----U3---- ------U4------- M- -D- --Q-- ---O--- ----H---- O(1) 000 000000 0000000000 000000000000000 00 000 00000 0000000 000000000 N(1) 000 000000 0000000000 000000000000000 00 000 00000 0000000 000000000 C(1) 000 000000 0000000000 000000000000000 00 000 00000 0000000 000000000 H(1) 000 000000 0000000000 000000000000000 00 000 00000 0000000 000000000 H(2) 000 000000 0000000000 000000000000000 00 000 00000 0000000 000000000 H(3) 000 000000 0000000000 000000000000000 00 000 00000 0000000 000000000 KAPPA 000000 KAPPA 000000 KAPPA 000000 KAPPA 000000 EXTCN 0000000 OVTHP 0 SCALE 1 END KEY The KEY table defines which parameters are to be refined. "0" means don't refine and any other entry, usually "1" means refine. The layout for the atoms is self explanatory. The XD manual & tutorial gives the order in which the U's and multipole parameters are given. In general, the KEY table written by the import program XDINI will be satisfactory for an initial model, but is the part of the input which needs changing most.

  26. Jyväskylä Summer School on Charge Density August 2007 The XDLSM Commands !GROUP2 atom1 atom2 ... KEEP kappa 1 2 3 4 KEEP charge group1 !KEEP rigid group1 !RESET bond C(1) H(1) 1.09 ... WEIGHT -2.0 .0 .0 .0 .0 0.3333 !SWAT g 0.00 U 0.00 SKIP obs 0. 1.d10 *sigobs 3. 1.d06 sinthl 0. 2. !PRINT sinthl .0 2. obs 0. 15. delta 0. 10. *del% 80 100 extcn 80. 100. *abssc !EXTCN *iso aniso *type_1 type_2 type_3 distr_g *distr_l msc_0 msc_1 DMSDA 1.1 1.8 FOUR fmod1 4 2 0 0 fmod2 -1 2 0 0 !CON num1 par1/iat1 num2 par2/iat2 ... = num0 In XDLSM (as in all programs) placing an "!" mark as the first character comments out the commands. The KEEP kappa command ensures that the kappa' parameters for all l values of the deformation valence are the same The KEEP charge ensures that the sum of the monopole populations Pv equals the total valence population.

  27. Jyväskylä Summer School on Charge Density August 2007 The Results of Refinement A set of positional, thermal motion and multipole parameters which provide the best fit to the data. These parameters can be used to reconstruct and analyse the electron density (do not use Fourier methods). CAVEATS 1. Because of the complexity of the model, least-squares procedure may not provide a unique solution. 2. The refinement of the mutipole parameters may be difficult if the structure is non-centrosymmetric, because of correlations between phases and odd-order multipoles. 3. The accuracy of the final parameters depends crucially on the quality of the experimental data. Systematic errors are the worst, but even random errors can degrade the results A. El Hauouzi et al (1996) Acta Cryst.A52, 291. C. Lecomte et al (1999) Acta Cryst.A55 1038.

  28. Jyväskylä Summer School on Charge Density August 2007 An Interesting Tale ... In 1992, Howard et al reported a charge density study on 2-methyl-4-nitroaniline (MNA) which showed a threefold enhancement of the molecular dipole moment on crystallisation, to 23D with an error of 8D. Became a classic reference. New results of Whitten, Spackman et al in 2006 suggest that this result is quite unreasonable. After a very careful data collection and refinement, they estimate that the true result is ~ 12(1) D, i.e. an enhancement of 25-30%. This result is also close to their theoretical work. The discrepancies with the previous work is a result of unstable refinement of the scale factor and use of anisotropic thermal parameters for the H atoms. S. T. Howard et al (1992) J. Chem. Phys.97, 5616. A. E. Whitten, M. A Spackman et al (2006) J. Phys. Chem. A, 110, 8763.

  29. Jyväskylä Summer School on Charge Density August 2007 Fourier Maps in XD Two programs in XD XDFFT – calculates Fourier over whole unit cell – used for reporting residuals XDFOUR – can calculate Fourier in an arbitary plane – useful for investigations FOUR fmod1 4 2 0 0 fmod2 -1 2 0 0 MODULE *XDFFT SELECT *fobs *fmod1 fmod2 snlmin 0. snlmax 2. sig 3. phase 0. SELECT gridsize 0.2 scale 1. npeak 10 nhole 10 neutron gridf peakf END XDFFT MODULE *XDFOUR SELECT *fobs *fmod1 fmod2 print snlmin 0. snlmax 2. GRID *3-points perp cryst ATOM label ato(1) symm 1 trans 0 0 0 *mark on plot ATOM label ato(2) symm 1 trans 0 0 0 *mark on plot ATOM label ato(3) symm 1 trans 0 0 0 *mark on plot LIMITS xmin -2.0 xmax 2.0 nx 50 LIMITS ymin -2.0 ymax 2.0 ny 50 LIMITS zmin 0.0 zmax 0.0 nz 1 END XDFOUR command in XDLSM to write XD.FOU file XD.FOU contains Fobs and two types of Fcalc based on the models indicated in the FOUR command

  30. Jyväskylä Summer School on Charge Density August 2007 Fourier Maps in XD Two programs in XD XDFFT – calculates Fourier over whole unit cell – used for reporting residuals XDFOUR – can calculate Fourier in an arbitary plane – useful for investigations FOUR fmod1 4 2 0 0 fmod2 -1 2 0 0 MODULE *XDFFT SELECT *fobs *fmod1 fmod2 snlmin 0. snlmax 2. sig 3. phase 0. SELECT gridsize 0.2 scale 1. npeak 10 nhole 10 neutron gridf peakf END XDFFT MODULE *XDFOUR SELECT *fobs *fmod1 fmod2 print snlmin 0. snlmax 2. GRID *3-points perp cryst ATOM label ato(1) symm 1 trans 0 0 0 *mark on plot ATOM label ato(2) symm 1 trans 0 0 0 *mark on plot ATOM label ato(3) symm 1 trans 0 0 0 *mark on plot LIMITS xmin -2.0 xmax 2.0 nx 50 LIMITS ymin -2.0 ymax 2.0 ny 50 LIMITS zmin 0.0 zmax 0.0 nz 1 END XDFOUR command in XDLSM to write XD.FOU file fmod1 4 2 0 0 means (a) multipole model up to l = 4 (b) thermal motion up to anisotropic (c) no anomalous dispersion (d) no extinction

  31. Jyväskylä Summer School on Charge Density August 2007 Fourier Maps in XD Two programs in XD XDFFT – calculates Fourier over whole unit cell – used for reporting residuals XDFOUR – can calculate Fourier in an arbitary plane – useful for investigations FOUR fmod1 4 2 0 0 fmod2 -1 2 0 0 MODULE *XDFFT SELECT *fobs *fmod1 fmod2 snlmin 0. snlmax 2. sig 3. phase 0. SELECT gridsize 0.2 scale 1. npeak 10 nhole 10 neutron gridf peakf END XDFFT MODULE *XDFOUR SELECT *fobs *fmod1 fmod2 print snlmin 0. snlmax 2. GRID *3-points perp cryst ATOM label ato(1) symm 1 trans 0 0 0 *mark on plot ATOM label ato(2) symm 1 trans 0 0 0 *mark on plot ATOM label ato(3) symm 1 trans 0 0 0 *mark on plot LIMITS xmin -2.0 xmax 2.0 nx 50 LIMITS ymin -2.0 ymax 2.0 ny 50 LIMITS zmin 0.0 zmax 0.0 nz 1 END XDFOUR command in XDLSM to write XD.FOU file fmod1 –1 2 0 0 means (a) spherical atom model (b) thermal motion up to anisotropic (c) no anomalous dispersion (d) no extinction

  32. Jyväskylä Summer School on Charge Density August 2007 Fourier Maps in XD Two programs in XD XDFFT – calculates Fourier over whole unit cell – used for reporting residuals XDFOUR – can calculate Fourier in an arbitary plane – useful for investigations FOUR fmod1 4 2 0 0fmod2 -1 2 0 0 MODULE *XDFFT SELECT *fobs *fmod1 fmod2 snlmin 0. snlmax 2. sig 3. phase 0. SELECT gridsize 0.2 scale 1. npeak 10 nhole 10 neutron gridf peakf END XDFFT MODULE *XDFOUR SELECT *fobs *fmod1 fmod2 print snlmin 0. snlmax 2. GRID *3-points perp cryst ATOM label ato(1) symm 1 trans 0 0 0 *mark on plot ATOM label ato(2) symm 1 trans 0 0 0 *mark on plot ATOM label ato(3) symm 1 trans 0 0 0 *mark on plot LIMITS xmin -2.0 xmax 2.0 nx 50 LIMITS ymin -2.0 ymax 2.0 ny 50 LIMITS zmin 0.0 zmax 0.0 nz 1 END XDFOUR *fobs *fmod1 means calculate a difference Fourier with coefficients based on Fcalc from model 1 and Fobs – this map is a full difference Fourier and should be featureless

  33. Jyväskylä Summer School on Charge Density August 2007 Fourier Maps in XD *fobs *fmod1 Residual map These are very important for checking the quality of data and of the refinement Contours at 0.05eÅ-3

  34. Jyväskylä Summer School on Charge Density August 2007 Fourier Maps in XD *fobs *fmod2 Experimental deformation map These are equivalent to the difference maps obtained with a SHELX refinement. Shows the bonding density peaks Contours at 0.05eÅ-3

  35. Jyväskylä Summer School on Charge Density August 2007 Fourier Maps in XD *fmod1 *fmod2 Dynamic model map These show the difference between Fcalc (spherical) and Fcalc (multipole). Similar to experimental deformation map. Does not contain experimental noise, but does contain effects of thermal motion. Contours at 0.05eÅ-3

  36. Jyväskylä Summer School on Charge Density August 2007 XDPROP – calculation of properties XDPROP performs a number of tasks. The input parameters are the multipole populations from the refinement program XDLSM. From these the static density (and associated properties) can be computed. topological analysis – finds critical points in scalar field (density or Laplacian) and seaches for bond paths (molecular graph). Graphical display of gradient vector plots. Gives the topology of the molecule “extracted” from the crystal Program TOPXD gives the topology of the crystal. atomic charges and higher moments – these can be calculated in a number of ways, either from the multipole parameters of by numerical integration of the derived density interaction energies – between two or more fragments of the total lattice energy d-orbital populations – from multipole parameters Properties are obtained as lists of numbers and also in graphical form (2D and 3D maps).

  37. Jyväskylä Summer School on Charge Density August 2007 XDPROP – topological analysis Concepts of topological analysis dealt with in another lecture. Shown here is the molecular graph for formamide, giving the bond paths (in gold), the bond critical points (in red) and the eigenvectors of the Hessian (red = major axis, green = minor axis of curvature). This POV-Ray picture is producesd by the WinXD GUI CPSEARCH BOND C(1) H(3) CPSEARCH SHELL O(1) RMIN 1.20 RMAX 1.20 NRAD 1 NANG 15 15 CUT 0.01 CPSEARCH POINT 1.2 -0.3 1.3 CPSEARCH START xd.cps cpsearch bond rmin 0.9 rmax 1.7 BPATH O(1) C(1) ALGRITHM 2 BPATH N(1) C(1) ALGRITHM 2 BPATH N(1) H(1) ALGRITHM 2 BPATH N(1) H(2) ALGRITHM 2 BPATH C(1) H(3) ALGRITHM 2

  38. Jyväskylä Summer School on Charge Density August 2007 XDPROP – topological analysis Gradient vector plots show the division of the molecule into atomic basins Also shows bond paths and bcp’s ODESOLVE *rk bs eps 1e-6 stepi 0.01 TRAJPLT origin atom C(1) TRAJPLT xaxis atom N(1) Xdim1 -2.0 Xdim2 2.5 TRAJPLT yaxis atom H(3) Ydim1 -2.0 Ydim2 2.0 TRAJPLT params Circle 0.1 ATrad 0.05 CPrad 0.05 CPgrid 0.1 CPlim 0.01 TRAJPLT mark *atoms *labels *bonds *cps *basins hbonds TRAJPLT *plot *plane npath 36 *zcut 0.3 *xytol 0.3 *all select O(1)

  39. Jyväskylä Summer School on Charge Density August 2007 XDPROP – calculation of charges The concept of atomic charges is a central one in chemistry. Unfortunately it is a very hazy concept and not one deeply founded in quantum mechanics. It is only through AIM theory that an unambiguous definition of atomic charge has achieved. AIM derived charges are often larger than “chemical intuition” expects and this has led to considerable criticism. XDPROP provides several ways to calculate net atomic charges: (a) directly from the refined valence populations of the atoms (b) using Hirshfeld’s stockholder’s approach (c) using a fit to the electrostatic potential (d) using Bader’s Quantum Theory of Atoms in Molecules (AIM) ! Atomic/Molecular moments from pseudoatoms : MULTMOM ! ! Atomic/Molecular from STOCKHOLDER partitioning: STOCKMOM atoms *all select ato(1) ato(2) ... ! Atomic charges fitting electrostatic potential: QFIT grid 11 length 7.0 width 1.0 constrain false CONSTRAIN ato(1) ato(2) ... R. F. W. Bader and C. Matta (2004) J. Phys Chem A. 108, 8385 F. L. Hirshfeld (1977). Theor. Chim. Acta, 44, 129

  40. Jyväskylä Summer School on Charge Density August 2007 XDPROP – electrostatic potential XDPROP can calculate maps of the electrostatic potential. These may be used to show sites of chemical reactivity. In general (and always for isolated atoms) the ESP is positive, but on chemical bond formation, some areas might achieve a negative potential. One visually attractive way of displaying the ESP is as a colour coded isosurface (usually of the density).

  41. Jyväskylä Summer School on Charge Density August 2007 XDPROP – d-orbital populations The multipole populations can be directly related to the d-orbital populations in transition metal compounds. Not unique, but depends on the chosen local coordinate system. Usually best if this system is chosen to correspond to symmetry axes (actual or idealised) of the compound. An optimal coordinate system minimises the cross populations. A. Holladay, P. C. Leung & P. Coppens (1983) Acta Cryst. A39, 377 J. R. Sabino & P. Coppens (2003). Acta Cryst. A59, 127

  42. Jyväskylä Summer School on Charge Density August 2007 Geometry calculations XDGEOM Geometry calculations carried out using XDGEOM. Uses variance- covariance matrix xd.cov (if available) to determine correct su’s for derived parameters, distances, angles, torsions • Provides • Table of xyz, Uijs, distances, angles, torsions • Tables of multipole parameters • Writes a CIF xd_geo.cif of same (some will be moved to xd_lsm.cif in due time. e.g. xyz, Uijs) • Generally positional parameters (hence interatomic distances, angles) are not very sensitive to model (spherical or multipole), but of course …. Aromatic C-H SHELX (X-ray) 0.96Å neutron 1.083Å K2SO4 tutorial data set SHELX XD S-O1 1.4837(4) 1.4838(3) S-O2 1.4717(4) 1.4716(3) S-O3 1.4830(3) 1.4832(2)

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