Transcript Experimental Aspects of Charge Density Studies

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
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).
Jyväskylä Summer School on Charge Density August 2007
The XD Program System
module
task
XDINI
importing data to XD
XDLSM
least-squares refinement
XDGEOM
calculation of tables of geometries,
ADPs, multipolar parameters and errors
XFOUR
calculation of Fourier maps
XDFFT
fast Fourier transform program
XDPROP
calculation of one-electron properties
XDGRAPH
visualization
TOPXD
full topological analysis of crystal
structures
Jyväskylä Summer School on Charge Density August 2007
The XD Program System
Jyväskylä Summer School on Charge Density August 2007
The XD Program System
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
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 Cryst 1997, 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
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
Jyväskylä Summer School on Charge Density August 2007
<name>
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
Jyväskylä Summer School on Charge Density August 2007
number of atoms
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
Jyväskylä Summer School on Charge Density August 2007
Parameters for atom O(1)
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
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
.
positional parameters
.
.
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
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
.
Occupancy - not refinable !
.
.
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
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
.
anisotropic thermal parameters U11 U22 U33 U12 U13 U23
.
.
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
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
.
multipole parameters - currently only Pv and P00 are present
.
.
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
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
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
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
Jyväskylä Summer School on Charge Density August 2007
The XD.HKL Reflection File
XD
-5
-5
-5
-5
-5
-5
-5
-5
-5
-5
-5
.
.
.
-7
-7
-7
-7
-6
-6
-6
-6
-6
-6
-5
1
2
3
4
1
2
3
4
5
6
1
F^2
1
1
1
1
1
1
1
1
1
1
1
NDAT
5.300
74.050
2.740
11.410
21.890
0.540
5.140
3.090
94.190
17.450
2.680
6
0.790
2.480
1.540
10.700
1.880
1.210
0.860
1.030
2.830
13.830
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)
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
O
CHFW
N
CHFW
C
CHFW
H
CHFW
END SCAT
.
.
END
SPHV
CHFW
CHFW
CHFW
CHFW
DEFV
CSZD
CSZD
CSZD
CSZD
1S
2
2
2
-1
2S
-2
-2
-2
0
3S
0
0
0
0
4S
0
0
0
0
2P
-4
-3
-2
0
3P
0
0
0
0
4P
0
0
0
0
3D
0
0
0
0
4D
0
0
0
0
4F
0
0
0
0
5S
0
0
0
0
5P
0
0
0
0
6S
0
0
0
0
6P
0
0
0
0
5D
0
0
0
0
7S
0
0
0
0
6D
0
0
0
0
5F
0
0
0
0
DELF'
0.0110
0.0060
0.0030
0.0000
DELF'' NSCTL
0.0060 0.580
0.0030 0.936
0.0020 0.665
0.0000 -0.374
XDLSM
Divided into sections - one main section and eight other sections giving
commands for the main program modules.
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
O
CHFW
N
CHFW
C
CHFW
H
CHFW
END SCAT
.
.
END
SPHV
CHFW
CHFW
CHFW
CHFW
DEFV
CSZD
CSZD
CSZD
CSZD
1S
2
2
2
-1
2S
-2
-2
-2
0
3S
0
0
0
0
4S
0
0
0
0
2P
-4
-3
-2
0
3P
0
0
0
0
4P
0
0
0
0
3D
0
0
0
0
4D
0
0
0
0
4F
0
0
0
0
5S
0
0
0
0
5P
0
0
0
0
6S
0
0
0
0
6P
0
0
0
0
5D
0
0
0
0
7S
0
0
0
0
6D
0
0
0
0
5F
0
0
0
0
DELF'
0.0110
0.0060
0.0030
0.0000
DELF'' NSCTL
0.0060 0.580
0.0030 0.936
0.0020 0.665
0.0000 -0.374
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
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
O
CHFW
N
CHFW
C
CHFW
H
CHFW
END SCAT
.
.
END
SPHV
CHFW
CHFW
CHFW
CHFW
DEFV
CSZD
CSZD
CSZD
CSZD
1S
2
2
2
-1
2S
-2
-2
-2
0
3S
0
0
0
0
4S
0
0
0
0
2P
-4
-3
-2
0
3P
0
0
0
0
4P
0
0
0
0
3D
0
0
0
0
4D
0
0
0
0
4F
0
0
0
0
5S
0
0
0
0
5P
0
0
0
0
6S
0
0
0
0
6P
0
0
0
0
5D
0
0
0
0
7S
0
0
0
0
6D
0
0
0
0
5F
0
0
0
0
DELF'
0.0110
0.0060
0.0030
0.0000
DELF'' NSCTL
0.0060 0.580
0.0030 0.936
0.0020 0.665
0.0000 -0.374
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.
Jyväskylä Summer School on Charge Density August 2007
The ATOM Table
ATOM
O(1)
N(1)
C(1)
H(1)
H(2)
H(3)
DUM0
END ATOM
ATOM0
C(1)
C(1)
N(1)
N(1)
N(1)
C(1)
0.0000
AX1 ATOM1
X O(1)
Z N(1)
X C(1)
Z H(1)
Z H(2)
Z H(3)
0.0000 0.0000
ATOM2
N(1)
O(1)
O(1)
C(1)
C(1)
O(1)
AX2 R/L TP TBL KAP LMX SITESYM
Y
R
2 1
1
4 m
Y
R
2 2
2
4 mm2
Y
R
2 3
3
4 m
Y
R
1 4
4
1 cyl
Y
R
1 4
4
1 cyl
Y
R
1 4
4
1 cyl
CHEMCON
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.
Jyväskylä Summer School on Charge Density August 2007
The ATOM Table
ATOM
O(1)
N(1)
C(1)
H(1)
H(2)
H(3)
DUM0
END ATOM
ATOM0
C(1)
C(1)
N(1)
N(1)
N(1)
C(1)
0.0000
O atom m
AX1 ATOM1
X O(1)
Z N(1)
X C(1)
Z H(1)
Z H(2)
Z H(3)
0.0000 0.0000
ATOM2
N(1)
O(1)
O(1)
C(1)
C(1)
O(1)
AX2 R/L TP TBL KAP LMX SITESYM
Y
R
2 1
1
4 m
Y
R
2 2
2
4 mm2
Y
R
2 3
3
4 m
Y
R
1 4
4
1 cyl
Y
R
1 4
4
1 cyl
Y
R
1 4
4
1 cyl
CHEMCON
C atom m
N atom mm2
H atom cyl
Formamide HC(=O)NH2
Jyväskylä Summer School on Charge Density August 2007
The KEY Table
KEY
O(1)
N(1)
C(1)
H(1)
H(2)
H(3)
KAPPA
KAPPA
KAPPA
KAPPA
EXTCN
OVTHP
SCALE
END KEY
xyz --U2-000 000000
000 000000
000 000000
000 000000
000 000000
000 000000
000000
000000
000000
000000
0000000
0
1
----U3---0000000000
0000000000
0000000000
0000000000
0000000000
0000000000
------U4------000000000000000
000000000000000
000000000000000
000000000000000
000000000000000
000000000000000
M00
00
00
00
00
00
-D000
000
000
000
000
000
--Q-00000
00000
00000
00000
00000
00000
---O--0000000
0000000
0000000
0000000
0000000
0000000
----H---000000000
000000000
000000000
000000000
000000000
000000000
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.
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.
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.
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.
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
command in XDLSM to write XD.FOU file
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
END XDFFT
MODULE *XDFOUR
SELECT
*fobs *fmod1 fmod2 print snlmin
GRID
*3-points perp cryst
ATOM
label ato(1) symm 1 trans 0 0 0
ATOM
label ato(2) symm 1 trans 0 0 0
ATOM
label ato(3) symm 1 trans 0 0 0
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
peakf
0. snlmax 2.
*mark on plot
*mark on plot
*mark on plot
XD.FOU contains Fobs and two types of Fcalc based on the models indicated in the FOUR
command
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
command in XDLSM to write XD.FOU file
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
END XDFFT
MODULE *XDFOUR
SELECT
*fobs *fmod1 fmod2 print snlmin
GRID
*3-points perp cryst
ATOM
label ato(1) symm 1 trans 0 0 0
ATOM
label ato(2) symm 1 trans 0 0 0
ATOM
label ato(3) symm 1 trans 0 0 0
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
peakf
0. snlmax 2.
*mark on plot
*mark on plot
*mark on plot
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
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
command in XDLSM to write XD.FOU file
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
END XDFFT
MODULE *XDFOUR
SELECT
*fobs *fmod1 fmod2 print snlmin
GRID
*3-points perp cryst
ATOM
label ato(1) symm 1 trans 0 0 0
ATOM
label ato(2) symm 1 trans 0 0 0
ATOM
label ato(3) symm 1 trans 0 0 0
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
peakf
0. snlmax 2.
*mark on plot
*mark on plot
*mark on plot
fmod1 –1 2 0 0 means (a) spherical atom model (b) thermal motion up to anisotropic
(c) no anomalous dispersion (d) no extinction
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
END XDFFT
MODULE *XDFOUR
SELECT
*fobs *fmod1 fmod2 print snlmin
GRID
*3-points perp cryst
ATOM
label ato(1) symm 1 trans 0 0 0
ATOM
label ato(2) symm 1 trans 0 0 0
ATOM
label ato(3) symm 1 trans 0 0 0
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
peakf
0. snlmax 2.
*mark on plot
*mark on plot
*mark on plot
*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
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
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
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
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).
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
CPSEARCH POINT 1.2 -0.3
CPSEARCH START xd.cps
cpsearch bond rmin 0.9 rmax
BPATH O(1) C(1) ALGRITHM
BPATH N(1) C(1) ALGRITHM
BPATH N(1) H(1) ALGRITHM
BPATH N(1) H(2) ALGRITHM
BPATH C(1) H(3) ALGRITHM
1.20
1.3
1.7
2
2
2
2
2
RMAX
1.20
NRAD 1
NANG
15
15
CUT
0.01
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)
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
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).
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
Jyväskylä Summer School on Charge Density August 2007
Geometry calculations XDGEOM
Geometry calculations carried out using XDGEOM. Uses variancecovariance 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
S-O1
S-O2
S-O3
SHELX
XD
1.4837(4) 1.4838(3)
1.4717(4) 1.4716(3)
1.4830(3) 1.4832(2)