EXAMPLESAll made with XD – could bedone with other programs like
JANA, Valray, Molly etc.

Cheiron School 2010

1

K2SO4 ‐ ongoing work

Schmøkel, M. S. Unpublished results
Cheiron School 2010

2

K2SO4 ‐ ongoing work
S

O

K

Data overview – K2SO4Space group
Detector
Wavelength, Å
μ*r
Temperature, K
Crystal size
Resolution, Å# meas refl
# unique refl
Rint
# parameters
R(F2), all dataSO4‐tetrahedra surrounded by K+;
Oxygen: Octahedral coordination sphere;
K: 9‐coordinated to O‐atoms

APS
Pnma
Apex2
0.41327
0.00781830x30x20 μm3
0.37
49029
4393
0 044 (<N> = 11
0.044
11.2)
2)
95
0.018

Motivation:
Network structure, impossible at conventionalsourceSchmøkel, M. S. Unpublished results
Cheiron School 20103

K2SO4
With extinction,,R(F2) = 1.69%

No extinction,
R(F2) = 1.83%
Five most affected reflections
0
0
0
3
2

2
1
4
0
1

0 0.1752 1 26485.000 26602.000 -117.650
3 0.1741 1 21087.000 20547.000 539.680
0 0.3505 1 22238.000 22263.000 -25.892
1 0.2087 1 10378.000 10414.000 -36.374
1 0.1686 1 6755.900 6874.400 -118.490

95.7
96.6
98.2
98.6
98.8

Schmøkel, M. S. Unpublished results
Cheiron School 20104

K2SO4OO
SOO

Schmøkel, M. S. Unpublished results
Cheiron School 20105

Hydrogenbonding
Cheiron School 20106

Hydrogen bonds

Enzyme catalysis

The catalytic triade cleavage of peptide bonds

Low Barrier Hydrogen Bonding
Herbstein et al, Acta Cryst. Sect B 1999,55, 767‐787
Schiøtt et al,
al Proc Natl.
Natl Acad
Acad. Sci 1998
1998,95,
95 12799‐12802
Schiøtt et al, J. Am. Chem. Soc. 1998, 120, 12117‐12125
Madsen et al, J. Am. Chem. Soc. 1998, 120, 10045‐10051

Overgaard et al, Chem. Eur. J 2001, 3756
3756‐3767
3767

Cheiron School 20107

X N study of ”biobrint”
X‐N
biobrint
Refinement details
Data overview – Biobrint
NSLS
Space group
Detector
Wavelength, ÅTTemperature,
K
Resolution, Å# collected refl
# unique refl
Rint
# parameters
R(F2), all data

H ber
Huber
C2/c

IP
0.643
28
0.38
98132
15657
0 030
0.030

point detector
0.5513
10(1)
0.98
16382
3187
0 016
0.016
1128
0.035

Motivation:
Anomaly in HB distances, multicomponent crystal,
active site analogue, excellent crystals
Overgaard et al, Chem. Eur. J 2001, 3756‐3767
Cheiron School 20108

Biobrint – a model for the catalytic triad•••

Cheiron School
9 2010Theh bondingb di pattern resembles
bl thehgeometry in the catalytic triad involvedin enzymatic action.
HB’s are:d(N‐H) d(N‐‐‐O)
N1A‐H1A‐‐‐O1A 1.046 2.613
N3A‐H3A‐‐‐O8
1.056 2.685
N1B‐H1B‐‐‐O1B 1.049 2.676
An anomaly in HB2

Accuracy in synchrotron studies
Atomic Displacement Parameters|U(x-ray)-U(neutron)|σ(U)= 1.42|U(x-ray)-U(neutron)|= 0.0009Å2

U(x-ray)= 1.011(16)U(neutron)

75 unique atoms (25 H)
Catalytic triad model

Ab iinitio
i i theoryhExperimentd orbitals necessary
Cheiron School 201010

Biobrint – electron density modelling•••

U‐values: Extracting Uij’s from N study: The H atom adp’s were taken directly from
N without scaling (<Uii(X)/Uii(N)> = 1
1.011(16))
011(16))
H‐positions: The positions of the H atoms were directly copied from N values
Multipoles: For all three H listed all dipoles and quadropoles refined
H(??)

•

000 000000 .... 10 111 11111 0000000 000000000

Significance:

From output listing:
M1
D1+
D1D0
Q0
Q1+
Q1
Q1-

0.719900
0.129500
0.008500
0.002000-0.048600
0.011400-0.008500
0 008500-0.000030-0.000006
0.000006-0.000018-0.000028-0.000043
0.000029-0.000024
0 000024

Q2+

0.112600-0.000010

Q2-0.066800

0.000021

Cheiron School
11 20100.719870
0.129494
0.008482
0.001972-0.048643
0.011429-0.008524
0 008524

0.028197
0.020020
0.014671
0.012943
0.018678
0.020080
00.016129016129

512
587
651
705
759
813
867

-3
-4
4
-3
-3
-3
-3
-3
3

0.112590

0.020783

932-40.066821

0.021843996-3

H and Ehb of HB’s

}

( )

3
1 2
2 23
53
G (rbcp ) =3πρ (rbcp ) + ∇ ρ (rbcp )106h 2
V (rbcp ) =∇ ρ (rbcp ) − 2G (rbcp )4m

Hbcp = ‐0.13 hartree Å‐3; EHB = 18.1 kcal mol‐1.

→

E HB = 0.5 ∗ V (rbcp )Hbcp = ‐0.61 hartree Å‐3; EHB = 42.3 kcal mol‐1.

Cheiron School
12 2010

Source function from theo wavefunctions•

Useful in analysis of HB’s as a tool to discriminate between types: What is
important is the H contribution to the bcp:
30.5
%

23.4
%

4.9%

d(X---O) decreases from left to right•

The trend is that the stronger HB’s are followed by an increase in thecontribution from the H atom.

Cheiron School
13 2010

Source function from experiment•

Added in XD2006 is the TOPINT keyword to calculate source function
contributions – to be compared to theoretical values.
valuesSOURCE
refpoint
5.673506
2.156185
2.299098! O(1A)-H(1A)
SOURCE
refpoint
9.897701
0.896144
4.688383! O(8) -H(3A)
SOURCE
refpoint
13.550304
2.847093
0.784550! O(1B)-H(1B)
TOPINT spheres H(2B) 0.256 H(4B) 0.257 ..... (FOR ALL ATOMS)TOPINT atomst**allll select
l t N(1B) H(1B)%‐contributions to HB2

6.1%

H3A
O8
N3A
O9
N1A

EXP
6.1
34.8
18
18.3
3
8.4
4.3

Cheiron School
14 2010

THEO
4.9
35.0
21
21.8
8
8.3
3.9

Hydrogen atomic charges•

One could reasonably ask what the integrated charge within the H atomic
basin is?

CGEN alim -0.5 1.5 blim -0.5 1.5 clim -0.5 1.5
ATBP Spheres O(8) 0.806 O(9) 0.824 N(7) 0.867 C(12) 0.424 C(13) 0.636
ATBP *atoms H(1A) iZFS nvi 100 IRsur 0 *IRSav Rest Debug Phi 48 Th 36 Rad 120 Accur
1.D-3

•

The value of the integrated Laplacian describes the accuracy of theintegration

q(HX1) = 0.60

q(H3A) = 0.53
q(H1A) = 0.57
q(H1B) = 0.57

Cheiron School
15 2010

X N study of a HB system
X‐N
Refinement details
Data overview – OxHy
D3Space group
Detector
Wavelength, ÅTTemperature,
K
Resolution, Å# collected refl
# unique refl
Rint
# parameters
R(F2), all data

Residuals close to K+, which are
reduced significantly byrefinement of anharmonicity
on the K atom

H ber
Huber
P‐1

Apex2
0.45
15
0.38
160430
14266
0 077
0.077
483
0.052

point detector
0.5513
11(1)
0.357
15020
10210
0 01110.0111548
0.034

Motivation:
Very strong hydrogen bonds, test example for D3

W. Morgenroth, J. Appl. Cryst., 2008, 41, 846‐853.
Cheiron School 201016

X N study of a HB system
X‐N
Parameter comparisons
IAM parameters:
The average difference in positionis, <δX> = 0.0002(5)while the average difference in U‐
value
l is
i <δU
δUij>=0.007(23)0 007(23)UIJXN comparison
D3<ΔU><ΔU2>1/2<ΔUX,ii/ΔUN,ii><(ΔU/σ(ΔU))( / ( ))2>1/2

0.00050(30)0.00059
0.89(11)
6.66

Multipole parameters:
307 multipole parameters refined,and <δPlm> = 0.06(9).
For the monopoles only, the average
deviation, <δPv> = 0.05(14)Cheiron School 201017

X N study of a HB system
X‐N
How well do the data fit?

Cheiron School 201018

X N study of a HB system
X‐N
How well do the data fit?

Cheiron School 201019

X N study of a HB system
X‐N
Laplacian map

H l b D3
Hasylabd(O‐H)=1.089 Å, d(O‐‐‐O)=2.471 Å, d(H‐‐O)=1.382 ÅCheiron School 201020

Cobalt dimer

Cheiron School 201021

Co dimer
Co‐dimer
Refinement details
Data overview – Co2(CO)6(HC2C6H10OH),
ZZ’ = 2
D3
Space group
Detector
W l
Wavelength,th ÅTemperature, K
Resolution, Å# unique refl
# parameterstR(F2), all data

Apex2

P‐1
MarCCD165 Apex2
0 47690.47690 71070.7107
15
100
0.42
0.45
40270
31948
1228
785
0.024
0.026

Motivation:
Presence or not of Co‐Co & details of Co‐C2 bonding

J. Overgaard, H. F. Clausen, J. A. Platts, B. B. Iversen, JACS, 2008, 130, 3834.
Cheiron School 201022

Co dimer
Co‐dimerA
Agreement
factorsf& redundancy
d d

D3

Apex2

Based on the internal agreement
factors, the two systems behave
relatively equal

Cheiron School 201023

Co dimer
Co‐dimer
Data statistics

Significance of synchrotron data higher.
Effect of thermal smearing visible on
Apex2 data.

Cheiron School 2010

Based on the multipole models, theaverage ratio in 0.05 Å‐1 shells ofreciprocal space are closer to ideal 1.0
for D3 data.

24

Co dimer
Co‐dimerGeometry comparison
Geometry – Co2(CO)6(HC2C6H10OH)
D3
Co‐Co
2.4633(1),2.4653(1)Co‐C(O)
1.791‐1.836
C(11)‐C(12) 1.3421(4), 1.3399(4)Apex2
2.4648(1), 2.4666(1)1.791‐1.836
1.3433(7), 1.3401(6)Comparison of D3 vs Apex2 structural models is 0.2%, andthe average difference between same bond lengths is
0.06%!!

Cheiron School 201025

Co dimer
Co‐dimer
Multipole modelKappa
pp parameters:p
D3/Apex2
Co
0.999(2), 0.95(2)1.012(1), 0.865(5)O(CO)
0 98 ( ) 0.78(1)0.985(1),0 8( )
1.014(1), 1.00(1)C(sp3)
0.914(2), 0.827(5)1.009(1), 0.834(5)C(CO)
0.940(2), 0.883(7)1.066(1), 0.897(6)C(alkyne) 0.912(2), 0.75(1)1 023(2) 0.758(8)1.023(2),0 758(8)Cheiron School 2010

Theory0.9721(4), 1.014
0 990 (3) 00.9901(3),
0.998
998
N/A
0.966,0.863
0.9218, 0.774

26

Co dimer
Co‐dimer
Topology comparison
For comparisonpa theoretical calculation
was done using CAS‐SCF methods. This
showed the molecule to be a singlet di‐radical.
Quantum Topological Molecular
Similarity showed the two models to berather different (QTMS‐value of 3.5; forp‐NH2 and p‐NO2 it is 0.37). However,
without the C‐O bonds, the value ismuch
h llower at 0
0.8.Why?
8 Wh ?

J A
J.
A. Platts
Platts, G.
G J.
J S.
S Evans,
Evans M.
M P.
P Coogan,
Coogan J.
J Overgaard,
Overgaard Inorg.
Inorg Chem.
Chem 2007,46,
2007 46 6291.
6291
P. L. A. Popelier, J. Phys. Chem. A 1999, 103, 2883.
Cheiron School 201027

Co dimer
Co‐dimerElectron density in the ”infamous” polar carbonyl bondIn such a polar bond, the sign of
the Laplacian is strongly
dependent on the exact positionof the bcp. Here:
Synchrotron model: ∇2ρ +40 eÅ‐5
Conventional model: ∇2ρ ‐10 eÅ‐5

Cheiron School 201028

Co dimer
Co‐dimerElectron density in the Co‐C2 triangles

In this region, the density is extremely
flat and the topology is affected by small
errors in the data as well as model
insufficiencies. Not all Co‐C bond paths
found.

Cheiron School 201029

Co dimer
Co‐dimerElectron density in the Co‐C2 triangles

This is illustrated by the density
curvatures along paths in thisplane. Only small valleys are foundto show minima.
Possible explanations:¾Crystalyppackingg¾Asymmetric ligand¾Model dependency¾Measurement errors¾...

Cheiron School 201030

Co dimer
Co‐dimerElectron density in the Co‐C2 triangles

Directly from theory

MM on theoreticalstructure factors

Cheiron School 201031

Coordination
polymers
Cheiron School 201032

Mn based CP
Mn‐based
Refinement details
Data overview – Mn2C4H12O12
D3Space group
Detector
Wavelength, ÅTemperature, K
Resolution, Å# unique refl
# parameters
R(F2), all data

Apex2

P21/c
MarCCD165 Apex2
0.55
0.7107
100
100
1.56
1.18
15080
7212
263
263
0.043
0.024

Motivation:
Magnetic interaction pathways. Comparison with
APS (6).
R. D. Poulsen et al, Chem. Eur. J. 2007, 13, 9775.
Cheiron School 201033

Mn based CP
Mn‐based
Data comparisons

The HO data are relatively higher at thesynchrotron,despite identical temperatures.

Cheiron School 2010

The significance in Apex compared to D3 ishigher for the weak data but lower for thestrong data.

34

Mn based CP
Mn‐based
Thermal parameters

The thermal parameters arellower
ffor theh D3 bby ca 10%which relates well to therelatively higher intensities forD3 HO ddata.
tCheiron School 201035

Mn based CP
Mn‐based
Deformation density maps
The static deformation density maps in the plane of the water molecule show interesting
features.
Apex2
Hasylab D3
κ = 0.999

κ = 0.993

TheoryAPSκ = 0.963
κ = 0.963

κ = 0.963

Cheiron School 201036

Fe & Zn‐basedZn based CP
Refinement details
Data overview – M2C4H12O12Z
Zn
Space group
Detector
Wavelength, ÅTTemperature,t
K
Resolution, Å# meas refl
# unique refl
Ri t
Rint
# parameters
R(F2), all data

F
Fe

P21/c
MarCCD165
0.50
0.47686
15
15
0.45
0.44
154531
50762
7314
8212
0 045
0.045
0 040
0.040
342
344
0.02150.0254

Motivation:
Magnetic interaction pathways. Comparison with
Mn‐complex.
Mads R. V. Jørgensen et al, unpublished results
Cheiron School 201037

Fe & Zn‐basedZn based CP
Refinement details
Almost exactly parabolic in shape in the residual density analysis

Fe

Zn

Mads R. V. Jørgensen et al, unpublished results
Cheiron School 201038

Fe & Zn‐basedZn based CP
Atomic charges

Atom
Zn(1)
Fe(1)
Mn(1)
Zn(2)
Fe(2)
Mn(2)

PΩ
2.04
1.69
1.68
2.00
1 96
1.96
1.60

V001
51.8
60.8
66.8
52.8
62 4
62.4
71.2

Dipole moment
0.0
0.0
0.0
0.0
00
0.0
0.0

Quadrupole Moments‐4.80, ‐4.81, ‐4.79‐5.41,
5.41, ‐5.42,
5.42, ‐5.22
5.22‐5.52, ‐5.43, ‐5.54‐4.84, ‐4.86, ‐4.80‐5 40 ‐5.49,‐5.40,‐5 49 ‐5.05‐5 05‐5.67, ‐5.74, ‐5.77

Mads R. V. Jørgensen et al, unpublished results
Cheiron School 201039

Fe & Zn‐basedZn based CP
d‐orbital populations
Zn1
Fe1
Fe1 (ERD(6))
Mn1
Mn1 (ERD)
Zn2
Fe2
Fe2 (ERD)
Mn2
Mn2 (ERD)

dx2‐y2
1.97

dz2
2.00

dxy
1.91

dyz
1.98

dxz
1.97

SUM
9.83

Max. unpaired
N/A(20.0)
1.03(16.6)(20.3)
1.22(19.6)(19.4)
1.39(22.4)(20.1)
1.37(22.0)(20.0)
1.21(19.5)

6.21

3.79

1.30
(21.0)
1.12(21.5)

0.99(15.9)
1.19(22.7)

1.34(21.6)
1.09(20.8)

1.19(19.1)
0.92(17.6)

1.39(22.4)
0.91(17.4)

6.21

3.77

5.23

4.43

0.91
(17.4)
2.12

1.32(25.2)
1.94

0.91(17.4)
1.88

1.25(23.9)
1.98

0.84(16.1)
1.94

5.23

4.09

9.87

N/A

(21.5)
1.23(20.7)
0.98(19.7)
0.95(16.0)
1.18(19.0)
1.55(26.0)
1.09(20.1)
1.19(20.0)
1.80(19.7)
1.03(17.3)
0.92

5.95

3.95

5.95

3.86

(16.4)
1.06(19.8)(19.8)
1.11(20.9)(18.3)
1.07(20.0)(30.0)
1.07(20.1)(15.6)
1.02(19.1)

5.32

4.67

0.89
(16 7)(16.7)

1.37(25 7)(25.7)

0.89(16 8)(16.8)

1.26(23 6)(23.6)

0.92(17 3)(17.3)

5.32

4.43

Mads R. V. Jørgensen et al, unpublished results
Cheiron School 201040

Cr wheel complex
Cr‐wheel
Refinement details
Data overview – Cr8F8(C5H9O2)16
Space group
Detector
Wavelength, ÅTemperature, K
Resolution, Å# meas refl
# unique refl
# parameters
R(F2), all data

NSLS
P21/c
SMART1000
0.643
16(5)
0.55
165264
37733
1582
0.039

Motivation:
Electrostatic potential, host‐guest chemistry

Overgaard et al, Chem Eur. J. 2002, 12, 2775-2786
Cheiron School 201041

Host guest chemistry
Host‐guest

Cheiron School 201042

Host guest chemistry
Host‐guest

Residual density
Single crystal synchrotron data

Deformation densityy mapp

Cheiron School 201043

Inorganic analogue to the cyclodextrins
Fantastic inclusion properties, stable, cheap, non-toxic=> used for molecular protection in pigments, food etc

Cyclodextrinerd anf f electrons maylead to novel chemistry(including magnetism)
Cheiron School 201044

X‐ray Electrostatic Potential

Cheiron School 201045