polymorphism tnb text&suppl - wiley-vch · 2004. 2. 18. · crystal data and structure refinement...
TRANSCRIPT
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Supporting Information
for
Angew. Chem. Int. Ed. Z52253
© Wiley-VCH 200369451 Weinheim, Germany
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Polymorphism of 1,3,5-trinitrobenzene induced by trisindane additive**
Praveen K. Thallapally, Ram K. R. Jetti, Amy K. Katz, H. L. Carrell, Kuldeep Singh,
Kakali Lahiri, Sambasivarao Kotha, Roland Boese,* Gautam R. Desiraju*
[*] Prof. G. R. Desiraju, Dr. P. K. Thallapally
School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
Fax: (+91) 40-2301-0567
E-mail: [email protected]
Prof. Dr. R. Boese, Dr. R. K. R. Jetti
Institut für Anorganische Chemie, Universität Duisburg-Essen, Standort Essen,
Universitätstrasse 5-7, D-45177 Essen, Germany
Fax: (+49) 201-183-2535
E-mail: [email protected]
Dr. H. L. Carrell, A. K. Katz
The Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue,
Philadelphia, PA 19111, USA
Prof. S. Kotha, K. Singh, Dr. K. Lahiri
Department of Chemistry, Indian Institute of Technology, Powai, Mumbai, 400 076,
India
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Form I
Form II
Form III
TI
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Table 1. Crystal data and structure refinement for TNB Form I .
Identification code TNB Form I
Empirical formula C6 H3 N3 O6
Formula weight 213.11 Da
Density (calculated) 1.729 g cm-3
F(000) 1728
Temperature 183(2) K
Crystal size 0.43 x 0.21 x 0.07 mm
Crystal color colorless
Crystal description plate
Wavelength 0.71073 Å
Crystal system orthorhombic
Space group Pbca
Unit cell dimensions a = 12.587(11) Å α = 90°
b = 9.684(9) Å β = 90°
c = 26.86(2) Å γ = 90°
Volume 3274(5) Å3
Z 16
Cell measurement reflections used 1658
Cell measurement theta min/max 2.76° to 18.16°
Diffractometer control software Bruker AXS SMART Vers. 5.054 1997/98
Diffractometer measurement device Siemens SMART CCD area detector system
Diffractometer measurement method Full sphere data collection
in omega at 0.3° scan width
two runs with 720 frames, phi = 0°, 270°
and two runs with 436 frames, phi = 88°, 180°
Theta range for data collection 2.22° to 28.75°
Completeness to theta = 28.75° 98.5 %
Index ranges -16
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Computing structure refinement Bruker AXS SHELXTL Vers.6.10, DOS/WIN95/NT/2000
Refinement method Full-matrix least-squares on F2
Reflections collected 36564
Independent reflections 4188 [R(int) = 0.1760]
Data / restraints / parameters 1396 / 0 / 271
Goodness-of-fit on F2 0.831
Weighting details w = 1/[σ2 (Fo2)+ (0.0635*P)2]
where P = (Fo2+2Fc2)/3
Final R indices [I>2sigma(I)] R1 = 0.0450, wR2 = 0.0985
R indices (all data) R1 = 0.1883, wR2 = 0.1422
Largest diff. peak and hole 0.188 and -0.191 eÅ-3
Treatment of hydrogen atoms Riding model on idealized geometries
with the 1.2 fold isotropic displacement
parameters of the equivalent Uij of the
corresponding carbon atom
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Table 1. Crystal data and structure refinement for TNB Form II
Identification code Form II
Empirical formula C6 H3 N3 O6
Formula weight 213.11
Temperature 120(2) K
Wavelength 0.71073 Å
Crystal system Orthorhombic
Space group Pca21
Unit cell dimensions a = 9.2970(19) Å, α = 90°
b = 18.730(4) Å, β = 90°
c = 9.6330(19) Å, γ = 90°
Volume 1677.4(6) A3
Z, Calculated density 8, 1.688 Mg/m3
Absorption coefficient 0.155 mm-1
F(000) 864
Crystal size 0.3 x 0.3 x 0.1 mm
Theta range for data collection 2.45 to 27.88°
Limiting indices 0
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Table 1. Crystal data and structure refinement for TNB Form III .
Identification code TNB Form III
Empirical formula C6 H3 N3 O6
Formula weight 213.11 Da
Density (calculated) 1.717 g cm-3
F(000) 432
Temperature 183(2) K
Crystal size 0.57 x 0.35 x 0.15 mm
Crystal color yellow
Crystal description plate
Wavelength 0.71073 Å
Crystal system monoclinic
Space group P 21/c
Unit cell dimensions a = 12.896(5) Å α = 90°
b = 5.723(2) Å β = 98.190(8)°
c = 11.287(5) Å γ = 90°
Volume 824.5(6) Å3
Z 4
Cell measurement reflections used 1353
Cell measurement theta min/max 3.19° to 27.32°
Diffractometer control software Bruker AXS SMART Vers. 5.054 1997/98
Diffractometer measurement device Siemens SMART CCD area detector system
Diffractometer measurement method Full sphere data collection
in omega at 0.3° scan width
two runs with 720 frames, phi = 0°, 270°
and two runs with 436 frames, phi = 88°, 180°
Theta range for data collection 3.19° to 28.30°
Completeness to theta = 28.30° 97.8 %
Index ranges -17
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Computing structure solution Bruker AXS SHELXTL Vers.6.10, DOS/WIN95/NT/2000
Computing structure refinement Bruker AXS SHELXTL Vers.6.10, DOS/WIN95/NT/2000
Refinement method Full-matrix least-squares on F2
Reflections collected 4936
Independent reflections 2008 [R(int) = 0.0331]
Data / restraints / parameters 1221 / 0 / 136
Goodness-of-fit on F2 0.962
Weighting details w = 1/[σ2 (Fo2)+ (0.1095*P)2]
where P = (Fo2+2Fc2)/3
Final R indices [I>2sigma(I)] R1 = 0.0609, wR2 = 0.1462
R indices (all data) R1 = 0.0967, wR2 = 0.1705
Largest diff. peak and hole 0.419 and -0.231 eÅ-3
Treatment of hydrogen atoms Riding model on idealized geometries
with the 1.2 fold isotropic displacement
parameters of the equivalent Uij of the
corresponding carbon atom
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Table 1. Crystal data and structure refinement for TI.
Identification code TI
Empirical formula C15 H18
Formula weight 198.29 Da
Density (calculated) 1.172 g cm-3
F(000) 432
Temperature 203(2) K
Crystal size 0.45 x 0.32 x 0.21 mm
Crystal color colorless
Crystal description block
Wavelength 0.71073 Å
Crystal system monoclinic
Space group P21/c
Unit cell dimensions a = 11.920(3) Å α = 90°
b = 6.0733(13) Å β = 110.670(4)°
c = 16.584(4) Å γ = 90°
Volume 1123.4(4) Å3
Z 4
Cell measurement reflections used 2165
Cell measurement two theta min/max 5.196° to 47.370°
Diffractometer control software Bruker AXS SMART Vers. 5.054 1997/98
Diffractometer measurement device Siemens SMART CCD area detector system
Diffractometer measurement method Full sphere data collection
in omega at 0.3° scan width
two runs with 720 frames, phi = 0°, 270°
and two runs with 436 frames, phi = 88°, 180°
Theta range for data collection 1.83° to 27.00°
Completeness to theta = 27.00° 99.4 %
Index ranges -15
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Computing structure refinement Bruker AXS SHELXTL Vers. 6.10 DOS/WIN95/NT/2000
Refinement method Full-matrix least-squares on F2
Reflections collected 12490
Independent reflections 2443 [R(int) = 0.0696]
Data / restraints / parameters 1428 / 0 / 136
Goodness-of-fit on F2 0.974
Weighting details w = 1/[σ2 (Fo2)+ (0.0589P)2+0.5439P]
where P = (Fo2+2Fc2)/3
Final R indices [I>2sigma(I)] R1 = 0.0559, wR2 = 0.1260
R indices (all data) R1 = 0.1051, wR2 = 0.1610
Largest diff. peak and hole 0.208 and -0.139 eÅ-3
Treatment of hydrogen atoms Riding model on idealized geometries
with the 1.2 fold isotropic displacement
parameters of the equivalent Uij of the
corresponding carbon atom
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Crystal structure of TI
view along b-axis
view along a-axis
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Powder X-ray Diffraction
Powder diffraction data were collected on a Siemens D5000 Powder X-ray Diffractometer with 7° OED. The sample was obtained by grinding the crystals grown from methanol solution of Form I and micro crystals of pure TNB. The powder diffractogram recorded is shown below. The powder patterns for Form I, II and III are simulated using the program, Platon.[1] There were no discrepancies noted between the experimental and simulation in terms of 2θ values for Form I and Pure TNB; the experimental pattern was found to be consistent in several samples. This shows there is no phase transition in the pure sample and is same as Form I. In contrast, the simulated powder patterns of form II and III shows that indeed they are different from Form I and are formed due to the additive, TI.
[1] Platon–version 1.05, 2002: A. L. Spek, Acta Crystallogr. 1990, A46, C34.
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DSC Diffrential scanning thermograms for Form I and pure TNB were recorded on
NETZSCH, Phoenix DSC 2004. The thermograms are shown below. There were no
additional peaks in the thermograms indicating phase transition.
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Melting Point Melting point of crystals of Form I and Form III were recorded on Olympus BX40 hot
stage microscope connected with Wagner & Munz Poly Therm A heater. The melting
point pictures are shown below. The Melting Point (MP) analysis shows that the Form I
crystals melts at lower temperature (mp: 121.8 °C) than Form III crystals (mp: 122.7 °C)
which suggests that Form I is kinetic and From III is thermodynamic.
Form I crystals
Form I crystal at room temperature
Melting of Form I crystal at 122.7 °C
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Form III crystals
Form III crystal at room temperature
Melting of Form III crystal at 122.7 °C
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Morphology of Form I
Crystal faces have been calculated using BDFH method in Morphology module in
Cerius2 program. Atom-atom potentials were estimated using Dreiding 2.21 force field
and atomic charges were estimated using the charge equilibration method. Cerius2,
Accelrys, Cambridge (UK). See www.accelrys.com
Morphology of Form I Form I : Pbca (two molecules in the asymmetric unit) ------------------
specified minimum slice thickness gave rise to too many faces. Minimum slice thickness actually used is 3.000 Angstroms. The total surface area is 2308.7288 units Area of face ( 4 0 2) is 0.0000 units List Areas by form Form { 1 0 2} accounts for 27.27 percent of the total area.
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Form { 1 1 1} accounts for 39.42 percent of the total area. Form { 0 0 2} accounts for 33.31 percent of the total area.
Calculate Angle between 4 0 2 and -4 0 2 is Angle between normals to ( 4 0 2) and ( -4 0 2) is 153.4763 degrees Internal angle between ( 4 0 2) ) and ( -4 0 2) is 26.5237 degrees. Aspect ratio is : 2.3754 List of First Two Faces -------------------------------------------------------------- H K L Distance Color D-spacing Area Corners ( 0 0 2) 7.5182 PINK 13.3011 384.5252 6 ( 0 0 -2) 7.5182 PINK 13.3011 384.5252 6 ( 1 0 2) 10.9599 PINK 9.1241 157.3730 4 ( -1 0 2) 10.9599 PINK 9.1241 157.3730 4 ( -1 0 -2) 10.9599 PINK 9.1241 157.3730 4 ( 1 0 -2) 10.9599 PINK 9.1241 157.3730 4
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Table 3. Dihedral angles of TNB polymorphs
Form I Form II Form II I
τ1 5.5 1.6 3.5
τ2 4.1 13.5 6.7
τ3 31.9 4.2 8.7
τ4 6.6 4.3
τ5 9.9 3.9
τ6 10.4 2.5
Table 4. Geometrical parameters of hydrogen bonds
Interaction d (Å)a D (Å) θ (º)
Form I C–H···O 2.98 3.84 137.1
C–H···O 2.21 3.29 173.0
C–H···O 2.25 3.26 155.0
C–H···O 2.87 3.90 160.4
C–H···O 2.90 3.93 159.0
N–O···O 3.04 157.0
N–O···O 2.97 151.0
N–O···N 2.86 152.0
N–O···N 2.97 142.2
Form II C–H···O 2.35 3.41 165.5
C–H···O 2.45 3.48 158.7
C–H···O 2.41 3.48 170.1
C–H···O 2.63 3.48 134.9
C–H···O 2.27 3.31 159.2
C–H···N 3.08 4.13 164.0
C–H···N 2.69 3.70 154.1
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C–H···N 2.81 3.84 158.1
N–O···O 3.00 153.0
N–O···O 3.14 156.6
N–O···O 2.97 139.3
N–O···N 2.84 143.0
N–O···N 2.97 146.0
N–O···N 2.78 159.0
Form III C–H···O 2.69 3.73 161.1
C–H···O 2.46 3.21 125.3
C–H···O 2.43 3.40 147.6
C–H···O 2.34 3.40 166.0
C–H···O 2.85 3.78 144.1
N–O···O 2.94 144.6
N–O···N 2.99 124.2
N–O···N 2.989 124.0
N–O···N 2.99 150.2
N–O···N 3.01 140.0
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Cambridge Structural Database (CSD)
The N-O···N interactions were searched in aromatic nitro compounds in the CSD. The search was performed using CSD 5.23 April 2002 version. The following screens were used: R-factor < or = 7.5, no disorder, no ions, only organics, 3D coordinates present.
Scatter plot of N···O interactions in CSD
The N···O distances in the Forms I, II and III are shown with colour in the figure. Blue
circle (Form I), Red square (Form II), Pink triangle (Form III). The N···O interaction in
Form II is one of the shortest such interactions in CSD.
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Supramolecular Synthons
H
O2N
O2N
N
O
O NO
O
N
O
O
NO
OH
N
OO H
NOO
HN O
O
H
O2N
H
NO O
H
NO
O
H
N
O
O
NO2
NO2
N
O
O
N OO
HO2N
I (Form I) II (Form II)
III (Form II) IV (Form III)
Hits = 2 Hits = 342
Hits = 0 Hits = 6
The occurrences of the above supramolecular synthons in Forms I, II and III was
searched for aromatic nitro compounds in the Cambridge Structural Database (CSD). The
search was performed using CSD 5.23 April 2002 version. There are only 2 hits for
synthon I (Form I), 0 hits for synthon III (Form II) and 6 hits for synthon IV (Form III).
However, synthon II in Form II (hits 342) is very commonly observed in the CSD. The
N-O···N distance in synthon II which is observed in Form II is one of the shortest in
CSD.