S23
Submitted to Chem. Commun.
Version 1 of October 13, 2003
Supplementary Information
Excavations in molecular crystals
Erwan Le Fur, Eric Demers, Thierry Maris and James D. Wuest*
Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada. E-mail: ; Fax: +1 514 343 7586; Tel: +1 514 343 6266
Contents
I. Selected experimental procedures (S2-S4)
II. Crystal structure of tecton 2 • 3 DMSO • 1 acetone • n H2O (S5-S13)
III. Crystal structure of tetrol 3, as prepared from crystals of tecton 2 by hydrolysis in the solid state (S14-S23)
Selected experimental procedures
Tetrakis[4-[(2,4-dichloro-1,3,5-triazin-6-yl)amino]phenyl]methane (5). Tetrakis(4-amino-phenyl)methane (4) was prepared by a published procedure (F. A. Neugebauer, H. Fischer and R. Bernhardt, Chem. Ber., 1976, 109, 2389), modified by using THF instead of ethyl acetate in the reduction of tetrakis(4-nitrophenyl)methane. A solution of tetrakis(4-aminophenyl)methane (4; 0.761 g, 2.00 mmol) in acetone (16 mL) was added dropwise at 0 °C to a stirred solution of cyanuric chloride (1.51 g, 8.19 mmol) in acetone (24 mL). The resulting mixture was kept at 0 °C for 1 hour, treated with Na2CO3 (0.869 g, 8.20 mmol), and poured into water (160 mL). The precipitate was separated by filtration, washed, and dried to give tetrakis[4-[(2,4-dichloro-1,3,5-triazin-6-yl)amino]phenyl]methane (5; 1.48 g, 1.52 mmol, 76%) as a colorless solid: mp >310 °C; 1H NMR (400 MHz, DMSO-d6, 25 °C) d 7.18 (d, 8H, 3J = 8.7 Hz), 7.55 (d, 8H, 3J = 8.7 Hz), 11.18 (s, 4H); 13C NMR (75.4 MHz, DMSO-d6, 25 °C) d 64.1, 121.7, 131.7, 135.8, 143.8, 164.6, 169.7, 170.7; MS (FAB, 3-nitrobenzyl alcohol) m/e 969. Anal. Calcd for C37H20Cl8N16: C, 45.71; H, 2.07; N, 23.05. Found: C, 46.03; H, 2.09; N, 22.61.
Tetrakis[4-[[4-amino-2-chloro-1,3,5-triazin-6-yl]amino]phenyl]methane (6). A solution of tetrakis[4-[(2,4-dichloro-1,3,5-triazin-6-yl)amino]phenyl]methane (5; 0.250 g, 0.257 mmol) in dioxane (10 mL) was stirred at 0 °C and treated with concentrated aqueous ammonia (5 mL). The resulting white suspension was kept at 0 °C for 12 h, then excess ammonia was removed by partial evaporation of the mixture under reduced pressure. The concentrate was poured into water (20 mL), and the precipitated solid was separated by filtration, washed twice with water (10 mL), and dried under vacuum to give tetrakis[4-[[4-amino-2-chloro-1,3,5-triazin-6-yl]amino]phenyl]methane (6; 0.217 g, 0.242 mmol, 94%) as a light yellow solid. To effect crystallization, the compound (0.050 g, 0.056 mmol) was first dissolved in DMSO (10 mL). The solution was then filtered and divided into 10 portions, which were placed in open 4 mL vials and transferred to a closed chamber containing CH3CN. Crystals were obtained within several days: mp >250°C ; 1H NMR (300 MHz, DMSO-d6, 90 °C) d 7.05 (d, 8H, 3J = 8.7 Hz), 7.19 (bs, 8H), 7.64 (d, 8H, 3J = 8.7 Hz), 9.63 (bs, 4H); 13C NMR (75.4 MHz, DMSO-d6, 25 °C) d 62.8, 119.7, 130.8, 137.0, 141.4, 164.1, 167.2, 168.6. Anal. Calcd for C37H28Cl4N20 + 1 DMSO: C, 45.75; H, 4.11; N, 24.81. Found: C, 45.42; H, 3.60; N, 24.96.
Tetrakis[4-[[4-amino-2-(2-hydroxyethyl)amino-1,3,5-triazin-6-yl]amino]phenyl]methane (3). A mixture of tetrakis[4-[(4-amino-2-chloro-1,3,5-triazin-6-yl)amino]phenyl]methane (6; 0.300 g, 0.335 mmol), excess ethanolamine (12 mL), and THF (5 mL) was stirred and heated at 110 °C for 5 h. The mixture was then poured into a mixture of ice and water (50 mL), and the resulting precipitate was separated by filtration, washed four times with water (20 mL), and dried under vacuum to give tetrakis[4-[[4-amino-2-(2-hydroxyethyl)amino-1,3,5-triazin-6-yl]amino]phenyl]methane (3; 0.305 g, 0.307 mmol, 92%) as a light yellow solid: mp >250°C; 1H NMR (300 MHz, DMSO-d6, 90 °C) d 3.36 (dt, 8H, 3J = 5.9 Hz, 3J = 5.8 Hz), 3.53 (t, 8H, 3J = 5.9 Hz), 4.25 (s, 4H), 5.90 (bs, 8H), 6.18 (t, 4H, 3J = 5.8 Hz), 6.99 (d, 8H, 3J = 8.8 Hz), 7.66 (d, 8H, 3J = 8.8 Hz), 8.41 (bs, 4H); 13C NMR (75.4 MHz, DMSO-d6, 25 °C) d 43.0, 60.5, 62.4, 118.6, 130.7, 138.6, 140.0, 164.5, 166.4, 167.2; HRMS (electrospray) calcd for C45H53N24O4 m/e 993.46820, found 993.46814.
Tetrakis[4-[[4-amino-2-(2-acetoxyethyl)amino-1,3,5-triazin-6-yl]amino]phenyl]methane (2). Excess acetic anhydride (5 mL) was added to tetrakis[4-[(4-amino-2-(2-hydroxyethyl)amino-1,3,5-triazin-6-yl)amino]phenyl]methane (3; 0.050 g, 0.050 mmol) and pyridine (0.68 mL, 8.4 mmol), and the resulting suspension was stirred at 25 °C for 24 h. The mixture was then concentrated by partial evaporation under reduced pressure, and the resulting precipitate was separated by filtration, washed twice with water (10 mL), and dried under vacuum to give tetrakis[4-[[4-amino-2-(2-acetoxyethyl)amino-1,3,5-triazin-6-yl]amino]phenyl]methane (2; 0.049 g, 0.042 mmol, 84%) as a light yellow solid. To effect crystallization, the compound (0.040 g, 0.034 mmol) was first dissolved in DMSO (0.8 mL). The solution was then filtered and divided into 8 portions, which were placed in open 4 mL vials and transferred to a closed chamber containing a 5:1 mixture of acetone and water. Crystals suitable for X-ray diffraction were obtained within 48 h: mp >250°C; 1H NMR (300 MHz, DMSO-d6, 90 °C) d 1.96 (s, 12H), 3.48 (dt, 8H, 3J = 5.9 Hz, 3J = 4.5 Hz), 4.12 (t, 8H, 3J = 5.9 Hz), 5.99 (bs, 8H), 6.48 (t, 4H, 3J = 4.5 Hz), 6.98 (d, 8H, 3J = 8.7 Hz), 7.66 (d, 8H, 3J = 8.7 Hz), 8.52 (bs, 4H); 13C NMR (75.4 MHz, DMSO-d6, 25 °C) d 21.0, 40.5, 62.4, 63.0, 118.6, 130.7, 138.6, 140.1, 164.6, 166.3, 167.2, 170.7; MS (FAB, 3-nitrobenzyl alcohol) m/e 1162 (M + 1).
CRYSTAL AND MOLECULAR STRUCTURE OF
C53 H60 N24 O8 COMPOUND (JIW249)
Equipe WUEST
Département de chimie, Université de Montréal,
C.P. 6128, Succ. Centre-Ville, Montréal, Québec, H3C 3J7 (Canada)
Solvent: DMSO/acetone/H2O
Table 1. Crystal data and structure refinement for C53 H60 N24 O8.
Identification code JIW249
Empirical formula C53 H60 N24 O8
Formula weight 1161.25
Temperature 293(2)K
Wavelength 1.54178 Å
Crystal system, Space group Tetragonal, I41/a
Unit cell dimensions a = 25.6644(3) Å a = 90°
b = 25.6644(3) Å b = 90°
c = 12.2028(3) Å g = 90°
Volume 8037.5(2)Å3
Z 4
Density (without solvent) 0.960 g/cm3
Absorption coefficient 0.567 mm-1
F(000) 2440
Crystal size 0.41 x 0.14 x 0.14 mm
Theta range for data collection 3.44 to 72.95°
Index ranges -31 £ h £ 30, -31 £ k £ 31, -12 £ £ 14
Reflections collected 32725
Independent reflections 3976 [Rint = 0.055]
Absorption correction Semi-empirical from equivalents
Max. and min. transmission 1.0000 and 0.3300
Refinement method Full-matrix least-squares on F2
Data / restraints / parameters 3976 / 0 / 193
Goodness-of-fit on F2 1.097
Final R indices [I>2sigma(I)] R1 = 0.0824, wR2 = 0.1885
R indices (all data) R1 = 0.1568, wR2 = 0.2306
Largest diff. peak and hole 0.202 and -0.235 e/Å3
Table 2. Atomic coordinates (x 104) and equivalent isotropic
displacement parameters (Å2 x 103) for C53 H60 N24 O8.
Ueq is defined as one third of the trace of the orthogonalized
Uij tensor.
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x y z Ueq
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O(1) 8588(1) 2201(1) 1352(3) 89(1)
O(2) 8282(1) 2635(1) 2815(3) 97(1)
N(1) 8768(1) 3781(1) -836(2) 50(1)
N(2) 8184(1) 4095(1) 382(2) 49(1)
N(3) 7521(1) 3541(1) 1108(2) 49(1)
N(4) 8180(1) 3197(1) -72(2) 48(1)
N(5) 7570(1) 4404(1) 1577(3) 78(1)
N(6) 7545(1) 2676(1) 695(3) 60(1)
C(1) 10000 2500 -3750 34(1)
C(2) 9671(1) 2854(1) -2986(3) 37(1)
C(3) 9657(1) 3390(1) -3033(3) 44(1)
C(4) 9357(1) 3687(1) -2323(3) 48(1)
C(5) 9056(1) 3451(1) -1525(3) 40(1)
C(6) 9079(1) 2913(1) -1431(3) 46(1)
C(7) 9379(1) 2624(1) -2149(3) 43(1)
C(8) 8362(1) 3678(1) -152(3) 43(1)
C(9) 7763(1) 3998(1) 1013(3) 49(1)
C(10) 7758(1) 3152(1) 576(3) 47(1)
C(11) 7781(2) 2194(1) 343(4) 66(1)
C(12) 8095(2) 1929(2) 1193(4) 85(1)
C(13) 8629(2) 2553(2) 2188(5) 80(1)
C(14) 9145(2) 2804(2) 2188(5) 108(2)
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Table 3. Hydrogen coordinates (x 104) and isotropic displacement
parameters (Å2 x 103) for C53 H60 N24 O8.
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x y z Ueq
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H(1) 8864 4102 -849 60
H(5A) 7298 4364 1982 93
H(5B) 7717 4704 1532 93
H(6) 7245 2658 1006 72
H(3) 9856 3560 -3562 53
H(4) 9359 4048 -2383 58
H(6) 8891 2746 -882 55
H(7) 9387 2264 -2071 51
H(11A) 8003 2265 -284 79
H(11B) 7508 1959 102 79
H(12A) 7903 1921 1877 102
H(12B) 8163 1572 971 102
H(14A) 9138 3104 2658 162
H(14B) 9233 2909 1457 162
H(14C) 9401 2561 2451 162
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Table 4. Anisotropic parameters (Å2 x 103) for C53 H60 N24 O8.
The anisotropic displacement factor exponent takes the form:
-2 p2 [ h2 a*2 U11 + ... + 2 h k a* b* U12 ]
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U11 U22 U33 U23 U13 U12
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O(1) 73(2) 79(2) 116(3) 8(2) 10(2) 8(2)
O(2) 75(2) 118(3) 99(3) 5(2) 23(2) -9(2)
N(1) 48(2) 31(1) 71(2) -7(1) 19(1) -4(1)
N(2) 42(2) 36(2) 69(2) -4(1) 16(1) 0(1)
N(3) 38(2) 41(2) 67(2) -5(1) 5(1) -1(1)
N(4) 39(2) 38(2) 65(2) 1(1) 12(1) 0(1)
N(5) 70(2) 44(2) 119(3) -19(2) 45(2) -8(2)
N(6) 49(2) 37(2) 93(3) 2(2) 12(2) -5(1)
C(1) 31(2) 31(2) 39(4) 0 0 0
C(2) 30(2) 31(2) 50(2) -1(1) 0(1) 2(1)
C(3) 42(2) 34(2) 57(2) 2(2) 11(2) -5(1)
C(4) 45(2) 30(2) 70(3) 0(2) 13(2) -3(1)
C(5) 34(2) 34(2) 53(2) -5(2) 3(2) 2(1)
C(6) 46(2) 42(2) 51(2) 4(2) 12(2) -3(1)
C(7) 43(2) 30(2) 56(2) 2(1) 9(2) 2(1)
C(8) 34(2) 35(2) 60(2) 0(2) 3(2) 1(1)
C(9) 41(2) 41(2) 66(3) -8(2) 10(2) 1(1)
C(10) 37(2) 38(2) 66(3) 1(2) 1(2) 1(1)
C(11) 69(3) 39(2) 90(3) -4(2) 7(2) -7(2)
C(12) 76(3) 50(2) 128(4) 5(3) 13(3) 0(2)
C(13) 69(3) 72(3) 98(4) 15(3) 4(3) 1(2)
C(14) 70(3) 122(5) 133(5) 4(4) 1(3) -19(3)
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Table 5. Bond lengths [Å] and angles [°] for C53 H60 N24 O8
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S23
O(1)-C(13) 1.367(6)
O(1)-C(12) 1.458(5)
O(2)-C(13) 1.192(5)
N(1)-C(8) 1.362(4)
N(1)-C(5) 1.404(4)
N(2)-C(8) 1.334(4)
N(2)-C(9) 1.349(4)
N(3)-C(9) 1.331(4)
N(3)-C(10) 1.338(4)
N(4)-C(8) 1.323(4)
N(4)-C(10) 1.347(4)
N(5)-C(9) 1.343(4)
N(6)-C(10) 1.345(4)
N(6)-C(11) 1.442(4)
C(1)-C(2)#1 1.551(3)
C(1)-C(2)#2 1.551(3)
C(1)-C(2)#3 1.551(3)
C(1)-C(2) 1.551(3)
C(2)-C(3) 1.379(4)
C(2)-C(7) 1.397(4)
C(3)-C(4) 1.387(4)
C(4)-C(5) 1.383(4)
C(5)-C(6) 1.386(4)
C(6)-C(7) 1.384(4)
C(11)-C(12) 1.480(6)
C(13)-C(14) 1.473(6)
C(13)-O(1)-C(12) 118.9(4)
C(8)-N(1)-C(5) 130.6(3)
C(8)-N(2)-C(9) 113.9(3)
C(9)-N(3)-C(10) 113.7(3)
C(8)-N(4)-C(10) 114.0(3)
C(10)-N(6)-C(11) 125.1(3)
C(2)#1-C(1)-C(2)#2 106.1(2)
C(2)#1-C(1)-C(2)#3 111.20(12)
C(2)#2-C(1)-C(2)#3 111.20(12)
C(2)#1-C(1)-C(2) 111.20(12)
C(2)#2-C(1)-C(2) 111.20(12)
C(2)#3-C(1)-C(2) 106.1(2)
C(3)-C(2)-C(7) 116.0(3)
C(3)-C(2)-C(1) 125.0(3)
C(7)-C(2)-C(1) 119.0(2)
C(2)-C(3)-C(4) 122.4(3)
C(5)-C(4)-C(3) 120.7(3)
C(4)-C(5)-C(6) 118.1(3)
C(4)-C(5)-N(1) 116.8(3)
C(6)-C(5)-N(1) 125.1(3)
C(7)-C(6)-C(5) 120.3(3)
C(6)-C(7)-C(2) 122.5(3)
N(4)-C(8)-N(2) 126.3(3)
N(4)-C(8)-N(1) 119.8(3)
N(2)-C(8)-N(1) 113.9(3)
N(3)-C(9)-N(5) 117.8(3)
N(3)-C(9)-N(2) 125.9(3)
N(5)-C(9)-N(2) 116.4(3)
N(3)-C(10)-N(6) 116.1(3)
N(3)-C(10)-N(4) 126.0(3)
N(6)-C(10)-N(4) 117.9(3)
N(6)-C(11)-C(12) 114.5(4)
O(1)-C(12)-C(11) 110.1(3)
O(2)-C(13)-O(1) 122.6(5)
O(2)-C(13)-C(14) 126.4(6)
O(1)-C(13)-C(14) 110.9(5)
S23
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Symmetry transformations used to generate equivalent atoms:
#1 -y+5/4,x-3/4,-z-3/4 #2 y+3/4,-x+5/4,-z-3/4 #3 -x+2,-y+1/2,z+0
Table 6. Torsion angles [°] for C53 H60 N24 O8.
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S23
C(2)#1-C(1)-C(2)-C(3) -112.7(4)
C(2)#2-C(1)-C(2)-C(3) 5.2(3)
C(2)#3-C(1)-C(2)-C(3) 126.3(3)
C(2)#1-C(1)-C(2)-C(7) 70.00(18)
C(2)#2-C(1)-C(2)-C(7) -172.0(3)
C(2)#3-C(1)-C(2)-C(7) -51.0(2)
C(7)-C(2)-C(3)-C(4) -2.3(5)
C(1)-C(2)-C(3)-C(4) -179.6(3)
C(2)-C(3)-C(4)-C(5) 0.0(5)
C(3)-C(4)-C(5)-C(6) 2.5(5)
C(3)-C(4)-C(5)-N(1) 179.5(3)
C(8)-N(1)-C(5)-C(4) 164.2(3)
C(8)-N(1)-C(5)-C(6) -19.1(5)
C(4)-C(5)-C(6)-C(7) -2.6(5)
N(1)-C(5)-C(6)-C(7) -179.3(3)
C(5)-C(6)-C(7)-C(2) 0.3(5)
C(3)-C(2)-C(7)-C(6) 2.2(5)
C(1)-C(2)-C(7)-C(6) 179.7(3)
C(10)-N(4)-C(8)-N(2) 3.8(5)
C(10)-N(4)-C(8)-N(1) -175.9(3)
C(9)-N(2)-C(8)-N(4) -3.3(5)
C(9)-N(2)-C(8)-N(1) 176.5(3)
C(5)-N(1)-C(8)-N(4) -0.2(5)
C(5)-N(1)-C(8)-N(2) 180.0(3)
C(10)-N(3)-C(9)-N(5) -175.9(3)
C(10)-N(3)-C(9)-N(2) 5.2(5)
C(8)-N(2)-C(9)-N(3) -1.7(5)
C(8)-N(2)-C(9)-N(5) 179.5(3)
C(9)-N(3)-C(10)-N(6) 176.5(3)
C(9)-N(3)-C(10)-N(4) -4.6(5)
C(11)-N(6)-C(10)-N(3) -169.7(3)
C(11)-N(6)-C(10)-N(4) 11.3(6)
C(8)-N(4)-C(10)-N(3) 0.5(5)
C(8)-N(4)-C(10)-N(6) 179.4(3)
C(10)-N(6)-C(11)-C(12) 92.6(5)
C(13)-O(1)-C(12)-C(11) 96.6(5)
N(6)-C(11)-C(12)-O(1) -74.4(5)
C(12)-O(1)-C(13)-O(2) 2.4(7)
C(12)-O(1)-C(13)-C(14) -177.6(4)
S23
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Symmetry transformations used to generate equivalent atoms:
#1 -y+5/4,x-3/4,-z-3/4 #2 y+3/4,-x+5/4,-z-3/4 #3 -x+2,-y+1/2,z+0
Table 7. Bond lengths [Å] and angles [°] related to the hydrogen
bonding for C53 H60 N24 O8.
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D-H ..A d(D-H) d(H..A) d(D..A) <DHA
N(1)-H(1) N(3)#4 0.86 2.46 3.288(4) 161.9
N(5)-H(5A) N(2)#5 0.86 2.12 2.975(4) 174.6
N(6)-H(6) O(2)#6 0.86 2.11 2.907(4) 153.3
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Symmetry transformations used to generate equivalent atoms:
#1 -y+5/4,x-3/4,-z-3/4 #2 y+3/4,-x+5/4,-z-3/4
#3 -x+2,-y+1/2,z+0 #4 -y+5/4,x-1/4,z-1/4
#5 y+1/4,-x+5/4,z+1/4 #6 -x+3/2,-y+1/2,-z+1/2
ORTEP view of the C53 H60 N24 O8 compound with the numbering scheme adopted. Ellipsoids drawn at 30% probability level. Hydrogens represented by sphere of arbitrary size.
Experimental details
X-ray crystallographic data for JIW249 were collected from a single crystal mounted on a glass fiber. Data were collected using a Bruker Platform diffractometer, equipped with a Bruker SMART 2K charge-coupled device (CCD) area detector, using the program SMART and normal focus sealed-tube source graphite-monochromated Cu-Ka radiation. The crystal-to-detector distance was 4.908 cm, and the data collection was carried out in 512 x 512 pixel mode, utilizing 4 x 4 pixel binning. The initial unit cell parameters were determined by a least-squares fit of the angular setting of strong reflections, collected by a 9.0 degree scan in 30 frames over four different parts of the reciprocal space (120 frames total). One complete sphere of data was collected, to better than 0.8 Å resolution. Upon completion of the data collection, the first 101 frames were recollected in order to improve the decay correction analysis.
The space group I41/a was determined based on systematic absences and intensity statistics. A successful direct-methods solution was calculated, which provided most non-hydrogen atoms from the E-map. Several full-matrix least-squares/difference Fourier cycles were performed, which located the remainder of the non-hydrogen atoms. In this way, the host network could easily be found and refined, but no resolved solvent molecules (DMSO/acetone/H2O) could be found within the cavities. Most solvent molecules were disordered to such an extent that few significant difference peaks were found by Fourier difference. Refining the structure with isolated solvent peaks for modeling the disordered solvent gave a residual R1 close to 20% at this point, even though what appeared to be a correct solution was found. The data were treated with the Platon/Squeeze option to remove as much of the effects of solvent disorder as possible.
Platon found a potential solvent void of 3166 Å3 in the unit cell volume of 8037.5 Å3, or 39%. The Squeeze option found 760 electrons of diffuse scattering, a value giving 18 DMSO solvent molecules per unit cell or 4.5 per molecule of tecton. This figure is close to the value of 3.5 DMSO per tecton found by NMR, but acetone and H2O may also be included in the cavities in the unit cell (see text).