Download citation
Download citation
link to html
In the title macrocyclic poly­amine, C24H38N6·5H2O, the centrosymmetric poly­amine mol­ecules are stacked in rows, and between these mol­ecules there are channels along the a axis. The intermolecular hydrogen bonds formed between the water and poly­amine, together with those formed between water mol­ecules, generate an extensive hydrogen-bonding network.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270100007095/gd1091sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270100007095/gd1091Isup2.hkl
Contains datablock I

CCDC reference: 150354

Comment top

Macrocyclic complexes play a key role in the modelling of metallobiosites (Fenton & Ōkawa, 1993), and in the development of systems for activating substrate molecules (Vigato et al., 1990). Our current studies focus on macrocyclic polyamines in which the relative positions of the donor atoms in the ring are deigned to hold pairs of coordinated transition metal ions at specified distances. The distance between these two metal ions is considered to be an important factor in increasing the efficiency in activation of substrates. Recently, it was reported that the title compound, (I), and its analogues can accelerate the hydrolysis of bis(p-nitrophenyl)phosphate and ATP (Ragunathan & Schneider, 1996; Lu et al., 1997). On the other hand, these compounds and their metal complexes are good receptors for inorganic phosphates and RNA (Nation et al., 1996; Li et al., 1997). Therefore, the structure of the title compound may prove useful for understanding the mechanisms of hydrolysis and for the dsign of new compounds. \sch

Fig. 1. is the ORTEP representation of compound (I). The centrosymmetric macrocycle adopts a chair-like conformation, with one diethylene triamine moiety flipped down and the other flipped up. While in its analogue 3,7,11,19,23,27-hexaazatricyclo [27.3.1.113,17]tetratriaconta-1(32),13,15,17 (34),29 (33),30-hexaene hexahydrobromide dihydrate, (II), although the molecule is still in the chair conformation, in this case, it is the two phenyl rings that flipped down and flipped up and the two phenyl rings are nearly perpendicular to the plane of the macrocyclic arms (Liobet et al., 1994). These differences may depend both on the different states of protonation and on the different plaing of the aromatic substituents, para in (I) and meta in (II). The C—C and C—N bond lengths in (I) are almost equal to those in (II). In the crystal, the macrocyclic molecules are arranged in stacks (Fig. 2), and the macrocycles of the molecules form an apparent channel along the a axis. The water molecules [O11, O12, O14, O15 and their symmetry-related partners] link different polyamine molecules by hydrogen bonds (Table 2) to form a supermolecule.

Experimental top

The title compound was synthesized in a similar procedure used by others (Chen & Martell, 1991). To an MeCN solution of diethylene triamine an equivalent amount of terephthalaldehyde was added slowly at room temperature. Several hours later, a white precipitate was obtained. The white solid was reduced with sodium borohydride in ethanol for 5 h. The solvent was then removed in vacuo, and the residue was extracted with chloroform. The product was purified by recrystallization from MeCN, the pure compound dissolved in an appropriate amount of hot water and prismatic single crystals suitable for crystallographic analysis were obtained by crystallization from water.

Refinement top

Hydrogen atoms were found from the difference map and were refined isotropically with fixed isotropic displacement parameters 1.2 × isotropic Ueq of the atoms to which they attached. To make the refinement stable, several restraints were used to fix the O—H and N—H bond distances as well as H—O—H angles. No suitable positions were found from the difference map for the hydrogen atoms attached to the disordered oxygen atoms O15 and O15'.

Computing details top

Data collection: XSCANS (Siemens, 1994); cell refinement: XSCANS; data reduction: SHELXTL (Sheldrick, 1997); program(s) used to solve structure: SHELXTL; program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Figures top
[Figure 1] Fig. 1. Structure of the title compound showing 50% probability displacement ellipsoids with numbering scheme. The water molecules were omitted for clarity. Symmetry code: (A) 1 − x, 1 − y, 1 − z.
[Figure 2] Fig. 2. The unit cell of the title compound, hydrogen atoms are omitted for clarity.
3,6,9,16,19,22-hexaazatricyclo[22.2.2.211,14]triaconta-11,13,24,26,27, 29-hexaene pentahydrate top
Crystal data top
C24H38N6·5H2ODx = 1.218 Mg m3
Mr = 500.68Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, PnmaCell parameters from 29 reflections
a = 7.451 (3) Åθ = 7.8–9.2°
b = 19.709 (6) ŵ = 0.09 mm1
c = 18.587 (8) ÅT = 293 K
V = 2729.6 (18) Å3Prism, colourless
Z = 40.40 × 0.20 × 0.20 mm
F(000) = 1096
Data collection top
Bruker P4
diffractometer
Rint = 0.034
Radiation source: sealed tubeθmax = 25.0°, θmin = 2.1°
Graphite monochromatorh = 18
2θ/ω scansk = 231
3241 measured reflectionsl = 122
2474 independent reflections3 standard reflections every 97 reflections
1770 reflections with I > 2σ(I) intensity decay: 4.9%
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.064Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.197Only H-atom coordinates refined
S = 1.03 w = 1/[σ2(Fo2) + (0.1131P)2 + 1.2637P]
where P = (Fo2 + 2Fc2)/3
2474 reflections(Δ/σ)max < 0.001
244 parametersΔρmax = 0.36 e Å3
21 restraintsΔρmin = 0.31 e Å3
Crystal data top
C24H38N6·5H2OV = 2729.6 (18) Å3
Mr = 500.68Z = 4
Orthorhombic, PnmaMo Kα radiation
a = 7.451 (3) ŵ = 0.09 mm1
b = 19.709 (6) ÅT = 293 K
c = 18.587 (8) Å0.40 × 0.20 × 0.20 mm
Data collection top
Bruker P4
diffractometer
Rint = 0.034
3241 measured reflections3 standard reflections every 97 reflections
2474 independent reflections intensity decay: 4.9%
1770 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.06421 restraints
wR(F2) = 0.197Only H-atom coordinates refined
S = 1.03Δρmax = 0.36 e Å3
2474 reflectionsΔρmin = 0.31 e Å3
244 parameters
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Hydrogen atoms were found from different map and were refined isotropically with fixed isotropic thermal parameters 1.2 times equivalent isotropic Ueq of the atoms they attached. To make the refinement stable, several restraints were used to fix the O—H and N—H bond distances as well as H—O—H angles. No suitable positions were found from the different map for the hydrogen atoms attached to the disordered oxygen atoms O15 and O15'.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
N10.7066 (4)0.65895 (14)0.38227 (15)0.0685 (8)
H1N0.693 (2)0.6886 (11)0.3503 (13)0.082*
N21.0172 (3)0.65199 (11)0.48594 (13)0.0505 (6)
H2N0.928 (3)0.6762 (14)0.4981 (17)0.061*
N30.9297 (3)0.63938 (10)0.64678 (11)0.0440 (6)
H3N0.855 (3)0.6545 (14)0.6158 (12)0.053*
C10.8571 (4)0.61237 (17)0.37799 (17)0.0562 (7)
H1A0.954 (5)0.6358 (15)0.3460 (17)0.067*
H1B0.815 (5)0.5718 (18)0.3541 (18)0.067*
C20.9454 (5)0.59274 (14)0.44828 (16)0.0504 (7)
H2A0.859 (5)0.5695 (16)0.4766 (16)0.061*
H2B1.057 (4)0.5618 (16)0.4368 (15)0.061*
C31.1400 (4)0.63528 (15)0.54497 (15)0.0496 (7)
H3A1.191 (4)0.6785 (16)0.5635 (16)0.060*
H3B1.244 (4)0.6066 (15)0.5247 (16)0.060*
C41.0594 (4)0.59784 (14)0.60828 (15)0.0476 (7)
H4A1.013 (4)0.5569 (16)0.5922 (16)0.057*
H4B1.156 (4)0.5842 (15)0.6424 (16)0.057*
C50.8274 (4)0.60255 (14)0.70239 (15)0.0483 (7)
H5A0.737 (4)0.6374 (14)0.7268 (15)0.058*
H5B0.910 (4)0.5890 (14)0.7398 (17)0.058*
C60.7235 (4)0.54177 (13)0.67558 (13)0.0427 (6)
C70.5920 (4)0.54929 (14)0.62383 (14)0.0486 (7)
H70.562 (4)0.5932 (16)0.6063 (16)0.058*
C80.5026 (4)0.49400 (14)0.59559 (16)0.0497 (7)
H80.411 (4)0.4990 (15)0.5556 (16)0.060*
C90.5414 (4)0.42834 (13)0.61831 (14)0.0462 (7)
C100.6665 (4)0.42099 (14)0.67200 (15)0.0501 (7)
H100.705 (4)0.3755 (16)0.6913 (16)0.060*
C110.7579 (4)0.47635 (14)0.70054 (15)0.0485 (7)
H110.846 (4)0.4736 (14)0.7347 (17)0.058*
C120.4526 (5)0.36756 (15)0.58191 (19)0.0603 (8)
H12A0.416 (5)0.3813 (17)0.5295 (19)0.072*
H12B0.545 (5)0.3269 (17)0.5794 (18)0.072*
O111.1218 (4)0.75000.70300 (15)0.0537 (7)
H211.056 (3)0.7145 (3)0.6875 (15)0.064*
O121.1879 (5)0.75000.39151 (18)0.0713 (10)
H221.131 (4)0.7145 (3)0.4118 (16)0.086*
O130.7169 (5)0.75000.53880 (19)0.0744 (9)
H230.623 (4)0.75000.5695 (17)0.089*
H330.663 (5)0.75000.4958 (11)0.089*
O141.4852 (6)0.75000.6552 (2)0.1123 (16)
H241.3667 (19)0.75000.664 (3)0.135*
H341.532 (7)0.75000.6997 (15)0.135*
O150.579 (2)0.75000.2565 (5)0.107 (3)0.559 (14)
O15'0.723 (2)0.75000.2534 (6)0.096 (4)0.441 (14)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0705 (17)0.0521 (15)0.083 (2)0.0111 (14)0.0109 (14)0.0134 (13)
N20.0622 (15)0.0354 (12)0.0541 (13)0.0049 (11)0.0059 (12)0.0033 (10)
N30.0543 (13)0.0343 (11)0.0435 (12)0.0004 (10)0.0018 (10)0.0047 (9)
C10.0555 (17)0.0534 (17)0.0596 (17)0.0092 (15)0.0082 (15)0.0043 (14)
C20.0559 (17)0.0383 (14)0.0571 (17)0.0100 (13)0.0019 (14)0.0034 (12)
C30.0515 (15)0.0465 (15)0.0509 (15)0.0103 (14)0.0002 (13)0.0027 (12)
C40.0568 (17)0.0393 (14)0.0468 (15)0.0016 (13)0.0027 (13)0.0026 (12)
C50.0579 (16)0.0482 (15)0.0386 (13)0.0042 (14)0.0005 (13)0.0051 (12)
C60.0500 (14)0.0442 (14)0.0338 (12)0.0039 (12)0.0065 (11)0.0013 (10)
C70.0566 (17)0.0419 (15)0.0474 (15)0.0001 (13)0.0040 (13)0.0064 (12)
C80.0504 (15)0.0480 (15)0.0507 (15)0.0020 (13)0.0053 (14)0.0026 (13)
C90.0430 (15)0.0435 (14)0.0521 (15)0.0023 (12)0.0053 (12)0.0008 (12)
C100.0525 (16)0.0402 (14)0.0577 (17)0.0042 (13)0.0054 (14)0.0066 (13)
C110.0509 (16)0.0523 (16)0.0424 (14)0.0048 (13)0.0001 (13)0.0050 (12)
C120.0638 (19)0.0452 (16)0.072 (2)0.0042 (15)0.0003 (17)0.0124 (15)
O110.0656 (18)0.0370 (14)0.0585 (16)0.0000.0099 (15)0.000
O120.095 (3)0.0416 (15)0.078 (2)0.0000.0199 (18)0.000
O130.081 (2)0.069 (2)0.073 (2)0.0000.0030 (18)0.000
O140.080 (3)0.196 (5)0.061 (2)0.0000.003 (2)0.000
O150.162 (9)0.095 (5)0.065 (4)0.0000.033 (6)0.000
O15'0.161 (10)0.069 (4)0.058 (4)0.0000.015 (7)0.000
Geometric parameters (Å, º) top
N1—C11.451 (4)C5—H5B0.97 (3)
N1—C12i1.457 (4)C6—C71.381 (4)
N1—H1N0.841 (8)C6—C111.394 (4)
N2—C21.463 (3)C7—C81.381 (4)
N2—C31.466 (4)C7—H70.95 (3)
N2—H2N0.847 (10)C8—C91.392 (4)
N3—C41.455 (4)C8—H81.01 (3)
N3—C51.475 (4)C9—C101.373 (4)
N3—H3N0.853 (10)C9—C121.526 (4)
C1—C21.513 (4)C10—C111.391 (4)
C1—H1A1.04 (3)C10—H101.01 (3)
C1—H1B0.97 (4)C11—H110.92 (3)
C2—H2A0.95 (3)C12—N1i1.457 (4)
C2—H2B1.05 (3)C12—H12A1.05 (3)
C3—C41.513 (4)C12—H12B1.06 (4)
C3—H3A0.99 (3)O11—H210.902 (10)
C3—H3B1.03 (3)O12—H220.900 (10)
C4—H4A0.93 (3)O13—H230.901 (10)
C4—H4B1.00 (3)O13—H330.895 (10)
C5—C61.511 (4)O14—H240.898 (11)
C5—H5A1.06 (3)O14—H340.899 (10)
C1—N1—C12i115.3 (3)N3—C5—C6115.1 (2)
C1—N1—H1N119.7 (11)N3—C5—H5A108.0 (15)
C12i—N1—H1N118.3 (11)C6—C5—H5A109.1 (16)
C2—N2—C3114.0 (2)N3—C5—H5B108.0 (18)
C2—N2—H2N107 (2)C6—C5—H5B110.2 (17)
C3—N2—H2N114 (2)H5A—C5—H5B106 (2)
C4—N3—C5114.3 (2)C7—C6—C11117.5 (3)
C4—N3—H3N107 (2)C7—C6—C5120.6 (2)
C5—N3—H3N108 (2)C11—C6—C5121.9 (3)
N1—C1—C2116.8 (3)C6—C7—C8121.5 (3)
N1—C1—H1A106.6 (17)C6—C7—H7120.1 (18)
C2—C1—H1A107.7 (18)C8—C7—H7118.4 (18)
N1—C1—H1B107 (2)C7—C8—C9121.2 (3)
C2—C1—H1B109 (2)C7—C8—H8121.8 (17)
H1A—C1—H1B109 (3)C9—C8—H8116.9 (17)
N2—C2—C1111.6 (2)C10—C9—C8117.4 (3)
N2—C2—H2A111.6 (19)C10—C9—C12122.2 (3)
C1—C2—H2A107.8 (19)C8—C9—C12120.3 (3)
N2—C2—H2B105.8 (17)C9—C10—C11121.8 (3)
C1—C2—H2B108.5 (16)C9—C10—H10123.1 (17)
H2A—C2—H2B112 (3)C11—C10—H10114.9 (17)
N2—C3—C4116.4 (2)C10—C11—C6120.5 (3)
N2—C3—H3A107.8 (17)C10—C11—H11124.7 (19)
C4—C3—H3A107.5 (17)C6—C11—H11114.7 (19)
N2—C3—H3B108.6 (17)N1i—C12—C9115.6 (3)
C4—C3—H3B108.4 (17)N1i—C12—H12A108 (2)
H3A—C3—H3B108 (2)C9—C12—H12A108.8 (19)
N3—C4—C3111.8 (2)N1i—C12—H12B106.1 (18)
N3—C4—H4A113 (2)C9—C12—H12B109.4 (18)
C3—C4—H4A108.8 (19)H12A—C12—H12B109 (3)
N3—C4—H4B108.6 (17)H23—O13—H33102.6 (15)
C3—C4—H4B109.9 (18)H24—O14—H34102.5 (16)
H4A—C4—H4B104 (3)
Symmetry code: (i) x+1, y+1, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N···O150.84 (2)2.29 (2)3.097 (9)162 (2)
N2—H2N···O130.85 (2)2.27 (3)3.115 (4)172 (2)
N3—H3N···O130.85 (2)2.58 (3)3.361 (4)153 (2)
O11—H21···N30.90 (2)1.91 (2)2.810 (3)175 (2)
O12—H22···N20.90 (2)2.03 (2)2.903 (4)162 (2)
O13—H23···O14ii0.90 (3)1.90 (3)2.768 (6)162 (3)
O14—H24···O110.90 (2)1.96 (2)2.850 (5)169 (5)
O14—H34···O11iii0.90 (3)1.93 (3)2.825 (5)177 (5)
Symmetry codes: (ii) x1, y, z; (iii) x+1/2, y+3/2, z+3/2.

Experimental details

Crystal data
Chemical formulaC24H38N6·5H2O
Mr500.68
Crystal system, space groupOrthorhombic, Pnma
Temperature (K)293
a, b, c (Å)7.451 (3), 19.709 (6), 18.587 (8)
V3)2729.6 (18)
Z4
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.40 × 0.20 × 0.20
Data collection
DiffractometerBruker P4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
3241, 2474, 1770
Rint0.034
(sin θ/λ)max1)0.594
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.064, 0.197, 1.03
No. of reflections2474
No. of parameters244
No. of restraints21
H-atom treatmentOnly H-atom coordinates refined
Δρmax, Δρmin (e Å3)0.36, 0.31

Computer programs: XSCANS (Siemens, 1994), XSCANS, SHELXTL (Sheldrick, 1997), SHELXTL.

Selected geometric parameters (Å, º) top
N1—C11.451 (4)C1—C21.513 (4)
N2—C21.463 (3)C3—C41.513 (4)
N2—C31.466 (4)C5—C61.511 (4)
N3—C41.455 (4)C9—C121.526 (4)
N3—C51.475 (4)
C2—N2—C3114.0 (2)N3—C5—C6115.1 (2)
C4—N3—C5114.3 (2)C7—C6—C5120.6 (2)
N1—C1—C2116.8 (3)C11—C6—C5121.9 (3)
N2—C2—C1111.6 (2)C10—C9—C12122.2 (3)
N2—C3—C4116.4 (2)C8—C9—C12120.3 (3)
N3—C4—C3111.8 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N···O150.84 (2)2.29 (2)3.097 (9)162.4 (16)
N2—H2N···O130.85 (2)2.27 (3)3.115 (4)172 (2)
N3—H3N···O130.85 (2)2.58 (3)3.361 (4)153 (2)
O11—H21···N30.902 (16)1.911 (16)2.810 (3)175 (2)
O12—H22···N20.901 (19)2.03 (2)2.903 (4)162 (2)
O13—H23···O14i0.90 (3)1.90 (3)2.768 (6)162 (3)
O14—H24···O110.898 (18)1.96 (2)2.850 (5)169 (5)
O14—H34···O11ii0.90 (3)1.93 (3)2.825 (5)177 (5)
Symmetry codes: (i) x1, y, z; (ii) x+1/2, y+3/2, z+3/2.
 

Follow Acta Cryst. C
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds