Tris(1H-benzimidazol-2-ylmethyl)-amine-solvent adducts

Article abstract of DOI:10.1107/S0108270105023553

The tris(1H-benzimidazol-2-ylmethyl)amine (ntb) molecule crystallizes in different solvent systems, resulting in two kinds of adduct, namely the monohydrate, C₂₄H₂₁N₇·H₂O or ntb·H₂O, (I), and the acetonitrile-methanol-water (1/0.5/1.5) solvate, C₂₄H₂₁N₇·C₂H ₃N·0.5CH₄O·1.5H₂O or ntb·1.5H₂O·0.5MeOH·MeCN, (II). In both cases, ntb adopts a tripodal mode to form hydrogen bonds with a solvent water molecule via two N-H...O and one O-H...N hydrogen bond. In (I), the ntb·H₂O adduct is further assembled into a two-dimensional network by N-H...N and O-H...N hydrogen bonds, while in (II), a double-stranded one-dimensional chain structure is assembled via N-H...O and O-H...O hydrogen bonds, with the acetonitrile molecules located inside the cavities of the chain structure.

Full text of DOI:10.1107/S0108270105023553

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
redetermined the structure and located all the H atoms. The
crystal structural analyses of the adducts (I) and ntbÁMeCNÁ-
0.5MeOHÁ1.5H2O, (II), revealed that the recognition of water
molecules by ntb is speci®c in both adducts, but the extension
of the hydrogen bonds is different, depending on the inclusion
of different solvent molecules.
ISSN 0108-2701
Tris(1H-benzimidazol-2-ylmethyl)-
amine±solvent adducts
Xue-Li Zhang, Sheng-Run Zheng, Yong-Ru Liu, Xiang-Li
Zheng and Cheng-Yong Su*
School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou
510275, People's Republic of China, and State Key Laboratory of Organometallic
Chemistry, Shanghai Intitute of Organic Chemistry, Chinese Academy of Science,
Shanghai 200032, People's Republic of China
Correspondence e-mail: cedc63@zsu.edu.cn
Received 11 July 2005
Accepted 22 July 2005
Online 10 August 2005
Our structure determination of (I) shows that all imine and
amine groups of the ntb molecules and the water molecules
are involved in hydrogen-bond formation (Table 1). The ntb
molecule adopts a tripodal mode, with two NH groups and one
imine N atom directed towards the water molecule, which is
held by forming two DÁ Á ÁA-type NÐHÁ Á ÁO and one AÁ Á ÁD-
type NÁ Á ÁHÐO hydrogen bond, as shown in Fig. 1. Such a
hydrogen-bonding environment is speci®c for recognition of
the water molecule because of its tetrahedral hydrogen-
bonding geometry. The remaining H atom of the water mol-
ecule forms an OÐHÁ Á ÁN hydrogen bond with one `outside'
imine N atom belonging to a neighbouring ntb molecule. In
addition, one more imine N atom and one NH group of a
neighbouring ntb molecule form NÐHÁ Á ÁN hydrogen bonds,
resulting in a two-dimensional network parallel to (101), as
depicted in Fig. 2.
The tris(1H-benzimidazol-2-ylmethyl)amine (ntb) molecule
crystallizes in different solvent systems, resulting in two kinds
of adduct, namely the monohydrate, C24H21N7ÁH2O or
ntbÁH2O, (I), and the acetonitrile±methanol±water (1/0.5/1.5)
solvate, C24H21N7ÁC2H3NÁ0.5CH4OÁ1.5H2O or ntbÁ1.5H2OÁ-
0.5MeOHÁMeCN, (II). In both cases, ntb adopts a tripodal
mode to form hydrogen bonds with a solvent water molecule
via two NÐHÁ Á ÁO and one OÐHÁ Á ÁN hydrogen bond. In (I),
the ntbÁH2O adduct is further assembled into a two-
dimensional network by NÐHÁ Á ÁN and OÐHÁ Á ÁN hydrogen
bonds, while in (II), a double-stranded one-dimensional chain
structure is assembled via NÐHÁ Á ÁO and OÐHÁ Á ÁO
hydrogen bonds, with the acetonitrile molecules located inside
the cavities of the chain structure.
Comment
The tripodal compound tris(2-benzimidazolylmethyl)amine
(ntb) is a versatile ligand which possesses three imine N atoms
and three amine NH groups. The three imine N atoms can act
as coordination donors to form various metal complexes
(Moon et al., 2002; Su, Kang, Mu et al., 1998), while the three
amine NH groups are potential hydrogen-bond donors (Su,
Kang, Liu et al., 1998; Su et al., 2000). Since the three benz-
imidazolyl (Bim) arms can rotate freely about the methylene
(±CH2±) groups and the three imine N atoms can also behave
as hydrogen-bond acceptors, ntb is a good candidate for
formation of hydrogen-bonded adducts via speci®c steric
intermolecular recognition. We have been interested in the
assembly of supramolecular aggregates with ntb-related
compounds and report here two kinds of ntbÁsolvent adducts
formed via multiple hydrogen bonds. The adduct ntbÁH2O, (I),
has been reported previously (Zhou et al., 1999), but the
structure was not fully determined or re®ned as no allowance
was made for any of the H atoms in the structure. We have
Figure 1
A view of (I), showing the atom-labelling scheme. Displacement
ellipsoids are drawn at the 50% probability level. Dashed lines indicate
hydrogen bonds.
Acta Cryst. (2005). C61, o533±o536
DOI: 10.1107/S0108270105023553
# 2005 International Union of Crystallography o533

organic compounds
Figure 2
A view of the hydrogen-bonded two-dimensional network in (I) in the (101) plane. Dashed lines indicate hydrogen bonds. [Symmetry codes: (i) x
1
2
,
1
1
1
1
y + , z + ; (ii) x + , y
,
2
z + 12; (iii) x + 1, y, z + 1; (iv) x + 1, y + 1, z + 1.]
2
2
2
When ntb crystallized in a hydrated MeOH/MeCN solution,
adduct (II) was obtained. In this compound, all imine and
amine groups of the ntb molecules are involved in hydrogen
bonding (Table 2). Our structure determination shows that the
water molecule is recognized by ntb in exactly the same way as
in (I) (details are given in Table 2). As in (I), there are two
DÁ Á ÁA-type NÐHÁ Á ÁO and one AÁ Á ÁD-type NÁ Á ÁHÐO
hydrogen bond, as shown in Fig. 3. The ntb molecule takes on
the same tripodal conformation in both (I) and (II), with one
imine N atom and two NH groups pointing `inside', and
leaving two imine N atoms and one NH group directed
`outside' of the ntbÁH2O moiety.
The analysis of (II) was slightly complicated by disorder.
The methanol molecule (O3/C4 in Fig. 3) lies adjacent to an
inversion centre, with the methyl C atom at such a short
Ê
intermolecular distance [2.298 (7) A from C4 at (2
x, y,
z)] that it can be present with an occupancy of no more than
0.5. Occupancy re®nement showed unequivocally that while
methanol atom C4 is only present with 0.5 occupancy, the
O-atom site has unit occupancy, implying that this site
(labelled as O2 and O3 in Fig. 3) must contain a 0.5-occupancy
water molecule (O2) as well as the 0.5-occupancy methanol
atom O3.
One of the two outside imine N atom forms an NÁ Á ÁHÐO
hydrogen bond with the 0.5-occupancy methanol/water site
(Fig. 3). Water molecule O1 forms its fourth OÐHÁ Á ÁO
Figure 3
A view of (II), showing the atom-labelling scheme. Displacement
ellipsoids are drawn at the 50% probability level. Dashed lines indicate
hydrogen bonds. Atoms O2 and O3 were constrained to share the same
site.
ꢀ
o534 Zheng et al. C24H21N7ÁH2O and C24H21N7ÁC2H3NÁ0.5CH4OÁ1.5H2O
Acta Cryst. (2005). C61, o533±o536

organic compounds
Figure 4
The hydrogen-bonded chain structure in (II), viewed along the a axis. Dashed lines indicate hydrogen bonds and guest acetonitrile molecules are shown
in space-®lling mode. [Symmetry code: (vii) x 1, y, z.]
Compound (I)
hydrogen bond with a neighbouring 0.5-occupancy methanol/
water site, thus generating
one-dimensional ntbÁ-
H2OÁ Á ÁMeOH/H2OÁ Á ÁntbÁH2OÁ Á ÁMeOH/H2O chain, as
a
Crystal data
3
C24H21N7ÁH2O
Dx = 1.261 Mg m
Mo Kꢁ radiation
Mr = 425.49
Monoclinic, P21=n
depicted in Fig. 4. Since there remains one outside imine N
atom and one outside NH group for each ntb molecule, two
such one-dimensional chains are connected by the formation
of NÐHÁ Á ÁN hydrogen bonds, resulting in a double-stranded
chain along the a axis (Fig. 4). The acetonitrile molecules are
located inside the cavities of such double-stranded chains,
with only van der Waals contacts to the hydrogen-bonded
chains.
Cell parameters from 7855
re¯ections
Ê
a = 9.9731 (6) A
ꢂ = 4.2±26.3ꢁ
ꢃ = 0.08 mm
T = 293 (2) K
Ê
b = 12.3273 (7) A
1
Ê
c = 18.2323 (11) A
ꢀ = 91.508 (1)ꢁ
V = 2240.7 (2) A
Z = 4
3
Ê
Block, colourless
0.28 Â 0.2 Â 0.18 mm
Data collection
Bruker SMART 1K CCD
diffractometer
' and ! scans
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
Tmin = 0.873, Tmax = 1.000
15554 measured re¯ections
6455 independent re¯ections
4526 re¯ections with I > 2ꢄ(I)
Rint = 0.019
ꢂmax = 30.0ꢁ
The difference between (I) and (II) is that there is in (II) an
additional site, equally occupied by methanol and water O =
atoms, which disrupts the direct hydrogen bonding of the
`enclosed' water molecule to a neighbouring ntb molecule as
in (I).
h = 12 ! 14
k = 16 ! 17
l = 24 ! 25
Re®nement
Re®nement on F2
R[F2 > 2ꢄ(F2)] = 0.040
wR(F2) = 0.115
S = 1.03
6455 re¯ections
310 parameters
H atoms treated by a mixture of
independent and constrained
re®nement
w = 1/[ꢄ2(F2o) + (0.0637P)2]
where P = (F2o + 2Fc2)/3
(Á/ꢄ)max = 0.001
Experimental
Ntb was prepared from the condensation reaction between nitrilo-
triacetate and 1,2-diaminobenzene in diethylene glycol (yield 85%).
Single crystals of (I) suitable for X-ray analysis were obtained by slow
evaporation from a 98% methanol solution at room temperature.
Single crystals of (II) were obtained by slow evaporation from a 98%
methanol/acetonitrile solution at room temperature.
3
Ê
Áꢅmax = 0.20 e A
3
Ê
0.16 e A
Áꢅmin
Extinction correction: SHELXL97
=
Extinction coef®cient: 0.0042 (11)
ꢀ
Acta Cryst. (2005). C61, o533±o536
Zheng et al.
C24H21N7ÁH2O and C24H21N7ÁC2H3NÁ0.5CH4OÁ1.5H2O o535

organic compounds
Ê
of 0.93±0.97 A and Uiso(H) values set at 1.5 (methyl H atoms) and 1.2
Table 1
Hydrogen-bond geometry (A, ) for (I).
ꢁ
Ê
(other H atoms) times Ueq(C). The O- and N-bound H atoms were
located in difference Fourier maps and re®ned with isotropic
displacement parameters [for the OH group in (II), Uiso(H) =
1.5Ueq(O)]. In (II) (as noted in the Comment), the methanol O atom
was found to share a site with a water O atom. The site-occupancy
re®nement of the methyl C atom indicated an occupancy of 0.5, while
that of the O atom was close to unity. The water (O2) and methanol
(O3) O atoms were then assigned occupancies of 0.5 and constrained
to lie at the same site. Only one H atom could be located at the O2/O3
site, and this was assigned unit occupancy. The missing 0.5-occupancy
water H atom is presumably disordered. Difference maps showed
that the H atoms of the methanol and acetonitrile methyl groups in
(II) are diffuse, and these were allowed for as six H-atom sites with
appropriate occupancy.
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
N11ÐH11AÁ Á ÁO1
N21ÐH21Á Á ÁO1
N31ÐH31Á Á ÁN23v
O1ÐH11Á Á ÁN13vi
O1ÐH12Á Á ÁN33
0.913 (14)
0.973 (15)
0.906 (13)
0.856 (15)
0.924 (17)
1.938 (14)
1.886 (15)
1.943 (13)
2.000 (16)
1.903 (17)
2.8380 (12)
2.8579 (12)
2.8406 (12)
2.8410 (12)
2.8223 (12)
168.2 (12)
177.3 (13)
170.4 (11)
167.0 (13)
173.4 (13)
Symmetry codes: (v) x ‡ 1; y ‡ 1; z; (vi) x ‡ 32; y
;
z ‡ 12.
1
2
Compound (II)
Crystal data
C24H21N7ÁC2H3NÁ0.5CH4OÁ1.5H2O
Z = 2
Dx = 1.246 Mg m
Mo Kꢁ radiation
Cell parameters from 28
re¯ections
ꢂ = 4.6±12.6ꢁ
ꢃ = 0.08 mm
T = 293 (2) K
Block, colourless
0.75 Â 0.65 Â 0.50 mm
3
For (I), data collection: SMART (Siemens, 1993); cell re®nement:
SAINT (Siemens, 1995); data reduction: SAINT. For (II), data
collection: CAD-4 EXPRESS (Enraf±Nonius, 1994); cell re®nement:
CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo,
1995). For both compounds, program(s) used to solve structure:
SHELXS97 (Sheldrick, 1997); program(s) used to re®ne structure:
SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL
(Bruker, 1997); software used to prepare material for publication:
SHELXTL.
Mr = 491.58
Triclinic, P1
a = 9.778 (4) A
Ê
Ê
b = 9.995 (2) A
Ê
c = 14.397 (6) A
1
ꢁ = 103.34 (1)ꢁ
ꢀ = 98.16 (1)ꢁ
ꢆ = 102.34 (1)ꢁ
3
Ê
V = 1310.1 (8) A
Data collection
Siemens P4 diffractometer
!±2ꢂ scans
Absorption correction: scan
(North et al., 1968)
Tmin = 0.885, Tmax = 0.938
5999 measured re¯ections
5066 independent re¯ections
3752 re¯ections with I > 2ꢄ(I)
Rint = 0.047
ꢂmax = 26.0ꢁ
This work was supported by the NNSF of China (grant No.
20303027) and the Programme for New Century Excellent
Talents in Universities of China.
h = 1 ! 12
k = 11 ! 11
l = 17 ! 17
3 standard re¯ections
every 197 re¯ections
intensity decay: none
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: FG1867). Services for accessing these data are
described at the back of the journal.
Re®nement
Re®nement on F2
R[F2 > 2ꢄ(F2)] = 0.045
wR(F2) = 0.113
S = 1.01
5066 re¯ections
358 parameters
H atoms treated by a mixture of
independent and constrained
re®nement
w = 1/[ꢄ2(F2o) + (0.0463P)2
+ 0.303P]
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(Á/ꢄ)max = 0.001
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Ê
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Áꢅmin
3
Ê
0.17 e A
=
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N11ÐH11AÁ Á ÁO1
N21ÐH21Á Á ÁO1
N31ÐH31Á Á ÁN23iii
O1ÐH11Á Á ÁO2vii/O3vii
O1ÐH12Á Á ÁN33
O2ÐH2Á Á ÁN13
0.90 (2)
0.86 (2)
0.91 (2)
0.91 (2)
0.90 (2)
0.95 (3)
2.01 (2)
2.03 (2)
1.91 (2)
1.91 (3)
1.90 (2)
1.82 (3)
2.910 (2)
2.886 (2)
2.826 (2)
2.806 (2)
2.798 (2)
2.772 (2)
177 (2)
174.0 (18)
176.3 (17)
168 (2)
179 (2)
176 (3)
Symmetry codes: (iii) x ‡ 1; y; z ‡ 1; (vii) x 1; y; z.
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All H atoms, except those on O and N atoms involved in hydrogen-
bond formation, were included as riding atoms, with CÐH distances
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ꢀ
o536 Zheng et al. C24H21N7ÁH2O and C24H21N7ÁC2H3NÁ0.5CH4OÁ1.5H2O
Acta Cryst. (2005). C61, o533±o536