N,N′-Dimethylbenzamidine and derivatives: Preparations, structures, and hydrogen bond networks therein

Article abstract of DOI:10.1016/j.molstruc.2008.03.018

Reported herein are the syntheses of N,N′-dimethylbenzamidine (HDMBA, 1) and its phenyl substituted derivatives HYDMBA with phenyl substituents Y as 3-CH₃O (2), and 3-CF₃ (3), and the determination of single crystal structures of com

Full text of DOI:10.1016/j.molstruc.2008.03.018

Journal of Molecular Structure 890 (2008) 90–94
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
N,N0-Dimethylbenzamidine and derivatives: Preparations, structures,
and hydrogen bond networks therein
*
Wei-Zhong Chen, Guo-Lin Xu, Conrad G. Jablonski, Tong Ren
Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 4790, USA
a r t i c l e i n f o
a b s t r a c t
Reported herein are the syntheses of N,N0-dimethylbenzamidine (HDMBA, 1) and its phenyl substituted
derivatives HYDMBA with phenyl substituents Y as 3-CH3O (2), and 3-CF3 (3), and the determination of
single crystal structures of compounds 1–3. In addition, the crystal structures of the salts of 1 with HBF4
(1a), oxalic acid (1b), terephthalic acid (1c), and 2 with HCl (2d) are also reported. Interesting configura-
tions and H-bonding patterns due to the orientation of two methyl groups were observed.
Ó 2008 Elsevier B.V. All rights reserved.
Article history:
Received 13 December 2007
Received in revised form 12 March 2008
Accepted 12 March 2008
Available online 21 March 2008
Dedicated to the memory of Professor Al
Cotton
Keywords:
Benzamidine
Hydrogen bonding
Crystal structures
1. Introduction
dimethylbenzamidinate) [10]. A series of diruthenium compounds
supported by N,N0-dialkylbenzamidinate have been prepared and
Ligands containing amidine group have played important roles
in both coordination and organometallic chemistry [1–3]. Fre-
quently utilized amidine ligands include N,N0-diarylformamidines
(HDArF), 2-anilinopyrdines (Hap), guanidines, and benzamidines,
as shown in Chart 1. The DArF ligands have been used extensively
to support both the transition metal and main group metal com-
plexes [2,4], especially as the bridging ligand in bimetallic paddle-
wheel motifs [5]. In addition, amidinates have also found
applications such as ancillary ligands for Ziegler-Natta catalysts
[6] and molecular precursors for ALD (atomic layer deposition)
[7]. The strong electron donor nature of amidinates also renders
a unique redox richness of the resultant complexes. In an extreme
case, W2(hpp)4 (Hhpp = 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-
a]pyrimidine) was found to be more electropositive than Cs metal
[8].
become valuable platforms for both the exploration of charge
mobility along metal-alkynyl backbone and the building blocks
of molecular wires and molecular diodes [11]. N,N0-Dialkylbenz-
i
t
amidine with bulky alkyl groups such as Pr, Bu, and cyclohexyl
can be readily prepared from the reactions between an appropriate
carbodiimide (RN@C@NR) and alkyl lithium (LiR0). Such an easy
preparation is unavailable for homolog of smaller R such as methyl
and ethyl because of the instability of the corresponding carbodii-
mides. Described in this contribution are the synthesis of N,N0-dim-
ethylbenzamidine (HDMBA) and its phenyl-substituted derivatives
(Chart 2), their crystal structures and intermolecular hydrogen
bonding patterns therein.
2. Results and discussion
A major focus area in our laboratory is to use the diruthenium
alkynyl compounds supported by amidinates including DArF and
ap (Chart 1) as the building blocks of molecular wires and molec-
ular devices [9]. Our particular interest in N,N0-dialkylbenzamidi-
nates is rooted in their ability to support paddlewheel dinuclear
transition metal compounds without hindering axial ligation,
which was first demonstrated by Cotton and coworkers with the
synthesis of Cr2(DMBA)4 and Re2(DMBA)4Cl2 (DMBA = N,N0-
2.1. Syntheses
N,N0-Dimethylbenzamidine (1) was synthesized from N-meth-
ylbenzamide in two steps (Scheme 1) with an overall yield of ca.
40% using a procedure slightly modified from that in the literature
[12]. The same procedure was used for the preparation of com-
pounds 2 and 3, where appropriately substituted N-methylbenza-
mides were used and yields were between 40% and 80%. The
salts of amidines with various acids, as defined in Table 1, were
generated in methanol solutions and crystallized upon the intro-
duction of ether via vapor diffusion.
* Corresponding author. Tel.: +1 765 494 5466; fax: +1 765 494 0239.
E-mail address: tren@purdue.edu (T. Ren).
0022-2860/$ - see front matter Ó 2008 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2008.03.018

W.-Z. Chen et al. / Journal of Molecular Structure 890 (2008) 90–94
91
Table 1
Salts formed between amidine and acid (ratio, designation)
HBF4
Oxalic
Terephthalic
HCl
–
N
N
H
N
N
1
2
1:1, 1a
–
1:2, 1b
–
3:4, 1c
–
H
1:1, 2d
HDArF
Hap
NHR'
N
R
R
N
N
N
N
H
R
H
R
N
N
H
Hhpp
guanidine
Chart 1. Common amidines.
benzamidine
Y
Compound
Y
H
1
2
3
m-OCH3
m-CF3
Me
Fig. 1. ORTEP plot of molecule 1 at 30% probability level. Selected bond lengths (Å)
and angles (°): C1AN1, 1.351(2); C1AN2, 1.282(2); C1AC4, 1.494(2); N1AC1AN2,
120.0(2).
Me
N
N
H
Chart 2. HDMBA and derivatives.
2.2. Crystal structures
The structures of compounds 1, 2, 3, 1a, 1b, 1c, and 2d were
determined through single crystal X-ray diffraction studies, and
the respective ORTEP plots including one packing diagram for 1
are shown in Figs. 1–8. The amidine group of all neutral com-
pounds 1–3 adopts the same E,Z-configuration, where the amino
(designated as N1) N-methyl group is trans- to the Cipso (C4) center
and the imino (N2) N-methyl group is cis- to the Cipso center.
The amino hydrogen (H1) was located from the difference map
in each of 1–3 and successfully refined, which confirms a localized
N1AH1 bond. Among the neutral compounds, two CAN bonds can
be unambiguously assigned as amino CAN bond (C1AN1, 1.349–
1.353 Å) and imino CAN double bond (C1AN2, 1.268–1.297 Å) on
the basis of bond lengths. Limited literature precedents of the
HDMBA-type structures include those of N,N0-dimethyl-4-nitro-
benzamidine [13] and N,N0-dimethyl-4-halobenzamidine (halo-
gen = Br and I) [14], where the configurations of amidine group
are identical to those of compounds 1–3 [13].
Fig. 2. ORTEP plot of molecule 2 at 30% probability level. Selected bond lengths (Å)
and angles (°): C1AN1, 1.345(2); C1AN2, 1.280(2); C1AC4, 1.500(2); N1AC1AN2,
120.5(2).
Neutral compounds 1–3 engage zig-zag intermolecular hydro-
gen bonding in the crystalline state. As illustrated by Fig. 4 for crys-
tal 1, compounds 1–3 form a one-dimensional H-bonding chain in
solid state, where the amino H center interacts with the imino N
center from the adjacent molecule. The formation of the same type
1D H-bonding chain should be expected for N,N0-dimethyl-4-nitro-
benzamidine, except that the coordinate of the amino hydrogen
was not reported in that structure [13]. The hydrogen bonding pat-
tern of HDMBA compounds also contradicts the patterns observed
for HDArF and Hap, where the head-to-tail dimer is predominant
(see Chart 3) [3,15].
Fig. 3. ORTEP plot of molecule 3 at 30% probability level. Selected bond lengths (Å)
and angles (°): C1AN1, 1.349(4); C1AN2, 1.268(3); C1AC4, 1.508(4); N1AC1AN2,
120.8(3).
compound 1 by HBF4 resulted in compound 1a, and its crystal
structure is shown in Fig. 5. As shown in Fig. 5, both of the N-bound
hydrogen atoms were located from the difference map and suc-
cessfully refined, and each interacts with a BFꢀ4 . Notably, the
C1AN1 (1.304(6) Å) and C1AN2 (1.312(6) Å) bond lengths are
identical within the experimental errors, indicating that the posi-
tive charge is delocalized over the entire amidinium unit. Thus,
each NAH ꢁ ꢁ ꢁ BFꢀ4 pair accounts for one half of the salt bridge.
Two F atoms from each BFꢀ4 are involved in the salt bridge, which
led to a one-dimension chain of ion-pairs.
Compounds 1–3 can be readily protonated by both strong and
weak protic acids, and the resultant ions form aggregates primarily
via the formation of one or several salt bridges. The protonation of
Ar
Ar
Ar
MeNH2
SOCl2
Me
Me
Me
Me
N
N
O
N
H
Cl
N
H
Scheme 1. Synthesis of HDMBA.

92
W.-Z. Chen et al. / Journal of Molecular Structure 890 (2008) 90–94
Fig. 4. Intermolecular H-bonding diagram of molecule 1.
Fig. 5. H-bonding diagram of molecule 1a.
Fig. 7. Simplified H-bonding diagram of molecule 1c.
Fig. 8. H-bonding diagram of molecule 2d.
Fig. 6. Simplified H-bonding diagram of molecule 1b.
terephthalic acid molecule. More intricate 3D network was formed
through various salt bridges between H1+ and terephthalate, while
free terephthalic acids form a linear chain through hydrogen bond-
ing. Previously, the salt bridge formation was described for the pair
of N,N0-diethylbenzamidine and ferrocenecarboxylic acid, where
hydrogen bonding interaction is limited within the pair [16].
Crystal 2d is a HCl salt of compound 2, and the asymmetric unit
contains one unit of [H2]Cl and a water molecule. As shown in
Fig. 8, the chloride interacts with three different H centers: one
hydrogen from water and two hydrogens from different amidini-
um groups, and the latter interactions resulted in a one-dimen-
sional chain of salt bridges.
The co-crystallization of compound 1 with oxalic acid resulted
in a salt [Hꢁ1]2(oxalate) (1b). The asymmetric unit of 1b contains
one [H1]+ and one half of an oxalate, and an inversion center bi-
sects the oxalate. Similar to 1a, both of the N-bound hydrogen
atoms were located and refined, and a delocalized amidinium unit
was implicated by the equal CAN bond lengths. The oxalate oxygen
centers engage hydrogen bonding with one or two [H1]+, which
results in a 2D H-bonding network shown in Fig. 6. A 2:1 salt,
[Hꢁ1]2(terephthalate) (1c, Fig. 7), was formed when 1 was co-crys-
tallized with terephthalic acid. In addition to a unit of [Hꢁ1]2(tere-
phthalate), the asymmetric unit of 1c contains one half of a free

W.-Z. Chen et al. / Journal of Molecular Structure 890 (2008) 90–94
93
was added dropwise to a 50 mL aqueous methylamine solution
(generated in situ from 18 g of methylamine hydrochloride with
11 g of NaOH in water) in 20 min at 0 °C. The resultant mixture
was warmed to room temperature and stirred for another 3 h.
The mixture was then treated with NaOH (aq) and extracted with
CH2Cl2 (3 ꢂ 50 mL). The organic layer was collected and the sol-
vent was removed by rotavapor to yield a sticky solid. Further
recrystallization from CH2Cl2 and hexanes gave a pure white solid
(10 g, 71.4%). Data for 1: 1H NMR: 7.29–7.27 (m, 3H, aromatic),
7.16–7.14 (m, 2H, aromatic), 4.18 (s, 1H, NH), 2.77 (s, 6H, NCH3);
13C NMR: 161.5, 135.8, 129.2, 128.8, 127.9, 27.0; MS-FAB (m/e):
147 [M+ꢀH]; IR (t/cmꢀ1): 3205, 2938, 1629, 1540, 1402, 1336,
1158, 1038, 1003, 915, 774, 701.
Ar
H
C
Ar
Ar
Ar
H
Me
Ar
N
H
N
N
H
N
N
N
Me
Me
N
H
N
H
N
H
N
N
N
Me
Ar
C
H
Ar
Ar
HDArF
HDMBA
Hap
Chart 3. Hydrogen bonding patterns in amidines.
3. Conclusion
4.3. Preparation of 2
Our results revealed that the amidine group in N,N0-dimethyl-
benzamidines adopt an E,Z-configuration, which results in a 1D
zig-zag hydrogen bonding chain. Upon protonation, the salt
bridges between amidinium and anion also result in various ex-
tended networks.
N,N0-Dimethyl-3-methoxyl-benzamidine (2) was prepared in
65% yield using the same procedure as that of 1 from N-methyl-
3-methoxyl-benzamide instead of N-methylbenzamide. Data for
2: 1H NMR: 7.26–7.21 (m, 1H, aromatic), 6.84–6.70 (m, 3H, aro-
matic), 4.17 (s, 1H, NH), 3.73 (s, 3H, OCH3), 2.79 (s, 6H, NCH3);
13C NMR: 161.2, 159.9, 137.3, 129.9, 120.2, 114.8, 113.4, 55.7;
MS-FAB (m/e): 179 [M+H]; IR (t/cmꢀ1): 3196, 2928, 1623, 1558,
1404, 1337, 1140, 1050, 1013, 892, 787, 715.
4. Experimental
4.1. General
Benzoyl chloride, 3-methoxylbenzoic acid, 4-bromobenzoyl
chloride, terephthalic acid, thionyl chloride were purchased from
ACROS, 3-trifluoromethylbenzoic acid was purchased from OAK-
WOOD, and methylamine hydrochloride was purchased from Al-
drich. Synthesis of N,N0-dimethylbenzamidine (1) was modified
from that of the literature [12], and some detailed description is gi-
ven below. 1H and 13C NMR spectra were recorded on a Bruker
AVANCE300 NMR spectrometer, with chemical shifts (d) refer-
enced to the residual CHCl3 and the solvent CDCl3, respectively.
Infrared spectra were recorded on a Perkin-Elmer 2000 FT-IR spec-
trometer using KBr disks.
4.4. Preparation of 3
N,N0-Dimethyl-3-trifloromethyl-benzamidine (3) was prepared
in 46% yield using the same procedure as that for 1 from N-
methyl-3-trifluoromethyl-benzamide instead of N-methylbenza-
mide. Data for 3: 1H NMR: 7.51–7.42 (m, 4H, aromatic), 4.15 (s,
1H, NH), 2.86 (s, 6H, NCH3); 13C NMR: 167.2, 159.7, 136.7, 131.6,
129.4, 126.1, 124.9, 122.4, 27.2; MS-FAB (m/e): 215 [M+ꢀH]; IR
(t/cmꢀ1): 3205, 2943, 1629, 1558, 1406, 1329, 1167, 1071, 907,
809, 704.
4.5. X-ray data collection, processing, and structure analysis and
refinement
4.2. Preparation of 1
A 100 mL round-bottomed flask was charged with 20 g of N-
methylbenzamide (prepared from the treatment of benzoyl chlo-
ride with methylamine in water) and 20 mL thionyl chloride. The
mixture was heated to reflux until the cease of gas evolution from
the reaction mixture (about 2 h). The excess thionyl chloride was
distilled off under a reduced pressure and the residue was further
distilled under reduced pressure (ca. 0.1 torr) to yield a colorless li-
quid (14 g, 61%). The distilled product from the preceding reaction
Single crystals of 1–3, were grown via either diffusion of hex-
anes into a CH2Cl2 solution (1) or slow evaporation of hexanes/
CH2Cl2 solutions (2 and 3). Salts 1a, 1b, 1c, and 2d were prepared
by dissolving appropriate amidine and acid with ethanol in a small
vial, which was then enclosed in a larger vial containing ether.
Crystals suitable for X-ray diffraction study were harvested after
24 h. The X-ray intensity data were measured at 300 K on a Bruker
SMART1000 CCD-based X-ray diffractometer system using MoKa
Table 2
Crystallographic data for compounds 1, 1a–c, 2, 2d, and 3
1
2
3
1a
1b
1c
2d
Formula
FW
Space group
a (Å)
b (Å)
c (Å)
C9H12N2
148.21
Pbca
8.6624(6)
11.3426(8)
18.391(1)
90
C10H14N2O
178.23
Pbca
8.3555(8)
8.4040(7)
29.080(3)
90
C10H11F3N2
216.21
P21/c
9.228(2)
13.411(3)
8.622(2)
98.356(5)
1055.7(4)
4
C9H13N2 BF4
236.02
P21/n
10.662(2)
7.726(1)
13.732(2)
90.507(3)
1131.1(3)
4
C20H26N4O4
386.45
P21/n
9.0756(5)
9.9715(6)
11.4323(7)
95.931(1)
1029.1(1)
2
C30H33N4O6
545.60
P21/c
9.6208(7)
19.308(1)
15.340(1)
94.229(1)
2841.7(4)
4
C10H17ClN2O2
232.71
P21/c
11.4889(7)
10.4510(7)
10.9843(7)
111.722(2)
1225.24(1)
4
b (°)
V (Å3)
Z
1807.0(2)
8
2042.0(3)
8
T (°C)
27
27
27
27
27
27
27
k (MoKa) (Å)
0.71073
1.09
0.075
0.040
0.110
0.71073
1.160
0.077
0.042
0.111
0.71073
1.360
0.120
0.059
0.129
0.71073
1.386
0.129
0.097
0.334
0.71073
1.247
0.088
0.044
0.120
0.71073
1.275
0.090
0.048
0.136
0.71073
1.262
0.296
0.040
0.116
qcalc (g cmꢀ3
l (mmꢀ1)
)
R1 (I > 2r (I))
wR2 (I > 2r (I))
GOF
1.01
1.05
0.83
1.01
1.01
1.01
1.05

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W.-Z. Chen et al. / Journal of Molecular Structure 890 (2008) 90–94
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5. Supporting Information available
Crystallographic data for the structural analysis have been
deposited with the Cambridge Crystallographic Data Center, CCDC
670438–670443 for compounds 1, 1a–c, 2, 2d, and 3, respectively.
Copies of this information may be obtained free of charge from, The
Director, CCDC, 12 Union Road, Cambridge CB2 1EZ, UK, (Fax: +44
1233 336033; email: deposit@ccdc.cam.ac.uk or www: http://
ccdc.cam.ac.uk).
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Acknowledgement
T. Ren, S. Radak, Y.-H. Ni, G.-L. Xu, C. Lin, K.L. Shaffer, V. DeSilva, J. Chem.
Crystallogr. 32 (2002) 197;
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B. Xi, G.-L. Xu, J.-W. Ying, H.-L. Han, A. Cordova, T. Ren, J. Organomet. Chem 693
(2008) 1656.
This work is supported by the National Science Foundation
(Grants Nos. CHE 0242623/0553564 and CHE 0715404).
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