Egan, Simon

Forsyth, Craig M.

Moloney, Gerard P.

Stoermer, Martin J.

University of Queensland eSpace

(Z)-N'-(1H-benzo[d]imidazol-2-yl)-arylimidamide adducts of 2-aminobenzimidazole 
and aromatic nitriles: Structural and spectroscopic proof of regiochemical and 
stereochemical outcomes. 
 
 
Martin J. Stoermer1*, Simon Egan2, Craig M. Forsyth3, and Gerard P. Moloney2  
 
1 Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, 
The University of Queensland, St. Lucia, 4072, Queensland, Australia; 2Department 
of Medicinal Chemistry, Victorian College of Pharmacy, Monash University (now 
Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, 
Parkville Victoria, 3052, Australia. 3School of Chemistry, Monash University Clayton 
Victoria 3800, Australia. 
 
*Corresponding author 
Dr. Martin J. Stoermer 
Division of Chemistry and Structural Biology, Institute for Molecular Bioscience  
University of Queensland 
Brisbane, Queensland 4072, Australia 
E-mail: martin.stoermer@uq.edu.au 
Twitter: @MartinStoermer 
Abstract 
 
 
The selection of a core scaffold or template is of enormous importance in medicinal 
chemistry. Benzimidazoles are a recurring fragment in medicinal chemistry, and the 
2-amino derivative is a versatile example in lead generation. Alkylated and acylated 
examples abound, however, alternative linkage chemistries leading do more diverse 
structures are needed. Here we discuss the regiochemistry of nucleophilic addition of 
2-aminobenzimidazole to nitriles, leading to imidamide (amidine) adducts. 
Additionally, we use extensive NMR analysis and ultimately X-ray crystallography to 
demonstrate both the regiochemistry and stereochemistry of the addition products, 
arising from derivatisation of the exocylic 2-amino group. 
 
 
Keywords: aminobenzimidazole, nucleophilic addition, X-ray crystallography, 
regiochemistry, imidamide. 
  
Introduction 
 
Benzimidazoles are common fragments and scaffolds found in drug discovery and 
development programs and in several marketed drugs including omeprazole, 
telmisartan, and albendazole. Their combination of synthetic tractability, hydrophobic 
B ring and heterocyclic A ring containing up to 3 attachment points for elaboration 
into drug-like molecules make benzimidazoles attractive synthons for medicinal 
chemistry (Figure 1). The 2-amino derivative (1) is similarly frequently found in the 
medicinal chemistry literature as a starting material or scaffold with the additional 
virtue of being a low-basicity guanidine mimetic1 with a pKa some 5 log units lower 
than a free guanidine group such as that found in the amino acid arginine. 
 
 
Figure 1. Marketed drugs containing benzimidazoles and 2-aminobenzimidazole (1), 
a scaffold for medicinal chemistry 
 
As mentioned above, 2-aminobenzimidazole (1) can in principal be used as a scaffold 
for the attachment of up to 3 substituents, based upon relatively straightforward 
alkylation and acylation chemistries at both ring nitrogen atoms and the exocyclic 
amine. The general trends of this reactivity have been examined in some detail and 
reviewed in journals2 and monographs3. Interestingly much of the literature dates from 
the pre-NMR era and relied on infra-red spectroscopy for confirmation of the 
regiochemical outcomes. Later work unequivocally confirmed the regiochemistry of 
initial alkylation or acylation reactivity by using small-molecule crystal structure 
determination (see Table S1, Supporting Information for examples). Sometimes 
additional crystallographic evidence is obtained where the lead or drug candidate has 
been co-crystallised in complex with its biological target, e.g. for HIV-1 protease4 
(Figure 2) and IRAK-4 kinase5, although in the latter case the compounds were 
prepared by alternative routes to avoid structural ambiguity. 
 
N
H
N
NH2
(1)
Substituent 
Attachment points
Hydrophobic
region B A
omeprazole (Antiulcer)
O
S
NO
H
N
N
O N
N
N
N
HO
O
telmisartan (Antihypertensive)
albendazole (anthelmintic)
S
H
N
NH
N
O
O
 
Figure 2. 2-aminobenzimidazole-containing inhibitor SD146 bound to HIV protease4 
(PDB code 1QBT). Inhibitor and hydrogen-bonded aspartate residues shown in stick 
format. Hydrogen bonds displayed as dashed lines. Figure prepared using Pymol 
(www.schrodinger.com). 
 
In brief alkylation occurs first on one endocyclic nitrogen to produce compounds of 
general structure (2) (Figure 3). A subsequent second alkylation step generally 
produces the 1,3-disubstituted compounds (3)3a. If the second reaction is an acylation 
then the products obtained (4) have the 1,2-regiochemistry3b. If the initial reaction is 
an acylation then initially the most electrophilic endocyclic nitrogen N(3) reacts with 
the acylating agent to produce benzimidazolinium intermediates of type (5) which 
undergo an acyl migration to produce the 2-acylamino compounds (6)6. 
 
 
Figure 3. Regiochemical outcomes of alkylation/acylation of 2-aminobenzimidazole  
N
H
N
NH2
(1)
1 “2”
3
N
H
N
NH2
N
N
NH2
(7) (5)
N
N
NH2
N
H
N
N
H
alkyl
O R
HN R’
R’ CN acyl halide
alkyl halide rearrangement
(2) (6)
R
ON
H
N
N
(8)
R’
H2N
or
N
H
N
N
H
(taut-8)
R’
HN
alkyl halide
N
N
NH
alkyl
alkyl(3)
acyl halide
N
N
N
H
(4)
R
Oalkyl
We were interested in using alternative methodologies to simple acylation and 
alkylation, thus broadening the range of linkage methods available to the medicinal 
chemist. In this study we wished to produce imidamide (amidine) analogues (7 or 8) 
of compounds such as (4) and (6). These products are isosteric with those produced 
by acylation, however have different hydrogen bonding capabilities. For example, 
replacing (6) with (8) adds an additional hydrogen bond donor, and depending on the 
tautomeric state, relocates a hydrogen bond acceptor. For more information on the 
effects of these changes on physiochemical properties such as octanol/water partition 
coefficient (LogP), and polar surface area (PSA) see the Supporting Information.  The 
amidine products could be conceptually derived most simply by thermal or acid-
catalysed addition of (1) to nitriles. There are few literature examples7,8 of such 
compounds, which have been proposed to react at N2 giving (taut-8), a tautomer of 
(8). Of concern to us however was the lack of any structural or conclusive 
spectroscopic evidence for this tautomeric, regiochemical or stereochemical outcome. 
The NMR spectra provided in the two publications for the single compound (8a, 
R’=Ph) were somewhat contradictory and the regiochemistry of addition was implied 
from the products obtained after subsequent reactions steps, often under harsh 
oxidative or heating conditions which may have promoted rearrangement. 
 
Results and Discussion 
 
In our hands the previous report7 using tin(IV) chloride catalysis suffered from 
extensive hydrolysis of the desired product (8a) to the simple benzoyl derivative. We 
therefore chose initially to prepare compounds derived from 2-aminobenzimidazole 
(1) and benzonitrile and isonicotinitrile by simple thermal addition in the absence of 
tin (IV) catalyst thus avoiding the harsh alkaline workup (Scheme 1). The reactions 
proceeded smoothly albeit in moderate yields both in solution (8a) and the melt (8b).  
 
Scheme 1. Preparation of aromatic nitrile adducts with 2-aminobenzimidazole 
 
Compounds such as (8) are complex organic bases, consisting of a heterocyclic 
guanidine fused to a benzamidine moiety. We were particularly interested to study the 
regiochemistry of protonation of compounds (8) and the effect of this upon imine-
amine tautomerism that has previously been studied for acylation products (6)9. 
Accordingly, the simple benzonitrile product (8a) was most conveniently purified by 
HPLC in acidic medium yielding the product as a TFA salt. Analysis of the resultant 
1H and 13C NMR spectra clearly indicated the presence of symmetry on both the 
benzimidazole and phenyl rings as only 5 aromatic CH signals and 4 quaternary 
carbons were observed, whereas in the neutral adduct (8b), asymmetry in the 
benzimidazole ring resulted in 6 aromatic CH and 5 quaternary carbons being 
observed. In addition, the neutral adduct (8b) was also analysed by natural abundance 
N
H
N
NH2
(1)
N
H
N
N
(8a)
NH2
PhCN
DMF
N
H
N
N
(8b)
NH2
N
isonicotinitrile
neat
N
H
H
N
N
(8a TFA salt)
NH2
N
H
N
N
N
N
HPLC CF3CO2
-
HH
H-bond
15N NMR (HSQC/HMBC/DEPT) spectroscopy which clearly indicated that the two 
NH protons at 10.47 and 8.86 ppm were attached to the same nitrogen atom (at 102.4 
ppm). The difference in chemical shift of these two NH protons is likely attributable 
to the presence of an internal hydrogen bond for one NH to N3 of the benzimidazole 
scaffold (Scheme 1). This strongly implied that the addition products were obtained 
with the Z-geometry about the amidine double bond. Macromodel analysis of the 
possible E- and Z-isomers (Supporting Information) strongly supported the NMR 
observation of the stabilising intramolecular hydrogen bond for the Z-isomers, 
whereas in the E-isomers this hydrogen bond is absent and the additional steric clash 
of the phenyl or pyridyl rings results in an out of plane twist in the structures. This 
also has significant effects on the molecular volume and polar surface area. A 
similarly downfield shifted NH had been reported for a neutral form of (8a) without 
comment7. These results strongly support the amidation reaction occurring at the 
exocyclic NH2 group, analogous to acylation chemistry3b, although here also an 
intermediate N(3) benzimidazolinium species followed by rearrangement to (8) 
cannot be ruled out. Further compounds (8c-e) were prepared, purified and 
characterised in the same manner as (8a), albeit in lower yields (Figure 4). Analogues 
(8c-e) were all found by NMR to possess the same symmetry in the benzimidazole 
ring, indicating uniform initial protonating on the N3 nitrogen.  
 
 
Figure 4. Further arylimidamide adducts (8c-e) of 2-aminobenzimidazole prepared in 
this work as their TFA salts.  
 
As ultimate proof for the regiochemistry of addition and protonation states for adducts 
of type (8), we undertook a small molecule crystal structure analysis of (8b), prepared 
as the picrate salt10. As well as confirming the regiochemistry of addition, the X-ray 
structure also showed that the amidine double bond was in the Z-configuration. The 
picrate ring is involved in an offset π-π interaction with the B ring of two 
benzimidazole moieties. Near symmetry in the benzimidazole B ring is revealed as 
both nitrogen atoms are protonated, and all the ring bond lengths with the exception 
of the two A ring benzimidazole C-N bonds (0.011Å) are all within 0.006Å of the 
symmetrical pair. One of these is involved in a hydrogen bond with the 2-nitro group 
of the picrate molecule (H-O distances 2.013, 2.545Å), whilst the one proton from the 
amidino NH2 group is hydrogen bonded (H-O distances 2.059Å) to the picrate 
phenoxide oxygen (Figure 5). The amidino group itself displays evidence of 
N
H
N
N
H2N
N
H
N
N
H2N
N
H
N
N
H2N
Br
(8c) (8d) (8e)
CF3CO2-
N
H
H
N
N
H2N
N
H
H
N
N
H2N
N
H
H
N
N
H2N
Br
(8c TFA salt) (8d TFA salt) (8e TFA salt)
CF3CO2- CF3CO2-
delocalisation. Whilst the tautomer with two hydrogens on one nitrogen appears 
preferred, the two C-N bonds are of similar length (1.320, 1.316Å), and the N(3)-
C(8)-N(5) group is out of plane with the pyridine ring. 
 
   A      B 
  
Figure 5. Crystal structure of (8b), picrate salt10. A: Bond lengths observed for the 
imidamide in the crystal structure. B: Hydrogen bonds (red dotted lines) between 
amidine NH2 group and picrate phenoxide anion. 
 
Conclusion 
 
Thermal addition of 2-aminobenzimidazole to aromatic nitriles gives products 
analogous to acylation reactions, with substitution occurring on the exocyclic NH2 
group. The products are obtained in the Z-configuration about the amidine double 
bond. Initial protonation of these complex fused guanidine-amidine products occurs 
on the benzimidazole. 
 
 
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1.316Å
1.320Å
1.353Å
1.342Å1.398Å
1.393Å
1.386Å1.390Å
1.388Å 1.392Å
1.398Å 1.396Å
N
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(Z)-N'-(1H-Benzo[d]imidazol-2-Yl)-arylimidamide adducts of 2-aminobenzimidazole and aromatic nitriles: structural and spectroscopic proof of regiochemical and stereochemical outcomes

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(Z)-N'-(1H-Benzo[d]imidazol-2-Yl)-arylimidamide adducts of 2-aminobenzimidazole and aromatic nitriles: structural and spectroscopic proof of regiochemical and stereochemical outcomes

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