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1.  Ethyl 7-oxo-7H-benzo[de]imidazo[5,1-a]iso­quinoline-11-carboxyl­ate–tri­fluoro­acetic acid (1/1) 
The structure of the title tri­fluoro­acetic acid adduct, C17H12N2O3·C2HF3O2, contains a tri­fluoro­acetic acid mol­ecule hydrogen bonded to the imine N atom of the imidazole ring of a nearly planar four-fused-ring system (r.m.s. deviatiation = 0.013 Å). The carb­oxy­lic acid group of the triflouro­acetic acid mol­ecule is twisted with respect to the mean plane of the four-fused-ring sytem by 75.9 (2)°. A short intra­molecular C—H⋯O hydrogen bond occurs. In the crystal, the adduct mol­ecules are arranged into stacks along the b axis via π–π inter­actions between imidazole rings and between imidazole and one of the benzene rings [centroid–centroid distances 3.352 (2) and 3.485 (2) Å, respectively]. Molecules are linked via C—H⋯O hydrogen bonds, forming an alternating polymeric head-to-head/tail-to-tail stepped chain approximately along the a-axis direction and tilted on an axis bisecting the b and c axes.
PMCID: PMC3685112  PMID: 23795131
2.  5H-Imidazo[4,5-f][1,10]phenanthroline 
The title mol­ecule, C13H8N4, is is essentially planar [r.m.s. deviation for all non-H atoms = 0.025 (3) Å]. In the crystal, mol­ecules are connected through one weak bifurcated N—H⋯(N,N) hydrogen bond and three π–π stacking inter­actions between pyridine and imidazole rings [centroid–centroid distance = 3.631 (8) Å] and between pyridine and benzene rings [centroid–centroid distances = 3.675 (5) and 3.666 (2) Å].
PMCID: PMC3344565  PMID: 22590327
3.  Crystal structure of 5-amino-5′-chloro-6-(4-chloro­benzo­yl)-8-nitro-2,3-di­hydro-1H-spiro­[imidazo[1,2-a]pyridine-7,3′-indolin]-2′-one including an unknown solvent mol­ecule 
The asymmetric unit of the title compound, C21H15Cl2N5O4, contains two independent mol­ecules (A and B) having similar conformations. The amine (NH2) group forms an intra­molecular hydrogen bond with the benzoyl group, giving an S(6) ring motif in both mol­ecules. The central six-membered rings adopt sofa conformations and the imidazole rings are planar (r.m.s deviations = 0.0150 and 0.0166 Å). The pyridine and imidazole rings are inclined to one another by 3.54 (1) and 3.03 (1)° in mol­ecules A and B, respectively. In the crystal, mol­ecules are linked by N—H⋯O hydrogen bonds, forming chains along the a axis which enclose R 2 2(16) ring motifs. The rings are linked by weak N—H⋯O and C—H⋯O hydrogen bonds and C—H⋯π inter­actions forming sheets lying parallel to (001). A region of disordered electron density, most probably disordered solvent mol­ecules, occupying voids of ca 753 Å3 for an electron count of 260, was treated using the SQUEEZE routine in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155]. Their formula mass and unit-cell characteristics were not taken into account during refinement.
PMCID: PMC4186207  PMID: 25309286
crystal structure; spiro; imidazole; pyridine-indoline C—H⋯π inter­actions; hydrogen bonding
4.  3-[(1-Isobutyl-1H-imidazo[4,5-c]quinolin-4-yl)amino]­benzoic acid 
In the title compound, C21H20N4O2, the statistically planar 1H-limidazole ring [maximum deviation = 0.003 (1) Å] makes dihedral angles of 1.33 (9) and 8.23 (7)°, respectively, with the essentially planar fused pyridine ring [maximum devation = 0.018 (1) Å] and the pendant benzene ring, which is attached to the pyridine ring by an —NH— group. An intra­molecular C—H⋯N inter­action, which generates an S(6) ring, helps to estalish the mol­ecular conformation. In the crystal, the mol­ecules are linked by N—H⋯O, C—H⋯O and O—H—N hydrogen bonds, which generate bifurcated R 1 2(6) and R 2 2(9) ring motifs, resulting in supra­molecular [001] chains. The crystal structure also features weak π–π stacking [centroid–centroid distance = 3.5943 (9) Å] and C—H⋯π inter­actions.
PMCID: PMC3213588  PMID: 22091165
5.  5-Amino-6-benzoyl-8-nitro-2,3-di­hydro-1H-spiro­[imidazo[1,2-a]pyridine-7,3′-indolin]-2′-one dimethyl sulfoxide monosolvate 
In the title compound C21H17N5O4·C2H6OS, the central six-membered ring derived from 1,4-di­hydro­pyridine adopts a distorted boat conformation with a small puckering amplitude of 0.127 (3) Å. The sums of bond angles around the pyridine N atom [358.7 (2)°] and the other imidazolidine N atom [60 (2)°] indicate that these atoms are in sp2 hybridization, leading to an essentially planar imidazolidine ring. The last heterocycle, an oxindole moiety, is also nearly planar with an r.m.s. deviation of 0.0185 (1) Å. The amine NH2 group forms an intra­molecular hydrogen bond with the benzoyl group, giving a S(6) motif. In the crystal, N—H⋯O hydrogen bonds lead to the formation of chains along the c-axis direction. Within the chains there are further N—H⋯O and C—H⋯O hydrogen bonds enclosing R 2 2(14) ring motifs. The chains are linked via N—H⋯O and C—H⋯O hydrogen bonds involving the dimethyl sulfoxide solvent mol­ecule which acts as both an acceptor and a donor..
PMCID: PMC4011289  PMID: 24860398
6.  2-(2-Fur­yl)-1H-imidazo[4,5-f][1,10]phenanthroline-3,7-diium dichloride monohydrate 
The organic cation of the title salt, C17H12N4O2+·2Cl−·H2O, is nearly planar, the dihedral angle between two pyridine rings being 2.53 (16)° and that between the pyridinum and furan rings being 4.17 (19)°. Mol­ecules are linked via N—H⋯O, N—H⋯Cl and O—H⋯Cl hydrogen bonds, forming a three-dimensional framework and π–π stacking inter­actions help to stabilize the crystal structure [the imidazole–pyridine and imidazole–benzene centroid–centroid distances are 3.501 (3) and 3.674 (3) Å; respectively].
PMCID: PMC2968264  PMID: 21581942
7.  3-Ethyl-5-(4-meth­oxy­phen­oxy)-2-(pyridin-4-yl)-3H-imidazo[4,5-b]pyridine 
In the title compound, C20H18N4O2, the imidazopyridine fused ring system is almost perpendicular to the benzene ring [dihedral angle = 87.6 (5)°]. The pyridine ring makes a dihedral angle of 35.5 (5)° with the mean plane of the imidazopyridine fragment. The crystal structure is stabilized by an aromatic π–π stacking inter­action between the phenyl rings of neighbouring mol­ecules [centroid–centroid distance = 3.772 (2) Å, inter­planar distance = 3.546 (2) Å and slippage = 1.286 (2) Å].
PMCID: PMC3152004  PMID: 21837144
8.  6-(2-Chloro­benz­yl)-1-(4-chloro­phen­yl)-7-hy­droxy-2,3-dihydro-1H-imidazo[1,2-a]pyrimidin-5-one 
The title compound, C19H15Cl2N3O2, was obtained by a one-step cyclo­condensation of 2-amino-1-(4-chloro­phen­yl)imidazoline with diethyl (2-chloro­benz­yl)malonate under basic conditions. In the crystalline state, the mol­ecule exists as the 7-hy­droxy-5-oxo tautomer. The dihedral angles between the fused imidazopyrimidine and aromatic chloro­phenyl and chloro­benzyl rings are 14.2 (1) and 70.7 (1)°, respectively. The conformation of the mol­ecule is influenced by the intra­molecular C—H⋯O and C—H⋯N hydrogen bonds, giving a nearly planar five-ring fused system [maximum deviation from the mean plane = 0.296 (2) Å]. In the crystal structure, strong inter­molecular O—H⋯O hydrogen bonds link the mol­ecules into chains along the c axis. These chains are further stabilized by weak C—H⋯Cl and π–π inter­actions [centroid–centroid distance = 3.6707 (12) Å].
PMCID: PMC3009369  PMID: 21588948
9.  2-(7,8-Diphenyl-1H-imidazo[4,5-f]quinoxalin-2-yl)phenol methanol disolvate 
The title compound, C27H18N4O·2CH4O, is a unsymmetrically substituted quinoxaline. An intra­molecular O—H⋯N hydrogen bond involving the hydr­oxy and imino groups generates an S(6) ring motif. Inter­molecular C—H⋯O and N—H⋯O hydrogen bonds form an R 2 1(7) ring motif involving a methanol O atom and two H atoms of the imidazole and benzene rings, respectively. The latter links neighbouring mol­ecules into one-dimensional extended chains along the a axis. The two benzene rings are inclined towards each other, as indicated by the dihedral angle of 52.13 (10)°. The phenol ring is almost coplanar with the basic quinoxaline unit, making a dihedral angle of 2.43 (6)°. The short distances between the centroids of the five- and six-membered rings prove the existence of π–π inter­actions [centroid–centroid distances = 3.5234 (9)–3.7885 (10) Å]. The crystal structure is stabilized by intra­molecular O—H⋯N, inter­molecular O—H⋯O, N—H⋯O and C—H⋯O (× 2) hydrogen bonds and weak inter­molecular C—H⋯π and π–π inter­actions.
PMCID: PMC2960492  PMID: 21201724
10.  5-Amino-5′-bromo-6-(4-methyl­benzo­yl)-8-nitro-2,3-di­hydro-1H-spiro­[imidazo[1,2-a]pyridine-7,3′-indolin]-2′-one including an unknown solvate 
In the title compound, C22H18BrN5O4, the central six-membered ring, derived from 1,4-di­hydro­pyridine, adopts a distorted boat conformation with a puckering amplitude of 0.197 (3) Å, the imidazole ring adopts a twisted conformation with a puckering amplitude of 0.113 (3) Å, and the oxindole moiety is planar with an r.m.s. deviation of 0.0125 Å. Two intra­molecular N—H⋯O hydrogen bonds are formed, each closing an S(6) loop. In the crystal, strong N—H⋯O hydrogen bonds lead to the formation of zigzag chains along the c axis. These are consolidated in the three-dimensional crystal packing by weak N—H⋯O hydrogen bonding, as well as by C—H⋯O, C—H⋯Br and C—H⋯π inter­actions. A small region of electron density well removed from the main mol­ecule was removed with the SQUEEZE procedure in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155] following unsuccessful attempts to model it as a plausible solvent mol­ecule. The unit-cell characteristics do not take into account this feature of the structure.
PMCID: PMC4120621  PMID: 25161594
crystal structure
11.  1-Isobutyl-4-meth­oxy-1H-imidazo[4,5-c]quinoline 
In the title compound, C15H17N3O, the 1H-imidazo[4,5-c]quinoline ring system is approximately planar, with a maximum deviation of 0.036 (1) Å. The C—N—C—C torsion angles formed between this ring system and the isobutyl unit are −99.77 (16) and 79.71 (17)°. In the crystal, inter­molecular C—H⋯O hydrogen bonds link the mol­ecules into chains along the c axis.
PMCID: PMC3200859  PMID: 22058955
12.  1-(6-Chloro-1-methyl-1H-imidazo[4,5-c]pyridin-4-yl)-3-(2-chloro­phen­yl)urea 
In the title compound, C14H11Cl2N5O, the plane of the 1H-imidazo[4,5-c]pyridine ring system [r.m.s. deviation = 0.087 (19) Å] makes a dihedral angle of 4.87 (10)° with the terminal phenyl ring. An intra­molecular N—H⋯N hydrogen bond stabilizes the mol­ecular conformation. In the crystal, N—H⋯O hydrogen bonds link the mol­ecules into inversion dimers. These dimers are connected by π–π inter­actions between imidazole rings [shortest centroid–centroid distance = 3.4443 (14) Å].
PMCID: PMC3998316  PMID: 24764877
13.  6-Bromo-3-methyl-2-phenyl-3H-imidazo[4,5-b]pyridine 
The two fused five- and six-membered rings building the mol­ecule of the title compound, C13H10BrN3, are approximately planar, the largest deviation from the mean plane being 0.004 (2) Å. The dihedral angle between the imidazo[4,5-b]pyridine mean plane and that of the phenyl ring is 41.84 (11)°. The structure is held together by slipped π–π stacking between symmetry-related mol­ecules, with an inter­planar distance of 3.583 (1) Å and a centroid–centroid vector of 3.670 (2) Å.
PMCID: PMC3151993  PMID: 21837081
14.  3-{[5-(4-Bromo­phen­yl)imidazo[2,1-b][1,3,4]thia­diazol-2-yl]meth­yl}-1,2-benzoxazole 
In the title compound, C18H11BrN4OS, the imidazothia­diazole and benzisoxazole rings are individually planar with maximum deviations of 0.025 (3) 0.015 (4) Å, respectively, and are inclined at an angle of 23.51 (7)° with respect to each other. The planes of the imidazothia­diazole and bromo­phenyl rings are inclined at an angle of 27.34 (3)°. In the crystal, inter­molecular C—H⋯N inter­actions result in chains of mol­ecules along the b and c axes. Moreover, C—H⋯O inter­actions result in centrosymmetric head-to-head dimers with R 2 2(24) graph-set motifs. The mol­ecular packing is further stabilized by π–π stacking inter­actions between the imidazole rings with a shortest centroid–centroid distance of 3.492 (3) Å. In addition, C—H⋯π inter­actions are observed in the crystal structure.
PMCID: PMC3050133  PMID: 21522661
15.  8H-Chromeno[2′,3′:4,5]imidazo[2,1-a]isoquinoline 
The title compound, C18H12N2O, comprises two aromatic fragments, viz., imidazo[2,1-a]isoquinoline and benzene, linked by oxygen and methyl­ene bridges. Despite the absence of a common conjugative system within the mol­ecule, it adopts an essentially planar conformation with an r.m.s. deviation of 0. 036 Å. In the crystal, due to this structure, mol­ecules form stacks along the b axis by π⋯π stacking inter­actions, with shortest C⋯C distances in the range 3.340 (4)–3.510 (4) Å. The mol­ecules are bound by inter­molecular C—H⋯O inter­actions within the stacks and C—H⋯π inter­actions between the stacks.
PMCID: PMC2983581  PMID: 21580448
16.  Crystal structures of methyl 3-phenyl-4,5-di­hydro-1H,3H-benzo[4,5]imidazo[2,1-c][1,4]oxazepine-4-carboxyl­ate and methyl 1-methyl-3-phenyl-4,5-di­hydro-1H,3H-benzo[4,5]imidazo[2,1-c][1,4]oxazepine-4-carboxyl­ate 
In two benzo[4,5]imidazo[2,1-c][1,4]oxazepine-4-carboxyl­ates, the seven-membered oxazepane rings both have a twist-chair conformation. The dihedral angle between the phenyl ring and the benzimidazole ring system is significantly smaller in one of the compounds, viz. 73.42 (10) compared to 83.07 (17)°.
The title compounds, C19H18N2O3, (I), and C20H20N2O3, (II), differ only by a methyl substituent on the seven-membered oxazepine ring in (II). In both compounds, these rings have a twist-chair conformation. The phenyl ring makes a dihedral angle of 73.42 (10)° with the benzimidazole ring system mean plane (r.m.s. deviation = 0.015 Å) in (I) and 83.07 (7)° in (II) (r.m.s. deviation = 0.026 Å). The methyl carboxyl­ate groups are planar to within 0.031 (2) in (I) and 0.003 (2) Å in (II). They are inclined to the phenyl and benzimidazole ring system by 33.78 (16) and 87.56 (14)°, respectively, in (I) and by 53.04 (12) and 60.22 (11)°, respectively, in (II). In the crystal of (I), mol­ecules stack in a herringbone fashion and are linked by C—H⋯O hydrogen bonds, forming chains along [100]. In the crystal of (II), there are no significant inter­molecular inter­actions present.
PMCID: PMC4257324  PMID: 25484732
crystal structure; oxazepine; benzimidazole; angiogenesis; natural products.
17.  2-Isobutyl-6-(4-meth­oxy­phen­yl)imidazo[2,1-b][1,3,4]thia­diazole 
In the title compound, C15H17N3OS, the dihedral angle between the statistically planar imidazo[2,1-b][1,3,4]thia­dia­zole fused-ring system (r.m.s. deviation = 0.002 Å) and the methyoxbenzene ring is 4.52 (6)°. In the crystal, mol­ecules are arranged into columns and stacked down the a axis. The crystal structure is stabilized by weak C—H⋯π and π–π inter­actions [centroid–centroid separations = 3.6053 (8) and 3.7088 (7) Å].
PMCID: PMC3051798  PMID: 21522949
18.  2-Isobutyl-6-phenyl­imidazo[2,1-b][1,3,4]thia­diazole 
In the title compound, C14H15N3S, the imidazo[2,1-b][1,3,4]thia­diazole fused-ring system is close to planar, with a maximum deviation of 0.042 (1) Å, and the dihedral angle between it and the phenyl ring is 24.21 (6)°. The isobutyl group is disordered over two sets of sites in a 0.899 (9):0.101 (9) ratio. In the crystal, weak aromatic π–π stacking inter­actions involving the imidazole and thia­diazole rings with a centroid–centroid distance of 3.8067 (7) Å occur.
PMCID: PMC3051612  PMID: 21522948
19.  6-Bromo-1-(1,2-propadien­yl)-3-(2-propyn­yl)-1H-imidazo[4,5-b]pyridin-2(3H)-one 
The reaction of propargyl bromide and 6-bromo-1,3-dihydro­imidazo[4,5-b]pyridin-2-one in refluxing dimethyl­formamide yields the title compound, C12H8BrN3O, which features nitro­gen-bound propadienyl and propynyl substituents. The imidazolopyridine fused ring is planar (r.m.s. deviation = 0.012 Å); the propadienyl chain is coplanar with the fused ring as it is conjugated with it, whereas the propynyl chain is not as the nitro­gen-bound C atom is a methyl­ene linkage. The acetyl­enic H atom is hydrogen bonded to the carbonyl O atom of an adjacent mol­ecule, forming a helical chain runnning along the b axis.
PMCID: PMC2983773  PMID: 21580600
20.  7-Benzyl-3-methyl-6-phenyl­imidazo[2,1-b][1,3]thia­zol-7-ium chloride 0.75-hydrate 
Theasymmetric unit of the title salt, C19H17N2S+·Cl−·0.75H2O, contains two symmetrically independent formula units of the carbenium salt along with three water mol­ecules. The water mol­ecules are only 50% occupated, and one of them is positioned in a hydro­phobic pocket not forming any hydrogen bonds. The conformation of the independent cations is very similar, with dihedral angles of 61.0 (2) and 61.5 (3)° between the benzene rings. They form quasi-centrosymmetric couples via π–π stacking inter­actions between the benzene and imidazo[2,1-b]thia­zole rings [centroid–centroid distances = 3.718 (3) and 3.663 (3) Å]. In the crystal, O—H⋯Cl hydrogen bonds lead to the formation of a helical anion–water chain along the c-axis direction. The cations connect to the anion–water chain through C—H⋯Cl inter­actions, generating a three-dimensional supra­molecular network. O—H⋯S hydrogen bonds and C—H⋯O inter­actions also occur.
PMCID: PMC3793749  PMID: 24109336
21.  2-(8-Bromo­imidazo[1,2-a]pyridin-2-yl)-N′-[(E)-4-diethyl­amino-2-hy­droxy­benzyl­idene]acetohydrazide dihydrate 
In the title compound, C20H22BrN5O2·2H2O, the Schiff base mol­ecule exists in an E conformation with respect to the acyclic C=N bond. An S(6) ring motif is formed via an intra­molecular O—H⋯N hydrogen bond. The dihedral angle between the imidazo[1,2-a]pyridine system and the benzene ring is 84.62 (5)°. In the crystal, N—H⋯O, O—H⋯O, O—H⋯N, C—H⋯O and C—H⋯Br hydrogen bonds link the mol­ecules into a three-dimensional network. The crystal packing is further stabilized by C—H⋯π and π–π inter­actions [centroid–centroid distance = 3.5365 (7) Å].
PMCID: PMC3297878  PMID: 22412681
22.  Crystal structure of zwitterionic 3-(2-hy­droxy-2-phospho­nato-2-phosphono­eth­yl)imidazo[1,2-a]pyridin-1-ium monohydrate (minodronic acid monohydrate): a redetermination 
A redetermination of the crystal structure of minodronic acid monohydrate was carried out in order to provide accurate atomic coordinates and geometry information, whose knowledge is fundamental to elucidate the presumed polymorphism of the compound at room temperature.
In a previous study, the X-ray structure of the title compound, C9H12N2O7P2·H2O, was reported [Takeuchi et al., (1998 ▶). Chem. Pharm. Bull. 46, 1703–1709], but neither atomic coordinates nor details of the geometry were published. The structure has been redetermined with high precision as its detailed knowledge is essential to elucidate the presumed polymorphism of minodronic acid monohydrate at room temperature. The mol­ecule crystallizes in a zwitterionic form with cationic imidazolium[1,2a]pyridine and anionic phospho­nate groups. The dihedral angle formed by the planes of the pyridine and imidazole rings is 3.55 (9)°. A short intra­molecular C—H⋯O contact is present. In the crystal, mol­ecules are linked by O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds and π–π inter­actions [centroid-to-centroid distance = 3.5822 (11) Å], forming a three-dimensional structure.
PMCID: PMC4331878
crystal structure; bis­phospho­nate; polymorphism; minodronic acid; hydrogen bonds; redetermination
23.  2-Methyl-6-(trifluoro­meth­yl)imidazo[1,2-a]pyridine-3-carbonitrile 
In the title compound, C10H6F3N3, the imidazo[1,2-a]pyridine group is essentially planar with a maximum deviation of 0.021 (1) Å. The F atoms in the trifluoro­methyl group and the methyl H atoms are each disordered over two sets of sites with refined site occupancies of 0.68 (1):0.32 (1). In the crystal, mol­ecules are linked into infinite chains through two C—H⋯N inter­actions forming R 2 2(12) and R 2 2(8) hydrogen-bond ring motifs. These chains are stacked along the a axis.
PMCID: PMC3052008  PMID: 21522335
24.  3-[2-(6-Bromo-2-phenyl-3H-imidazo[4,5-b]pyridin-3-yl)eth­yl]-1,3-oxazolidin-2-one 
In the title mol­ecule, C17H15BrN4O2, the fused-ring system is essentially planar, the largest deviation from the mean plane being 0.015 (2) Å, and forms dihedral angles of 37.8 (2) and 35.5 (2)° with the phenyl and oxazolidine rings, respectively. The conformation adopted by the mol­ecule is stabilized by an intra­molecular π⋯π inter­action [centroid–centroid distance = 3.855(2) Å] between oxazolidine and phenyl rings. The crystal packing features inter­molecular C—H⋯N and C—H⋯O inter­actions.
PMCID: PMC3089183  PMID: 21754415
25.  6-(4-Chloro­phen­yl)-3-methyl­imidazo[2,1-b]thia­zole 
In the title compound, C12H9ClN2S, the imidazo[2,1-b]thia­zole fragment is planar (r.m.s. deviation = 0.003 Å), and the benzene ring is twisted slightly [by 5.65 (6)°] relative to this moiety. In the crystal, mol­ecules are linked by π–π stacking inter­actions into columns along [010]. The mol­ecules within the columns are arranged alternatively by their planar rotation of 180°. Thus, in the columns, there are the two types of π–π stacking inter­actions, namely, (i) between two imidazo[2,1-b]thia­zole fragments [inter­planar distance = 3.351 (2) Å] and (ii) between an imidazo[2,1-b]thia­zole fragment and the phenyl ring [inter­planar distance = 3.410 (5) Å]. There are no short contacts between the columns.
PMCID: PMC3884351  PMID: 24454127

Results 1-25 (166392)