Structural Investigation of Weak Intermolecular Interactions (Hydrogen

Article pubs.acs.org/crystal

Structural Investigation of Weak Intermolecular Interactions (Hydrogen and Halogen Bonds) in Fluorine-Substituted Benzimidazoles Marta Pérez-Torralba,*,† M. Á ngeles García,† Concepción López,† M. Carmen Torralba,*,‡ M. Rosario Torres,‡ Rosa M. Claramunt,† and José Elguero§ †

Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias, Universidad Nacional de Educación a Distancia (UNED), Senda del Rey 9, E-28040 Madrid, Spain ‡ Departamento de Química Inorgánica I and CAI de Difracción de Rayos-X, Facultad de Ciencias Químicas, Universidad Complutense de Madrid (UCM), E-28040 Madrid, Spain § Instituto de Química Médica, Centro de Química Orgánica “Manuel Lora-Tamayo”, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain S Supporting Information *

ABSTRACT: The structures of five fluorinated benzimidazoles and one intermediate (an open double amide) have been determined by X-ray crystallography. In the analysis of these heterocycles, particular attention has been paid to N−H···H hydrogen bonds and to fluorine−fluorine intermolecular contacts. Thus, one of the shortest F···F distances ever reported, 2.596(3) Å, has been observed in 4,5,6,7-tetrafluoro-1H-benzimidazole-2(3H)-one. The 13C, 15N, and 19F solid-state NMR data for all benzimidazoles are also given.

■

INTRODUCTION After hydrogen bonds (HB),1 the most studied of the related weak interactions are halogen bonds (XB).2 The competition between these two interactions as well as their interplay to determine the crystal packing of organic halogen derivatives is a subject of interest today.3 Most the studies related to XB concerns the heaviest halogen atoms, I and Br, less concerns Cl, and much less concerns F, because the interaction energy decreases in this order.4 Having been working on polyfluorinated heterocycles, we decided to study the structure of six derivatives bearing four fluorine atoms on the benzene ring (Scheme 1) by X-ray crystallography and solid-state NMR, an interesting combination of techniques.5 This article deals with compounds 1−6 (compound 6 was obtained as a side-product of the synthesis of 2). The systematic names of the compounds of Scheme 1 are 4,5,6,7-tetrafluoro-1H-benzimidazole (1); 4,5,6,7-tetrafluoro-2(trifluoromethyl)-1H-benzimidazole (2); 4,5,6,7-tetrafluoro1H-benzimidazole-2(3H)-one (3); 4,5,6,7-tetrafluoro-1-methyl-1H-benzimidazole-2(3H)-one (4); 4,5,6,7-tetrafluoro-1,3dimethyl-1H-benzimidazole-2(3H)-one (5); and N,N-(perfluoro-1,2-phenylene)bis(2,2,2-trifluoroethanamide) (6). The simultaneous presence of four adjacent fluorine atoms and one or two N−H groups (save in 5) makes the compounds © 2014 American Chemical Society

Scheme 1. Two-Dimensional Formulae and Ring Atoms Numbering of Compounds 1−6

of Scheme 1 interesting candidates to observe different kinds of weak interactions. The literature on 4,5,6,7-tetrafluoro-1H-benzimidazoles covers such compounds as the parent compound 1 (a metalfree organic magnetic material),6 the 2-methyl derivative,7 2trifluoromethyl derivative 2 (an antibacterial and herbicidal Received: March 31, 2014 Revised: April 30, 2014 Published: May 19, 2014 3499

dx.doi.org/10.1021/cg500442k | Cryst. Growth Des. 2014, 14, 3499−3509

Crystal Growth & Design

Article

Table 1. Fluorine···Fluorine Intermolecular Interactions use the CSD yes yes yes no yes yes no yes no yes no no no no no no yes no no no no no no no no no yes yes yes yes no yes no no yes no no no yes no

Types I and II yes

yes yes

yes

yes yes yes yes yes yes yes yes

yes

d(F···F) Å

for or against

a b 2.84 2.80 c 2.88 2.85 2.89 3.09 2.86, 2.95 2.77 2.63 2.80 2.78 3.03 2.78 2.86 2.87 ∼2.9 d 2.76 2.66 2.76 2.69 ∼2.6 2.85 2.92 2.97 2.82 2.81 2.92

for against for for against against for for against against against for for for for for for for doubtful for for for for doubtful for for against for doubtful for for for for doubtful for for for for against for

b 2.93 2.89 2.9 2.83 2.64e 2.9 2.66

notes polar flattening Desiraju

Desiraju Desiraju, inversion center Csp3 Csp3 olefinic Csp2 Csp3

not centrosymmetric Csp3

polar flattening due to packing? 1.1 GPa: 2.61 Å Desiraju, due to packing

homohalogen F···F heterohalogen F···X

monolayer on Au(111) between two BF4− anions not on the fingerprint plot Csp3

ref 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52

a Definition of the radii considering the flattening. bA statistical survey. cNo short F···F contacts are observed. d“F···F close contacts”. eDue to disorder this value may be underestimated.

compound),8 the 2-amino derivative,8 and an important 2substituted free radical.9 Concerning F···F interactions (a homohalogen interaction), there is an abundant bibliography, both theoretical10 and crystallographic. We have summarized the available crystallographic information in Table 1, with the first column reporting whether the authors have used the Cambridge Structural Data Base,11 the second, if they have classified the halogen bonds in the well-known three classes of Sakurai, Sundaralingam, and Jeffrey (Figure 2),12 the third column reports de shortest F···F distance in Å (the sum of van der Waals radii is 2.94 Å), and the fourth column reporting, in a simplified way, whether the authors agree or disagree with the existence of F···F halogen bonds. Finally, the fifth column contains some comments: if the author discussed the notion of “polar flattening”, if one of the authors is “Desiraju”, the hybridization of the carbon atom (sp2,

sp3), the pressure when different from atmospheric pressure (about 101 kP), etc. It has been pointed out that fluorine/fluorine interactions play a unique role precisely because they are very weak if not negligible. This behavior originates in the low polarizability of the fluorine atom that leads to limited attractive interatomic dispersion forces. Today, with the exception of Desiraju,14,18,22,39 most authors consider that F···F intermolecular contacts are due to an attractive force based not only on crystallographic but also on computational results (closed-shell interactions).29,34,47 Several cases in Table 1, where the authors doubted the existence of halogen bonds, correspond to Csp3−F bonds.21,23,31 In one case it has been mentioned that the F···F halogen bond does not appear in the fingerprint plot.51 A plot of the data of Table 1 is represented in Figure 1 (blue halfpoints). 3500



Article

reason we decided to explore those potentially present in the structures of Scheme 1.

■

EXPERIMENTAL SECTION

Materials. The compounds prepared and investigated in this study (1−6) are presented in Scheme 1. All were synthesized following standard procedures,53 and its purity was checked by differential scanning calorimetry (DSC) using a Seiko DSC220C connected to a model SSC5200H disk station. Thermograms (sample size 0.004 g) were recorded with a scan rate of 5.0 °C. Compound 1 (4,5,6,7-tetrafluoro-1H-benzimidazole). Mp = 233.9 °C (EtOH). Lit.54 mp =232−233 °C. 19F NMR (379.5 MHz, DMSOd6): δ(ppm) = −156.1 (F4, F7), −167.3 (F5, F6). Compound 2 (4,5,6,7-tetrafluoro-2-(trifluoromethyl)-1H-benzimidazole) Mp = 163.5 °C (EtOH). Lit.54 mp = 161−162 °C. 19F NMR (379.5 MHz, DMSO-d6): δ (ppm) = −154.9 (F4, F7), −163.9 (F5, F6), −63.6 (CF3). Compound 3 (4,5,6,7-tetrafluoro-1H-benzimidazole-2(3H)-one). Mp = 302.2 °C (EtOH). Lit.8 mp =302.5−306.0 °C. 19F NMR (379.5 MHz, DMSO-d6): δ (ppm) = −160.5 (F4, F7), −170.2 (F5, F6). Compound 4 (4,5,6,7-tetrafluoro-1-methyl-1H-benzimidazole2(3H)-one). Mp = 225.5 °C (hexane/ethyl acetate). Anal. Calcd for C8H4F4N2O (%): C, 43.65; H, 1.83; N, 12.73. Found: C, 42.82; H, 2.05; N, 12.85. 19F NMR (379.5 MHz, DMSO-d6): δ (ppm) = −160.7 (F4), −166.2 (F7), −169.4 (F5), −169.8 (F6). Compound 5 (4,5,6,7-tetrafluoro-1,3-dimethyl-1H-benzimidazole2(3H)-one). Mp = 107.9 °C (hexane/ethyl acetate). Anal. Calcd for C9H6F4N2O (%): C, 46.17; H, 2.58; N, 11.96. Found: C, 45.34; H, 2.68; N, 12.14. 19F NMR (379.5 MHz, CDCl3): δ (ppm) = −166.0 (F4, F7), −167.5 (F5, F6). Compound 6 (N,N-(perfluoro-1,2-phenylene)bis(2,2,2-trifluoroethanamide). Mp = 168 °C (EtOH). Lit.54 mp =166−167 °C. 19F NMR (379.5 MHz, DMSO-d6): δ (ppm) = −142.7 (F4, F7), −156.0 (F5, F6), −73.9 (CF3). Crystal Data Collection and Refinement. Crystals of good quality for X-ray diffraction analyses were obtained for compound 1 (AcOEt), compound 2 (CH2Cl2/hexane), compound 3 (EtOH), compound 4, polymorph A (AcOEt), compound 4, polymorph B (CDCl3), compound 5 (DMF), and compound 6 (DMSO). The data collection for all compounds was carried out at 293(2) K on a Bruker Smart CCD diffractometer using graphite-monochro-

Figure 1. Number of examples vs. F···F distances in Å.

If the sum of the van der Waals radii (2.94 Å) is considered the borderline, then (i) several authors reported F···F contacts beyond it; (ii) there are many examples with values lower than 2.94 Å; (iii) Olejniczak, Katrusiak, and Vij38 have reported an example where the pressure reduces the F···F distance from 2.85 to 2.61 Å, offering the possibility to move the cutoff at 2.85 Å. Note that a decrease of 0.24 Å is considerable considering the steep increase in energy of the left branch of a Morse potential. An important aspect concerning this question is that centrosymmetric F···F bonds (Type I) can be due to crystal packing, while noncentrosymmetric ones (Type II) are surer proofs of halogen bonding (Figure 2).18,22,39−41,46,47 For this reason, the results of ref 30 are very significant. The question of the polar flattening of fluorine atoms has been discussed in this context,13,34 but today it seems to have disappeared from the literature. In summary, Table 1 together with Figures 1 and 2 show that F···F interactions are widespread covering a wide range of distances and types but that they are still controversial. For this

Figure 2. Three classes of halogen bonds. Top, the original Sakurai, Sundaralingam, and Jeffrey classification;12 middle, that reported in ref 4a (see p 190); bottom, those present in compound 1 (this work). In almost all cases they correspond to C−X···X−C interactions (exception B−F···F−B).50 3501



Article

Table 2. Crystal Data and Structure Refinement for 1, 2, 3, 4 polymorph A, 4 polymorph B, 5, and 6 crystal data

1

2

3

4 polymorph A

4 polymorph B

5

6

identification code empirical formula formula weight crystal system space group unit cell dimensions a(Å) b (Å) c (Å) α (deg) β (deg) γ (deg) volume (Å3) Z density (calculated) (Mg/m3) absorption coefficient (mm−1) F(000) theta range (deg) for data collection index ranges

CCDC-981 681

CCDC-981 682

CCDC-981 683

CCDC-981 684

CCDC-981 685

CCDC-981 686

CCDC-981 687

C7H2F4N2 190.11 monoclinic C2/c

C8H1F7N2 258.11 monoclinic P21/n

C7H2F4N2O1 206.11 monoclinic P21/c

C8H4 F4N2O1 220.13 monoclinic P21/n

C8H4F4N2O1 220.13 triclinic P1̅



18.342(5) 7.221(2) 21.239(6)

7.898(5) 13.628(8) 9.602(6)

13.723(15) 4.884(5) 11.259(12)

11.258(1) 5.4872(5) 13.546(1)

24.123(5) 4.3561(9) 18.078(4)

9.733(1) 15.198(2) 18.133(2)

90.928(5)

112.516(12)

100.854(18)

101.503(2)

101.365(5)

94.256(3)

2812.7(1) 16 1.796

954.7(1) 4 1.796

741.0(1) 4 1.847

820.02(1) 4 1.783

5.009(1) 8.499(2) 10.854(2) 103.871(4) 101.076(4) 104.493(4) 418.42(2) 2 1.747

1862.4(7) 8 1.670

2674.9(6) 8 1.848

0.186

0.206

0.194

0.182

0.178

0.165

0.220

1504 1.92−25.00

504 2.74−25.00

408 1.51−27.00

440 2.15−27.99

220 2.01−25.02

944 1.72−25.00

1456 1.75−25.00

−17 ≤ h ≤ 21 −8 ≤ k ≤ 8 −25 ≤ l ≤ 24 7856

−9 ≤ h ≤ 7 −16 ≤ k ≤ 16 −10 ≤ l ≤ 11 7091

−13 ≤ h ≤ 17 −6 ≤ k ≤ 4 −14 ≤ l ≤ 14 5894

−14 ≤ h ≤ 14 −7 ≤ k ≤ 7 −17 ≤ l ≤ 13 7291

−5 ≤ h ≤ 5 −10 ≤ k ≤ 8 −12 ≤ l ≤ 12 3198

−28 ≤ h ≤ 22 −5 ≤ k ≤ 5 −21 ≤ l ≤ 21 13251

−11 ≤ h ≤ 11 −18 ≤ k ≤ 17 −21 ≤ l ≤ 21 20210

2468 [0.1411]

1678 [0.1503]

1623 [0.0920]

1962 [0.0372]

1432 [0.0262]

3282 [0.3606]

4668 [0.0649]

99.5

99.7

100

99.0

97.5

100

98.8

2468/0/237

1678/0/154

1623/0/127

1962/0/137

1432/0/137

3282/0/289

4668/0/433

0.983

0.997

0.990

0.995

1.002

0.985

0.998

0.0615 (1226)

0.0660 (595)

0.0402 (908)

0.0362 (1123)

0.0482 (790)

0.0875 (735)

0.0522 (2030)

0.1698

0.1744

0.1152

0.1045

0.1815

0.2565

0.1465

reflections collected independent refln [R(int)] completeness to theta (%) data/restraints/ parameters goodness-of-fit on F2 R1 (reflns obsd) [I > 2σ(I)]a wR2 (all data)b a

R1 = Σ||Fo| − |Fc||Σ|Fo|. wR2 = b

{Σ[w(Fo2

− Fc )

2 2

]Σ[w(Fo2)2]}. Kel-F end-caps. Operating conditions involved 2.9 μs 90° 1H pulses and decoupling field strength of 86.2 kHz by TPPM sequence. 13C spectra were originally referenced to a glycine sample, and then the chemical shifts were recalculated to the Me4Si (for the carbonyl atom δ(glycine) = 176.1 ppm) and 15N spectra to 15NH4Cl and then converted to nitromethane scale using the relationship: δ15N(nitromethane) = δ15N(ammonium chloride) − 338.1 ppm. The typical acquisition parameters for 13C CPMAS were spectral width, 40 kHz; recycle delay, 5−50 s; acquisition time, 30 ms; contact time, 2−4 ms; and spin rate, 12 kHz. In order to distinguish protonated and unprotonated carbon atoms, the non-quaternary suppression (NQS) experiment by conventional cross-polarization was recorded; before the acquisition the decoupler is switched off for a very short time of 25 ms,56,57 and for 15N CPMAS were spectral width, 40 kHz; recycle delay, 5−50 s; acquisition time, 35 ms; contact time, 7−9 ms; and spin rate, 6 kHz. Solid-state 19F (376.94 MHz) NMR spectra were obtained on a Bruker WB 400 spectrometer using a MAS DVT BL2.5 X/F/H double resonance probehead. Samples were carefully packed in 2.5 mm diameter cylindrical zirconia rotors with Kel-F end-caps. Samples were spun at the magic angle at rates of 25 kHz, and the experiments were carried out at ambient probe temperature.

mated Mo−Kα radiation (λ = 0.71073 Å) operating at 50 kV and 35 mA with the exception of compound 4, polymorph A, and compound 5 that were measured at 50 kV and 30 mA. In all cases, the data were collected over a hemisphere of the reciprocal space by combination of three exposure sets, each exposure of 20 s and covered 0.3° in ω. The first 100 frames were recollected at the end of the data collection to monitor crystal decay, and no appreciable decay was observed. A summary of the fundamental crystal and refinement data is given in Table 2. The structures were solved by direct methods and refined by full-matrix least-squares procedures on F2 (SHELXL-97).55 All non-hydrogen atoms were refined anisotropically. All hydrogen atoms were included in calculated positions and refined riding on the respective carbon atoms, with some exceptions concerning to all hydrogen atoms bonded to nitrogen atoms which were located in a Fourier synthesis and refined riding on the respective bonded atoms. Further crystallographic details for the structure reported in this paper may be obtained from The Cambridge Crystallographic Data Center, on quoting the depository numbers CCDC 981681−981687. NMR Experiments. Solid-state 13C (100.73 MHz) and 15N (40.60 MHz) CPMAS NMR spectra were obtained on a Bruker WB 400 spectrometer at 300 K using a 4 mm DVT probehead. Samples were carefully packed in a 4 mm diameter cylindrical zirconia rotors with 3502



Article

Table 3. Distances and Angles of Hydrogen Bonds (Å and °) for Compounds 1−6 compound 1 2 3 4-A 4-B 5 6

D−H···A N11−H11···N32 N12−H12···N31#1 N1−H1···N3 #2 N1−H1···O1 #3 N3−H3···O1 #4 N3−H3···O1 #5 N3−H3···O1 #6 N12−H12···O11 N32−H32···O21 N31−H31···O22 #7 N11−H11···O12 #7

symmetry operations #1 #2 #3 #4 #5 #6

x − 1/2, y − 1/2, z x − 1/2, −y + 1/2, z − 1/2 −x, −y, −z + 2 −x, y + 1/2, −z + 3/2 −x + 1, −y + 2, −z −x, −y + 1, −z

#7 x − 1, y, z

d(D−H)

d(H···A)

d(D···A)

∠(DHA)

1.04 1.10 1.02 0.89 0.99 0.96 0.89

1.77 1.73 1.86 1.93 1.83 1.85 1.88

2.813(4) 2.831(4) 2.868(6) 2.817(3) 2.818(3) 2.800(2) 2.767(4)

176.1 176.5 171.3 170.2 173.4 171.1 171.1

0.93 0.97 0.96 0.90

1.98 1.89 1.86 2.08

2.891(4) 2.830(4) 2.766(4) 2.905(4)

164.2 164.3 157.2 151.2

Table 4. Distances and Angles of F···F contacts (Å and °) for Compounds 1−5 C−F···F−Ca

d(F···F)

∠C−F···F

C−F···F−C

1

C42−F42···F52−C52

2.805(4)

89.9(4)

2.776(4)

2 3

C61−F61···F61−C61 no F···F contacts C4−F4···F7−C7

131.5(2) 132.1(2) 126.4(3)

2.914(3)

C5−F5···F5−C5 C5−F5···F6−C6 C6−F6···F7−C7

2.596(3) 2.938(1) 2.878(2)

4-B

C5−F5···F5−C5 C6−F6···F7−C7

2.846(4) 2.936(4)

5

C51−F51···F61−C61

2.88(1)

C72−F72···F72−C72

2.89(1)

compound

4-A

a

81.5(5) 169.1(1) 161.9(2) 167.1 84.4(9) 160.0(1) 127.2(3) 85.2(2) 96.2(2) 98.1(8) 172.8(8) 89.5(6) 163.6(7)

centrosymmetricb

type

−x, y, −1/2 − z

yes

I

166.2(4)

−x, y, 1/2 − z

yes

I

153.3(7)

x, 1/2 − y, 1/2 + z

no

II

180.0(6) 75.1(5) 25.3(3)

1 − x, 2 − y, 2 − z −x, −y, −z 1/2 − x, −1/2 + y, 1/2 − z

yes yes no

I I II

180.0(4) 122.8(3)

3 − x, 2 − y, 1 − z 2 − x, 1 − y, 1 − z

yes yes

I I

36(7)

1 − x, −1/2 + y, 1/2 − z

no

II

130(2)

l2 − x, −1/2 + y, 1.5 − z

no

II

symmetry operations

Atoms numbered according to Figure 3. bCentrosymmetric or noncentrosymmetric F···F interactions.

Typical parameters for single pulse 19F MAS NMR spectra were spectral width, 75 kHz; pulse width, 2.5 μs; recycle delay, 10 s; scans, 128; and spin rate, 25 kHz. The typical acquisition parameters 19F{1H} MAS were: spectral width, 75 kHz; recycle delay, 10 s; pulse width, 2.5 μs and proton decoupling field strength of 100 kHz by SPINAL-64 sequence; recycle delay, 10 s; acquisition time, 25 ms; 128 scans; and spin rate, 25 kHz. The 19F spectra were referenced to ammonium trifluoroacetate sample, and then the chemical shifts were recalculated to the CFCl3 δ(CF3COONH4+) = −72.0 ppm.

■

As a common general feature, these compounds are quite planar due to the presence of the two aromatic rings. The existence of the methyl groups as substituent in the nitrogen atoms does not modify the planarity of the molecule. The bond distances and angles are in agreement with the expected ones for this kind of compound. The presence of the carbonyl group induces some electronic changes in the imidazole ring that is seen in the lengthening of the C2−N3 bond distance and in a higher deviation of C2 atom from the molecular plane. Moreover, all the compounds show one or more interactions by strong linear hydrogen bonds, which leads to the formation of chains that, in some cases, can exhibit additional interactions via π−π and/or F···F contacts spreading out the dimensionality of the structure in the crystal. Although compound 1 was previously described it is interesting to remark its main features. It crystallizes in the monoclinic C2/c space group. The asymmetric unit contains two crystallographically different molecules (Figure 3), named types 1 and 2, which are almost coplanar and alternate in a head to head fashion. Each molecule of one type forms two asymmetric hydrogen bonds with two adjacent ones of another type: N11−H11···N32 and N12−H12···N31 with distances of 1.77 and 1.73 Å, respectively (Table 3). These interactions are extended along the [110] direction giving rise to chains which are stacked showing several weak π−π contacts between the

RESULTS AND DISCUSSION

Crystal Structures. The structure of compound 1 has been previously described. We decided to crystallize it again because the structure reported in the CSD (REVPAK)58 came from a 2006 Ph.D. Thesis (P. M. Lahti and P. Taylor), and it was cited but without any Supporting Information in ref 6b. It was determined at 293 K from a crystal obtained in nonspecified conditions. Our sample was crystallized in AcOEt, and the crystal obtained was identical to REVPAK. The distances and angles of the hydrogen bonds for compounds 1−6 are summarized in Table 3, and the geometrical data for the main interaction F···F of compounds 1−5 are in Table 4. An ORTEP plot for compounds 1−5 is displayed in Figure 3. 3503



Article

Figure 3. ORTEP plot (20% probability) showing the labeling scheme for compounds 1−5.

molecule rings [shortest distance of 3.33(6) Å]. Additional contacts between fluorine atoms of different chains, F42···F52′ [distances of 2.805(4) Å] and F61···F61′ [distance of 2.776(4) Å], are also observed (Figure 4). Compound 2 crystallizes in the monoclinic P21/n space group with one molecule per asymmetric unit. The molecules form symmetric hydrogen bonds N1−H1···N3 (distance of 1.86 Å) with the adjacent ones achieving chains along [101]. The sterically demanding CF3 substituent forces the adjacent molecules to be rotated 76.3(3)°. There are not observed significant contacts between the fluorine atoms of different molecules due to their relative disposition inside the chains that prevent their interactions. That fact as well as the absence of π−π contacts between the neighboring chains results in a monodimensional network (Figure 5). Compound 3 crystallizes in a monoclinic space group, P21/c, with one molecule in the asymmetric unit. In this case, the structure can be described by almost planar dimeric units formed by a doubly symmetric hydrogen bond N1H1···O1

between two opposite molecules, with a distance of 1.93 Å. There are observed significantly strong F···F interactions of these units through F5 [distance of 2.596(3) Å] of both molecules in the dimer with the F5 atoms of adjacent dimers leading to the formation of chains along [120]. Simultaneously, each dimer in one chain interacts with four dimeric units of different chains, which are tilted 54.9(2)°, by additional symmetric H-bonds through N3−H3···O1 (distance 1.83 Å), showing the O atoms a bifurcate fashion (Figure 6). For that reason, the molecular interactions of the dimeric units are extended in a tridimensional way. Additional symmetric F···F interactions through both F4 and F7 [distances of 2.914(3) Å] can be observed in the crystal structure. The compound 4 displays a structure based on dimeric units formed by hydrogen bonds. For this compound, two polymorphs can be described depending on the additional π−π interactions between the imidazole rings or imidazole with phenyl rings and intermolecular F···F interactions between the fluorine atoms of the different layers (Figure 7). 3504



Article

Figure 4. View along the b axis showing the F···F contacts between the chains in 1.

dimers inside the layer are tilted about 56° relative to the direction of the chain. On the other hand, additional interactions between fluorine atoms [F6···F7, distance of 2.878(2) Å] of different layers twist them 90° with respect to the following one (Figure 7a). Polymorph B crystallizes in a triclinic P1̅ space group, also with one independent molecule. As in polymorph A, the layers consist of chains of dimers formed by hydrogen bonds (distance N3−H3···O1 of 1.88 Å) but, in this case, with the dimers linked by F5···F5′ [distance of 2.846(4) Å]. The chains so formed are stacked by π−π interactions between the imidazole and the phenyl rings [shortest distance of 3.32(7) Å]. Additional weaker symmetric fluorine interactions [F6···F6′ and F7···F7′ distances of 2.936(4) Å] between dimeric units of adjacent chains originate laddered chains extending the dimensionality in the crystal (Figure 7b). Compound 5 crystallizes in a monoclinic P21/c space group containing two different molecules per asymmetric unit. Each molecule independently is almost planar, but they are displayed perpendicular to each other with an angle of about 78°. Each type of molecule interacts in a different way with the neighboring ones. If they are named as molecules type 1 and 2, several interactions are observed among molecules of same type (Figure 8). So, the molecules of type 1 interact weakly through F···F interactions (F51 and F61 atoms) with two adjacent ones that are situated parallel but in different levels [F51···F61′ and F61···F5″ distances of 2.88(1) Å]. These interactions, extended along the b axis, form a stacking along that direction. On the other hand, the contacts between type 2 molecules through F72···F72 atoms of adjacent molecules [distances of 2.89(1) Å] also form a stacking along the b axis. The only contact between both types of molecules deals with interactions between O11 atom of the molecules 1 and the methyl group of neighboring molecules 2 that are found in different levels [O11···H92′ distance of 2.59(8) Å; O11···C92′ distance of 3.37(1) Å]. No significant π−π interactions between the phenyl or imidazole rings are observed. Compound 6 crystallizes in a monoclinic P21/c space group. The asymmetric unit contains two different molecules named 1 and 2 (Figure 9). The molecules are not planar because the CF3CO fragments are clearly out of the molecular plane

Figure 5. View of the chain formed by H-bonds in 2.

Figure 6. View of the F···F and H-bonding interactions among the tilted chains formed by dimeric units in 3.

Polymorph A crystallizes in a monoclinic P21/n space group containing one molecule per asymmetric unit. Its crystalline structure consists of dimers formed by symmetric hydrogen bonding interactions N3−H3···O1 of neighboring molecules (distance of 1.85 Å). These dimers are in an almost planar disposition and interact with neighboring dimeric units through symmetric F···F interactions [F5···F6, distance of 2.938(1) Å] giving rise to slightly laddered chains along [2̅10]. The presence of short contacts between the imidazole rings [shortest distance of 3.34(3) Å] forms layers parallel to the (001) plane. The 3505



Article

Figure 7. View of the different F···F interactions between the dimers in 4 which lead to a different molecular packing in the crystal: (a) polymorph A; (b) polymorph B.

defined by the phenyl ring. Molecules type 1 and 2 are partially overlapped in an opposite way allowing a double hydrogen bond between them. They are also slightly tilted with a dihedral angle between their molecular planes of 22.2(2)°. The relative positions of the hydrogen atoms in the NH groups, pointing to the O atoms of neighboring molecules, favor these interactions. So, each molecule forms four different hydrogen bonds with their adjacent molecules: N12−H12···O11; N32−H32···O21; N31−H31···O22; N11−H11···O12 (Table 3) giving rise to a chain along the a axis in which the molecules 1 and 2 are alternated. Several fluorine contacts between the different chains can be observed which spread out the dimensionality of the interactions. The distances F41···F62 and F41···F72 are about 2.84 Å being in an usual range found for this type of contacts, however, it is noteworthy the stronger symmetric interaction between adjacent chains through F42 with a distance F···F of 2.677(3) Å and angle C42F42···F42 of 98.4(2)° [the torsion angle C42F42···F42C42 is 180(3)°] (Figure 10). The F···F contacts determined in this work are represented in Figure 11 (red squares). The distribution is similar to that of the literature (half-blue points) and includes one of the shortest

F···F distances ever reported [2.596(3) Å]. The 2.6 Å from ref 37 is an approximate value, the 2.61 Å from ref 38 corresponds to a 1.1 GPa pressure, the 2.64 Å distance corresponds to a disordered tetrafluoroborate anion,50 and only the 2.63 value of ref 24 is devoid of ambiguity. Unfortunately, our value corresponds to a type I situation and our type II situation corresponds to distances between 2.88 and 2.91 Å. As it is well-known, π−π interactions play an important role in the packing arrangement of the molecules, and the presence of the fluorine atoms in the phenyl ring in compounds 1−5 could, a priori, modify them. Weak π−π contacts between the different rings were found in compounds 1, 4-A, and 4-B. However, there has not been found a clear relationship between the presence of the fluorine as substituents and the existence or not of those π−π interactions as it is deduced by comparing the structures of 1−3 with their non F-substituted homologous ones,59 in which weak partial π−π contacts between the rings are observed. In conclusion, the formation of strong linear Hbonds between the molecules is the driving force for the packing arrangement achieving chains whose dimensionality is extended by the formation of additional F···F contacts. Finally, the presence of different substituents on the imidazole ring 3506



Article

Figure 8. View along the b-axis showing the different interactions in both types of molecules in 5.

Figure 10. View along the a axis showing the chains formed by Hbonds as well as the interchain F···F interactions in 6.

Figure 11. Number of examples vs. F···F distances in Å including those determined in the present work.

Figure 9. An ORTEP plot (20% probability) for compound 6.

■

CONCLUSIONS In this paper we have explored the behavior of five tetrafluorinated benzimidazoles in search of intermolecular interactions and the relative importance of HBs vs. XBs. Note that the fluorine atoms of the CF3 group in compound 2 do not play any significant role as far as XBs are concerned. The simultaneous presence of both interactions in most compounds (note that in compound 5 no HBs are present) led to a rich wealth of different packings, including a new example of polymorphism and some short F···F contacts. We hope that the results here presented will prove useful to other structural studies where fluorine atoms are present such as in anion···π interactions,61 or in medicinal chemistry.2l,62 Further solid-state NMR studies of perfluorinated aromatic derivatives together with DFT periodic calculations are necessary to attain the level of NMR crystallography.5f

seems to exert a certain influence on the overlapping of the aromatic rings in adjacent chains, hindering, in some cases, their interactions via π−π contacts. Solid-State NMR Spectroscopy. The 13C and 15N CPMAS and the 19F MAS results are reported in Table 5. In the case of compound 4 the spectra correspond to a mixture of both polymorphs. In these series of compounds, the splittings are less related to the presence of one or two independent molecules in the crystal than to the unresolved interaction with the fluorine atoms. For instance, compound 1 with two independent molecules show no splittings, while compound 2 with only one independent molecule shows C2 and F7 split. In the case of compound 3, the broadening due to extensive dipolar couplings between 19F atoms (natural abundance 100%)60 blurred the small difference in chemical shifts between F4/F7 and F5/F6. 3507



Article

Table 5. Solid-State 13C, 15N, and 19F NMR Chemical Shifts (ppm) of Compounds 1−5 13

C2

C3a

C4

C5

C6a

C7a

C7a

other

1 2

141.8 146.3 143.0 157.1 156.0 155.7 153.7

125.8 126.5

136.9 136.6

136.9 136.6

136.9 136.6

136.9 136.6

118.6 119.5

119.5 (CF3)

112.3 112.6 112.8 114.1b

132.2 132.8 133.1 132.2

132.2 135.5 134.5 136.3 19 F MAS

132.2 132.8 133.1 132.2

112.3 114.8

29.0 (CH3)

114.8b

28.6 (CH3)

5

a

C CPMAS

compound

3 4

a

a

132.2 135.4 134.5 136.3 15 N CPMAS and

compound

N1

N3

F4

F5

F6

F7

other

1 2 3 4 5

−223.9 −228.5 −262.4 −263.2 −268.7

−146.8 −153.1 −262.4 −265.2 −268.7

−155.0 −152.2 −160 (vb) −160.3 −165.6

−162.0 −160.4

−156.7 −150.5

−164.6 −164.3; −166.3

−63.1 (CF3)

−167.1 −165.5

−168.0 −163.6

−168.5 −168.9

These signals are complex multiplets. bThese signals can be interchanged.

■

Resnati, G. IUCrJ 2014, 1, 5−7. (n) Mukherjee, A.; Desiraju, G. R. IUCrJ 2014, 1, 49. (3) (a) Aakeröy, C. B.; Fasulo, M.; Schultheiss, N.; Desper, J.; Moore, C. J. Am. Chem. Soc. 2007, 129, 13772. (b) Gonnade, R. G.; Shashidhar, M. S.; Bhadbhade, M. M. J. Indian Inst. Sci. 2007, 87, 149. (c) Aakeröy, C. B.; Chopade, P. D.; Ganser, C.; Desper, J. Chem. Commun. 2011, 47, 4688. (4) (a) Halogen Bonding. Fundamentals and Applications; Metrangolo, P., Resnati, G., Eds.; Struct. Bonding (Berlin) 2008, 126, 1. (b) Metrangolo, P.; Resnati, G.; Pilati, T.; Biella, S. Struct. Bonding (Berlin) 2008, 126, 105. (c) Fourmigué, M. Struct. Bonding (Berlin) 2008, 126, 181. (d) Merz, K.; Vasylyeva, V. CrystEngComm 2010, 12, 3989. (e) Chopra, D.; Guru Row, T. N. CrystEngComm 2011, 13, 2175. (f) Primagi, A.; Cavallo, G.; Metrangolo, P.; Resnati, G. Acc. Chem. Res. 2013, 46, 2686. (5) (a) Baldy, A.; Elguero, J.; Faure, R.; Pierrot, M.; Vincent, E.-J. J. Am. Chem. Soc. 1985, 107, 5290. (b) Etter, M. C.; Vojta, G. M. J. Mol. Graphics 1989, 7, 3. (c) Elguero, J.; Cano, F. H.; Foces-Foces, C.; Llamas-Saíz, A.; Limbach, H.-H.; Aguilar-Parrilla, F.; Claramunt, R. M.; López, C. J. Heterocycl. Chem. 1994, 31, 695. (d) Anulewicz, R.; Wawer, I.; Krygowski, T. M.; Männle, F.; Limbach, H.-H. J. Am. Chem. Soc. 1997, 119, 12223. (e) Claramunt, R. M.; Cornago, P.; Torres, V.; Pinilla, E.; Torres, M. R.; Samat, A.; Lokshin, V.; Valés, M.; Elguero, J. J. Org. Chem. 2006, 71, 6881. (f) NMR Crystallography; Harris, R. K., Wasylischen, R. E., Duer, M. J., Eds.; Wiley: Chichester, 2009. (6) (a) Sridlar, R.; Perumal, P. T. Synth. Commun. 2004, 34, 735. (b) Lahti, P. M. Adv. Phys. Org. Chem. 2011, 45, 93 (the structure is reported on p 151). (7) Troitskaya, V. I.; Rudyk, V. I.; Yakobson, G. G.; Yagupol’skii, L. M. Chem. Heterocycl. Compd. 1982, 1232. (8) (a) Brooke, G. M.; Burdon, J.; Tatlow, J. C. J. Chem. Soc. 1961, 802. (b) Bishop, B. C.; Chelton, E. T. J.; Jones, A. S. Biochem. Pharmacol. 1964, 13, 751. (c) Burton, D. E.; Lambie, A. J.; Ludgate, J. C. L.; Newbold, G. T.; Percival, A.; Saggers, D. T. Nature 1965, 208, 1166. (9) Seber, G.; Freitas, R. S.; Mague, J. T.; Paduan-Filho, A.; Gratens, X.; Bindilatti, V.; Oliveira, N. F., Jr.; Yoshioka, N.; Lahti, P. M. J. Am. Chem. Soc. 2012, 134, 3825. (10) (a) Alkorta, I.; Elguero, J. Struct. Chem. 2004, 15, 117. (b) Grabowski, S. J.; Sadlej, A. J.; Sokalski, W. A.; Leszczynski, J. Chem. Phys. 2006, 327, 151. (c) Sánchez-Sanz, G.; Trujillo, C.; Alkorta, I.; Elguero, J. Comp. Theor. Chem. 2012, 991, 124. (d) Matta, C. F.; Castillo, N.; Boyd, R. J. J. Phys. Chem. A 2005, 109, 3669. (e) Goedecke, C.; Sitt, R.; Frenking, G. Inorg. Chem. 2012, 51, 11259. (11) Allen, F. H. Acta Crystallogr. 2002, B58, 380. (12) Sakurai, T.; Sundaralingam, M.; Jeffrey, G. A. Acta Crystallogr. 1963, 16, 354.

ASSOCIATED CONTENT

S Supporting Information *

Crystallographic information file. This material is available free of charge via the Internet at http://pubs.acs.org.

■

AUTHOR INFORMATION

Corresponding Authors

*E-mail: [email protected] (M.P.-T.). *E-mail: [email protected] (M.C.T.). Notes

The authors declare no competing financial interest. In Memoriam of Professor Alan Roy Katritzky.

■

ACKNOWLEDGMENTS This work was financed by the Spanish MICINN (CTQ201016122).

■

REFERENCES

(1) (a) Jeffrey, G. A. An Introduction to Hydrogen Bonding; Oxford University Press: Oxford, 1997. (b) Desiraju, G. R.; Steiner, T. The Weak Hydrogen Bond in Structural Chemistry and Biology, IUCr Monographs on Crystallography; Oxford University Press: Oxford, 1999. (c) Gilli, G.; Gilli, P. The Nature of the Hydrogen Bond: Outline of a Comprehensive Hydrogen Bond Theory, IUCr Monographs on Crystallography; Oxford University Press: Oxford, 2009. (2) (a) Metrangolo, P.; Resnati, G. Chem.Eur. J. 2001, 7, 2511. (b) Reichenbächer, K.; Süss, H. I.; Hulliger, J. Chem. Soc. Rev. 2005, 34, 22. (c) Politzer, P.; Lane, P.; Concha, M. C.; Ma, Y.; Murray, J. S. J. Mol. Model. 2007, 13, 305. (d) Metrangolo, P.; Meyer, F.; Pilati, T.; Resnati, G.; Terraneo, G. Angew. Chem., Int. Ed. 2008, 47, 6144. (e) Bertani, R.; Sgarbossa, P.; Venzo, A.; Lelj, F.; Amati, M.; Resnati, G.; Pilati, T.; Metrangolo, P.; Terraneo, G. Coord. Chem. Rev. 2010, 254, 677. (f) Cavallo, G.; Metrangolo, P.; Pilati, T.; Resnati, G.; Sansotera, M.; Terraneo, G. Chem. Soc. Rev. 2010, 39, 3772. (g) García, M. A.; Cabildo, P.; Claramunt, R. M.; Pinilla, E.; Torres, M. R.; Alkorta, I.; Elguero, J. Inorg. Chim. Acta 2010, 363, 1332. (h) Berger, R.; Resnati, G.; Metrangolo, P.; Weber, E.; Hulliger, J. Chem. Soc. Rev. 2011, 40, 3496. (i) Metrangolo, P.; Resnati, G. Cryst. Growth Des. 2012, 12, 5835. (j) Bauzá, A.; Alkorta, I.; Frontera, A.; Elguero, J. J. Chem. Theory Comput. 2013, 9, 5201. (k) Alkorta, I.; Sánchez-Sanz, G.; Elguero, J. CrystEngComm 2013, 15, 3178. (l) Wilcken, R.; Zimmermann, M. O.; Lange, A.; Joerger, A. C.; Boeckler, F. M. J. Med. Chem. 2013, 56, 1363. (m) Metrangolo, P.; 3508



Article

(13) Nyburg, S. C.; Faerman, C. H. Acta Crystallogr. 1985, B41, 274. (14) Desiraju, G. R.; Parthasarathy, R. J. Am. Chem. Soc. 1989, 111, 8725. (15) Schwiebert, K. E.; Chin, D. N.; MacDonald, J. C.; Whitesides, G. M. J. Am. Chem. Soc. 1996, 118, 4018. (16) Vishnumurthy, K.; Guru Row, T. N.; Venkatesan, K. J. Chem. Soc. Perkin Trans. 2 1997, 615. (17) Thalladi, V. R.; Weiss, H. C.; Bläser, D.; Boese, R.; Nangia, A.; Desiraju, G. R. J. Am. Chem. Soc. 1998, 120, 8702. (18) Thalladi, V. R.; Weiss, H.-C.; Boese, R.; Nangia, A.; Desiraju, G. R. Acta Crystallogr. 1999, B55, 1005. (19) Kowalik, J.; VanDerveer, D.; Clower, C.; Tolbert, L. M. Chem. Commun. 1999, 2007. (20) Fernández-Castañ o, C.; Foces-Foces, C.; Cano, F. H.; Claramunt, R. M.; Escolástico, C.; Fruchier, A.; Elguero, J. New J. Chem. 1997, 21, 195. (21) Wolff, J. J.; Gredel, F.; Oesez, T.; Irngartinger, H.; Pritzkow, H. Chem.Eur. J. 1999, 5, 129. (22) Madhavi, N. N. L.; Desiraju, G. R.; Bilton, C.; Howard, J. A. K.; Allen, F. H. Acta Crystallogr. 2000, B56, 1063. (23) Dautel, O. J.; Fourmigué, M. J. Org. Chem. 2000, 65, 6479. (24) Bach, A.; Lentz, D.; Luger, P. J. Phys. Chem. A 2001, 105, 7405. (25) Vangala, V. R.; Nangia, A.; Lynch, V. M. Chem. Commun. 2002, 1304. (26) Choudhury, A. R.; Urs, U. K.; Guru Row, T. N.; Nagarajan, K. J. Mol. Struct. 2002, 605, 71. (27) Bianchi, R.; Forni, A.; Pilati, T. Chem.Eur. J. 2003, 9, 1631. (28) Choudhury, A. R.; Guru Row, T. N. Cryst. Growth Des. 2004, 4, 47. (29) Hibbs, D. E.; Overgaard, J.; Platts, J. A.; Waller, M. P.; Hursthouse, M. B. J. Phys. Chem. B 2004, 108, 3663. (30) Chopra, D.; Nagarajan, K.; Guru Row, T. N. Cryst. Growth Des. 2005, 5, 1035. (31) Halper, S. R.; Cohen, S. M. Inorg. Chem. 2005, 44, 4139. (32) Hulme, A. T.; Price, S. L.; Tocher, D. A. J. Am. Chem. Soc. 2005, 127, 1116. (33) Choudhury, A. R.; Guru Row, T. N. CrystEngComm 2006, 8, 265. (34) Chopra, D.; Cameron, T. S.; Ferrara, J. D.; Guru Row, T. N. J. Phys. Chem. A 2006, 110, 10465. (35) Chopra, D.; Guru Row, T. N. Cryst. Growth Des. 2008, 8, 848. (36) Schwarzer, A.; Weber, E. Cryst. Growth Des. 2008, 8, 2862. (37) Subramanian, S.; Park, S. K.; Parkin, S. R.; Podzorov, V.; Jackson, T. N.; Anthony, J. E. J. Am. Chem. Soc. 2008, 130, 2706. (38) Olejniczak, A.; Katrusiak, A.; Vij, A. J. Fluorine. Chem. 2008, 129, 173. (39) Thakur, T. S.; Kirchner, M. T.; Bläser, D.; Boese, R.; Desiraju, G. R. CrystEngComm 2010, 12, 2079. (40) Barceló-Oliver, M.; Estarellas, C.; García-Raso, A.; Terrón, A.; Frontera, A.; Quiñonero, D.; Mata, I.; Molins, E.; Deyà, P. M. CrystEngComm 2010, 12, 3758. (41) Vasylyeva, V.; Merz, K. J. Fluorine Chem. 2010, 131, 446. (42) Collas, A.; De Borger, R.; Amanova, T.; Blockhuys, F. CrystEngComm 2011, 13, 702. (43) Nayak, S. K.; Reddy, M. K.; Guru Row, T. N.; Chopra, D. Cryst. Growth Des. 2011, 11, 1578. (44) Nayak, S. K.; Reddy, M. K.; Chopra, D.; Guru Row, T. N. CrystEngComm 2012, 14, 200. (45) Chopra, D. Cryst. Growth Des. 2012, 12, 541. (46) Vasylyeva, V.; Shishkin, O. V.; Maleev, A. V.; Merz, K. Cryst. Growth Des. 2012, 12, 1032. (47) Baker, R. J.; Colavita, P. E.; Murphy, D. M.; Platts, J. A.; Wallis, J. D. J. Phys. Chem. A 2012, 116, 1435. (48) Huston, S. M.; Wang, J.; Loth, M. A.; Anthony, J. E.; Conrad, B. R.; Dougherty, D. B. J. Phys. Chem. C 2012, 116, 21465. (49) Pérez-Medina, C.; López, C.; Cabildo, M. P.; Claramunt, R. M.; Torralba, M. C.; Torres, M. R.; Alkorta, I.; Elguero, J. J. Mol. Struct. 2012, 1022, 139.

(50) Durá, G.; Carrión, M. C.; Jalón, F. A.; Rodríguez, A. M.; Manzano, B. R. Cryst. Growth Des. 2013, 13, 3275. (51) Madura, I. D.; Czerwinska, K.; Jakubczyk, M.; Pawelko, A.; Adamczyk-Wózniak, A.; Sporzynski, A. Cryst. Growth Des. 2013, 13, 5344. (52) Putta, A.; Mottishaw, J. D.; Wang, Z.; Sun, H. Cryst. Growth Des. 2014, 14, 350−356. (53) Alvarez-Builla, J.; Vaquero. J. J.; Barluenga, J., Eds. Modern Heterocyclic Chemistry; Wiley-VCH: Weinheim, 2011; Vols. I-II. (54) Heaton, A.; Hill, M.; Drakesmith, F. J. Fluorine Chem. 1997, 81, 133. (55) Sheldrick, G. M. SHELX97, Program for Refinement of Crystal Structure; University of Göttingen: Göttingen, Germany, 1997. (56) Murphy, P. D. J. Magn. Reson. 1983, 52, 343. (57) Alemany, L. B.; Grant, D. M.; Alger, T. D.; Pugmire, R. J. J. Am. Chem. Soc. 1983, 105, 6697. (58) Allen, F. H. Acta Crystallogr. Sect. B 2002, 58, 380. (59) González-Padilla, J. E.; Rosales-Hernández, M. C.; PadillaMartínez, I. I.; García-Báez, E. V.; Rojas-Lima, S.; Salazar-Pereda, V. Acta Crystallogr. Sect. C 2014, 70, 55. (60) Robbins, A. J.; Ng, W. T. K.; Jochym, D.; Keal, T. W.; Clark, S. J.; Tozer, D. J.; Hodgkinson, P. Phys. Chem. Chem. Phys. 2007, 9, 2389. (61) Giese, M.; Albrech, M.; Repenko, T.; Sackmann, J.; Valkonen, A.; Rissanen, K. Eur. J. Org. Chem. 2014, 2435. (62) Ilardi, E. A.; Vitaku, E.; Njardson, J. T. J. Med. Chem. 2014, 57, 2832.

3509


Structural Investigation of Weak Intermolecular Interactions (Hydrogen

Recommend Documents