Synthesis, crystal structure and Hirshfeld surface analysis of 2-(perfluoro­phen­yl)acetamide in comparison with some related compounds

Novikov, A.P.; Bezdomnikov, A.A.; Grigoriev, M.S.; German, K.E.

doi:10.1107/S2056989021013359

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Volume 78| Part 1| January 2022| Pages 80-83

https://doi.org/10.1107/S2056989021013359

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Synthesis, crystal structure and Hirshfeld surface analysis of 2-(perfluorophenyl)acetamide in comparison with some related compounds

Anton P. Novikov,^a,^b ^* Alexey A. Bezdomnikov,^b Mikhail S. Grigoriev ^b and Konstantin E. German ^b

^aPeoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya, St, 117198, Moscow, Russian Federation, and ^bFrumkin Institute of Physical Chemistry and Electrochemistry Russian, Academy of Sciences, 31 Leninsky Prospekt bldg 4, 119071 Moscow, Russian Federation
^*Correspondence e-mail: tony.novickoff@yandex.ru

Edited by A. S. Batsanov, University of Durham, England (Received 24 November 2021; accepted 15 December 2021; online 1 January 2022)

The molecular and crystal structures of the title compound, C₈H₄F₅NO, were examined by single-crystal X-ray diffraction and Hirshfeld surface analysis. The title compound was synthesized by a new method at the interface of aqueous solutions of LiOH and pentafluorophenylacetonitrile. In the crystal, hydrogen bonds and π–halogen interactions connect the molecules into double layers. Analysis of the Hirshfeld surface showed that the most important contributions to the crystal packing are made by F⋯F (30.4%), C⋯F/F⋯C (22.9%), O⋯H/H⋯O (14.9%), H⋯F/F⋯H (14.0%) and H⋯H (10.2%) contacts. The Hirshfeld surfaces of analogues of the title compound were compared and the effect of perfluorination on the crystal packing was shown.

Keywords: crystal structure; hydrogen bonds; Hirshfeld surface analysis; acetamide; perfluorophenyl.

CCDC reference: 2128969

1. Chemical context

The development of effective methods for the formation of an amide bond CONR₂ is of great importance because of the high synthetic value of amides, their industrial applications and pharmacological interest (Massolo et al., 2020 ). The addition of functional groups such as –F, –Cl etc. can improve the catalytic or biological activity of the corresponding coordination compounds (Naumann, 2003 ).

The title compound was previously obtained (Barbour et al., 1961 ) using 2,3,4,5,6-pentafluorobenzoic acid as the starting compound, but its crystal structure was not studied. In this work, we have synthesized 2–(perfluorophenyl) acetamide, 1, from pentafluorophenylacetonitrile and determined its crystal structure. We have analysed the Hirshfeld surface of this compound and compared it with those of 2-(4-chlorophenyl) acetamide, 2 (OCETAT; Ma et al., 2011 ) and 2-phenylacetamide, 3 (SAWHAC; Skelton et al., 2017 ).

2. Structural commentary

The title compound crystallizes in the space group P2₁/c with four molecules in the unit cell. All H atoms in the phenyl ring are replaced by fluorine atoms. The asymmetric unit is illustrated in Fig. 1. Carbon atom C7 is in the plane of the imidazole ring. The acetamide group is twisted relative to the Ph-ring with a C2—C1—C7—C8 torsion angle of 107.61 (14)°. This angle is larger than in the 3-chloro-4-hydroxyphenyl acetamide (Davis et al., 2005 ). Torsion angles C8—C7—C1—C6 and C1—C7—C8—N2 are −74.35 (15) and 134.77 (12)°, respectively. This conformation is probably a consequence of intermolecular hydrogen bonds and steric factors.

Figure 1
Molecular structure of the title compound, including atom labelling. Displacement ellipsoids are drawn at the 50% probability level.

3. Supramolecular features

The hydrogen-bond system is shown in Fig. 2. In the structure, there are three hydrogen bonds. Two relatively strong hydrogen bonds are formed between the amino group and the oxygen atom of the carbonyl group. The shortest hydrogen bond N2—H2B⋯O1ⁱⁱ [symmetry code: (ii) x, −y + $[{3\over 2}]$ , z − $[{1\over 2}]$ ] is 2.8795 (14) Å (Table 1). The structure also contains one short contact of the type C—H⋯F with a C7—H7B⋯F1ⁱⁱⁱ [symmetry code: (iii) x, −y + $[{1\over 2}]$ , z − $[{1\over 2}]$ ] distance of 3.3764 (15) Å, but this cannot be called a hydrogen bond (Howard et al., 1996 ). The structure contains a short contact between the fluorine atoms F4 and F4^iv [symmetry code: (iv) −x + 1, −y + 2, −z + 1], whose length of 2.6649 (18) Å is shorter then the sum of the van der Waals radii (Mantina et al., 2009 ). However, according to the recommendations of Cavallo et al. (2016 ), it cannot be considered to be a halogen bond.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2A⋯O1ⁱ	0.853 (19)	2.062 (19)	2.9120 (15)	174.3 (16)
N2—H2B⋯O1ⁱⁱ	0.869 (18)	2.053 (19)	2.8795 (14)	158.7 (16)
Symmetry codes: (i) ; (ii) $[x, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ .

Figure 2
View showing hydrogen bonds in 1. [Symmetry codes: (i) −x, −y + 2, −z + 1; (ii) x, −y + $[{3\over 2}]$ , z − $[{1\over 2}]$ .]

The crystal packing can be represented as layered, as shown in Fig. 3. The hydrogen bonds bind molecules inside double layers parallel to (100). This type of packing can be found in the structure of 5,5-dichloro-6-hydroxydihydropyrimidine-2,4(1H,3H)-dione (Novikov et al., 2020 ).

Figure 3
Crystal packing of 1 showing the double layers.

4. Hirshfeld surface analysis

Crystal Explorer 21 was used to calculate the Hirshfeld surfaces and two-dimensional fingerprint plots (Spackman et al., 2021 ). The donor–acceptor groups are visualized using a standard (high) surface resolution and the d_norm surfaces are mapped over a fixed colour scale of −0.542 (red) to 1.121 (blue) a.u., as illustrated in Fig. 4a. The most important hydrogen bonds, N2—H2A⋯O1ⁱ are N2—H2B⋯O1ⁱⁱ, are shown by red spots on the surface. A weak red spot may indicate the presence of a π-interaction between the C atom of the ring and the F atom of another ring. There are no π-stacking interactions of the molecules, which can be seen from the absence of characteristic triangles in Fig. 4b. However, a bright spot on the shape-index surface may indicate the presence of a π-halogen interaction. The overall two-dimensional fingerprint map for the title compound is shown in Fig. 5a. The fingerprint plots show that the F⋯F contacts (30.4%) make the largest contribution to the overall packing of the crystal. Contacts of the C⋯F/F⋯C type also make a significant contribution (22.9%). This can also be related to the presence of a π—F interaction in the structure. The short distances C1⋯F2ⁱⁱⁱ [symmetry code: (iii) x, −y + $[{1\over 2}]$ , z − $[{1\over 2}]$ ] and C4⋯F5^v [symmetry code: (v) x, −y + $[{3\over 2}]$ , z + $[{1\over 2}]$ ], which are 3.079 (2) and 3.110 (2) Å, respectively, confirm this fact (Novikov et al., 2021 ; Zhuo et al., 2014 ). The O⋯H/H⋯O and H⋯F/F⋯H hydrogen bonds also make a significant contribution to the Hirshfeld surface area (28.9% in total). In addition, van der Waals interactions (H⋯H) contribute 10.2%. The contribution of other contacts is less than 8% in total and is not discussed in this work.

Figure 4
Hirshfeld surface mapped over (a) d_norm and (b) shape-index to visualize the interactions in the title compound.

Figure 5
(a) The full two-dimensional fingerprint plot for the title compound, together with those delineated into (b) F⋯F, (c) C⋯F/F⋯C, (d) O⋯H/H⋯O, (e) H⋯F/F⋯H and (f) H⋯H contacts.

An analogous methodology was applied to construction of Hirshfeld surfaces for similar benzenamide derivatives with one Cl substituent and an unsubstituted six-membered ring. The effect of perfluorination is evident from the comparison made in Fig. 6. On going from the title compound 1 to compound 3, the halogen bonds disappear. Moreover, if only one hydrogen atom in the ring is replaced by chlorine, the proportion of halogen and π-halogen bonds is significantly reduced. However, in the transition from compound 1 to 3, the contribution of van der Waals interactions increases.

Figure 6
Percentage contributions of contacts to the Hirshfeld surface in the title compound and for related compounds.

5. Database survey

A search in the Cambridge Structural Database (CSD, Version 5.42, update of September 2021; Groom et al., 2016 ) gave only a few results for phenyl acetamide. We have found no compound with a fluorine-substituted phenyl ring similar to the title compound. In 3 (SAWHAC; Skelton et al., 2017), the H atoms in the phenyl ring are not substituted, and this compound crystallizes in space group C2/c different from 1. In 2 (OCETAT; Ma et al., 2011) the hydrogen atom in the para-position to the acetamide group is substituted with chlorine. FIXCEV (Davis et al., 2005) contains a chlorine atom at the meta-position and a hydroxo-group at the para-position to the amido group. However, as a result of the presence of a hydroxo group, a different system of hydrogen bonds and packing is present in the structure, as is the case in the structure of BHXPAM10 (McMillan et al., 1975 ), where there are two bromine atoms and two hydroxo groups.

6. Synthesis and crystallization

A saturated aqueous solution of LiOH (0.5 mL, at 298 K) and 2,3,4,5,6-pentafluorophenylacetonitrile (0.5 mL) were placed in a 1.5 mL screw-neck vial. The closed vial was shaken in a water bath at 383 K until the organic phase turned dark red (30 min). The closed vial with the resulting two-phase system was left for three days at 298 K, and slow growth of the crystal phase at the interface of water-2,3,4,5,6-pentafluorophenylacetonitrile was observed. The obtained crystals were identified as 2-(pentafluorophenyl)acetamide by X-ray structural analysis.

7. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. N- and C-bound H atoms were refined isotropically [U_iso(H) = 1.2U_eq(N,C)].

Table 2
Experimental details

Crystal data
Chemical formula	C₈H₄F₅NO
M_r	225.12
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	100
a, b, c (Å)	14.4934 (5), 5.8247 (2), 9.7836 (3)
β (°)	90.870 (2)
V (Å³)	825.83 (5)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.20
Crystal size (mm)	0.2 × 0.15 × 0.06

Data collection
Diffractometer	Bruker KAPPA APEXII area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2008 )
T_min, T_max	0.888, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	10007, 2394, 1868
R_int	0.032
(sin θ/λ)_max (Å⁻¹)	0.703

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.036, 0.101, 1.02
No. of reflections	2394
No. of parameters	148
H-atom treatment	Only H-atom coordinates refined
Δρ_max, Δρ_min (e Å⁻³)	0.41, −0.22
Computer programs: APEX2 and SAINT (Bruker, 2008), SHELXS (Sheldrick, 2008 ), SHELXL2018/3 (Sheldrick, 2015 ) and OLEX2 (Dolomanov et al., 2009 ).

Supporting information

CCDC reference: 2128969

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989021013359/zv2012sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989021013359/zv2012Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989021013359/zv2012Isup3.cml

checkCIF report

Computing details top

Data collection: SAINT (Bruker, 2008); cell refinement: APEX2 (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS (Sheldrick, 2008); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

2-(2,3,4,5,6-Pentafluorophenyl)acetamide top

Crystal data top

C₈H₄F₅NO	F(000) = 448
M_r = 225.12	D_x = 1.811 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 14.4934 (5) Å	Cell parameters from 2651 reflections
b = 5.8247 (2) Å	θ = 3.8–30.0°
c = 9.7836 (3) Å	µ = 0.20 mm⁻¹
β = 90.870 (2)°	T = 100 K
V = 825.83 (5) Å³	Fragment, colourless
Z = 4	0.2 × 0.15 × 0.06 mm

Data collection top

Bruker KAPPA APEXII area-detector diffractometer	1868 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.032
Absorption correction: multi-scan (SADABS; Bruker, 2008)	θ_max = 30.0°, θ_min = 4.2°
T_min = 0.888, T_max = 1.000	h = −20→20
10007 measured reflections	k = −7→8
2394 independent reflections	l = −13→13

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F² > 2σ(F²)] = 0.036	Only H-atom coordinates refined
wR(F²) = 0.101	w = 1/[σ²(F_o²) + (0.0514P)² + 0.2972P] where P = (F_o² + 2F_c²)/3
S = 1.01	(Δ/σ)_max < 0.001
2394 reflections	Δρ_max = 0.41 e Å⁻³
148 parameters	Δρ_min = −0.22 e Å⁻³
0 restraints

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
F1	0.18090 (6)	0.17229 (15)	0.56871 (9)	0.0236 (2)
F5	0.29215 (6)	0.86391 (15)	0.38309 (9)	0.0256 (2)
F2	0.33786 (6)	0.12487 (16)	0.71473 (9)	0.0277 (2)
F3	0.47319 (6)	0.44830 (17)	0.69860 (9)	0.0282 (2)
F4	0.44951 (6)	0.81691 (16)	0.53158 (10)	0.0291 (2)
C7	0.14592 (9)	0.5453 (2)	0.38358 (13)	0.0164 (2)
H7A	0.1111 (12)	0.407 (3)	0.3821 (17)	0.020*
H7B	0.1623 (11)	0.578 (3)	0.2907 (18)	0.020*
C2	0.24618 (9)	0.3351 (2)	0.55727 (13)	0.0160 (3)
C4	0.39563 (9)	0.4708 (3)	0.62489 (13)	0.0193 (3)
C5	0.38321 (9)	0.6590 (2)	0.54069 (14)	0.0190 (3)
C6	0.30222 (9)	0.6800 (2)	0.46574 (13)	0.0168 (3)
C1	0.23166 (8)	0.5202 (2)	0.47089 (12)	0.0142 (2)
C3	0.32681 (9)	0.3079 (2)	0.63280 (13)	0.0181 (3)
C8	0.08285 (8)	0.7324 (2)	0.43665 (12)	0.0138 (2)
O1	0.06484 (6)	0.74411 (16)	0.56027 (9)	0.0168 (2)
N2	0.04797 (8)	0.8763 (2)	0.34425 (11)	0.0178 (2)
H2A	0.0121 (12)	0.985 (3)	0.3679 (18)	0.021*
H2B	0.0642 (12)	0.868 (3)	0.2593 (19)	0.021*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
F1	0.0232 (4)	0.0218 (4)	0.0259 (4)	−0.0081 (3)	−0.0001 (3)	0.0061 (3)
F5	0.0335 (5)	0.0193 (4)	0.0240 (4)	−0.0024 (3)	0.0013 (3)	0.0094 (3)
F2	0.0301 (5)	0.0281 (5)	0.0247 (4)	0.0023 (4)	−0.0027 (3)	0.0139 (4)
F3	0.0200 (4)	0.0387 (5)	0.0257 (4)	0.0010 (4)	−0.0091 (3)	−0.0006 (4)
F4	0.0252 (4)	0.0281 (5)	0.0340 (5)	−0.0138 (4)	0.0018 (3)	−0.0017 (4)
C7	0.0203 (6)	0.0176 (6)	0.0111 (5)	0.0022 (5)	−0.0017 (4)	−0.0026 (5)
C2	0.0171 (6)	0.0169 (6)	0.0142 (6)	−0.0025 (5)	0.0015 (4)	−0.0001 (5)
C4	0.0171 (6)	0.0254 (7)	0.0153 (6)	0.0018 (5)	−0.0017 (4)	−0.0024 (5)
C5	0.0189 (6)	0.0195 (7)	0.0188 (6)	−0.0055 (5)	0.0026 (5)	−0.0032 (5)
C6	0.0221 (6)	0.0149 (6)	0.0134 (6)	0.0001 (5)	0.0021 (4)	0.0021 (4)
C1	0.0171 (5)	0.0155 (6)	0.0100 (5)	0.0012 (4)	0.0011 (4)	−0.0014 (4)
C3	0.0218 (6)	0.0187 (6)	0.0138 (6)	0.0027 (5)	0.0004 (4)	0.0040 (5)
C8	0.0148 (5)	0.0167 (6)	0.0100 (5)	−0.0013 (4)	−0.0004 (4)	−0.0007 (4)
O1	0.0217 (4)	0.0206 (5)	0.0082 (4)	0.0020 (4)	0.0009 (3)	0.0001 (3)
N2	0.0234 (5)	0.0226 (6)	0.0075 (5)	0.0059 (5)	0.0003 (4)	0.0001 (4)

Geometric parameters (Å, º) top

F1—C2	1.3454 (15)	C2—C3	1.3823 (18)
F5—C6	1.3485 (15)	C4—C5	1.381 (2)
F2—C3	1.3421 (15)	C4—C3	1.3795 (19)
F3—C4	1.3328 (15)	C5—C6	1.3800 (18)
F4—C5	1.3343 (15)	C6—C1	1.3844 (18)
C7—H7A	0.949 (18)	C8—O1	1.2430 (15)
C7—H7B	0.962 (17)	C8—N2	1.3272 (17)
C7—C1	1.5043 (17)	N2—H2A	0.853 (19)
C7—C8	1.5192 (18)	N2—H2B	0.869 (18)
C2—C1	1.3841 (18)

H7A—C7—H7B	107.0 (14)	F5—C6—C5	118.21 (12)
C1—C7—H7A	111.2 (10)	F5—C6—C1	118.86 (12)
C1—C7—H7B	110.0 (10)	C5—C6—C1	122.93 (12)
C1—C7—C8	111.83 (10)	C2—C1—C7	122.62 (12)
C8—C7—H7A	106.9 (10)	C2—C1—C6	116.14 (11)
C8—C7—H7B	109.7 (10)	C6—C1—C7	121.22 (12)
F1—C2—C1	119.95 (11)	F2—C3—C2	120.16 (12)
F1—C2—C3	117.70 (11)	F2—C3—C4	120.01 (12)
C3—C2—C1	122.34 (12)	C4—C3—C2	119.83 (12)
F3—C4—C5	120.14 (12)	O1—C8—C7	120.54 (11)
F3—C4—C3	120.43 (12)	O1—C8—N2	123.01 (12)
C3—C4—C5	119.43 (12)	N2—C8—C7	116.44 (11)
F4—C5—C4	119.96 (12)	C8—N2—H2A	120.7 (12)
F4—C5—C6	120.71 (12)	C8—N2—H2B	120.6 (12)
C6—C5—C4	119.32 (12)	H2A—N2—H2B	118.6 (16)

F1—C2—C1—C7	−2.11 (19)	C5—C4—C3—F2	−179.69 (12)
F1—C2—C1—C6	179.76 (11)	C5—C4—C3—C2	−0.4 (2)
F1—C2—C3—F2	−0.42 (19)	C5—C6—C1—C7	−177.73 (12)
F1—C2—C3—C4	−179.75 (12)	C5—C6—C1—C2	0.43 (19)
F5—C6—C1—C7	1.67 (18)	C1—C7—C8—O1	−46.31 (16)
F5—C6—C1—C2	179.83 (11)	C1—C7—C8—N2	134.77 (12)
F3—C4—C5—F4	1.0 (2)	C1—C2—C3—F2	−179.69 (12)
F3—C4—C5—C6	−179.62 (12)	C1—C2—C3—C4	1.0 (2)
F3—C4—C3—F2	−0.2 (2)	C3—C2—C1—C7	177.14 (12)
F3—C4—C3—C2	179.08 (12)	C3—C2—C1—C6	−1.00 (19)
F4—C5—C6—F5	0.16 (19)	C3—C4—C5—F4	−179.60 (12)
F4—C5—C6—C1	179.55 (12)	C3—C4—C5—C6	−0.2 (2)
C4—C5—C6—F5	−179.26 (12)	C8—C7—C1—C2	107.61 (14)
C4—C5—C6—C1	0.1 (2)	C8—C7—C1—C6	−74.35 (15)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···O1ⁱ	0.853 (19)	2.062 (19)	2.9120 (15)	174.3 (16)
N2—H2B···O1ⁱⁱ	0.869 (18)	2.053 (19)	2.8795 (14)	158.7 (16)

Symmetry codes: (i) −x, −y+2, −z+1; (ii) x, −y+3/2, z−1/2.

Acknowledgements

X-ray diffraction experiment was carried out at the Centre of Shared Use of Physical Methods of Investigation of IPCE RAS. This study was supported by the RUDN University Strategic Academic Leadership Program.

Funding information

Funding for this research was provided by: Ministry of Science and Higher Education of the Russian Federation (subject No. AAAA-A18-118040590105-4).

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