research communications
and Hirshfeld surface analysis of 5-hydroxypentanehydrazide
aDepartamento de Química, Universidade Federal do Paraná, Centro, Politécnico, Jardim das Américas, 81530-900, Curitiba-PR, Brazil
*Correspondence e-mail: marcelodoca@ufpr.br
Carboxyhydrazides are widely used in medicinal chemistry because of their medicinal properties and many drugs have been developed containing this 5H12N2O2 (1). The aliphatic compound can react both via the hydroxyl and hydrazide moieties forming derivatives, which can inhibit Mycobacterium tuberculosis catalase-peroxidase (KatG) and consequently causes death of the pathogen. In this work, the hydrazide was obtained via a reaction of a lactone with hydrazine hydrate. The colourless prismatic single crystals belong to the orthorhombic Pca21. Regarding supramolecular interactions, the compound shows classic medium to strong intermolecular hydrogen bonds involving the hydroxyl and hydrazide groups. Besides, the three-dimensional packing also shows weak H⋯H and C⋯H contacts, as investigated by Hirshfeld surface analysis (HS) and fingerprint plots (FP).
A suitable intermediate to obtain potential hydrazide drug candidates is the title compound 5-hydroxypentanehydrazide, CCCDC reference: 2345070
1. Chemical context
Carboxyhydrazides are non-alkaline compounds that can be identified as R1–NR2–NR3R4, where R1 is an acyl group and R2–R4 are typically hydrogen atoms or alkyl substituents. These compounds, particularly those in which R2–R4 are hydrogen atoms, present themselves as valuable functional groups for drug design, since compounds with this and its derivatives tend to have biological activity as antidepressants or antibiotics, for example (Narang et al., 2012). The medicinal potentiality led to the development of several drugs containing this such as isoniazid, furazolidone, and isocarboxazide (Gegia et al., 2017).
containing an acyl group as one of their substituents, thus they are of general formulavia the reaction of hydrazine (usually obtained from its hydrochloride or its hydrate) with acyl derivatives such as or (Huang et al., 2016). For example, (cyclic esters) promptly react with hydrazine hydrate in a such as methanol. In this work, δ-valerolactone was added to hydrazine to afford orthorhombic crystals of 5-hydroxypentanehydrazide 1 (Huang et al., 2016).
are usually formedCompound 1 was first synthesized by Karakhanov and collaborators in 1969 (Karakhanov et al., 1969). However, this is the first report describing the crystallographic features of 5-hydroxypentanehydrazide.
2. Structural commentary
The molecule of 5-hydroxypentanehydrazide (Fig. 1), crystallizes in the orthorhombic Pca21. The comprises a unique molecule of 1 with no atoms in special positions, as well as no solvent of crystallization. The C—N, C=O, and N—N bond lengths within the hydrazide group of 1.3376 (17) Å, 1.2375 (16) Å, and 1.4193 (14), respectively, are in agreement with the values reported for containing a hydrazide unit (Jensen, 1956; Lo et al., 2020; Kolesnikova et al., 2022). Moreover, the short and unbranched carbon chain formed by atoms C1, C2, C3, C4, and C5, is located in a plane (blue plane in Fig. 2) that makes an angle α of 54.8 (9)° relative to the plane containing the hydrazide atoms N1, N2, C1, C2 and O1 (grey plane in Fig. 2).
The aforementioned conformational features, linked to the orientation of the hydrazide group, are a relatively common characteristic in compounds containing these groups linked to carbon chains. The α angle of 54.8 (9)° observed in compound 1 is consistent with values reported in the literature, regardless of the carbon chain size. Noteworthy, values include 54.54° for a compound with a twelve-carbon chain (Jensen, 1956), 56.33° for a nine-carbon chain (Jensen & Lingafelter, 1961), and 57.08° for a six-carbon chain (Lee et al., 2016).
3. Supramolecular features
The three-dimensional packing of 1 (Fig. 3) is characterized by several intermolecular O–H⋯N and N–H⋯O hydrogen bonds involving the hydroxyl and hydrazine as hydrogen bond donor and acceptor groups (Table 1). Among them, the strongest ones, regarding shortest H⋯acceptor distances and most linear donor—H⋯acceptor angles, are the N1—H3⋯O1ii [2.03 (2) Å; 166 (2)°; symmetry code: (ii) x, y + 1, z] and O2—H4⋯N2i [1.92 (3) Å; 172 (2)°; symmetry code: (i) −x + 1, −y + 2, z + ], involving the hydrazine and hydroxyl as donor group, respectively, and carbonyl and hydrazine moieties as acceptor groups, respectively. Besides, the hydrazine moiety also promotes hydrogen bonds of medium-force: N2—H1⋯O2iii [2.10 (2) Å; 147.2 (18)°; symmetry code: (iii) −x + , y, z − ], N2—H2⋯O1iv [2.59 (2) Å; 144.0 (16)°; symmetry code: (iv) x − , −y + 1, z] and N2—H2⋯O2v [2.57 (2) Å; 122.0 (16)°; symmetry code: (v) −x + 1, 1 − y, z − ]. The latter promotes the formation of chains with a C(9) graph-set motif running in the c-axis direction. A weak hydrogen bond of type C—H⋯O is also present in the crystal packing. Notably, thanks to this weak interaction, the carbonyl group is the acceptor of a bifurcated hydrogen bond, sharing its electronic density with the C2—H2 and N2—H2 groups and resulting in a six-membered ring with an R21(6) graph-set motif in the b-axis direction (Fig. 4a). The formation of seven-membered rings with an R23(7) graph-set motif is observed involving the H1–N2–N1–C1–O1⋯H2vi⋯O2iii moiety in the a-axis direction [symmetry code: (iii) −x + , y, z − ; (vi) x + , −y + 1, z; Fig. 4b). Together, these interactions act cooperatively for the stability of 1 in the solid state (Sutor et al., 1962; Domagała & Grabowski, 2005).
The non-covalent interactions responsible for the crystal packing were also investigated by a Hirshfeld surface analysis (HS; Hirshfeld, 1977), performed with CrystalExplorer 21.5 (Spackman et al., 2021). The Hirshfeld surface provides a three-dimensional representation that elucidates molecular interactions through the mathematical distance functions di, denoting the distance from the surface to the nearest atom within it, and de, denoting the distance from the surface to the nearest atom outside of it. The normalization of the di and de distances by the van der Waals radius leads to the dnorm function, which enables the visualization of a surface that delineates regions involved in both accepting and donating intermolecular interactions. A key component of this analysis entails the generation of 2D fingerprint plots (FP), providing two-dimensional representations of the Hirshfeld surface.
Using the dnorm function, expressed by a colour scale, this method describes the strength of interatomic interactions. Red and blue indicate interatomic contacts where the distance between atoms is smaller or larger, respectively, than the sum of the van der Waals radii of the atoms involved, while white indicates contacts with distances close to the sum of the van der Waals radii.
In the case of compound 1, the red colour in Fig. 5a highlights the region of most intense contacts involving the nitrogen, oxygen and hydrogen atoms from the hydrazide and hydroxyl groups with adjacent oxygen atoms. Fig. 5b illustrates the nearest molecules within the crystal packing, delineating the spatial arrangement of the shortest interactions. Meanwhile, blue surfaces, which indicate longer-range interactions, arise mainly from H⋯H contributions.
Fingerprint plots (FP) were generated to quantify the contribution of each interatomic interaction to the supramolecular structure. For this purpose, the di (x axis) and de (y axis) distances, expressed in Ångstroms, of the HS are used. For 1, the percentages of the surface area correspond to 64.7% for H⋯H, 26.2% for O⋯H/H⋯O, 7.5% for N⋯H/H⋯N, 1.2% for C⋯H/H⋯C, 0.3% for O⋯C/C⋯O and 0.1% for O⋯O interactions, as shown in Fig. 6.
4. Database survey
A survey of the Cambridge Structural Database (CSD2023.2.0, version 5.45, November 2023; Groom et al., 2016) revealed several similar structures. 5-Hydroxypentanehydrazide was first synthesized as a byproduct of the reaction of dihydropyran and phenyl azide (Karakhanov et al., 1969) and has never had its structural properties discussed, although it was first obtained in its crystalline form. The synthesis and crystallographic characterization of other similar aliphatic hydrazide derivatives has been reported: t-butyl hydrazinecarboxylate (CSD refcode RENZUJ; Aitken & Slawin, 2022), α-cyanoacetohydrazide (CYACHZ; Chieh, 1973), n-dodecanoic acid hydrazide (DDEAHN; Jensen, 1956), hexanedihydrazide (MUYRIK; Lo et al., 2020), n-nonanoic acid hydrazide (NONACH; Jensen & Lingafelter, 1961) and n-octanoic acid hydrazide (ZZZOMM; Jensen & Lingafelter, 1953).
5. Synthesis and crystallization
To a round-bottom flask, δ-valerolactone (100 mg, 9.99 mmol), hydrazine hydrate (200 mg, 4.0 mmol) and 5 mL of methanol were added. The resulting solution was maintained stirring under reflux conditions for 24 h. The solution was then allowed to cool slowly to room temperature. After 20 minutes, a solid started to precipitate in the flask. The solid, which was filtered off and air dried, afforded 115.0 mg of colourless crystals of 5-hydroxypentanehydrazide (1) in 88.0% yield. The melting point (375–379 K) was in accordance with literature (Karakhanov et al., 1969).
6. Refinement
Crystal data, data collection and structure . The hydrogen atoms of the carbon chain were included in idealized positions with C—H distances set to 0.99 Å and refined using a riding model with Uiso(H) = 1.2Ueq(C); the other hydrogen atoms were located in difference-Fourier maps and were refined freely.
details are summarized in Table 2
|
Supporting information
CCDC reference: 2345070
https://doi.org/10.1107/S2056989024002871/vm2296sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989024002871/vm2296Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989024002871/vm2296Isup3.mol
Supporting information file. DOI: https://doi.org/10.1107/S2056989024002871/vm2296Isup4.cml
C5H12N2O2 | Dx = 1.320 Mg m−3 |
Mr = 132.17 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, Pca21 | Cell parameters from 9932 reflections |
a = 7.1686 (5) Å | θ = 4.2–28.7° |
b = 4.8491 (3) Å | µ = 0.10 mm−1 |
c = 19.1276 (14) Å | T = 100 K |
V = 664.90 (8) Å3 | Prism, colourless |
Z = 4 | 0.32 × 0.16 × 0.13 mm |
F(000) = 288 |
Bruker D8 Venture/Photon 100 CMOS diffractometer | 1567 independent reflections |
Radiation source: fine-focus sealed tube | 1527 reflections with I > 2σ(I) |
Detector resolution: 10.4167 pixels mm-1 | Rint = 0.029 |
φ and ω scans | θmax = 27.8°, θmin = 4.3° |
Absorption correction: multi-scan (SADABS; Krause et al., 2015) | h = −9→9 |
Tmin = 0.731, Tmax = 0.746 | k = −6→6 |
26421 measured reflections | l = −25→25 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.022 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.059 | w = 1/[σ2(Fo2) + (0.0379P)2 + 0.0769P] where P = (Fo2 + 2Fc2)/3 |
S = 1.08 | (Δ/σ)max < 0.001 |
1567 reflections | Δρmax = 0.21 e Å−3 |
98 parameters | Δρmin = −0.19 e Å−3 |
1 restraint | Absolute structure: Flack x determined using 732 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
Primary atom site location: dual | Absolute structure parameter: −0.1 (2) |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.58285 (13) | 0.44491 (18) | 0.38116 (6) | 0.0149 (2) | |
O2 | 0.71437 (14) | 0.7429 (2) | 0.71584 (5) | 0.0151 (2) | |
N1 | 0.51145 (15) | 0.8787 (2) | 0.34743 (5) | 0.0105 (2) | |
N2 | 0.42516 (17) | 0.7936 (2) | 0.28423 (6) | 0.0122 (2) | |
C1 | 0.58629 (18) | 0.6966 (3) | 0.39182 (6) | 0.0097 (2) | |
C3 | 0.58864 (17) | 0.6955 (2) | 0.52353 (6) | 0.0110 (2) | |
H3A | 0.453999 | 0.740443 | 0.525239 | 0.013* | |
H3B | 0.601004 | 0.492251 | 0.522213 | 0.013* | |
C4 | 0.68313 (18) | 0.8053 (3) | 0.58941 (6) | 0.0115 (3) | |
H4A | 0.818747 | 0.768536 | 0.586516 | 0.014* | |
H4B | 0.665552 | 1.007624 | 0.591765 | 0.014* | |
C5 | 0.60650 (19) | 0.6753 (3) | 0.65582 (7) | 0.0139 (3) | |
H5A | 0.476648 | 0.738769 | 0.663034 | 0.017* | |
H5B | 0.603920 | 0.472447 | 0.650158 | 0.017* | |
C2 | 0.67320 (18) | 0.8176 (2) | 0.45691 (6) | 0.0106 (2) | |
H2A | 0.654542 | 1.019919 | 0.456926 | 0.013* | |
H2B | 0.809132 | 0.781623 | 0.456417 | 0.013* | |
H1 | 0.514 (3) | 0.715 (4) | 0.2573 (12) | 0.024 (5)* | |
H2 | 0.345 (3) | 0.680 (4) | 0.2935 (10) | 0.016 (4)* | |
H3 | 0.517 (3) | 1.052 (4) | 0.3531 (11) | 0.020 (5)* | |
H4 | 0.664 (4) | 0.890 (5) | 0.7337 (13) | 0.034 (6)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0227 (5) | 0.0074 (4) | 0.0146 (4) | 0.0001 (3) | −0.0016 (4) | −0.0006 (3) |
O2 | 0.0204 (5) | 0.0158 (4) | 0.0092 (4) | 0.0034 (4) | −0.0026 (4) | −0.0033 (4) |
N1 | 0.0161 (5) | 0.0070 (5) | 0.0084 (5) | −0.0001 (4) | −0.0012 (4) | −0.0011 (4) |
N2 | 0.0160 (5) | 0.0111 (5) | 0.0094 (5) | −0.0012 (4) | −0.0029 (4) | −0.0016 (4) |
C1 | 0.0106 (5) | 0.0096 (5) | 0.0090 (6) | −0.0006 (4) | 0.0033 (4) | 0.0005 (4) |
C3 | 0.0127 (5) | 0.0120 (5) | 0.0082 (5) | −0.0013 (4) | 0.0005 (4) | 0.0012 (5) |
C4 | 0.0132 (6) | 0.0120 (6) | 0.0092 (5) | −0.0010 (4) | 0.0003 (5) | −0.0009 (5) |
C5 | 0.0170 (6) | 0.0166 (6) | 0.0081 (5) | −0.0031 (5) | −0.0008 (5) | −0.0007 (5) |
C2 | 0.0136 (6) | 0.0093 (5) | 0.0088 (5) | −0.0014 (5) | −0.0004 (5) | 0.0002 (4) |
O1—C1 | 1.2375 (16) | C3—C2 | 1.5303 (16) |
O2—C5 | 1.4223 (16) | C3—H3A | 0.9900 |
O2—H4 | 0.87 (3) | C3—H3B | 0.9900 |
N1—C1 | 1.3376 (17) | C4—C5 | 1.5208 (17) |
N1—N2 | 1.4193 (14) | C4—H4A | 0.9900 |
N1—H3 | 0.85 (2) | C4—H4B | 0.9900 |
N2—H1 | 0.91 (2) | C5—H5A | 0.9900 |
N2—H2 | 0.82 (2) | C5—H5B | 0.9900 |
C1—C2 | 1.5109 (16) | C2—H2A | 0.9900 |
C3—C4 | 1.5265 (16) | C2—H2B | 0.9900 |
C5—O2—H4 | 106.4 (17) | C5—C4—H4A | 109.1 |
C1—N1—N2 | 121.55 (11) | C3—C4—H4A | 109.1 |
C1—N1—H3 | 123.8 (15) | C5—C4—H4B | 109.1 |
N2—N1—H3 | 114.6 (15) | C3—C4—H4B | 109.1 |
N1—N2—H1 | 107.3 (14) | H4A—C4—H4B | 107.8 |
N1—N2—H2 | 108.6 (13) | O2—C5—C4 | 112.48 (10) |
H1—N2—H2 | 109.6 (19) | O2—C5—H5A | 109.1 |
O1—C1—N1 | 122.60 (12) | C4—C5—H5A | 109.1 |
O1—C1—C2 | 121.81 (11) | O2—C5—H5B | 109.1 |
N1—C1—C2 | 115.58 (11) | C4—C5—H5B | 109.1 |
C4—C3—C2 | 112.13 (10) | H5A—C5—H5B | 107.8 |
C4—C3—H3A | 109.2 | C1—C2—C3 | 111.87 (10) |
C2—C3—H3A | 109.2 | C1—C2—H2A | 109.2 |
C4—C3—H3B | 109.2 | C3—C2—H2A | 109.2 |
C2—C3—H3B | 109.2 | C1—C2—H2B | 109.2 |
H3A—C3—H3B | 107.9 | C3—C2—H2B | 109.2 |
C5—C4—C3 | 112.62 (10) | H2A—C2—H2B | 107.9 |
N2—N1—C1—O1 | −0.98 (19) | O1—C1—C2—C3 | −55.33 (16) |
N2—N1—C1—C2 | 180.00 (11) | N1—C1—C2—C3 | 123.70 (11) |
C2—C3—C4—C5 | −177.29 (11) | C4—C3—C2—C1 | 176.88 (10) |
C3—C4—C5—O2 | 170.30 (10) |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H4···N2i | 0.87 (3) | 1.92 (3) | 2.7865 (15) | 172 (2) |
N1—H3···O1ii | 0.85 (2) | 2.03 (2) | 2.8662 (14) | 166 (2) |
N2—H1···O2iii | 0.91 (2) | 2.10 (2) | 2.9068 (16) | 147.2 (18) |
N2—H2···O1iv | 0.82 (2) | 2.59 (2) | 3.2858 (16) | 144.0 (16) |
N2—H2···O2v | 0.82 (2) | 2.57 (2) | 3.0789 (14) | 122.0 (16) |
C2—H2A···O1ii | 0.99 | 2.57 | 3.4309 (15) | 145 |
Symmetry codes: (i) −x+1, −y+2, z+1/2; (ii) x, y+1, z; (iii) −x+3/2, y, z−1/2; (iv) x−1/2, −y+1, z; (v) −x+1, −y+1, z−1/2. |
Acknowledgements
The authors thank the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Edital PROIND 2020/UFPR and Coordenacão de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) for fellowships. The author's contributions are as follows. GAJ: methodology, writing – original draft; JSCN: formal analysis, resources; FSS: data curation, visualization; MLBR: validation; FGSP: investigation; PPD: writing, review and editing; MGMD: conceptualization, supervision.
Funding information
Funding for this research was provided by: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (grant No. 23038.003745/2021-31); Pró-Reitoria de Planejamento, Orçamentos e Finanças - UFPR - PROIND 2020 (grant No. 3527).
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