Molecular structure, hydrogen-bonding patterns and topological analysis (QTAIM and NCI) of 5-methoxy-2-nitroaniline and 5-methoxy-2-nitroaniline with 2-amino-5-nitropyridine (1:1) co-crystal

doi:10.1016/j.molstruc.2016.05.012

Journal of Molecular Structure

Volume 1119, 5 September 2016, Pages 505-516

https://doi.org/10.1016/j.molstruc.2016.05.012 Get rights and content

Highlights

•
Crystal structures of Nitroaniline derivatives were determined for first time.
•
The supramolecular structures were reinforced by C-H···O interactions.
•
Two types of topological analysis were performed QTAIM and NCI.
•
Their crystal packing exhibited layered structures.
•
In both compounds molecules pack avoiding C···C contacts between layers.

Abstract

In this work, we report an analysis of the molecular structure and the hydrogen-bonding patterns in the crystal structures of 5-methoxy-2-nitroaniline (1) and 5-methoxy-2-nitroaniline with 2-amino-5-nitropyridine (1:1) co-crystal (2). X-ray single crystal diffraction experiments were carried out to analyse the intermolecular forces in terms of geometrical criteria. These intermolecular interactions were also investigated through topological analysis of the electron density (ρ) employing QTAIM and NCI methods. Additionally, Raman spectroscopy was employed to analyse the vibrational characteristics of the entitled materials. The supramolecular structure of (1) is produced by crosslinked chains, which are primarily dominated by N-H···O hydrogen bonds. However, C-H···O interactions reinforce this connectivity. Furthermore, the molecules in (1) are connected through two-centre instead of the three-centre hydrogen-bonding interactions between the -NH₂ and -NO₂ groups commonly observed in nitroanilines. The asymmetric unit of (2) contains two symmetry-independent molecules of 5-methoxy-2-nitroaniline (5M2NA) and two symmetry-independent molecules of 2-amino-5-nitropyridine (2A5NP). The supramolecular structure of (2) is developed not only for N-H···O but also N-H···N and supportive C-H···O hydrogen bonds. The two symmetry-independent 2A5NP molecules bound to each other through two-centre hydrogen bonds between the -NH₂ and -NO₂ groups forming $C_{2}^{2} (16)$ chains. 5M2NA molecules bound to these chains forming $R_{2}^{2} (9)$ and $R_{2}^{2} (8)$ synthons. Experimental and theoretical results obtained in this work suggest that C-H···O interactions play an important role in the stabilization of these supramolecular structures.

Graphical abstract

Introduction

Nowadays, the non-linear optics (NLO) field is gaining attention in science and technology since its processes provide the basis for the development of frequency up-converters and optical switches [1]. For this reason, scientists are constantly carrying out investigations towards the development of high performance NLO materials with acceptable structural integrity in the solid-state [2]. Hence, there is a special interest in exploring organic molecules in view of their ability to act as building blocks for the design of a wide number of molecular architectures [3], [4], [5]. Furthermore, the relatively good hyperpolarizability (β) values of some of these compounds makes them even more attractive candidates for the development of highly efficient NLO materials [6], [7].

Among organic compounds, nitroaniline derivatives have displayed large β values due to the asymmetric charge distribution induced by the attachment of the electron-donating (-NH₂) and the electron-withdrawing (-NO₂) groups to the phenyl ring [8], [9], [10]. For instance, p-nitroaniline is a good example of a push–pull system due to the degree of conjugation induced by the location of the substituents -NH₂ and -NO₂ groups at para position to each other, which enhances its β value [11]. However, most of these compounds exhibit large molecular dipole moments, which leads for antiparallel molecular arrangements and consequently centrosymmetric crystal structures [12]. The latest characteristic vanishes second order NLO processes such as second harmonic generation (SHG) [13].

On the other hand, there is a continuous interest in understanding the role of weak interactions in the formation of molecular assemblies into predictable molecular arrays [14]. Particularly, non-covalent intermolecular interactions have received interest due to their key role on the molecular arrangement in crystals, because of their ability to control the intermolecular aggregation processes, based on the nature and polarity of the involved species [15]. It is well known that the hydrogen bond play an important role in controlling the molecular assemblies due to its directional characteristics [16]. For this reason, strong hydrogen bonds (N-H⋯O, O-H⋯O) are the most important elements in crystal engineering. However, in the absence of these conventional hydrogen bonds, weaker interactions are responsible for crystal packing [17]. One example of these weak hydrogen bonds is the C-H⋯X interactions. The C-H group is known to be a hydrogen-bond donor and it has been demonstrated that C-H⋯O, C-H⋯N, C-H⋯Cl and C-H⋯F interactions play a key role determining crystal packing [17], [18], [19]. The weakest kind of non-conventional hydrogen bonding is the X-H⋯π (X = O, N, C) interaction, but it is still important in molecular self-assembly and in the packing of organic crystals [20]. Note that it is hard to predict the supramolecular arrays into crystals [21].

In the case of nitroaniline derivatives, it was found that they usually associate through intermolecular hydrogen bonds between the -NH₂ and -NO₂ groups giving the development of infinite polar chains, which can be useful for the design of efficient NLO materials [22]. Furthermore, Panunto and co-workers found that the most common hydrogen-bonding pattern in these compounds involves a three-centred (bifurcated) N-H⋯(O₁)(O₂) interaction [23]. On the other hand, Ellena and co-workers found that in some cases the short-range ordering, which gives formation of dimers, is more stable than the chain development, giving rise to structures mainly stabilized by dimeric arrangements [24].

The analysis of electron density (ρ) topology using the Quantum Theory of Atoms in Molecules (QTAIM) [25] and Non-Covalent Interactions (NCI) method [26] has been used for identifying and classifying the inter-molecular interactions in molecular systems [27]. For example, QTAIM was used for describing the role of non-covalent interactions in possible crystallization mechanisms of isoxazole derivatives [28]. Besides, Koch and co-workers employed QTAIM to study the effect of intramolecular interactions in the conformation of the anti-AIDS drug 3´-azido-3´-deoxy-thymidine (AZT) [29]. From the analysis they concluded that a bifurcated intramolecular C-H···O hydrogen bond is responsible for the molecular conformation of the drug [29].

The NCI method has also been used for plotting and analysing non-covalent interactions [26], [30]. The NCI method is capable of mapping real-space regions where non-covalent interactions are important and is based exclusively on ρ and its gradient [30]. It is also a versatile and powerful tool for analysing intramolecular forces e.g. the method has been used not only for analysing molecular units, but also has been implemented for solid-sate periodic structures [30].

Herein we report the crystal structures of 5-methoxy-2-nitroaniline (1) and 5-methoxy-2-nitroaniline with 2-amino-5-nitropyridine (1:1) co-crystal, which were determined by the first time. Furthermore, with the aim to contribute to the existing investigations on the hydrogen bond formation in crystal structures of nitroaniline derivatives, we report here an analysis of the hydrogen-bonding patterns formed in (1) and (2) using X-ray diffraction data. Additionally, we have employed QTAIM and NCI methods mainly to analyse the existence of C-H⋯O interactions in these compounds. Raman spectroscopy was also used as complementary tool to understand the vibrational characteristics associated with the molecular structure of the entitled compounds.

Section snippets

Synthesis

5-Methoxy-2-nitroaniline (5M2NA) (≥97% pure), and 2-amino-5-nitropyridine (2A5NP) (≥97% pure) were obtained from Sigma–Aldrich and used without further recrystallization. Suitable crystals for single crystal X-ray diffraction (SCXRD) were grown from the solvent evaporation technique. Three crystallization experiments were set up at the laboratory: 1) 0.139 g (1 mmol) of 2A5NP were placed in a vessel and completely dissolved using 2 mL of commercial acetone; 2) 0.168 g (1 mmol) of 5M2NA were

Results and discussion

From the crystallization experiments, suitable single crystals for SCXRD analysis were obtained. Fig. S1 (see supplementary material) displays the morphology of the samples. 2A5NP crystallized with different morphologies, needles and plates in the centre of the vessel and blocks near the walls (see Figs. S1a and S1b, respectively). Single crystals of 2A5NP from the different morphologies were assessed via SCXRD experiments, but in all cases the unit cell matched to the one reported by Aakeröy

Conclusion

The analysis of the crystal structures of 5-methoxy-2-nitroaniline (1) and 5-methoxy-2-nitroaniline with 2-amino-5-nitropyridine (1:1) co-crystal (2) revealed that in these compounds there is no preference to form polar chains through the three-centre hydrogen-bonds commonly observed in nitroanilines. Besides, it was found that N-H···O hydrogen bonds dominate the self-assembly process in the supramolecular structures, which was more remarkable in (1). However, C-H···O interactions played an

Acknowledgements

The authors thank Consejo Nacional de Ciencia y Tecnología (CONACyT) México for funding in the following ways: Grant INFR-2014-01-225455 to acquire the single crystal X-ray diffractometer Bruker D8 QUEST, Grant No. 132856 and Grant 2014-01-226208 for supporting this work. We also thank Área de Cómputo Avanzado, Universidad de Sonora (ACARUS) for access to computational resources.

References (50)

J. Hernández-Paredes et al.
Spectrochim. Acta, Part A
(2015)
I. Cukrowski et al.
Comput. Theor. Chem.
(2015)
T.H. Tang et al.
J. Mol. Struct. (TEOCHEM)
(1990)
O.R. Evans et al.
Acc. Chem. Res.
(2002)
S.R. Marder
Chem. Comm.
(2006)
R.L. Gieseking et al.
J. Am. Chem. Soc.
(2015)
T.V. Timofeeva et al.
Cryst. Growth Des.
(2003)
O. Watanabe et al.
J. Mater. Chem.
(1993)
J. Zyss et al.
Adv. Mater.
(1993)
Y. Le Fur et al.
Chem. Mater.
(1996)

G.F. Lipscomb et al.

J. Chem. Phys.

(1981)

B.F. Levine et al.

J. Appl. Phys.

(1979)

S.P. Karna et al.

J. Chem. Phys.

(1991)

A. Dey et al.

Chem. Commun.

(2005)

R. Matsushima et al.

J. Mater. Chem.

(1993)

G.R. Desiraju

Angew. Chem. Int. Ed. Eng.

(1995)

A.J. Rybarczyk-Pirek et al.

Cryst. Growth Des.

(2015)

J. Hernández-Paredes et al.

CrystEngComm

(2015)

T.S. Thakur et al.

IUCrJ

(2015)

V.R. Thalladi et al.

J. Am. Chem. Soc.

(1998)

E. Bosch et al.

Cryst. Gowth Des.

(2015)

H. Suezawa et al.

Eur. J. Inorg. Chem.

(2002)

G.R. Desiraju

J. Am. Chem. Soc.

(2013)

D.Y. Curtin et al.

Chem. Rev.

(1981)

T.W. Panunto et al.

J. Amer. Chem. Soc.

(1987)

Cited by (18)

Exploring the intermolecular interactions in Co-crystals of 4-cyanopyridine with 4-bromobenzoic acid: Experimental and computational methods
2023, Materials Today: Proceedings
In present work, we have performed synthesis, quantitative and qualitative analysis of the different intermolecular interactions present in 4-Cyanopyridine:4-bromobenzoic acid(1:1) Co-crystal. The single crystal X-ray diffraction confirms the Co-crystal crystallizes in the P $\bar{1}$ space group with one molecule of 4-cyanopyridine and 4-bromobenzoic acid in the asymmetric unit. The Co-crystal is mainly stabilized by presence of strong C-H…O and O-H…N interactions. Computational studies confirms, along with strong hydrogen bonds C-H…Br, C-H…N, N…Br and π…π interactions plays a significant role in stabilizing the crystal packing. Lattice energy of the compound is calculated using PIXEL method. Hirshfeld surface analysis and fingerprint plots helped in analysing percentage contribution of each intermolecular interaction towards crystal packing. Topological properties of intermolecular interactions are studied based on QTAIM approach. CSD studies shows presence of isostructural polymorph of 4-Cyanopyridine:4-bromobenzoic acid Co-crystal. Later both polymorphs are compared using different computational tools.
New hydrate cocrystal of L-proline with 4-acetylphenylboronic acid obtained via mechanochemistry and solvent evaporation: An experimental and theoretical study
2022, Journal of Solid State Chemistry
Citation Excerpt :
QTAIM considers the electron density ρ(r) description and its topological analysis to obtain a molecule’s chemical information and properties [28,52]. For example, chemical properties such as the nature of the bonds between the atoms can be analysed using this theory [44–46]. Table 2 shows the general criteria established for the assessment of the topological properties in the (3, −1) bond critical points (BCPs) between every pair of nuclei to determine the nature of interactions [28,52,58,59]:
In this work, we present the formation of a new multi-component molecular complex by targeting the boronic acid moiety (-B(OH)₂) of 4-acetylphenylboronic acid with the carboxylate group (-COO^-) of l-proline using two different techniques: mechanochemistry and solvent evaporation. The experiments produced efficiently a new cocrystal named L-PRO4APBA. It was characterised to study its structural properties by X-ray powder diffraction (XRPD), infrared spectroscopy (FTIR), single-crystal X-ray diffraction (SCXRD), and quantum chemical methods based on QTAIM. Also, its thermal behaviour was analysed using a simultaneous DSC/TGA experiment. The results showed that L-PRO4APBA comprises discrete molecular units held together mainly by O–H⋯O and N–H⋯O hydrogen bonds. However, C–H⋯O, C–H⋯π, and other non-conventional interactions gave further stabilisation. Moreover, SCXRD showed that the asymmetric unit contains five independent molecules: two of l-proline (PRO1 and PRO2), two of 4-acetylphenylboronic acid (4APBA1 and 4APBA2) and one of water. PRO1 and PRO2 adopted different conformations with their carboxylate groups in equatorial and axial positions, respectively. This feature produced two independent helical chains running along the 2₁ screw axis in which 4APBA1 and 4APBA2 bound through the expected -B(OH)₂···⁻OOC- heterosynthon. Surprisingly, the presence of water molecules in the lattice did not disrupt the formation of this motif. However, water molecules played an essential role for the stabilisation of the 3D structure. These findings would set up the structural basis to continue exploring the formation of new cocrystals by combining l-proline with boronic acids.
Molecular structure, covalent and non-covalent interactions of an oxaborole derivative (L-PRO2F3PBA): FTIR, X-ray diffraction and QTAIM approach
2021, Journal of Molecular Structure
Citation Excerpt :
Also, the molecules are held together through the C9-H9B···O2#3 interaction, which has interaction energy of -1.25 kcal/mol. This value suggested the importance of the interaction to strengthen the molecular self-assembly [50]. The molecular graph showed the presence of a BCP and its corresponding bond path depicting an F1···O1#3 interaction (see Fig. 7).
Boron containing compounds have gained attention in the past decades due to their potential applications as pharmaceuticals. These materials comprise molecules such as boronic acids, iminoboronates and oxaboroles. The main idea is to develop molecular units that can interact with organic compounds and biological molecules for pharmaceutical and biological applications. Herein, we report the synthesis and characterisation of (3aS,7S)-1-(2-fluoropyridin-3-yl)-1-hydroxy-3-oxohexahydro-1H-pyrrolo[1,2-c][1,3,2]oxazaborol-7-ium-1-uide, which has been obtained by the reaction of the biologically active molecule L-proline with 2-fluoro-3-pyridineboronic acid in ethanol. The compound, namely L-PRO2F3PBA hereafter, was characterised by FTIR spectroscopy, single-crystal X-ray diffraction, and quantum chemical methods based on QTAIM to study its molecular structure, covalent and non-covalent interactions. The results showed the importance of a coordinate N→B dative bond for stabilising the molecules in the solid-state. Also, the molecular self-assembly occurs mainly by N-H···O, O-H···O and C-H···O non-covalent interactions. The ESP maps analysis showed that the molecules interacted so that electropositive zones attracted the electronegative zones to form dimeric pairs. Overall, the results suggested that the compound comprises functional groups that make it a good candidate for further studies in medicine, pharmacology, and biology.
Analysis of supramolecular interactions directing crystal packing of a trans,trans,trans-[diaquabis(4-quinolin-3-yl)-4H-1,2,4-triazole)bis(tricyanomethanide)iron(II)] complex: A combination of XRD, MEP, NBO, QTAIM, and NCI analyses
2021, Journal of Molecular Structure
The synthesis and structural characterization of a hydrated high-spin iron(II) complex [Fe(4-qtrz)₂(tcm)₂(H₂O)₂] are reported where 4-qtrz = 4-quinolin-3-yl-4H-1,2,4-triazole and tcm = tricyanomethide. The complex was prepared solvothermally and crystallizes in the triclinic space group P $\bar{1}$ with Z = 1, a = 8.5221(3) Å, b = 8.9343(5) Å, c = 10.0081(5) Å, α = 85.147(2)°, β = 77.166(2)°, γ = 83.784(2)°. The complex is centrosymmetric, with mutually trans pairs of water molecules, of tcm, and monodentate 4-qtrz coordinated via the triazole unit and a combination of O–H⋅⋅⋅N and C–H⋅⋅⋅N hydrogen bonds, forming a three-dimensional framework structure in which the shortest Fe⋅⋅⋅Fe distance is 8.5221(3) Å. An analysis of non-covalent interactions was conducted through reduced density gradient, quantum theory of atoms in molecules and natural bond orbitals. Accordingly, the important contributions of several intra- and inter-molecular hydrogen bonds stabilize the supramolecular structure. The hydrogen bonds occur by electron transfer from the tricyanomethanide nitrogen lone pairs to σ* orbitals in the triazole, quinoline and water moieties. Other hydrogen bonds are attributed to π(CN) → σ*, in triazole and quinoline, transfer. Additionally, a set of π⋅⋅⋅π* interactions between cyano groups (CN⋅⋅⋅CN), π(phenyl of quinoline)⋅⋅⋅π*(CN), and π[CC of C(CN)₃] to π*(phenyl of quinoline) were also observed.
Synthesis, crystal structure and dft studies of polyfunctionalized alkenes: A transition metal-free c(sp<sup>2</sup>)-h sulfenylation of electron deficient alkyne
2021, Journal of Molecular Structure
Citation Excerpt :
The non-covalent interactions largely affect the molecular architecture by controlling the aggregation process in crystals. [42] The role of strong hydrogen bonds (O—H····O, N—H····H, N—H····O etc.) is very significant in crystal packing [43]. Further, crystal packing in molecules devoid of these strong directional forces depends mainly upon weak interactions.
An efficient, novel and transition metal-free protocol has been developed for the synthesis of polyfunctionalized aminothioalkenes via direct CH sulfenylation of in situ generated enamines. The reaction was performed using a catalytic amount of inexpensive and nontoxic K₂CO₃ under mild reaction condition. All the reactions resulted in good to excellent yields. The cross-coupling reaction has been achieved by in situ aerobic oxidation at room temperature with good functional group tolerance. The molecular architecture and stereochemistry has been established by spectral data, X-ray single crystal diffraction studies and supported by Density Functional theory (DFT). Hirshfeld surface analysis has been used to explore the intramolecular and intermolecular interactions present in the case of 4a. Moreover, the intramolecular hyperconjugative interactions have been investigated using natural bond orbitals (NBOs) analysis and their intensity was categorized according to their second-order stabilization energy (E(2)). The electrostatic properties such as global reactivity descriptors, local reactivity descriptors, ESP and NLO have been investigated using DFT method and B3LYP/6–311+G(d) level of theory.
Synthesis, crystal structure, and non-covalent interactions in 4-hydrazinobenzoic acid hydrochloride
2020, Journal of Molecular Structure
Citation Excerpt :
On the other hand, the study of non-covalent interactions through the reduced gradient of density (NCIPlot) has gained popularity because of the advantages of this method in the characterization and location of interactions in molecular real-space [18,19]. The combination of these methods with those of X-ray crystallography have been important in identifying the basis of supramolecular structures, e.g. Hernandez-Paredes found the role of C–H⋯O interaction in the assembly of 5-methoxy-2-nitroaniline and its co-crystal with 2-amino-5-nitropyridine [20]. Consequently, this approach has gained popularity as a complement to crystallographic studies.
The compound 4-hydrazinobenzoic acid hydrochloride (4-HBA), C₇H₉O₂·Cl, has been synthesized and characterized by FT-IR spectroscopy and X-ray diffraction. The compound crystallizes as colourless needles in a triclinic system, space group Pˉ1 (Z = 2), and cell parameters a = 3.7176 (4) Å, b = 5.9133 (4) Å, c = 19.3631 (13) Å, α = 87.841 (6), β = 88.924 (6), γ = 80.203 (6), V = 419.13 (6) Å³. The component ions are linked by a combination of O–H⋯O, N–H⋯N and N–H⋯Cl hydrogen bonds to form a complex three-dimensional framework structure in which each cation is linked to two other cations, by O–H⋯O and N–H⋯N hydrogen bonds, and to five different anions, while each anion accepts hydrogen bonds from five different cations. Calculations on the Non-Covalent Interactions (NCI) amplify the crystallographic conclusions concerning the interionic hydrogen bonds.

View all citing articles on Scopus

View full text

Molecular structure, hydrogen-bonding patterns and topological analysis (QTAIM and NCI) of 5-methoxy-2-nitroaniline and 5-methoxy-2-nitroaniline with 2-amino-5-nitropyridine (1:1) co-crystal

Highlights

Abstract

Graphical abstract

Introduction

Section snippets

Synthesis

Results and discussion

Conclusion

Acknowledgements

Spectrochim. Acta, Part A

Comput. Theor. Chem.

J. Mol. Struct. (TEOCHEM)

Acc. Chem. Res.

Chem. Comm.

J. Am. Chem. Soc.

Cryst. Growth Des.

J. Mater. Chem.

Adv. Mater.

Chem. Mater.

J. Chem. Phys.

J. Appl. Phys.

J. Chem. Phys.

Chem. Commun.

J. Mater. Chem.

Angew. Chem. Int. Ed. Eng.

Cryst. Growth Des.

CrystEngComm

IUCrJ

J. Am. Chem. Soc.

Cryst. Gowth Des.

Eur. J. Inorg. Chem.

J. Am. Chem. Soc.

Chem. Rev.

J. Amer. Chem. Soc.