key: cord-281464-15ld7knm
authors: Belova, Natalya V.; Pimenov, Oleg A.; Kotova, Vitaliya E.; Girichev, Georgiy V.
title: Molecular structure and electron distribution of 4-nitropyridine N-oxide: Experimental and theoretical study of substituent effects
date: 2020-05-17
journal: J Mol Struct
DOI: 10.1016/j.molstruc.2020.128476
sha: 
doc_id: 281464
cord_uid: 15ld7knm

The molecular structure of 4-nitropyridine N-oxide, 4-NO(2)-PyO, has been determined by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and by quantum chemical calculations (DFT and MP2). Comparison of these results with those for non-substituted pyridine N-oxide and 4-methylpyridine N-oxide CH(3)-PyO, demonstrate strong substitution effects on structural parameters and electron density distribution. The presence of the electron-withdrawing –NO(2) group in para-position of 4-NO(2)-PyO results in an increase of the ipso-angle and a decrease of the semipolar bond length r(N→O) in comparison to the non-substituted PyO. The presence of the electron-donating –CH(3) group in 4-CH(3)-PyO leads to opposite structural changes. Electron density distribution in pyridine-N-oxide and its two substituted compounds are discussed in terms of natural bond orbitals (NBO) and quantum theory atoms in molecule (QTAIM).

Pyridine-N-oxide derivatives have attracted (a) great interest in chemistry and biotechnology because of their accentuated oxidizing properties, high polarity, and their ability to be both charge donors and acceptors. Heterocyclic compounds with N-oxide groups have achieved widespread utility foremost because of their pronounced biological activity [1] . In the literature we can find the evidence of bactericidal, analgesic, anticonvulsant, apoptotic, and antimicrobial activity of N-oxides [2, 3] . These properties allow to use N-oxides as inhibitor of HIV-1 reverse transcriptase [4, 5] , as antiviral agent against various SARS corona virus strains [6] , and as antiadhesive and quorum-sensitive inhibitor [7] . Some complexes with pyridine-N-oxides are used in agriculture to regulate plant growth rates [8] . According to numerous studies, the biochemical activity of N-oxides is due to the complexations with the metalloporphyrins in living organisms [9] [10] [11] . Obviously, the reactivity of N-oxides may vary due to different substituents in the ring [12] .

The variation of the substituents gives wide possibilities to chemical modifications of N-oxides and allows to change their complexing properties, and, as the result, to influence the biological activity.

Apparently, the substitution of pyridine-N-oxide with a strong electron-withdrawing -NO 2 group would lead to an electron density redistribution, and thus would widen the scope of its reactivity. It is often assumed that the presence of the nitro group in substituted pyridine-N-oxides is responsible for a substantial increase in the antifungal activity [13] . Nitro-pyridine-N-oxides are also known to be used in photonics for design and development of new organic nonlinear optical (NLO) materials [14] [15] [16] [17] [18] . In order to elucidate the factors underlying these and other properties of pyridine-N-oxides a detailed information about the structural properties as well as about the electron density distribution in the molecules is needed.

The available literature data about molecular structure of gaseous N-oxides is not sufficient.

Only four pyridine-N-oxides have been studied by gas-electron diffraction (GED). Chiang J.F. et al. [19, 20] carried out GED studies of pyridine-N-oxide and three of its para-substituted compounds. However, the structural data reported in [20] should be criticized. Thus, e.g. N-C bond lengths in 4-NO 2 -PyO, 4-Cl-PyO, 4-Me-PyO obtained by Chiang J.F. et al. [20] are even longer than r(C-C) in the benzene ring, and are strongly overestimated compared to the calculated values

[21] and X-ray crystallographic data [22, 23] . Furthermore, the CNC bond angle values in the pyridine ring of 4-NO 2 -PyO and 4-Cl-PyO given in Ref. [20] are not consistent with sp 2 hybridization of the nitrogen atom and do not agree with calculated [21] and X-ray data [22, 23] .

The discrepancies in molecular structure of substituted N-oxides according to GED by Chiang J.F. et al. [19, 20] and other methods motivated us to perform a new gas-electron diffraction study of 4substituted-N-oxide. The first GED reinvestigation was performed for 4-methylpyridine-N-oxide [24] because of the largest structural contradictions for this molecule. Now more sophisticated methods for the analysis of GED data are available, including the possibility of quantum chemical results to be used in the interpretation of the experimental data. This allows us to determine the structural parameters more precisely compared to the studies performed in 1982. The experimental structural data for 4-methylpyridine-N-oxide obtained in our study [24] are in a good agreement with the theoretical parameters as well as the experimental X-ray data.

The present work continues our research of substituted-N-oxide structures. We performed new gas-electron diffraction study of 4-nitropiridine-N-oxide (Fig.1 ). This molecule was chosen because of the substituent nature. The nitro-group is known to be strong electron-withdrawing, whereas the methyl group is a good electron donor. Thus, the comparison of 4-NO 2 -PyO structure with that of 4-Me-PyO allows to reveal the substituent effects. This work presents also a theoretical study (DFT and MP2) of the molecular structure of 4-NO 2 -PyO along with the related molecules.

Electron charge distribution was studied in the framework of NBO scheme. As an alternative to conventional Lewis model which was realized in NBO the topological analysis of ρ(r) in the framework of Bader's quantum theory of atoms in molecule (QTAIM) [25] was performed for 4-NO 2 -PyO in the present work.

The electron diffraction patterns and the mass spectra were recorded simultaneously using the techniques described previously [26, 27] . Two series of GED/MS experiments at two different nozzle-to-plate distances have been performed. The conditions of GED/MS experiments and the relative abundance of the ions in mass spectra of 4-NO 2 -PyO are shown in Tables 1 and S1, respectively. The temperature of molybdenum effusion cell was measured by a W/Re-5/20 thermocouple calibrated by melting points of Sn and Al. The wavelength of the fast electrons was determined from the diffraction patterns of polycrystalline ZnO. Optical densities were measured by a computer-controlled MD-100 (Carls Zeiss, Jena) microdensitometer [28] . The molecular intensities were obtained in the ranges 2.5÷23.9 Å -1 (short camera) and 1.3÷16.1 Å -1 (long camera).

The molecular intensities and the radial distributing curves are shown in Fig.2 and Fig.3 respectively. Figure 4 and Table S1 present the mass spectrum recorded simultaneously with GED data.

All quantum chemical calculations were performed using the GAUSSIAN 09 program set [29] . The hybrid DFT computational methods, namely Becke's three-parameter hybrid functional B3LYP [30-34] and Perdew-Burke-Ernzerh of hybrid functional PBE0 [35] , as well as second order Møller-Plesset perturbation theory, MP2, were used. The correlation-consistent basis sets augmented with diffuse functions (aug-cc-pVTZ) have been taken to describe the electronic shells of O, C, N and H atoms. Structure optimizations were followed by calculations of the vibrational frequencies in order to ensure that a minimum on the potential energy hyper-surface had been reached. All calculations have been performed for the closed-shell electronic state.

The geometrical parameters of the calculated equilibrium structure derived with different theory methods are given in Table 2 together with the experimental results.Vibrational amplitudes and corrections, Δr=r h1 −r a , were derived from theoretical force fields (B3LYP/aug-cc-pVTZ) by Sipachev's method (approximation with taking into account the nonlinear kinematic effects at the level of the first order perturbation theory for the transformation of Cartesian coordinates into internal coordinates), using the program SHRINK [36] [37] [38] . Selected values are listed in Table 3 (excluding non-bonded distances involving hydrogen).

The potential energy function of the internal rotation of the nitro group about the C1-N2 bond was investigated. For this purpose, we carried out relaxed potential energy surface scans by the variation of the dihedral angle τ(C2C1N2O3) in steps of 10° between 0° and 180° with B3LYP/aug-cc-pVTZ method. Analysis of this potential function (Fig.5) shows that there is only one stable geometric configuration with τ about 0° (see Figure 1 for atom numbering). It should be noted that the internal rotation barrier is a sufficiently large, 7.70 kcal/mol (B3LYP/aug-cc-pVTZ), 8 .00 kcal/mol (PBE0/aug-cc-pVTZ) or 7.16 kcal/mol (MP2/aug-cc-pVTZ).

The NBO 5G program [39] , implemented for natural orbital analysis in PC GAMESS [40] , was used to obtain the net atomic charges and Wiberg bond indexes. B3LYP/aug-cc-pVTZ wave functions were used in the NBO analyses.

The topological analysis of electron density distribution function ρ(r) for 4-NO 2 -PyO and PyO was carried out using AIMAll Professional software [41] . The visualization of molecular models are realized by CHEMCRAFT [42] program.

The heaviest ion in mass spectrum observed during the combined GED/MS experiment was [NO 2 -PyO] + (Fig.4 , Table S1 ). No ions were detected, which could arise from impurities.This According to quantum chemical calculations, a planar structure with C 2v overall symmetry of the molecule was assumed. Independent r h1 parameters were used to describe the molecular structure.

Starting parameters from B3LYP/aug-cc-pVTZ calculations were refined by a least-squares procedure of the molecular intensities. The differences between all C−C bond distances, N-O bond distances, and C-N bond distances as well as between all C−H bond distances were constrained to calculated values (B3LYP/aug-cc-pVTZ). Vibrational amplitudes were refined in groups with fixed differences. With the abovementioned assumptions, four bond distances and three bond angles (Table 2) were refined simultaneously with eight groups of vibrational amplitudes (Table 3) . Only two correlation coefficients had absolute values larger than 0.7: (r(N1-C3))/(r(C2-C3))=-0.90, and (∠N1C3C2)/( ∠C3N1C4) = -0.75. The best agreement factor is R f = 3.6%. Results of the least squares analysis are given in Table 2 (geometric parameters) and Table 3 (vibrational amplitudes).

The model with nitro group plane turned relative to the pyridine ring plane was also tested in the GED analysis. This refinement leads to R f = 3.71% for τ(C2C1N2O3) fixed at10° and R f = 4.00% for τ(C2C1N2O3) fixed at 15°. The statistical Hamilton criterion [44] at the 0.01 significance level distinctly reveals that the nitro group rotation angle relative to the plane of the pyridine ring is not more exceed than 12° because the critical value R f = 3.78%. Table 2 summarizes the structural parameters of 4-nitro-pyridine-N-oxide. We can note a perfect agreement between calculated and experimental molecular structure parameters. Thus, changing the calculation method has no significant influence on the values of structural parameters.

The differences in theoretical values for bond distances do not exceed 0.020 Å, whereas the calculated values of the bond angles are almost equal, independent of the theoretical level. Both, quantum chemistry and GED analysis result in C 2v overall symmetry of the molecule with a planar pyridine ring. The nitro-group is coplanar with the heterocycle plane. Obviously, this position provides a conjugation between the π-system of the pyridine ring and the NO 2 group. Furthermore, Figure 2 presenting the calculated (B3LYP/aug-cc-pVTZ) -NO 2 -group rotation potential curve clearly shows that changing of the torsional angle τ(C2C1N2O3) by more than for 12° leads to a significant increase in energy. M. Dakkouri and V. Typke performed theoretical investigation of the structure of 2-nitropyridine-N-oxide [45] . It is astonishing to note that the endocyclic bond lengths of the pyridine N-oxide ring is almost equal, independent of the position of the nitro group. Table 4 compares the structure of pyridine-N-oxide and its two substituted obtained by GED, X-ray and DFT. Taking into account that the structural parameters obtained by different methods have different physical meaning, we can note a good agreement of the values obtained in our research (therein and [24] ) with the theoretical results (therein and [21] ) and, also, with the parameters for the crystals [46, 47] in contrast to the values recommended by Chiang J. F. et al. [20] . Apparently, some increase of the semipolar N→O bond lengths in a crystal phase compared to the free molecules is due to intermolecular hydrogen bonding. All parameters presented in Table   4 confirm the hyperconjugation in the pyridine ring and the sp 2 hybridization concept of the nitrogen and carbon atoms in the ring. The exceptions are only the data by Chiang J. F. et al. [20] , which are rather strange as we mentioned above. Unfortunately, large uncertainties in GED parameters for PyO [19] do not allow a comparison of the experimental structures. Thus, we can compare only the values obtained in our GED study (therein and [24] ) and the calculated values.

The structural data for free molecules in Table 4 show that the insertion of the methyl or nitro group in para -position to the PyO has no significant effect on the structural parameters of the pyridine ring, excluding only the ipso-angle ∠ C2C1C5, which is changes from 117.7° in PyO to 115.9° in 4-Me-PyO and 119.9° in 4-NO 2 -PyO (B3LYP/aug-cc-pVTZ). It is interesting to note, that the substituent effects on the geometry of heterocyclic ring are rather similar to the tendencies for the benzene ring [48, 49] . Thus, the presence of the electron-withdrawing -NO 2 group leads to the increase of the ipso-angle, whereas electron-donating -CH 3 substituent produces the opposite effect.

Furthermore, the r(N1→O1) semipolar bond lengths appear to be also sensitive to a substituent nature. Thus, the presence of electron withdrawing-NO 2 group in 4-NO 2 -PyO results in a shortening of r(N→O) in comparison with PyO, while in 4-Me-PyO with the donor substituent the bond length N→O increases.

The calculated net atomic charges along with the Wiberg bond indexes for PyO and two its derivatives are summarized in Table 5 . In all three cases the C-C and C-N bond orders in the ring, as well as the values of the distances from Tables 2 and 4 show that these bonds do not correspond to either single nor double bonds. This confirms the existence of π-conjugation in the pyridine rings. The C1-N2 bond distance as well as Q(C1-N2) for 4-NO 2 

Analyzing the average values of bond length in the pyridine ring Chiang J.F. et al. [20] have (Table 4) do not change with the insertion of the substituent in para-position. To study the substituent effect on the aromaticity the nuclear independent chemical shifts NICS(1) have been calculated. NICS(1) values correspond to the negative isotropic shielding (in ppm) at 1 Å above the ring plane [50] [51] [52] . It is of important to note that in a vast number of papers it has been elaborately shown that (depending on the size of the ring) the in-plane aromaticity which is indicated by the isotropic NICS(0) value contains considerable contribution of in-plane σaromaticity resulting from the diamagnetic shielding of the σ electronic framework. Thus the NICS(1) value regards to be a better descriptor of the π contribution to aromaticity due to the apparent decrease of the local contributions of the σ framework at larger distances from the ring center. All NICS values were computed by employing the standard GIAO method implemented in Table 6 ) are in satisfactory agreement with the Wiberg bond indexes ( Table 5 ) and confirm that the bonds in the pyridine ring are neither single nor double. As additional criteria of π-bonding contribution the bond ellipticity ε is used in QTAIM.

Among the endocyclic bonds of 4-NO 2 -PyO molecule the highest value of ε = 0.233 is for C2-C3

bond. Accordingly, this bond possesses highest π-character in the ring (in comparison ε = 0.200 for benzene [53] ). Surprisingly, the ellipticity value ε = 0.172 for C1-N2 bond is rather large, that could be a sign of the partial π-character of this bond in spite of the delocalization index value (δ = 0.887) corresponds to single (sigma) bond, as well as a bond r(C1-N2) length.

The net atomic charges obtained by QTAM approach are presented in Figure 6 and in Table   7 . Some differences of the net atomic charges obtained by NPA, Natural Population Analysis, (Table 5 ) and by QTAIM approach (Table 7) should be noted, although the general trends in the values remain from PyO to 4-NO 2 -PyO. According to QTAIM results, the atomic charge on the ipso carbon atom C1 in 4-NO 2 -PyO significantly changes in comparison with PyO because of a neighbor to acceptor -NO 2 group. The electron density on C2, C5 and N1 atoms in 4-NO 2 -PyO is decreased also due to negative mesomeric effect which takes place inside the pyridine ring. The total charge q(ring) of the heterocyclic ring in PyO has a positive value +0.274e which is increased up to +0.626e when -NO 2 group has been introduced. Indeed, the electron-withdrawing -NO 2 group is a part of π-conjugated system of the molecule, and as result electron density is shifted from O1 atom and pyridine ring towards the substituent. The negative total charge of -NO 2 group q(R) has a value -0.529e, that additionally supports the suggestion mentioned above. We would like to point out the magnitude of electron density into pyridine ring is changed quantitatively but topologically electron density distribution does not changed dramatically between non-and substituted pyridine-N-oxides (see Figure 7 and Table 6 ). At the same time a decrease of the charge on O1 atom can lead to a decrease in the complex formation ability of the substance.

The redistribution of electron density in 4-NO 2 -PyO affects to geometrical structure of the pyridine ring. The introduction of-NO 2 is accompanied by an increase of ρ b from 0.323 a.u. in PyO to 0.325 a.u. in 4-NO 2 -PyO and of ellipticity value ε from 0.186 to 0.195 for C1-C2 bond, respectively (see Table 6 ). That leads to magnification of electrostatic repulsion between these bonds and as result the ipso-angle C2C1C5 is changed from 117.7° in PyO to 119.9° in 4-NO 2 -PyO (B3LYP/aug-cc-pVTZ).It is interesting to note the same tendency is observed for crystal data where the ipso-angle C2C1C5 increased from 117.9° to 120.5° (see Table 4 ).

We can suspect the similar changes in electron density for crystal phase as for free 

In our research we are trying to understand the influence of the nature of substituents on the properties of N-oxides. In this work the molecular structure of 4-nitropyridine N-oxide has been studied by GED/MS and quantum chemical calculations (DFT and MP2). Both, quantum chemistry and GED analyses resulted in the C 2v molecular symmetry with the planar pyridine ring and -NO 2 group which is coplanar to the six-membered heterocycle. Furthermore, the rotation of -NO 2groupmore than for 12° leads to the significant increase in energy. a Distances in Å and angles in degrees. For atom numbering see Figure 1 . b Uncertainties in r h1 σ=(σ sc 2 +(2.5σ LS ) 2 ) 1/2 (σ sc =0,002r, σ LS -standard deviation in least-squares refinement), for angles σ= 3σ LS . c p i -parameter refined independently. (p i ) -parameters calculated from the independent parameter p i by a difference ∆= p i -(p i ) from the quantum chemical calculations (B3LYP/aug-cc-pVTZ). [24] X-ray [46] B3LYP/augcc-pVTZ r(N1-O1) 1.281 (22) * q(ring) -total natural charge of the heterocyclic ring (C1-C2-C4-N1-C5-C3) q(R) -total natural charge of the substituent Table 6 . Bond lengths and topological parameters of ρ(r) * in some bond critical points of 4-nitropyridine-N-oxide and pyridine-N-oxide (B3LYP/aug-cc-pVTZ) * -ρthe electron density(a.u.). ∇ 2 ρ-the Laplacian(a.u.). λ 1 , λ 2 , λ 3 -electron density Hessian matrix eigenvalues (a.u.). H b -the total electronic energy density (a.u.). ε-the bond ellipticity. δthe electronic delocalization index. 

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Figure 6. The molecular graphs for PyO (left ) and 4-NO 2 PyO (right )molecules and net atomic charges (e). The bond critical points are green

This work was supported by the Ministry of education and science of the Russian Federation (the project FZZW-2020-0007). We would like to thank Prof. A. V. Belyakov for his help in quantum chemical calculation.

The molecule possesses C 2v molecular symmetry with the planar pyridine ring and -NO 2 group which is coplanar to the six-membered heterocycle.Quantum chemical calculations for non-substituted pyridine-N-oxide, PyO, and for 4methylpiridine-N-oxide, 4-MePyO, have been performed using DFT.Obtained molecular parameters for PyO, 4-NO 2 -PyO, and 4-MePyO confirm the π-conjugation in the pyridine ring and the sp 2 hybridization concept of the nitrogen and carbon atoms in the ring.Electron density distribution analysis has discussed in terms of natural bond orbitals (NBO) and quantum theory atoms in molecule (QTAIM) scheme.The presence of electron withdrawing -NO 2 group in 4-NO 2 -PyO results in a shortening of r(N→O) in comparison with PyO, the corresponding bond order increases, and the negative net charge on the oxygen atom decreases, while in 4-Me-PyO with the donor substituent all changes are opposite.According to QTAIM N→O semipolar bond is predominantly covalent and possess the cylindrical symmetry, at the same time the electron density concentration is substantially high that is usually appropriate to the bonds with large π-contribution.

☒ The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.☐The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: