Nitroxoline Molecule: Planar or Not? A Story of Battle between ÏâÏ

Article Cite This: J. Phys. Chem. A 2018, 122, 1691−1701

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Nitroxoline Molecule: Planar or Not? A Story of Battle between π−π Conjugation and Interatomic Repulsion Denis S. Tikhonov,*,† Dmitry I. Sharapa,*,‡ Arseniy A. Otlyotov,*,¶ Peter M. Solyankin,§,∥ Anatolii N. Rykov,† Alexander P. Shkurinov,§,∥ Olga E. Grikina,† and Leonid S. Khaikin†

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†

Department of Physical Chemistry, M. V. Lomonosov Moscow State University, GSP-1, 1-3 Leninskie Gory, 119991 Moscow, Russian Federation ‡ Lehrstuhl für Physikalische und Theoretische Chemie, Friedrich-Alexander-Universität Erlangen−Nürnberg, Egerlandstraße 3, 91058 Erlangen, Germany ¶ Ivanovo State University of Chemistry and Technology, Ivanovo 153000, Russia § Department of Physics and International Laser Center, Lomonosov Moscow State University, GSP-1, 1-62 Leninskie Gory, Moscow 119992, Russia ∥ Institute on Laser and Information Technologies of the Russian Academy of Sciences, Branch of the FSRC “Crystallography and Photonics” RAS, Svyatoozerskaya 1, 140700 Shatura, Moscow Region, Russia S Supporting Information *

ABSTRACT: The conformational properties of the nitro group in nitroxoline (8-hydroxy5-nitroquinoline, NXN) were investigated in the gas phase by means of gas electron diffraction (GED) and quantum chemical calculations, and also with solid-state analysis performed using terahertz time-domain spectroscopy (THz-TDS). The results of the GED refinement show that in the equilibrium structure the NO2 group is twisted by angle ϕ = 8 ± 3° with respect to the 8-hydroxyoquinoline plane. This is the result of interatomic repulsion of oxygen in the NO2 group from the closest hydrogen, which overcomes the energy gain from the π−π conjugation of the nitro group and aromatic system of 8-hydroxyoquinoline. The computation of equilibrium geometry using MP2/ccpVXZ (X = T, Q) shows a large overestimation of the ϕ value, while DFT with the cc-pVTZ basis set performs reasonably well. On the other hand, DFT computations with double-ζ basis sets yield a planar structure of NXN. The refined potential energy surface of the torsion vibration the of nitro group in the condensed phase derived from the THz-TDS data indicates the NXN molecule to be planar. This result stays in good agreement with the previous X-ray structure determination. The strength of the π-system conjugation for the NO2 group and 8-hydroxyoquinoline is discussed using NBO analysis, being further supported by comparison of the refined semiexperimental gas-phase structure of NXN from GED with other nitrocompounds.

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INTRODUCTION Nitroxoline or 8-hydroxy-5-nitroquinoline (hereafter NXN) is a biologically active substance (see Figure 1 for its structure and atom numbering).1−4 It is widely used as an antibiotic1,2 and also can demonstrates some anticancer activity.3,4 Therefore, studies of the structural properties of this molecule are of certain interest, but, surprisingly, they are quite rare. The structure of NXN in the solid state was determined using powder X-ray diffraction.5 It was further investigated by means of infrared (IR) and Raman spectroscopy, UV spectroscopy, and 1H and 13C NMR and quantum chemical calculations.6 The latest theoretical and experimental work on NXN is by Sasi et al.7 It is quite similar to the previous study, i.e., quantum chemical computations with interest in the structure and electron density/chemical descriptor properties along with IR and Raman spectra of a crystalline sample of NXN.6 Nevertheless, the latter research was also concentrated on the difference between the single NXN molecule and its dimer. Arjunan et al.6 considered that NXN has a planar structure at equilibrium geometry, while Sasi et al.7 omit from discussion the conformational properties of the nitro group in this molecule. © 2018 American Chemical Society

However, a structural analogue of NXN, 1-nitronaphthalene, shows a significant deviation from planar geometry.8,9 It is due to the interatomic repulsion between the oxygen in the NO2 group and the closest hydrogen atom.9 Both NXN and 1-nitronaphtalene were predicted to be planar based on theoretical and experimental studies.6,10 However, in the case of 1-nitronaphthalene, it was shown theoretically that it is a wrong conclusion.8,9 Therefore, we started this study with a hope of shedding some systematic experimental and theoretical light on the ground-state structural properties in bicyclic systems with a nitro group attached to the larger site of the system.

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EXPERIMENTAL DETAILS Quantum Chemical Calculations. General Considerations. All of the computations were performed using the following software: Received: November 17, 2017 Revised: January 18, 2018 Published: January 23, 2018 1691

DOI: 10.1021/acs.jpca.7b11364 J. Phys. Chem. A 2018, 122, 1691−1701

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The Journal of Physical Chemistry A

level of theory with Firefly 8. The internal coordinate describing internal rotation of the hydroxyl group was dihedral ∠(H− O8−C8−C9). Additional unrelaxed PES scans with DLPNOCCSD(T) approximations were performed in ORCA (DLPNOCCSD(T)/cc-pVTZ) and in Turbomole (ri-CCSD(T)/def2TZVPP), based on geometries obtained at the B3LYP/cc-pVTZ level of theory. Geometry Optimizations. Unconstrained geometry optimizations of NXN and constrained optimization of its planar configuration were performed at MP2(full)/cc-pwCVTZ, CCSD/ccpVDZ, MP2(fc)/cc-pVTZ, MP2(fc)/cc-pVQZ, PBE0/ccpVQZ, and PBE0-D3/cc-pVQZ levels of theory using Firefly 8 and Gaussian 09. Also, the geometry optimizations were performed for the B3LYP, PBE0, PBE, and TPSS DFT functionals with and without D3 correction and with both cc-pVDZ and cc-pVQZ basis sets. Additional geometry optimization of naphthalene and 8-hydroxyquinoline were performed using G09 at PBE/cc-pVDZ and PBE/cc-pVTZ levels of theory. The HOMO/LUMO energies were computed for the optimized structures at the same levels of theory. Computation of Force Fields and Spectra. Geometry optimization of NXN followed by quadratic and cubic force field computations were performed with B3LYP/cc-pVTZ using Gaussian 09. The anharmonic frequencies for NXN on the same level of theory were also computed at the same level using second-order vibrational perturbation theory (VPT2)44 as implemented in Gaussian 09. The harmonic spectra were also computed at the MP2(fc)/cc-pVTZ and MP2(fc)/cc-pVQZ levels. Gas Electron Diffraction (GED). GED Experiment. The GED experiment was carried out on the EG-100 M apparatus at Lomonosov Moscow State University. A sample of NXN with purity of 96% was purchased from Sigma-Aldrich and used with no further purification. The diffraction patterns were recorded on photo films (MACO EM-Film EMS), which were scanned using a calibrated commercial scanner Epson Perfection 4870 Photo. Diffraction patterns were recorded at long (LD) and short (SD) nozzle-to-film distances. Intensity curves were obtained from scanned images by UNEX software.45 Patterns of CCl4 recorded along with the substance under investigation were used to calibrate the wavelength of the electron beam.46 A summary of experimental conditions is given in Table 1.

Figure 1. Geometry of NXN and numeration of its atoms used in the current work.

• Firefly 8;11 • ORCA;12 • Gaussian 09.13 A number of different methodologies were employed, including MP214 (full and frozen core, “fc”), DLPNO-CCSD(T),15−17 DLPNO-NEVPT2,18 B3LYP,19−21 PBE0,22 PBE,23 BP86,24−26 TPSS,27 and ri (resolution of identity)28 methods. D3 dispersion corrections,29 natural orbitals occupation numbers (NOONs),30 fractional occupancy density (FOD) diagnostics,31,32 T1-33 and T2-diagnostics,34 and the cc-pVTZ35 basis set were used as implemented in the software used. The def236 and cc-pwCVTZ37 basis sets were taken from the EMSL Basis Set Exchange Library38,39 in the cases when they were not implemented. An application of counterpoise correction (cp)40 for the possible intramolecular basis set superposition error (BSSE)41,42 was done by division of the NXN molecule into two subsystems, namely, a NO−2 group and positive ion of 8-hydroxyquinoline (8-HQ+), where both parts were considered to be singlets. Thus, the correction formula was41,42 ΔEcp = E(8‐HQ+)8‐HQ++ NO−2 + E(NO−2 )8‐HQ++ NO−2 − E(8‐HQ+)8‐HQ+ − E(NO−2 )NO−2

where E(X)Y denotes the single-point energy computation of the fragment X in the Gaussian basis set corresponding to the fragment Y in the same geometry as they are in the same molecule. The natural bond orbital (NBO) analysis43 was performed as it is implemented in Gaussian 09. Scans of Potential Energy Surfaces. Several relaxed scans of the potential energy surface (PES) for internal rotation of nitro group were made. The scanned dihedral angle was ∠(C10− C5−N5−O1) = ϕ. Only the unique part of the surface was considered (i.e., ϕNO2 was changed from 0 to 90°). Note that for the PES, the symmetry E(ϕNO2) = E(−ϕNO2) holds true. The relaxed scans of the PES were performed as follows: • using Gaussian 09 software employing B3LYP, PBE0, PBE, and TPSS (with and without D3 correction) and with cc-pVDZ and cc-pVTZ basis sets, • with ORCA at the ri-MP2(fc)/cc-pVTZ and ri-MP2(full)/cc-pVTZ levels of theory, • using Firefly 8 with MP2(fc)/def2-TZVP, cp-MP2(fc)/def2TZVP, PBE0/def2-SVP, and PBE0/def2-TZVP approximations. The 2D-scan of the PES for simultaneous internal rotations of NO2 and OH groups was performed at the MP2(fc)/def2-TZVP

Table 1. Conditions of the GED Experiment parameter dnozzle−film Uacceleration Ifast electrons λelectrons Tnozzle presidual gas texposure srange # of inflection points

[mm] [kV] [μA] [Å] [°C] [Pa] [s] [Å−1]

SD

LD

193.9 60 2.4 0.050155 158 3 × 10−3 75 6.6−30.8 3

362.3 60 2.4 0.049739 157 4 × 10−3 39 3.4−20.0 1

Details about the Structure Refinement. The vibrational parameters (i.e., mean vibrational amplitudes l and distance corrections re − ra) with exclusion of the lowest vibrational mode were computed using the VibModule program47 from quadratic and cubic force fields at the B3LYP/cc-pVTZ level. The refinement procedure was stabilized by regularization48−51 combined partitially with rigid constraints of some of 1692


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The Journal of Physical Chemistry A the parameters.52 All of the dihedral angles were frozen at the values computed with the ri-MP2(full)/cc-pVTZ level of theory. All of the values for bond lengths and valence angles were refined independently with soft restrictions based on the MP2(full)/ccpwCVTZ parameters. The PES for torsion vibration depending on ϕNO2 was refined without any restrictions using the form 3

V

V(ϕ) = V0 + ∑k = 1 22k (1 − cos(2kϕ)), i.e., parameters V2, V4, and V6 were varied independently, and the V0 constant was adjusted from the condition V(ϕ) ≥ 0. The final solution (i.e., the choice of regularization parameter α) was obtained using the modified version of the heuristic criterion introduced in the previous work.53 The resulting radial distribution curve can be found in Figure 2. The amount of experimental GED information

Figure 3. Reference pulse of THz-TDS and its spectrum (in the inset).

Figure 2. Experimental (circles) and theoretical (solid line) radial distribution curves for NXN and their difference.

wGED and corrected standard deviations of the refined parameters were estimated as was recently proposed.53 The refinement was performed using UNEX software.45 Terahertz Time-Domain Spectroscopy. Experimental Setup. The transmission spectrum of polycrystalline NXN was recorded using a conventional terahertz time-domain spectroscopy (THz-TDS) system. More detailed description of the spectrometer and methods for signal treatment can be found in Nazarov et al.54 In brief, in the current setup, femtosecond laser irradiation of a LT-GaAs surface causes THz single pulse generation with an ultra-broad-band spectrum from 0.1 to 2.5 THz (i.e., from 3.3 to 83.4 cm−1); see Figure 3. This pulse is transmitted through the sample and then is probed by the same optical pulse with some delay; therefore, one can retrieve the time profile of the electric field for THz radiation and obtain a THz spectrum by applying Fourier transformation. To eliminate atmospheric water vapor, the absorption system was vented with pure nitrogen. The sample was prepared by pressing NXN powder into a tablet with 1.2 mm width and 12.5 mm diameter using a Specac hydraulic press at 5 tons load. The measured THz absorption coefficient is presented in Figure 4. The spectrum was collected at 6 °C. Interpretation of the Spectrum. The resulting spectrum in the trusted region reveals three distinct features (see Figure 4). Prediction of spectroscopic properties of nitro group torsion vibrations was performed using a harmonic approximation, VPT2 calculation, and a 1D torsion model (see further text). All of them indicate that the motion of interest has a small, but nonzero intensity in the IR spectrum. The position of the peaks matches

Figure 4. Trusted region of the THz-TDS spectrum for the NXN sample and its interpretation. Circles correspond to the measured signal, the dashed line is the background Gaussian, continuous gaussians represent the signals, and vertical lines are the computed transition frequencies in different quantum-chemical approximations and fits. The heights of the vertical lines representing the transitions E

( )

|n⟩ → |m⟩ are proportional to the ⟨n|d|m⟩2 ·exp − kTn , where d is the dipole moment and En is the energy of the vibrational level |n⟩.

the predicted region of frequencies. For example, both harmonic approximation and VPT2 at the B3LYP/cc-pVTZ level of theory give an estimation of the fundamental frequency ν = 29 cm−1. Therefore, we considered the found peaks as a NO2 group torsion vibrations signal rather then the lattice modes. The experimental line was approximated using the sum of four gaussians (three signal peaks + one background peak). Interpretation of the spectra and the result of the refinement of the PES are given in Table 2. The refinement was performed by fitting the transition frequencies obtained from the solution of the 1D Schrödinger equation55,56 ⎛ d ⎞ d + V (ϕ)⎟ ψk = Ek ψk ⎜ − B(ϕ) dϕ ⎝ dϕ ⎠  Ĥ

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neglectable multireference character, we performed some calculation to leave fewer questions on this item. First of all, we looked at MP2 NOONs and found occupation numbers of the HOMO and LUMO to be 1.89 and 0.096, respectively, being nearly independent from the applied basis set. Deviation of 0.1 from doubly occupied or unoccupied orbitals was stated to be on the border of the “gray zone”, and even worse, nonphysical negative NOONs were observed that were announced as other symptoms of possible multireference character.30 However, nearly the same HOMO−LUMO NOONs (and negative NOONs) were found for naphthalene and tBu-NO2. Thus, we assume that MP2 NOONs may overrate the multireference nature of the system. FOD diagnostic provides a value of 0.215 that can be compared with that of an anthracene molecule (NFOD = 0.249) for which no multireference treatment is normally needed.31 The largest amplitudes (T2 diagnostic) taken from DLPNO-CCSD rigid scan calculations are approximately 0.054 and are also well below values where one has to pay attention to multireference (should not exceed 0.15 according to F. Neese or even 0.2 according to C. D. Scherrill). T1 diagnostic is below 0.014 (with an “alarm bell” of 0.0233). Finally, we performed DLPNONEVPT2 calculations for different geometries using the def2TZVP basis set and an active space of 12 electrons on 11 orbitals (this active space was chosen based on the gaps between orbitals). Results appear to be virtually the same; the 22222200000 configuration is dominant with weight over 0.8, and the second is 22222020000 with weight of less than 0.035 irrespectively of the torsion angle ϕNO2 up to at least 30°. We find that to be a sign of applicability of the single-reference method for a given system. Internal Rotation of the Hydroxyl Group. The others may have doubts that the other conformers, arising from the internal rotations of the hydroxyl group, are absent at the temperatures of the GED experiment (400 K). To eliminate these fears, a 2D scan for internal rotations of NO2 and of OH groups was obtained at the MP2(fc)/def2-TZVP level of theory (see Figure 5). It is easy to see that the conformers where hydrogen of the OH group is turned the opposite way from the nitrogen in the quinoline (N1) are approximately 3000 cm−1 ≈ 4 × 103 K higher in the energy then those where the same hydrogen looks right to the N1. This large energy difference comes from the intramolecular hydrogen bond −OH···N1. Therefore, the internal rotation of the OH group is absent in the NXN.

Table 2. Experimental and Fitted Transition Frequencies (ν) in the THz-TDS Spectraa νexperimental

νFit1, νFit2

30(5) 37(5)

30 38 43 46 49

47(8)

interpretation 0 1 2 3 4

→ → → → →

1 2 3 4 5

a Experimental frequencies are the expectation values for fitted gaussians, while given errors are the gaussian’s standard deviations. All of the values of ν are in cm−1. The vibrational quantum numbers of vibrational frequencies correspond to the numbering of levels in a single potential well ϕ ∈ [−90°; 90°).

by varying the parameters of PES (V(ϕ)), where B(ϕ) is the kinematic function (see Lewis et al.55 or Kudich et al.56 for an explanation). The parametric form for V(ϕ) was the same as that in the case of GED. The procedure was carried out using in-house software LAMPA-IntRo.Ver.ta.57 Several fits were made using different initial relaxed PES scans for the values of B(ϕ) and initial V(ϕ). Fit1 corresponds to the MP2(fc)/def2-TZVP initial V(ϕ) and assumed B(ϕ) and dipole moments, while Fit2 is based on PBE0/def2-TZVP analogical values. Although all of the values in the correlation matrix were always equal to ±1, different fits yielded the same results for frequencies and the PES in the range from 0 to ∼500 cm−1. Therefore, these large correlations are probably caused by the unknown behavior of the PES in the unpopulated region, and the inverse problem itself in the region of the interest is well-posed.

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RESULTS AND DISCUSSION Disclaimer: What We Do Not Have in the Nitroxoline. Multireferece Nature of the Electronic Wave Function. One may have doubts on applicability of the single-reference methods for this molecule. There are lists of indicators of the multireference nature of the system, e.g., T2 diagnostics, FOD, MP2 NOON, and others, and it was shown that they are rarely consistent.58 In particular, widely used for estimation of multireference character, T1 diagnostics was shown to have a little to do with multireference itself.34 Whenever general logic and TD-DFT calculations of NXN6 suggest big a HOMO−LUMO gap and

Figure 5. Relaxed 2D PES scan for internal rotation of nitro and hydroxyl groups at the MP2(fc)/def2-TZVP level of theory. 1694


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The Journal of Physical Chemistry A Nitroxoline: Planar or Not? What Does the Quantum Chemistry Say? The question entitling the current subsection arises from the results of different quantum-chemical calculations. This is the result of two competing effects that are estimated differently in different quantum chemical approximations: • a π−π conjugation of the NO2 group and 8-hydroxyquinoline fragments that forces NXN to be planar, • an interatomic repulsion of O1 from the nearby hydrogen that tries to tilt the nitro group with respect to the 8-hydroxyquinoline bicycle. A systematic set of PES scans with different DFT functionals using basis sets of the cc-pVnZ family and with and without the D3 dispersion corrections, are shown in Figures 6−9. They

Figure 8. Relaxed scans for rotation of the NO2 group in NXN using the PBE functional.

Figure 6. Relaxed scans for rotation of NO2 the group in NXN using the B3LYP functional.

Figure 9. Relaxed scans for rotation of the NO2 group in NXN using the TPSS functional.

distortion of nonplanarity in all of the cases are quite small (see Table 3). The equilibrium values for the dihedral ∠ϕ (∠ϕe) does not exceed 16°. The barrier heights at ϕ = 0° (EBH) are also small (less than 30 cm−1 ≈ 0.1 kcal/mol). The next step involves probing the true ab initio methods, such as MP2 and coupled clusters. Unfortunately, the direct implication of the latter for such a large system with low symmetry in a reasonable computational effort is possible only at the CCSD/cc-pVDZ level (see Table 3); therefore, we had to use the DLPNO version of CCSD(T). The results are shown in Figure 10 and Table 3. The results of ORCA and Turbomole computations at DLPNOCCSD(T)/cc-pVTZ and ri-CCSD(T)/def2-TZVPP were essentially the same; therefore, only the first ones are given in the figures. What first comes to mind while comparing the ab initio results with the DFT is a significant increase of the barrier height and the deviation from planarity. The overall increase of nonplanarity with the increase of basis set in DFT as well as strong deformations of the planar structure in the case of MP2 looks similar to the intramolecular BSSE.41,42 In order to compensate for it, a rigid cp-MP2(fc)/def2-TZVP scan was made on the basis of the geometries obtained in the MP2(fc)/def2TZVP scan. However, the introduction of this correction barely

Figure 7. Relaxed scans for rotation of the NO2 group in NXN using the PBE0 functional.

show that switching from double-ζ basis sets to triple-ζ immediately yields NXN becoming nonplanar (except for the TPSS). The D3 correction makes the PES flatter and wider, but it does not make the structure planar or nonplanar, again except for the TPSS, where the NXN in the TPSS/cc-pVTZ case is planar, while in the case of TPSS-D3/cc-pVTZ it becomes nonplanar. It should be fair to notice that the values of the 1695


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The Journal of Physical Chemistry A Table 3. Values of ϕNO2 at the Equilibrium Geometry of NXN and Height of the Barrier at the Planar Conformation from Different Experimental Techniques and Computed Using Different Levels of Theorya

Therefore, the intramolecular BSSE in the presented calculations is probably small. The increase of the quality of MP2 calculation MP2(fc)/def2TZVP → ri-MP2(fc)/cc-pVTZ → ri-MP2(full)/cc-pVTZ → MP2(full)/cc-pwCVTZ yielded a decrease of the EBH and of the ∠eϕ. The DFT had exactly the opposite tendency, with an increase of the basis set size including the D3-correction. Therefore, we might conclude that MP2 and DLPNO-CCSD(T) estimate the interatomic repulsion to be significantly dominating over the π−π conjugation, while the DFT predicts this domination to be significantly less drastic. We should also note that all of these electronic and structural effects are an order of magnitude less than kT ≈ 280 cm−1 ≈ 0.8 kcal/mol, which is smaller than the chemical accuracy (1 kcal/mol).59,60 What about the Experiments? Gas Electron Diffraction. In the current study, an experimental PES of internal rotation of the nitro group in NXN was obtained on the basis of GED (see Figure 12). The resulting surface (both the parametric form and pointwise form with the errors) can be found in SI. Surprisingly, the PES is very close to that obtained from DFT calculation. However, the errors of the obtained PES are quite large due to the fact that only EBH computed at the MP2(fc)/def2TZVP level can be rejected in light of experimental findings. On the other hand, for the refined value ∠eϕ = 8°(3°), the obtained standard deviation is quite small. The values close to this are easily obtained via optimization using DFT with triple-ζ basis sets, while the only close enough ab initio computation made is MP2(full)/cc-pwCVTZ with ∠eϕ = 13° (see Table 3). In other words, the DFT easily reproduces the results of the experiment, while in the case of MP2, a large basis sets and “full” option should be used. Because the experimental value for EBH = 1 ± 154 cm−1 has a large uncertainty, we recommend the value obtained from MP2(full)/cc-pwCVTZ computation: EBH = 80 cm−1. We consider it to be better then MP2(fc)/cc-pVQZ because the cc-pwCVnZ basis set shows faster convergence to the CBS limit with respect to cc-pVnZ (see Coriani et al.61 or Tikhonov et al.62). A quite interesting thing is that nonplanarity of NXN is sufficiently smaller than that in the case of 1-nitronaphthalene.8,9 In the case of NXN, the nitro group is bent for ∠eϕ = 8°(3°) with respect to the bicyclic aromatic system (theoretical DFT values are ∠eϕ = 0−16°). In contrast, the analogical values computed for 1-nitronaphthalene are distributed between 23 and 60°.8 Geometrical structures of the closest environment near the NO2 group in NXN and 1-nitronaphthalene are very similar; therefore, we can also expect very similar interatomic repulsion forces acting on the nitro group. Therefore, the most probable explanation for this difference in conformations of the nitro group is that it is the result of 8-hydroxyquinoline being a better π-electron donor then the naphthalene. If it is so, then the π−π conjugation in NXN would be better then that in 1-nitronaphthalene, and it will have the power to fight with the interatomic repulsion, making the theoretical structure determination for NXN a less trivial case. This guess is supported by simple estimations of electrodonating powers63,64

Experimental method

∠eϕ

GED THzSp

8°(3°) 0°

EBH, cm−1 1 ± 154 0 ∠αϕ

method XRD

4° Double-ζ

method

∠eϕ

EBH, cm−1

DFT(-D3)b/cc-pVDZ

0°

0

method

∠eϕ

EBH, cm−1

MP2(fc)/ccpVDZ CCSD/ccpVDZ

27°

−

24°

96

method

∠eϕ

EBH, cm−1

ri-MP2(full)/ccpVTZ

26°

91

MP2(full)/ccpVTZ

27°

−

MP2(full)/ccpwCVTZ

13°

80

Triple-ζ method

∠eϕ

EBH, cm−1

B3LYP/cc-pVTZ

11°

4

B3LYP-D3/cc-pVTZ PBE0/cc-pVTZ

16° 8°

21 1

PBE0-D3/cc-pVTZ PBE/cc-pVTZ

12° 4°

7 0.1

PBE-D3/cc-pVTZ TPSS/cc-pVTZ TPSS-D3/cc-pVTZ

9° 0° 7°

1.7 0 0.2 Quadriple-ζ

∠eϕ

EBH, cm−1

PBE0/cc-pVQZ

8°

−

PBE0-D3/cc-pVQZ

9°

−

method

method

∠eϕ

EBH, cm−1

MP2(fc)/ccpVQZ

26°

−

EBH denotes the height of the barrier at ϕ = 0°. bDFT(-D3) = B3LYP, PBE, PBE0, and TPSS functionals with and without D3 corrections.

a

ω− = Figure 10. PES scans for rotation of the NO2 group in NXN using ab initio techniques.

(3ϵHOMO + ϵLUMO)2 (3I + A)2 ≈ 16(I − A) 16(ϵLUMO − ϵHOMO)

where I and A are the ionization energy and electron affinity, which were estimated in our case using Koopmans’s theorem as I ≈ −ϵHOMO and A ≈ −ϵLUMO; ϵ is the orbital’s energy.65 The HOMO/LUMO in the cases of these molecules under

changed the PES quantitatively (the change was smaller relative to the form of the PES) and did not change it qualitatively at all. 1696


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The Journal of Physical Chemistry A disscussion correspond to the π-systems; therefore, the computation of ω− does not need any additional features, such as a choice of orbitals. For the 8-hydroxyquinoline, ω− ≈ 0.3 hartree, while for 1-nitronaphthalene, this value is only ω− ≈ 0.2 hartree (at PBE/cc-pVDZ and PBE/cc-pVTZ levels of theory). There are two possible reasons for the better electrodonating properties of 8-hydroxyquinoline then those of naphthalene: 1. the presence of the OH group in the para-position with respect to the NO2 group, 2. the presence of the nitrogen N1 in the quinoline ring. A simple application of the resonance theory66 (see Figure 11) provides arguments for the first cause: the OH group can

Figure 12. Experimental (GED and THz-TDS) and some theoretical PESs for rotation of the NO2 group in NXN.

Figure 11. Resonance structures for the mesomeric effect in the NXN. Figure 13. Stacking of two NXN molecules in the crystal structure.5

donate electrons via a mesomeric effect. Unfortunately, the second effect cannot be estimated in terms of simple qualitative models. Therefore, it is safer to conclude that the better donor properties of the 8-hydroxyquinoline with respect to the naphthalene are caused by the OH group in the para-position with respect to the NO2 group. Terahertz Time-Domain Spectroscopy. Another experimental technique involved in this study is THz-TDS. The most important difference of this experiment for NXN is that the sample under study was in the form of a polycrystal. Therefore, for interpretation of the results, the comparison with XRD study of NXN should be implied.5 The molecule of NXN in the crystal is close to planar with a dihedral value of ϕ = 4° (see Table 3). Unfortunately, this value cannot be used to judge the equilibrium structure of NXN in this form because XRD refinement considers the atoms to be moving in the quadratic potential; therefore, their motions are represented by thermal ellipsoids.This supposition can lead to effects similar to the Morino− Bastiansen “shrinkage effect”, which distorts gas-phase structures.67,68 The other problem is that in the work Yatsenko et al.5 no error estimation was made for this particular parameter. Nevertheless, we can use ϕ = 4° as a supporting reference. Refinement of the PES based on the results of THz-TDS uniquely yields NXN being planar, with the potential as given in the Figure 12. This does not contradict the result of XRD. From the structure of the NXN unit cell, it could be supposed that stacking the NXN molecules one above another could compensate the intramolecular atomic repulsion of O1···H, making the planar geometry more favorable (see Figure 13). Comparison with the PES obtained from the gas-phase

Figure 14. NBO overlap (π(C5−C6) → π*(N5−O2)) at the PBE0/ cc-pVQZ level of theory reflects electron-withdrawing properties of the −NO2 group in the NXN molecule. The numeration of the atoms is the same as that defined in Figure 1.

experiment and calculations supports this result because the width of the potential well in the case of the crystal is smaller compared to that of the gas. This can be thought of as an indirect observation of the effect of surroundings in the condensed phase. Strength of π-System Conjugation. NBO Analysis. The role of a substituent (donor or acceptor of the electron density) in a molecule can be described based on the NBO calculations (see, e.g., Vogt et al.69,70). The PBE0/cc-pVQZ level of theory was chosen for the NBO analysis because it was shown to be quite accurate in reproducing the electron density.71 In the case of NXN, donor−acceptor interactions between NBOs of the bonds C5−C6, C5−C10, N5−O1, and N5−O2 were taken into account (see Figure 14 as an example). These interactions 1697


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The Journal of Physical Chemistry A Table 4. Experimental Equilibrium Geometrical Parameters (re, ∠) of the Nitro Group in Different Moleculesa re(N−O)

molecule NXN Nitrobenzene72 1,3,5-trinitrobenzene72 C(NO2)474 CF(NO2)375 CBr(NO2)375

re(N5−O1) 1.229(3)b

re(N5−O2) 1.226(3)b 1.219(2) 1.220(1)

re(N−O+)d 1.199(3) 1.210(1) 1.209(1)

re(N−O−)e 1.201(3) 1.211(1) 1.214(1)

re(C−N)

∠(ONO)

1.457(15)b 1.482(6) 1.477(3)

123.9(12)c 125.0(6) 126.0(6)

1.509(5) 1.517(4) 1.529(3)

129.2(17) 129.5(6) 128.3(4)

a

The values of uncertainties in parentheses are 3σ. bwGED = 100%.53 cwGED = 58%.53 dThe O+ atom has smaller projection of C−O+ on the main symmetry axis. eThe O− atom has larger projection of C−O− on the main symmetry axis.

and bromotrinitromethane (CBr(NO2)3).75 The following geometrical parameters can serve as indirect indicators for the conjugation: • N−O bond length, • ONO valence angle, • C−N bond length that connects the NO2 fragment with the rest of the molecule. The comparison can be found in Table 4. The uncertainties for the parameters of NXN are larger than those in the case of the other molecules due to several reasons: • NXN has a lower symmetry and larger number of atoms of second period, • the influence of a priori assumptions taken from quantum-chemical calculations in the errors is reduced via a recently introduced method in contrast to the nitrobenzene, CF(NO2)3, and CBr(NO2)3.53 The tendencies are as follows, with the increase of electrondonor properties of the molecular frame: 1. the N−O bond length is increased, 2. the ∠(ONO) and C−N bond length are decreased. The π-conjugation gives a better electron acceptance of the nitro group with comparison to the inductive effect found in CX(NO2)3 (X = NO2, F, Br). Also, the 8-hydroxyquinoline is found to be a better electron donor than the benzene ring. The last fact is in good agreement with the results of our NBO analysis (see the previous subsection). Nitrobenzene and 1,3,5trinitrobenzene are flat molecules,72 while GED refinement shows that the nitro group in NXN is bent by 8°(3°) with respect to that in 8-hydroxyquinoline. Nevertheless, we can conclude that the strong π-conjugation is still preserved even with the observed structural deformation.

can be divided into donor and acceptor ones with respect to the NO2 group: • NO2 group as an acceptor: • π(C5−C6) → π*(N5−O2) (stabilization energy E(2) = 28.2 kcal/mol); • σ(C5−C6) → σ*(N5−O1) (E(2) = 2.3 kcal/ mol); • σ(C5−C10) → σ*(N5−O2) (E(2) = 1.9 kcal/ mol); • NO2 group as a donor: • π(C5−C6) → π*(N5−O2) (E(2) = 2.8 kcal/ mol); • σ(C5−C6) → σ*(N5−O1) (E(2) = 0.9 kcal/ mol); • σ(C5−C10) → σ*(N5−O2) (E(2) = 1.1 kcal/ mol). Comparison of the total stabilization energies of the acceptor (E∑,ac(2) = 32.4 kcal/mol) and donor (E∑,d(2) = 4.8 kcal/mol) interactions of the nitro group indicates its electron-withdrawing properties in the NXN molecule. The analogous values for the nitrobenzene molecule calculated at the same level of theory are 27.3 and 4.9 kcal/mol, respectively. Therefore, the NO2 group possesses more electron-withdrawing properties in NXN than in the nitrobenzene molecule. It is important to note that the same calculations performed for NXN with the nitro group being perpendicular to the benzene fragment (ϕNO2 = 90°) provided values of E∑,ac(2) = 12.6 kcal/mol and E∑,d(2) = 2.9 kcal/mol. This significant decrease of total stabilization energy reflects weakening of π-conjugation between the aromatic system and NO2 substituent, making large deviations from planarity energetically unfavorable. The NO2 substituent causes significant changes in the geometry of the benzene ring in NXN as compared to that for unsubstituted 8-hydroxyquinoline (optimized geometries at the PBE0/cc-pVQZ level). The bond lengths C5−C10 and C5−C6 increase by 0.015 and 0.005 Å, respectively. The ipso angle C6−C5−C10 increases by 1.5°. The same deformation of the ipso angle was previously reported for nitrobenzene (see, e.g., Khaikin et al.,72 Dorofeeva et al.73). Structural Features of π-Systems Conjugation. NBO analysis is not the only way to look at conjugation of the NO2 group’s and 8-hydroxyquinoline’s π-systems in NXN. It is also possible to compare the structures of other molecules with nitro groups. Because in the current work a semiexperimental equilibrium (re) structure of NXN in the gas phase was obtained, it seems convenient to compare it to the other experimental and semiexperimental structures. In this case, we took the following set of molecules: nitrobenzene,72 1,3,5-trinitrobenzene,72 tetranitromethane (C(NO2)4),74 fluorotrinitromethane (CF(NO2)3),

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CONCLUSIONS According to gas electron diffraction (GED), the equilibrium structure of NXN in the gas phase is not planar, where the dihedral angle between the NO2 group and the 8-hydroxyquinoline bicycle is 8°(3°). This is the result of interatomic repulsion of O1 (see Figure 1) from the nearby hydrogen. It distorts the planar structure formed by the π−π conjugation of the NO2 group and 8-hydroxyquinoline fragment. However, the structural features of the refined NXN structure as well as NBO analysis indicate that the conjugation is kept even with this distortion. Due to a large uncertainty of the experimental estimation of planar nitroxoline’s barrier height, we recommend the value calculated at the MP2(full)/ cc-pwCVTZ level of theory (80 cm−1) as the highest-level ab initio value. 1698


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calculations, and Dr. A. Ya. Freidzon for valuable discussions on multireference calculations. D.S.T., L.S.K., and O.E.G.’s computations were carried out using the equipment of the shared research facilities of HPC computing resources at Lomonosov Moscow State University.79

In the case of the crystal, NXN turns out to be planar, which is due to the surrounding molecules. The nearby molecules compensate the interatomic repulsion in a single molecule. This result is in an agreement with previous XRD studies of NXN.5 Unfortunately, we should also conclude that some of the previous studies on NXN were using a wrong assumption that NXN is planar.6 This deviation from nonplanarity is similar to that found for 1-nitronaphthalene,8,9 but it is sufficiently smaller due to 8-hydroxyquinoline being a better π-electron donor than naphthalene. However, we should also note that these deviations from planarity are smaller in energy scale than the chemical accuracy (1 kcal/mol). In the end, we must conclude that NXN is a fine example of a molecule with several intramolecular noncovalent forces having an observable impact on the structure. We could call such species a “molecular dynamometer” because by measuring the structure of the molecule we are also indirectly measuring the relation of its intramolecular forces. Some other examples of molecules of such kind recently investigated by GED are 1,1′-bisdiamantane and 6,6′-bis(3-oxadiamantane),76 1-phenyl-3-(perfluorophenyl)propane,77 histamine,78 and 1,8-bis[(trimethylsilyl)ethynyl]anthracene.70 We hope that further experimental characterization of such molecular dynamometers both with GED and with spectroscopic techniques will yield an even better understanding (and computational models) for intramolecular and intermolecular noncovalent interactions.

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(1) Pelletier, C.; Prognon, P.; Bourlioux, P. Roles of Divalent Cations and pH in Mechanism of Action of Nitroxoline against Escherichia Coli Strains. Antimicrob. Agents Chemother. 1995, 39, 707−13. (2) Sobke, A.; Klinger, M.; Hermann, B.; Sachse, S.; Nietzsche, S.; Makarewicz, O.; Keller, P. M.; Pfister, W.; Straube, E. The Urinary Antibiotic 5-Nitro-8-Hydroxyquinoline (Nitroxoline) Reduces the Formation and Induces the Dispersal of Pseudomonas aeruginosa Biofilms by Chelation of Iron and Zinc. Antimicrob. Agents Chemother. 2012, 56, 6021−6025. (3) Jiang, H.; Taggart, J. E.; Zhang, X.; Benbrook, D. M.; Lind, S. E.; Ding, W.-Q. Nitroxoline (8-hydroxy-5-nitroquinoline) Is More a Potent Anti-Cancer Agent than Clioquinol (5-chloro-7-iodo-8-quinoline). Cancer Lett. 2011, 312, 11−17. (4) Mirković, B.; Renko, M.; Turk, S.; Sosič, I.; Jevnikar, Z.; Obermajer, N.; Turk, D.; Gobec, S.; Kos, J. Novel Mechanism of Cathepsin B Inhibition by Antibiotic Nitroxoline and Related Compounds. ChemMedChem 2011, 6, 1351−1356. (5) Yatsenko, A. V.; Paseshnichenko, K. A.; Chernyshev, V. V.; Schenk, H. Powder Diffraction Study of the Hydrogen Bonds in Nitroxoline and Its Hydrochloride. Acta Crystallogr., Sect. C: Cryst. Struct. Commun. 2002, 58, o19−o21. (6) Arjunan, V.; Balamourougane, P. S.; Kalaivani, M.; Raj, A.; Mohan, S. Experimental and Theoretical Quantum Chemical Investigations of 8-hydroxy-5-nitroquinoline. Spectrochim. Acta, Part A 2012, 96, 506−516. (7) Arun Sasi, B. S.; Twinkle, A.; James, C. Characteristics of the Molecular Electron Density, Delocalization Effect and Hydrogen Bonding Interaction of Nitroxoline. J. Mol. Struct. 2017, 1141, 524− 534. (8) Alparone, A.; Librando, V. Comment on: “FT-IR, FT-Raman and {UV} Spectral Investigation; Computed Frequency Estimation Analysis and Electronic Structure Calculations on 1-Nitronaphthalene” by M. Govindarajan and M. Karabacak [Spectrochim. Acta A 85 (2012) 251−260]. Spectrochim. Acta, Part A 2012, 98, 479−480. (9) Onchoke, K. K.; Hadad, C. M.; Dutta, P. K. Density Functional Theoretical Study of Nitrated Polycyclic Aromatic Hydrocarbons. Polycyclic Aromat. Compd. 2004, 24, 37−64. (10) Govindarajan, M.; Karabacak, M. FT-IR, FT-Raman and {UV} Spectral Investigation; Computed Frequency Estimation Analysis and Electronic Structure Calculations on 1-Nitronaphthalene. Spectrochim. Acta, Part A 2012, 85, 251−260. (11) Granovsky, A. A. Firefly version 8. http://classic.chem.msu.su/ gran/firefly/index.html (2017). (12) Neese, F. The ORCA Program System. Wiley Interdisciplinary Reviews: Computational Molecular Science 2012, 2, 73−78. (13) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; et al. Gaussian 09, revision D.01; Gaussian Inc.: Wallingford, CT, 2009. (14) Møller, C.; Plesset, M. S. Note on an Approximation Treatment for Many-Electron Systems. Phys. Rev. 1934, 46, 618−622. (15) Neese, F.; Wennmohs, F.; Hansen, A. Efficient and Accurate Local Approximations to Coupled-Electron Pair Approaches: An Attempt to Revive the Pair Natural Orbital Method. J. Chem. Phys. 2009, 130, 114108. (16) Huntington, L. M. J.; Hansen, A.; Neese, F.; Nooijen, M. Accurate Thermochemistry from a Parameterized Coupled-Cluster Singles and Doubles Model and a Local Pair Natural Orbital Based Implementation for Applications to Larger Systems. J. Chem. Phys. 2012, 136, 064101.

ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jpca.7b11364. Optimized Cartesian coordinates of NXN at MP2(full)/ cc-pwCVTZ and CCSD/cc-pVDZ levels of theory, Cartesian re coordinates of NXN refined from GED for the nearest-to-equilibrium conformation (ϕ = 9°), geometrical parameters of NXN refined from GED, computed PES for torsion vibration on the NO2 group in NXN at different levels of theory, refined PES of NXN from GED and THz-TDS, input file for the UNEX program for GED refinement of NXN, correlation table for GED refinement of NXN, GED scattering intensities for NXN, and THz-TDS spectrum of NXN (PDF)

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REFERENCES

AUTHOR INFORMATION

Corresponding Authors

*E-mail: [email protected] (D.S.T.). *E-mail: [email protected] (D.I.S.). *E-mail: [email protected] (A.A.O.). ORCID

Denis S. Tikhonov: 0000-0003-3167-3104 Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS D.I.S. thanks the Collaborative Research Centre SFB 953: “Synthetic Carbon Allotropes” and Regionales Rechenzentrum Erlangen for computational time. The authors thank Prof. G. V. Girichev for providing computational resources of the laboratory of molecular parameters (Ivanovo State University of Chemistry and Technology) for quantum-chemical calculations, Dr. Yu. V. Vishnevskiy for performing the ri-CCSD(T)/def2-TZVPP 1699


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