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Nitroxoline Molecule: Planar or Not? A Story of Battle between #–# Conjugation and Interatomic Repulsion Denis S Tikhonov, Dmitry I. Sharapa, Arseniy A. Otlyotov, Petr M. Solyankin, Anatolii N. Rykov, Alexander P. Shkurinov, Olga E. Grikina, and Leonid S. Khaikin J. Phys. Chem. A, Just Accepted Manuscript • DOI: 10.1021/acs.jpca.7b11364 • Publication Date (Web): 23 Jan 2018 Downloaded from http://pubs.acs.org on January 24, 2018

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The Journal of Physical Chemistry

Nitroxoline Molecule: Planar or Not? A Story of Battle Between π − π Conjugation and Interatomic Repulsion Denis Tikhonov,∗,† Dmitry I. Sharapa,∗,‡ Arseniy A. Otlyotov,∗,¶ Peter M. Solyankin,§,k Anatolii N. Rykov,† Alexander P. Shkurinov,§,k Olga E. Grikina,† and Leonid S. Khaikin† 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, and Department of Physics and International Laser Center, Lomonosov Moscow State University, GSP-1, 1-62 Leninskie Gory, Moscow 119992, Russia E-mail: [email protected]; [email protected]; [email protected]

∗

To whom correspondence should be addressed 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 ErlangenNürnberg, 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 k 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 †

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Abstract The conformational properties of the nitrogroup in nitroxoline (8-hydroxy-5-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 nitrogroup and aromatic system of 8-hydroxyoquinoline. The computation of equilibrium geometry using MP2/cc-pVXZ (X = T, Q) shows a large overestimation of the φ value, whilst DFT with 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 of nitrogroup in the condensed phase derived from the from 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-systems conjugation for the NO2 -group and 8-hydroxyoquinoline is discussed using NBO analysis, being further supported by comparison of the refined semi-experimental gas-phase structure of NXN from GED with other nitrocompounds.

Keywords American Chemical Society, LATEX

Introduction Nitroxoline or 8-hydroxy-5-nitroquinoline (hereafter NXN) is a biologically active substance (see Fig. 1 for its structure and atom numbering). 1–4 It is widely used as an antibiotic, 1,2 2


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and also can demonstrates some anticancer activity. 3,4 Therefore the studies of the structural properties of this molecule are of a certain interest, but, surprisingly, they are quite rare. The structure of NXN in 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 1 H and 13 C 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 the interest on the structure and electron density/chemical descriptors properties along with IR, Raman spectra of 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 the equilibrium geometry, while Sasi et al. 7 omit from discussion the conformational properties of nitro-group in this molecule. However, a structural analog 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 1nitronaphthalene it was shown theoretically that it is a wrong conclusion. 8,9 Therefore we started this study with a hope to shed some systematic experimental and theoretical light on the ground-state structural properties in bicyclic systems with a nitrogroup attached to the larger site of the system.

Experimental details Quantum chemical calculations General considerations All the computations were performed using the following software:

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Figure 1: Geometry of NXN and the 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 MP2 14 (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 cc-pVTZ 35 basis set were used as implemented in the software used. The def2 36 and cc-pwCVTZ 37 basis sets were taken from the EMSL Basis Set Exchange Library 38,39 in the cases when they are 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 NXN molecule into two subsystems, namely NO− 2 group and positive ion of 8-hydroxyquinoline (8-HQ+ ), where both parts were considered to

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be singlets. Thus the correction formula was: 41,42

, − E(8-HQ+ )8-HQ+ − E(NO− ∆ECP = E(8-HQ+ )8-HQ+ +NO−2 + E(NO− 2 )NO− 2 )8-HQ+ +NO− 2 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) analysis 43 was performed as it is implemented in Gaussian 09.

Scans of potential energy surfaces Several relaxed scans of potential energy surface (PES) for internal rotation of nitrogroups were made. The scanned dihedral angle was 6 (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 PES were performed as following: • 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)/def2-TZVP, PBE0/def2-SVP and PBE0/def2-TZVP approximations. The 2D-scan of PES for simultaneous internal rotations of NO2 - and OH-groups was performed at MP2(fc)/def2-TZVP level of theory with Firefly 8. The internal coordinate describing internal rotation of hydroxyl group was dihedral 6 (H–O8–C8–C9). Additional unrelaxed PES scans of with DLPNO-CCSD(T) approximations were performed in ORCA (DLPNOCCSD(T)/cc-pVTZ) and in Turbomole (ri-CCSD(T)/def2-TZVPP), based on geometries obtained at B3LYP/cc-pVTZ level of theory. 5



Geometry optimizations Unconstrained geometry optimizations of NXN and constrained optimization of its planar configuration were performed at MP2(full)/cc-pwCVTZ, CCSD/cc-pVDZ, MP2(fc)/ccpVTZ, MP2(fc)/cc-pVQZ, PBE0/cc-pVQZ 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, 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 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 fields 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 experiment The GED experiment was carried out on the EG-100 M apparatus at Lomonosov Moscow State University. A sample of NXN with purity 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 calibrated commercial scanner Epson Perfection 4870 Photo. Diffraction patterns were recorded at the long (LD) and short (SD) nozzle-to-film distances. Intensity curves were obtained from scanned images by

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UNEX software. 45 Patterns of CCl4 recorded along with the substance under investigation were used to calibrate the wavelength of the electron beam. 46 The summary of experimental conditions is given in Table 1. 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 193.9 60 2.4 0.050155 158 3 · 10−3 75 6.6 – 30.8 3

LD 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 program 47 from quadratic and cubic force fields at B3LYP/cc-pVTZ level. Refinement procedure was stabilized by regularization 48–51 combined partitially with rigid constrains of some of the parameters. 52 All the dihedral angles were frozen at the values computed with ri-MP2(full)/cc-pVTZ level of theory. All 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 φN O2 was refined without P any restrictions using the form V (φ) = V0 + 3k=1 V22k (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 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 wGED and corrected standard deviations of the refined parameters were

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estimated as it was recently proposed. 53 The refinement was performed using UNEX software. 45

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

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 a femtosecond laser irradiation of LT-GaAs surface causes the THz single pulse generation with ultrabroadband spectrum from 0.1 to 2.5 THz (i.e. from 3.3 to 83.4 8


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Figure 3: Reference pulse of THz-TDS and its spectrum (at the inset). cm−1 ), see Fig. 3. This pulse is transmitted through the sample and then is probed by the same optical pulse with some delay, so one can retrieve time profile of electric field for THz radiation and obtain a THz spectrum by applying Fourier transformation. For eliminating atmosphere water vapor 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. Measured THz absorption coefficient is presented at Fig. 4. The spectrum was collected at 6 ◦ C.

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Figure 4: Trusted region of THz-TDS spectrum for NXN sample and its’ interpretation. Circles correspond to the measured signal, dashed line is the background gaussian, continuous gaussians represent the signals, vertical lines are the computed transition frequencies in different quantum-chemical approximations and fits. The heights of the vertical lines repreEn 2 senting the transitions |ni → |mi are proportional to the hn|d|mi · exp − kT , where d is the dipole moment, and En is the energy of the vibrational level |ni. Interpretation of the spectrum The resulting spectrum in the trusted region reveals three distinct features (see Fig. 4). The prediction of spectroscopic properties of nitrogroup torsion vibrations were performed using harmonic approximation, VPT2 calculation and 1D torsion model (see further text). All of them indicate that the motion of interest has a small, but nonzero intensity in the 10


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IR spectrum. The position of the peaks matches the predicted region of frequencies. For example, both harmonic approximation and VPT2 at 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). The interpretation of the spectra and the result of the refinement of PES is given in the Table 2. The refinement was performed by fitting the transition frequencies obtained from solution of 1D Schrödinger equation 55,56 d d + V (φ) ψk = Ek ψk , − B(φ) dφ dφ {z } | ˆ H

by varying the parameters of PES (V (φ)), where B(φ) is the kinematic function (see Ref. Lewis et al. 55 or Kudich et al. 56 for the explanation). The parametric form for V (φ) was the same as 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 the values in correlation matrix were always equal to 1, different fits yielded in the same results for frequencies and PES in the range from 0 to ∼ 500 cm−1 . Therefore these large correlation 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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Table 2: Experimental and fitted transition frequencies (ν) in the THz-TDS spectra. Experimental frequencies are the expectation values for fitted gaussians, while given errors are the gaussian’s standard deviations. All 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◦ ). νexperimental 30(5) 37(5) 47(8)

νFit1 , νFit2 30 38 43 46 49

Interpretation 0→1 1→2 2→3 3→4 4→5

Results and discussion Disclaimer: what we do not have in the nitroxoline Multireferece nature of the electronic wavefunction One may have doubts on applicability of the singlereference methods for this molecule. There are list of indicators of multireference nature of the system, e.g. T2-diagnostics, FOD, MP2 NOON and other, 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 NXN 6 suggest big HOMO-LUMO gap and neglectable multireference character, we performed some calculation to leave less questions on this item. First of all we looked on MP2 NOONs and found occupation numbers of HOMO and LUMO to be 1.89 and 0.096 respectively, being nearly independent from applied basis set. Deviation of 0.1 from doubly occupied or unoccupied orbitals was stated to be on the border of “gray zone”, and even worse, nonphysical negative NOONs were observed, that were announced as other symptom 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 multireference nature of the system. FOD-diagnostic provides value of 0.215 that can be compared with anthracene molecule (NFOD = 0.249) for which no multireference treatment 12


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is normally needed. 31 Largest amplitudes (T2-diagnostic) taken from DLPNO-CCSD rigid scan calculations are approx. 0.054 and are also well below values where one have 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 “alarm bell” of 0.02 33 ). Finally, we performed DLPNO-NEVPT2 calculations for different geometries using def2-TZVP basis set and 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, 22222200000 configuration is dominant with weight over 0.8 and the second following is 22222020000 with weight of less than 0.035 irrespectively to torsion angle φNO2 up to at least 30 degrees. We find that to be a sign of applicability of single reference method for given system.

Internal rotation of 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 MP2(fc)/def2-TZVP level of theory (see Fig. 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 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.

Nitroxoline: planar or not? What does the quantum chemistry say? The question entitling 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: 13



Figure 5: Relaxed 2D PES scan for the internal rotation of nitro- and hydroxyl- groups at MP2(fc)/def2-TZVP level of theory. • a π − π conjugation of 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 nitrogroup with respect to the 8-hydroxyquinoline bicycle. A systematic set of PES scans with different DFT functionals, using basis sets of cc-pVnZ family, and with and without the D3 dispersion corrections, are shown in Figs. 6 – 9. They show that switching from double-ζ basis sets to triple-zeta immediately yields in NXN becoming nonplanar (except for the TPSS). The D3 correction makes the PES more flat and wide, but it does not make the structure planar or nonplanar, again except for the TPSS, where the NXN in TPSS/cc-pVTZ case is planar, while in case of TPSS-D3/ccpVTZ it becomes nonplanar. It should be fair to notice that the values of the distortion of nonplanarity in all the cases are quite small (see Table 3). The equilibrium values for the dihedral 6 φ (6 φe ) does not exceed 16◦ . The barrier heights at φ = 0◦ (EBH ) are also small (less then 30 cm−1 ≈ 0.1 kcal/mol). The next step involves probing the true-ab initio

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Figure 6: Relaxed scans for the rotation of NO2 -group in NXN using B3LYP functional. methods, such as MP2 and coupled-clusters. Unfortunately, the direct implication of latter for such a large system with low symmetry in a reasonable computational efforts is possible only at CCSD/cc-pVDZ level (see Table 3), therefore we had to use the DLPNO version of CCSD(T). The results are shown in Fig. 10 and in the Table 3. The results of ORCA and Turbomole computations at DLPNO-CCSD(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 planar structure in case of MP2 looks similar to the intramolecular BSSE. 41,42 In order to compensate it

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Figure 7: Relaxed scans for the rotation of NO2 -group in NXN using PBE0 functional. a rigid CP-MP2(fc)/def2-TZVP scan was made on the basis of the geometries obtained in MP2(fc)/def2-TZVP scan. However, the introduction of this correction barely changed the PES quantitatively (the change was smaller relative to the form of the PES) and did not changed it qualitatively at all. Therefore the intramolecular BSSE in the presented calculations is probably small. The increase of the quality of MP2 calculation MP2(fc)/def2-TZVP → ri-MP2(fc)/ccpVTZ → ri-MP2(full)/cc-pVTZ → MP2(full)/cc-pwCVTZ yielded in the decrease of the EBH and of the

6 e φ.

The DFT had exactly the opposite tendency with increasing of the

basis set size and the including the D3-correction. Therefore we might conclude that MP2 and DLPNO-CCSD(T) estimate the interatomic repulsion to be significantly dominating

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Figure 8: Relaxed scans for the rotation of NO2 -group in NXN using PBE functional. 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 have the order of magnitude less then kT ≈ 280 cm−1 ≈ 0.8 kcal/mol, which is smaller then 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 nitrogroup in NXN was obtained on the basis of GED (see Fig. 12). The resulting surface (both 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

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Figure 9: Relaxed scans for the rotation of NO2 -group in NXN using TPSS functional. obtained PES are quite large, due to the fact that only EBH computed at MP2(fc)/def2TZVP level can be rejected in the light of experimental findings. On the other hand, the refined value for

6 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 the only close enough ab initio computation made is MP2(full)/cc-pwCVTZ with

6 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. Since 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, since the cc-pwCVTZ basis set shows faster convergence to CBS limit

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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 theory. EBH denotes the height of the barrier at φ = 0◦ .

Method GED THzSp Method XRD

Experimental: 6 eφ ◦ 8 (3◦ ) 0◦

EBH , cm−1 1 ± 154 0 6 αφ 4◦

Double-ζ: 6 eφ Method Method EBH , MP2(fc)/cc-pVDZ 27◦ DFT(-D3)a /cc-pVDZ 0◦ 0 CCSD/cc-pVDZ 24◦ Triple-ζ: −1 6 6 eφ EBH , cm Method Method eφ ◦ B3LYP/cc-pVTZ 11 4 ri-MP2(full)/cc-pVTZ 26◦ B3LYP-D3/cc-pVTZ 16◦ 21 PBE0/cc-pVTZ 8◦ 1 MP2(full)/cc-pVTZ 27◦ PBE0-D3/cc-pVTZ 12◦ 7 PBE/cc-pVTZ 4◦ 0.1 MP2(full)/cc-pwCVTZ 13◦ PBE-D3/cc-pVTZ 9◦ 1.7 TPSS/cc-pVTZ 0◦ 0 ◦ TPSS-D3/cc-pVTZ 7 0.2 Quadriple-ζ: 6 6 eφ Method EBH , cm−1 Method eφ ◦ PBE0/cc-pVQZ 8 – MP2(fc)/cc-pVQZ 26◦ ◦ PBE0-D3/cc-pVQZ 9 — a – DFT(-D3) = B3LYP, PBE, PBE0, TPSS functionals with and without 6 eφ

cm−1

EBH , cm−1 — 96 EBH , cm−1 91 — 80

EBH , cm−1 — D3 corrections

with respect to cc-pVTZ (see Coriani et al. 61 or Tikhonov et al. 62 ). A quite interesting thing is that nonplanarity of NXN is sufficiently smaller than in the case of 1-nitronaphthalene. 8,9 In the case of NXN the nitrogroup is bend for with respect to bicyclic aromatic system (theoretical DFT values are

6 eφ

6 eφ

= 8◦ (3◦ )

= 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 a very similar interatomic repulsion forces acting on the nitrogroup. Therefore the most probable explanation for this difference in conformations of nitrogroup, that it is the result of 8-hydroxyquinoline being 19



Figure 10: PES scans for the rotation of NO2 -group in NXN using ab initio techniques. better π-electron donor, then the naphthalene. If it is so, then the π − π conjugation in NXN would be better then 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 powers: 63,64 (3I + A)2 (3HOMO + LUMO )2 ω = ≈ , 16(I − A) 16(LUMO − HOMO ) −

where I and A are the ionization energy and electron affinity, which were estimated in our case using Koopmans’ theorem as I ≈ −HOMO and A ≈ −LUMO , is the orbital’s energy. 65 The HOMO/LUMO in the cases of these molecules under disscussion correspond to the π systems, therefore the computation of ω − does not need any additional features, 20


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such as a choice of orbitals. The for 8-hydroxyquinoline ω − ≈ 0.3 Hartrees, whether for 1nitronaphthalene this value is only ω − ≈ 0.2 Hartrees (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 of naphthalene: 1. presence of the OH-group in the para-position with respect to NO2 -group, 2. presence of the nitrogen N1 in the quinoline ring. A simple application of the resonance theory 66 (see Fig. 11) provides arguments for the first cause: OH-group can donate electrons via mesomeric effect. Unfortunately, the second effect cannot be estimated in the 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 polycrystal. Therefore for the 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 the dihedral value of φ = 4◦ (see Table 3). Unfortunately, this value cannot be used to judge about the equilibrium structure of NXN in this form, since XRD refinement consider the atoms to be moving in the quadratic potential, therefore their motions are represented by the thermal ellipsoids. This supposition can lead to the effects similar to the Morino-Bastiansen “shrinkage effect”, that 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. The refinement of PES based on the results of THz-TDS uniquely yields in a NXN being planar with the potential shapes as given in the Fig. 12. This does not contradict with the result 21



Figure 11: Resonance structures for the mesomeric effect in the NXN. of XRD. From the structure of NXN unit cell it could be supposed that stacking the NXN molecule one above another could compensate the intramolecular atomic repulsion of O1· · · H making the planar geometry more favorable (see Fig. 13). The comparison with the PES obtained from the gas-phase experiment and calculations supports this result, since the width of the potential well in case of the crystal smaller comparing to the gas. This can be thought as a indirect observation of the effect of surroundings in the condensed phase.

22


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

Strength of the π systems 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 , Otlyotov et al. 70 ). The PBE0/cc-pVQZ level of theory was chosen for the NBO analysis since it was shown to be quite accurate in reproducing the electron density. 71 In the case of NXN donor-acceptor interactions between natural bond orbitals of the bonds C5–C6, C5–C10, N5–O1 and N5– O2 were taken into account (see Fig. 14 as an example). These interactions can be divided into donor and acceptor ones with respect to the NO2 -group:

23



Figure 13: Stacking of two NXN molecules in the crystal structure. 5 • NO2 -group as an acceptor: – π(C5 − C6) → π ∗ (N5 − O2) (stabilization energy E(2) = 28.2 kcal · mol−1 ); – σ(C5 − C6) → σ ∗ (N5 − O1) (E(2) = 2.3 kcal · mol−1 ); – σ(C5 − C10) → σ ∗ (N5 − O2) (E(2) = 1.9 kcal · mol−1 ); • NO2 -group as a donor: – π(C5 − C6) ← π ∗ (N5 − O2) (E(2) = 2.8 kcal · mol−1 ); 24


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Figure 14: The natural bond orbitals overlap (π(C5 − C6) → π ∗ (N5 − O2)) at PBE0/ccpVQZ level of theory reflects electron withdrawing properties of –NO2 -group in NXN molecule. The numeration of the atoms is the same as defined in Fig. 1. – σ(C5 − C6) ← σ ∗ (N5 − O1) (E(2) = 0.9 kcal · mol−1 ); – σ(C5 − C10) ← σ ∗ (N5 − O2) (E(2) = 1.1 kcal · mol−1 ). The comparison of the total stabilization energies of the acceptor (EP,ac (2) = 32.4 kcal · mol−1 ) and donor (EP,d (2) = 4.8 kcal · mol−1 ) interactions of the nitro-group indicates its electronwithdrawing 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-1, respectively. Therefore, 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 25



NXN with the nitro-group being perpendicular to the benzene fragment (φNO2 = 90◦ ) provided the values of EP,ac (2) = 12.6 kcal · mol−1 and EP,d (2) = 2.9 kcal · mol−1 . 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 unsubstituted 8-hydroxyquinoline (optimized geometries at 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 The NBO analysis is not the only way to look at the conjugation of NO2 -group’s and of 8hydroxyquinoline’s π-systems in NXN. It is also possible to compare the structures of other molecules with nitrogroups. Since in the current work semi-experimental equilibrium (re ) structure of NXN in the gas phase was obtained, it seems convenient to compare it to the other experimental and semi-experimental 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 ) and bromotrinitromethane (CBr(NO2 )3 ). 75 The following geometrical parameters can serve as an indirect indicators for the conjugation: • N–O bond length, • ONO valence angle, • the C–N bond length, that connects 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 then in case of the other molecules due to several reasons: • NXN has a lower symmetry and larger number of atoms of second period, 26


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Table 4: Experimental equlibrium geometrical parameters (re , 6 ) of nitrogroup in different molecules. The values of uncertainties in parentheses are 3σ. re (N − O)

Molecule

NXN Nitrobenzene 72 1,3,5-trinitrobenzene 72

re (N5 − O1) re (N5 − O2) 1.229(3)a 1.226(3)a 1.219(2) 1.220(1) re (N − O+ )c re (N − O− )d 1.199(3) 1.201(3) 1.210(1) 1.211(1) 1.209(1) 1.214(1)

re (C − N)

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

6

(ONO)

123.9(12)b 125.0(6) 126.0(6)

1.509(5) 129.2(17) C(NO2 )4 74 75 1.517(4) 129.5(6) CF(NO2 )3 1.529(3) 128.3(4) CBr(NO2 )3 75 a – w 53 GED = 100 %. b – w 53 GED = 58 %. c – the O atom has smaller projection of C–O on the main symmetry axis. + + d – the O atom has larger projection of C–O on the main symmetry axis. − −

• the influence of a priori assumptions taken from quantum chemical calculations in the errors is reduced via 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 electron-donor properties of the molecular frame 1. the N–O bond length is increased, 2. the 6 (ONO) and C–N bond length are decreased. The π-conjugation gives better electron acceptance of nitrogroup 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, then the benzene ring. The last fact is in a good agreement with the results of our NBO-analysis (see previous subsection). The nitrobenzene and 1,3,5trinitrobenzene are flat molecules, 72 while the GED refinement shows that nitrogroup in NXN is bent for 8◦ (3◦ ) with respect to 8-hydroxyquinoline. Nevertheless, we can conclude that the strong π-conjugation is still preserved even with the observed structural deformation.

27



Conclusions According to gas electron diffraction, the equilibrium structure of NXN in the gas phase is not planar, where the dihedral angle between NO2 group and the 8-hydroxyquinoline bicycle is 8◦ (3◦ ). This is the result of interatomic repulsion of O1 (see Fig. 1) from the nearby hydrogen. It distorts the planar structure formed by the π − π conjugation of NO2 group and 8-hydroxyquinoline fragments. 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. 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 8hydroxyquinoline being better π-electron donor, then 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 an “molecular dynamometer”, because by measuring the structure of the molecule we are also doing an inderect measuring of relation of its’ intramolecular forces. Some other recently investigated by GED examples of molecules of such kind 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 spectroscopic 28


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techniques will yield in an even better understanding (and computational models) for intramolecular and intermolecular noncovalent interactions.

Acknowledgement D.I.S. thank Collaborative Research Centre SFB 953: “Synthetic Carbon Allotropes” and Regionales Rechenzentrum Erlangen for the 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 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

Supporting Information Available Supporting information contains the following data. • Optimized Cartesian coordinates of NXN at MP2(full)/cc-pwCVTZ and CCSD/ccpVDZ levels of theory (S1 and S2). • Cartesian re -coordinates of NXN refined from GED for the nearest-to-equilibrium conformation (φ = 9◦ ), S3. • Geometrical parameters of NXN refined from GED (bonded distances, S4, and valence angles, S5). • Computed PES for torsion vibration on NO2 -group in NXN at different levels of theory (S6-S16). • Refined PES of NXN from GED and THz-TDS (S17, S18). • Input file for UNEX program for the GED refinement of NXN (S19). 29



• Correlation table for GED refinement of NXN (S20). • GED scattering intensities for NXN (S21). • THz-TDS spectrum of NXN (S22). This material is available free of charge via the Internet at http://pubs.acs.org/.

References (1) Pelletier, C.; Prognon, P.; Bourlioux, P. Roles of Divalent Cations and pH in Mechanism of Action of Nitroxoline against Escherichia Coli Strains. Antimicrobial Agents and Chemotherapy 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. Antimicrobial Agents and Chemotherapy 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 Letters 2016, 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 Crystallographica Section C 2002, 58, o19–o21.

30


Page 30 of 41

Page 31 of 41 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(6) Arjunan, V.; Balamourougane, P. S.; Kalaivani, M.; Raj, A.; Mohan, S. Experimental and Theoretical Quantum Chemical Investigations of 8-hydroxy-5-nitroquinoline. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2012, 96, 506 – 516. (7) Sasi, B. A.; Twinkle, A.; James, C. Characteristics of the Molecular Electron Density, Delocalization Effect and Hydrogen Bonding Interaction of Nitroxoline. Journal of Molecular Structure 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]. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2012, 98, 479 – 480. (9) Onchoke, K. K.; Hadad, C. M.; Dutta, P. K. Density Functional Theoretical Study of Nitrated Polycyclic Aromatic Hydrocarbons. Polycyclic Aromatic Compounds 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. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2012, 85, 251 – 260. (11) Granovsky, A. A. Firefly version 8, http://classic.chem.msu.su/gran/firefly/ index.html. (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.; Cheese-

31



man, 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. Physical Review 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. The Journal of Chemical Physics 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. The Journal of Chemical Physics 2012, 136, 064101. (17) Neese, F.; Hansen, A.; Liakos, D. G. Efficient and Accurate Approximations to the Local Coupled Cluster Singles Doubles Method using a Truncated Pair Natural Orbital Basis. The Journal of Chemical Physics 2009, 131, 064103. (18) Guo, Y.; Sivalingam, K.; Valeev, E. F.; Neese, F. SparseMapsâĂŤA Systematic Infrastructure for Reduced-Scaling Electronic Structure methods. III. Linear-Scaling Multireference Domain-Based Pair Natural Orbital N-electron Valence Perturbation Theory. The Journal of Chemical Physics 2016, 144, 094111. (19) Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange. The Journal of Chemical Physics 1993, 98, 5648–5652. (20) Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density. Phys. Rev. B 1988, 37, 785–789. (21) Vosko, S. H.; Wilk, L.; Nusair, M. Accurate Spin-Dependent Electron Liquid Corre-

32


Page 32 of 41

Page 33 of 41 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


lation Energies for Local Spin Density Calculations: a Critical Analysis. Canadian Journal of Physics 1980, 58, 1200–1211. (22) Adamo, C.; Barone, V. Toward Reliable Density Functional Methods without Adjustable Parameters: The PBE0 model. The Journal of Chemical Physics 1999, 110, 6158–6170. (23) Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple. Phys. Rev. Lett. 1996, 77, 3865–3868. (24) Becke, A. D. Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior. Phys. Rev. A 1988, 38, 3098–3100. (25) Perdew, J. P. Density-Functional Approximation for the Correlation Energy of the Inhomogeneous Electron Gas. Phys. Rev. B 1986, 33, 8822–8824. (26) Perdew, J. P.; Zunger, A. Self-Interaction Correction to Density-Functional Approximations for Many-Electron Systems. Phys. Rev. B 1981, 23, 5048–5079. (27) Tao, J.; Perdew, J. P.; Staroverov, V. N.; Scuseria, G. E. Climbing the Density Functional Ladder: Nonempirical Meta–Generalized Gradient Approximation Designed for Molecules and Solids. Phys. Rev. Lett. 2003, 91, 146401. (28) Ren, X.; Rinke, P.; Blum, V.; Wieferink, J.; Tkatchenko, A.; Sanfilippo, A.; Reuter, K.; Scheffler, M. Resolution-of-Identity Approach to Hartree–Fock, Hybrid Density Functionals, RPA, MP2 and GW with Numeric Atom-Centered Orbital Basis Functions. New Journal of Physics 2012, 14, 053020. (29) Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A Consistent and Accurate Ab Initio Parametrization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu. The Journal of Chemical Physics 2010, 132 .

33



(30) Gordon, M. S.; Schmidt, M. W.; Chaban, G. M.; Glaesemann, K. R.; Stevens, W. J.; Gonzalez, C. A Natural Orbital Diagnostic for Multiconfigurational Character in Correlated Wave Functions. The Journal of Chemical Physics 1999, 110, 4199–4207. (31) Grimme, S.; Hansen, A. A Practicable Real-Space Measure and Visualization of Static Electron-Correlation Effects. Angewandte Chemie International Edition 2015, 54, 12308–12313. (32) Bauer, C. A.; Hansen, A.; Grimme, S. The Fractional Occupation Number Weighted Density as a Versatile Analysis Tool for Molecules with a Complicated Electronic Structure. Chemistry – A European Journal 2017, 23, 6150–6164. (33) Lee, T. J.; Taylor, P. R. A Diagnostic for Determining the Quality of Single-Reference Electron Correlation Methods. International Journal of Quantum Chemistry 1989, 36, 199–207. (34) Liakos, D. G.; Neese, F. Interplay of Correlation and Relativistic Effects in Correlated Calculations on Transition-Metal Complexes: The (Cu2O2)2+ Core Revisited. Journal of Chemical Theory and Computation 2011, 7, 1511–1523, PMID: 26610142. (35) Dunning, T. H. Gaussian Basis Sets for Use in Correlated Molecular Calculations. I. The Atoms Boron through Neon and Hydrogen. The Journal of Chemical Physics 1989, 90, 1007–1023. (36) Weigend, F.; Ahlrichs, R. Balanced Basis Sets of split Valence, Triple Zeta Valence and Quadruple Zeta Valence Quality for H to Rn: Design and Assessment of Accuracy. Phys. Chem. Chem. Phys. 2005, 7, 3297–3305. (37) Peterson, K. A.; Dunning, T. H. Accurate Correlation Consistent Basis Sets for Molecular Core–Valence Correlation Effects: The Second Row Atoms Al–Ar, and the First Row Atoms B–Ne Revisited. The Journal of Chemical Physics 2002, 117, 10548–10560.

34


Page 34 of 41

Page 35 of 41 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(38) Schuchardt, K. L.; Didier, B. T.; Elsethagen, T.; Sun, L.; Gurumoorthi, V.; Chase, J.; Li, J.; Windus, T. L. Basis Set Exchange: A Community Database for Computational Sciences. Journal of Chemical Information and Modeling 2007, 47, 1045–1052, PMID: 17428029. (39) Feller, D. The Role of Databases in Support of Computational Chemistry Calculations. Journal of Computational Chemistry 1996, 17, 1571–1586. (40) Jensen, F. Introduction to Computational Chemistry; John Wiley & Sons, Inc, 1999. (41) Asturiol, D.; Duran, M.; Salvador, P. Intramolecular Basis Set Superposition Error Effects on the Planarity of Benzene and Other Aromatic Molecules: A Solution to the Problem. The Journal of Chemical Physics 2008, 128, 144108. (42) Asturiol, D.; Duran, M.; Salvador, P. Intramolecular Basis Set Superposition Error Effects on the Planarity of DNA and RNA Nucleobases. Journal of Chemical Theory and Computation 2009, 5, 2574–2581. (43) Weinhold, F.; Landis, C. R. Natural Bond Orbitals and Extensions of Localized Bonding Concepts. Chem. Educ. Res. Pract. 2001, 2, 91–104. (44) Barone, V. Anharmonic Vibrational Properties by a Fully Automated Second-Order Perturbative Approach. The Journal of Chemical Physics 2005, 122, –. (45) Vishnevskiy, Y. V. UNEX version 1.6, http://unexprog.org. 2015. (46) Shibata, S.; Iijima, K.; Tani, R.; Nakamura, I. Precise Measurement of Gas ElectronDiffraction Intensity by a Sector-Microphotometer Method. Reports of Faculty of Science, Shizuoka University 1974, 9, 33 – 40. (47) Vishnevskiy, Y. V.; Zhabanov, Y. A. New Implementation of the First-Order Perturbation Theory for Calculation of Interatomic Vibrational Amplitudes and Corrections in Gas Electron Diffraction. Journal of Physics: Conference Series 2015, 633, 012076. 35



(48) Bartell, L. S.; Romenesko, D. J.; Wong, T. C. In Molecular Structure by Diffraction Methods; Sim, G. A., Sutton, L. E., Eds.; The Chemical Society, Burlington House, London, 1975; Vol. 3; pp 72–79. (49) Kochikov, I. V.; Tarasov, Y. I.; Kuramshina, G. M.; Spiridonov, V. P.; Yagola, A. G.; Strand, T. G. Regularizing Algorithm for Determination of Equilibrium Geometry and Harmonic Force Field of Free Molecules from Joint Use of Electron Diffraction, Vibrational Spectroscopy and Ab Initio Data with Application to Benzene. J. Mol. Struct. 1998, 445, 243 – 258. (50) Mitzel, N. W.; Rankin, D. W. H. SARACEN – Molecular Structures from Theory and Experiment: the Best of Both Worlds. Dalton Transactions 2003, 3650 – 3662. (51) Vishnevskiy, Y. V.; Abaev, M. A.; Rykov, A. N.; Gurskii, M. E.; Belyakov, P. A.; Erdyakov, S. Y.; Bubnov, Y. N.; Mitzel, N. W. Structure and Bonding Nature of the Strained Lewis Acid 3-Methyl-1-boraadamantane: A Case Study Employing a New Data-Analysis Procedure in Gas Electron Diffraction. Chemistry – A European Journal 2012, 18, 10585–10594. (52) Dore, L.; Geise, H. J.; Alsenoy, C. V.; Enden, L. V. D.; Schäfer, L. The Molecular Orbital Constrained Electron Diffraction (MOCED) Structural Model of Quadricyclane Determined by Electron Diffraction Combined with Ab Initio Calculations of Potential and Geometrical Parameters. Journal of Molecular Structure 1985, 129, 299 – 314. (53) Tikhonov, D.; Vishnevskiy, Y. V.; Rykov, A. N.; Grikina, O. E.; Khaikin, L. S. SemiExperimental Equilibrium Structure of Pyrazinamide from Gas-Phase Electron Diffraction. How Much Experimental is It? Journal of Molecular Structure 2017, 1132, 20–27. (54) Nazarov, M.; Shkurinov, A.; Kuleshov, E.; Tuchin, V. Terahertz Time-Domain Spectroscopy of Biological Tissues. Quantum Electronics 2008, 38, 647.

36


Page 36 of 41

Page 37 of 41 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(55) Lewis, J.; Malloy, T. B.; Chao, T. H.; Laane, J. Periodic Potential Functions for Pseudorotation and Internal Rotation. Journal of Molecular Structure 1972, 12, 427 – 449. (56) Kudich, A.; Bataev, V.; Abramenkov, A.; Pupyshev, V.; Godunov, I. Theoretical Study of the Structure of Propanal in the First Excited Singlet and Triplet Electronic States: Three-Dimensional Model for Torsional and Inversion Vibrations. Journal of Molecular Structure: THEOCHEM 2003, 631, 39 – 51. (57) Tikhonov, D. LAMPA-IntRoVer.ta (Large Amplitude Motion Potential energy Analyzer – Internal Rotation Version. SymmeTricAl edition), https://sourceforge.net/ projects/edsoftware/files/LAMPA/LAMPA-IntRoVer.ta/. 2017. (58) Fogueri, U. R.; Kozuch, S.; Karton, A.; Martin, J. M. L. A Simple DFT-Based Diagnostic for Nondynamical Correlation. Theoretical Chemistry Accounts 2012, 132, 1291. (59) Pople, J. A. Quantum Chemical Models (Nobel Lecture). Angewandte Chemie International Edition 1999, 38, 1894–1902. (60) Petruzielo, F. R.; Toulouse, J.; Umrigar, C. J. Approaching Chemical Accuracy with Quantum Monte Carlo. The Journal of Chemical Physics 2012, 136, 124116. (61) Coriani, S.; Marchesan, D.; Gauss, J.; Hättig, C.; Helgaker, T.; Jørgensen, P. The Accuracy of Ab Initio Molecular Geometries for Systems Containing Second-Row Atoms. The Journal of Chemical Physics 2005, 123, 184107. (62) Tikhonov, D. S.; Sharapa, D. I.; Schwabedissen, J.; Rybkin, V. V. Application of Classical Simulations for the Computation of Vibrational Properties of Free Molecules. Phys. Chem. Chem. Phys. 2016, 18, 28325–28338. (63) Gázquez, J. L.; Cedillo, A.; Vela, A. Electrodonating and Electroaccepting Powers. The Journal of Physical Chemistry A 2007, 111, 1966–1970, PMID: 17305319.

37



(64) Domingo, L. R.; Ríos-Gutiérrez, M.; Pérez, P. Applications of the Conceptual Density Functional Theory Indices to Organic Chemistry Reactivity. Molecules 2016, 21 . (65) Putz, M. V. Koopmans’ Analysis of Chemical Hardness with Spectral-Like Resolution. The Scientific World Journal 2013, 2013, Article ID 348415. (66) Pauling, L. The Nature of the Chemical Bond and the Structure of Molecules and Crystals: An Introduction to Modern Structural Chemistry; G - Reference,Information and Interdisciplinary Subjects Series; Cornell University Press, 1960. (67) Bastiansen, O.; Trætteberg, M. The Influence of ThermalMotion on Structure Determination of Linear Molecules Using the Electron-Diffraction Method. Acta Crystallographica 1960, 13, 1108. (68) Morino, Y. The Effect of Thermal Vibration of Gaseous Molecules in Electron Diffraction Studies. Acta Crystallographica 1960, 13, 1107. (69) Vogt, N.; Savelyev, D. S.; Giricheva, N. I.; Islyaikin, M. K.; Girichev, G. V. Accurate Determination of Equilibrium Structure of 3-Aminophthalonitrile by Gas Electron Diffraction and Coupled-Cluster Computations: Structural Effects Due to Intramolecular Charge Transfer. The Journal of Physical Chemistry A 2016, 120, 8853–8861, PMID: 27797521. (70) Otlyotov, A. A.; Lamm, J.-H.; Blomeyer, S.; Mitzel, N. W.; Rybkin, V. V.; Zhabanov, Y. A.; Tverdova, N. V.; Giricheva, N. I.; Girichev, G. V. Gas-Phase Structure of 1,8-bis[(trimethylsilyl)ethynyl]anthracene: Cog-Wheel-Type vs. Independent Internal Rotation and Influence of Dispersion Interactions. Phys. Chem. Chem. Phys. 2017, 19, 13093–13100. (71) Medvedev, M. G.; Bushmarinov, I. S.; Sun, J.; Perdew, J. P.; Lyssenko, K. A. Density Functional Theory is Straying from the Path Toward the Exact Functional. Science 2017, 355, 49–52. 38


Page 38 of 41

Page 39 of 41 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(72) Khaikin, L. S.; Kochikov, I. V.; Grikina, O. E.; Tikhonov, D. S.; Baskir, E. G. IR Spectra of Nitrobenzene and Nitrobenzene-15N in the Gas Phase, Ab Initio Analysis of Vibrational Spectra and Reliable Force Fields of Nitrobenzene and 1,3,5-trinitrobenzene. Investigation of Equilibrium Geometry and Internal Rotation in These Simplest Aromatic Nitro Compounds with One and Three Rotors by Means of Electron Diffraction, Spectroscopic, and Quantum Chemistry Data. Structural Chemistry 2015, 26, 1651– 1687. (73) Dorofeeva, O. V.; Vishnevskiy, Y.; Vogt, N.; Vogt, J.; Khristenko, L.; Krasnoshchekov, S.; Shishkov, I.; Hargittai, I.; Vilkov, L. Molecular Structure and Conformation of Nitrobenzene Reinvestigated by Combined Analysis of Gas-Phase Electron Diffraction, Rotational Constants, and Theoretical Calculations. Structural Chemistry 2007, 18, 739–753. (74) Vishnevskiy, Y. V.; Tikhonov, D. S.; Schwabedissen, J.; Stammler, H.-G.; Moll, R.; Krumm, B.; Klapötke, T. M.; Mitzel, N. W. Tetranitromethane: A Nightmare of Molecular Flexibility in the Gaseous and Solid States. Angewandte Chemie International Edition 2017, 56, 9619–9623. (75) Klapötke, T. M.; Krumm, B.; Moll, R.; Rest, S. F.; Vishnevskiy, Y. V.; Reuter, C.; Stammler, H.-G.; Mitzel, N. W. Halogenotrinitromethanes: A Combined Study in the Crystalline and Gaseous Phase and Using Quantum Chemical Methods. Chemistry – A European Journal 2014, 20, 12962–12973. (76) Fokin, A. A.; Zhuk, T. S.; Blomeyer, S.; Pérez, C.; Chernish, L. V.; Pashenko, A. E.; Antony, J.; Vishnevskiy, Y. V.; Berger, R. J. F.; Grimme, S. et al. Intramolecular London Dispersion Interaction Effects on Gas-Phase and Solid-State Structures of Diamondoid Dimers. Journal of the American Chemical Society 2017, 139, 16696 – 16707, PMID: 29037036.

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(77) Blomeyer, S.; Linnemannstöns, M.; Nissen, J. H.; Paulus, J.; Neumann, B.; Stammler, H.-G.; Mitzel, N. W. Intramolecular ÏĂâĂŞÏĂ Interactions in Flexibly Linked Partially Fluorinated Bisarenes in the Gas Phase. Angewandte Chemie International Edition 2017, 56, 13259–13263. (78) Tikhonov, D. S.; Rykov, A. N.; Grikina, O. E.; Khaikin, L. S. Gas Phase Equilibrium Structure of Histamine. Physical Chemistry Chemical Physics 2016, 18, 6092–6102. (79) Voevodin, V. V.; Zhumatiy, S. A.; Sobolev, S. I.; Antonov, A. S.; Bryzgalov, P. A.; Nikitenko, D. A.; Stefanov, K. S.; Voevodin, V. V. Practice of "Lomonosov" Supercomputer. Open Systems J. 2012, 36–39, (In Russian).

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Nitroxoline Molecule: Planar or Not? A Story of ... - ACS Publications

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