Chalcogen - Nitrogen - Structural Chemistry Group

The gas-phase molecular structures of 1,3,2,4-benzodithiadiazine and 5,6,7,8-tetrafluoro-1,3,2,4-benzodithiadiazine have been investigated by ab initio calculations and electron diffraction using the SARACEN method of structural analysis. Important structural parameters for the parent compound were found to be: <r(S=N)> 1.546(3), r(S-N) 1.697(5), r(C-S) 1.784(5), and r(C-N) 1.393(6) Å. For the tetrafluoro derivative, these are: <r(S=N)> 1.552(3), r(S-N) 1.723(8), r(C-S) 1.812(9), and r(C-N) 1.396(7) Å. Furthermore, the GED experiment (Gas Electron Diffraction) quite convincingly demonstrates the nonplanarity of the former and the planarity of the latter in agreement with DFT calculations; but the results contradict calculations at the MP2 level. The effect of the fluorine atoms on the conformations of the molecules is discussed.

Blockhuys, F.; Hinchley, S.L.; Makarov, A.Yu.; Gatilov, Yu.V.; Zibarev, A.V.; Woollins, J.D.; Rankin, D.W.H. Chem. Eur. J. 2001, 7, 3592-3602.

A series of fluorinated 1,3,2,4-benzodithiadiazines has been prepared through both electrophilic and nucleophilic intramolecular ortho-cyclisation reactions, and the former route seems to be more effective. High regioselectivity of the ring-closing procedures is observed in both cases. The compounds have been characterised by X-ray crystallography and multinuclear (H, C, N and F) NMR spectroscopy. In accordance with GIAO calculations, N‹H› experiments and the effects observed on complete substitution of hydrogen by fluorine, the high-field signal in the N NMR spectra can be assigned to N-4 and the low-field signal to N-2. In the crystal, the 5,6,7-trifluoro and 5,6,8-trifluoro derivatives are planar, whereas the 6,8-difluoro derivative is bent along the S1...N4 line by 8.3°. According to NICS calculations the heterocycle moiety in this compound class is antiaromatic while the carbocycle is aromatic. The fluorine substituents increase the aromaticity - and in some cases (especially when a fluorine atom is present in the 8-position) the antiaromaticity - of the corresponding rings. One ortho-fluoro-containing starting material cyclises to a fluorinated 2,1,3-benzothiadiazole upon treatment with CsF instead of sulfenyl chloride. For another starting compound the planar (Z,E) configuration features a short intramolecular H...N contact, as evidenced by X-ray diffraction. Both the reaction pathways mentioned are also discussed.

Makarov, A.Yu.; Bagryanskaya, I.Yu.; Blockhuys, F.; Van Alsenoy, C.; Gatilov, Yu.V.; Knyazev, V.V.; Maksimov, A.M.; Mikhalina, T.V.; Platonov, V.E.; Shakirov, M.M.; Zibarev, A.V. Eur. J. Inorg. Chem. 2003, 77-88.

The gas-phase molecular structures of 6,8-difluoro-1,3,2,4-benzodithiadiazine and 5,6,7-trifluoro-1,3,2,4-benzodithiadiazine have been determined using quantum chemical calculations and electron diffraction via the SARACEN method of structural analysis. Of particular interest was the planarity or nonplanarity of the heterocyclic fragments of the molecules. It was shown that the difluoro compound is planar with respect to the heterocyclic fragment [folding angle: 0.0(5)° (figures in parentheses indicated e.s.d.s in the final digits)] and that the trifluoro compound probably deviates from planarity to a small extent [folding angle: 4.0(-30;+3)°; the large uncertainty in the value of this angle is due to the low-frequency, large-amplitude vibrational motion associated with the folding of the heterocyclic fragment]. Pertinent structural parameters from the electron diffraction data of the difluoro compound are av[r(S=N)] = 155.7(7) pm, r(S-N) = 175.8(5) pm, r(C-S) = 176.6(8) pm and r(C-N) = 141.6(2) pm. For the trifluoro compound the equivalent structural parameters are av[r(S=N)] = 155.5(7) pm, r(S-N) = 170.7(6) pm, r(C-S) = 180.6(8) pm and r(C-N) = 140.6(2) pm. The gas-phase electron diffraction structures have been compared with results from ab initio and DFT calculations and also with experimental solid-state structures.

Turner, A.R.; Blockhuys, F.; Van Alsenoy, C.; Robertson, H.E.; Hinchley, S.L.; Zibarev, A.V.; Makarov, A.Yu.; Rankin, D.W.H. Eur. J. Inorg. Chem. 2005, 572-581.

5,6,7,8-Tetrafluoro-3,1,2,4-benzothiaselenadiazine is prepared by an intramolecular nucleophilic cyclization mediated by CsF. According to an X-ray diffraction analysis, its heterocycle is bent along the Se(1)...N(4) line by 6.0(2)° in the crystal. Despite the obvious similarities between this benzothiaselenadiazine and its 1,3-dithia analogue with respect to molecular composition and shape, the crystal packing of the former is substantially different from that of the latter. An interesting consequence of this is the inclusion of atmospheric nitrogen in the crystal lattice of the selenium derivative. The molecular structure and bonding of the benzothiaselenadiazine have been investigated using quantum-chemical calculations at the DFT/B3LYP/6-311+G* level of theory, and the results have been compared to those of the benzodithiadiazine and their hydrocarbon analogues.

Makarov, A.Yu.; Tersago, K.; Nivesanond, K.; Blockhuys, F.; Van Alsenoy, C.; Kovalev, M.K.; Bagryanskaya, I.Yu.; Gatilov, Yu.V.; Shakirov, M.M.; Zibarev, A.V. Inorg. Chem. 2006, 45, 2221-2228.

The molecular structure of 1,3,2,4-benzodithiadiazine has been studied theoretically by a large number of computational methods. The results of calculations using different DFT functionals are compared with those obtained from HF, MP2, MP4(SDQ), QCISD and CCSD calculations. In addition, the influence of a number of basis sets on the calculated geometry was investigated. The results of the post-HF methods show that convergence of the geometrical parameters is already obtained for the relatively small 6-311+G* basis set. Taking the MP4(SDQ)/cc-pVTZ geometry as a reference the DFT/B1B95 functional appears to provide the best description of all the examined functionals.

Tersago, K.; De Dobbelaere, C.; Van Alsenoy, C.; Blockhuys, F. Chem. Phys. Lett. 2007, 434, 200-204.

Our Microreview highlights the most important advances in the heteroatom chemistry of 1,3,2,4-benzodithiadiazines (pi-excessive and formally antiaromatic heterocycles), covering methods for synthesis, nontrivial features of the molecular and pi-electronic structure, spectral properties, and reactivity, in particular the transformations into persistent pi-radicals. The chemistry of 1,3,2,4-benzodithiadiazines is compared to that of related chalcogen-nitrogen compounds, both cyclic and acyclic.

Blockhuys, F.; Gritsan, N.P.; Makarov, A.Yu.; Tersago, K.; Zibarev, A.V. Eur. J. Inorg. Chem. 2008, 655-672.

Roesky's ketone

The molecular and crystal structure of 5-oxo-1,3,2,4-dithiadiazole or Roesky's ketone is studied experimentally by re-determining the single crystal structure and theoretically by calculations at the density functional level of theory using an extended basis set. A comprehensive set of properties, consisting of orbital topologies, atomic charges, atomic and molecular dipoles, aromaticity parameters and Fukui functions of Roesky's ketone and a number of its constitutional isomers has been calculated in order to formulate a description of its structure, its aromaticity and reactivity.

Van Droogenbroeck, J.; Tersago, K.; Van Alsenoy, C.; Aucott, S.M.; Milton, H.L.; Woollins, J.D.; Blockhuys, F. Eur. J. Inorg. Chem. 2004, 3798-3805.

A joint experimental-theoretical spectroscopic study of Roesky's ketone is presented. The theoretical results of a vibrational analysis, calculated at the DFT/B3LYP/6-311+G* level of theory, have been compared with experimental data, consisting of Raman and IR frequencies in different phases, and the bands have been assigned to the normal vibrations of the molecule. Additionally, an analysis of the origin of the high intensity of the band assigned to the CO stretching mode was performed based on calculated stockholder charges and atomic dipoles. The results of theoretical calculations of the C and N NMR chemical shifts are compared to experimentally obtained shifts.

Tersago, K.; Van Droogenbroeck, J.; Van Alsenoy, C.; Herrebout, W.A.; van der Veken, B.J.; Aucott, S.M.; Woollins, J.D.; Blockhuys, F. Phys. Chem. Chem. Phys. 2004, 6, 5140-5144.

The molecular structure of Roesky's ketone is studied theoretically by HF, DFT and MP2 calculations and the results have been compared to the QCISD geometry. Within DFT the structure is calculated using an elaborate series of functionals. A number of extended basis sets were used to investigate their influence on the calculated geometry. Of the nineteen evaluated method/basis set combinations none can reproduce the complete QCISD geometry: methods that reproduce the geometry of the NSNS fragment, overestimate the CS bond length and vice versa. No systematic way to improve the overall geometry of Roesky's ketone is apparent from the data.

Van Droogenbroeck, J.; Tersago, K.; Van Alsenoy, C.; Blockhuys, F. Chem. Phys. Lett. 2004, 399, 516-521.

By means of a number of computationally more advanced methods the search for an acceptable overall calculated gas-phase geometry of Roesky's ketone is continued. The results of CCSD, QCISD and MP4(SDQ) calculations are compared with the results of different CASSCF and DFT calculations. The results obtained with the wave-function-based methods are better than those generated by a large number of different DFT functionals, especially for the description of the carbon-sulfur bond. However, even at the CCSD and QCISD levels of theory no convergence is achieved: upon increasing the level of theory from CCSD to CCSD(T) the quality of the description actually becomes worse.

Tersago, K.; Oláh, J.; Martin, J.M.L.; Veszprémi, T.; Van Alsenoy, C.; Blockhuys, F. Chem. Phys. Lett. 2005, 413, 440-444.

The experimental rotational spectrum of Roesky's ketone has been recorded and the experimental rotational constants have been determined. The latter have been used to evaluate the performance of a large number of quantum chemical methods combined with different basis sets, by comparing the calculated with the experimental values. The results of this comparison indicate that, in general, the wave-function-based methods perform better than those from Density Functional Theory. Four of the 42 investigated methos/basis set combinations prove to be the most valuable, i.e., MP4(SDQ)/(aug-)cc-pVTZ, B3PW91/cc-pV(T+d)Z and MPW1PW91/aug-cc-pVTZ, as they produce rotational constants with a root-mean-square deviation from the experimental values of only about 5 MHz.

Blockhuys, F.; Tersago, K.; Shlykov, S.A.; Konrad, A.; Christen, D. J. Mol. Struct. 2010, 978, 147-152.

Roesky's sulfoxide

The molecular structure of 1-oxo-1,2,4,3,5-trithiadiazole has been studied theoretically by a large number of computational methods. The results of calculations using different DFT functionals are compared with those obtained from HF, MP2, MP4(SDQ), QCISD and CCSD calculations. In addition, the influence of a number of basis sets on the calculated geometry was investigated. The results of the post-HF methods show that improving the level of theory from CCSD to CCSD(T) still has a considerable effect on the geometry. Taking the CCSD/cc-pVTZ geometry as a reference the DFT/B1B95/aug-cc-pVTZ combination appears to provide the most valuable description of all the examined functionals.

Tersago, K.; Van Alsenoy, C.; Woollins, J.D.; Blockhuys, F. Chem. Phys. Lett. 2006, 423, 422-426.

The molecular and crystal structure of 1-oxo-1,2,4,3,5-trithiadiazole has been studied experimentally by the determination of the crystal structure and theoretically at the DFT/B1B95/aug-cc-pVTZ level of theory. The combination of the geometrical data with a number of properties of 1-oxo-1,2,4,3,5-trithiadiazole, consisting of orbital topologies, Hirshfeld charges and bond orders, aromaticity parameters and Fukui functions, led to a description of its structure, aromaticity and reactivity. In addition, the nature of the long sulfur-sulfur bond has been investigated. The bands in the newly recorded infrared and Raman spectra have been assigned to the normal vibrations of the molecule, based on calculated vibrational data. The results of theoretical calculations of the N NMR chemical shifts have been compared to the experimentally obtained shifts.

Tersago, K.; Matuska, V.; Van Alsenoy, C.; Slawin, A.M.Z.; Woollins, J.D.; Blockhuys, F. Dalton Trans. 2007, 4529-4535.

The bonding and spectroscopic properties of 5-cyclopentadienyl-5-cobalta-1,3,2,4-dithiadiazole (i.e., a structure having a Co-N-S-N-S five-membered ring) have been studied, based on the results of theoretical calculations at the DFT/B3LYP level with the 6-311+G* basis set and on a redetermination of the single-crystal structure and experimental NMR spectra. A description of the bonding is provided based on a combination of geometrical data, electron densities, bond orders, and valencies, and a critical evaluation of the aromaticity of the compound is given based on several aromaticity criteria. In addition, a dipole analysis is performed and the reactive sites in this complex are located by means of atomic charges, molecular electrostatic potentials, Fukui functions and local softnesses.

Van Droogenbroeck, J.; Van Alsenoy, C.; Aucott, S.M.; Woollins, J.D.; Hunter, A.D.; Blockhuys, F. Organometallics 2005, 24, 1004-1011.

Cp*Rh(S2N2) was prepared as a microcrystalline solid by using [S4N3]Cl in liquid ammonia or [Bu2Sn(S2N2)]2. It was characterised by NMR, IR and Raman spectroscopy and mass spectrometry. Low-temperature crystal structures of Cp*Co(S2N2) and Cp*Ir(S2N2) were determined. The experimental characterisation of the Cp*M(S2N2) complexes was complemented by calculated geometries and bond orders at the DFT/B1B95 level of theory.

Matuska, V.; Tersago, K.; Kilian, P.; Van Alsenoy, C.; Blockhuys, F.; Slawin, A.M.Z.; Woollins, J.D. Eur. J. Inorg. Chem. 2009, 4483-4490.

Dithiadiazoles

The effect on the ring-closing fragment on the aromaticity of planar five-membered rings containing an NSNS fragment is investigated systematically. The influence of changing the group or period number of the ring-closing atom is studied as well as the effect of a substituent on this ring-closing element. Two sets of four five-membered ring systems were investigated. To reach a multidimensional description of the aromaticity, a robust set of geometrical, magnetic and energetic aromaticity criteria were combined. Pi-electron populations based on the stockholder scheme were calculated and lead to a quantity that correlates to the other aromaticity criteria. A third set of molecules was introduced to verify the conclusions.

Van Droogenbroeck, J.; Van Alsenoy, C.; Blockhuys, F. J. Phys. Chem. A 2005, 109, 4847-4851.

Sulfur-nitrogen silylenes

A new class of inorganic systems is introduced in which a silylene fragment is combined with a sulfur-nitrogen fragment. The properties of the resulting "sulfur-nitrogen silylenes" have been studied using quantum chemical calculations, focussing on isodesmic reaction energies, dimerization, electro- and nucleophilicity, and the singlet-triplet energy gap - a number of as yet unsuccessful attempts to prepare the compounds is also reported. These new systems are found to be stable silylenes in which the sulfur-nitrogen fragment stabilizes both the singlet and the triplet states through extensive electron delocalization.

Oláh, J.; Veszprémi, T.; Woollins, J.D.; Blockhuys, F. Dalton Trans. 2010, 39, 3256-3263.

Benzodichalcogenazolyl radicals

1,2,3-Benzodithiazolyl, 2,1,3-benzothiaselenazolyl and 1,2,3-benzodiselenazolyl radicals were generated by the reduction of the corresponding cations and investigated by pulse EPR and ENDOR in frozen chloroform solutions at 30 and 80 K. These methods, in combination with density functional theory calculations, were used to study the magnetic parameters of the radicals, namely the principal values of the nitrogen and proton hyperfine interactions and g-tensors. The spin density distribution was shown to be nearly the same for all investigated radicals and, therefore, replacement of sulfur by selenium leads to a limited perturbation of the radicals’ electronic structure. A high anisotropy of the g-tensors was found for the selenium-containing radicals.

Pivtsov, A.V.; Kulik, L.V.; Makarov, A.Yu.; Blockhuys, F. Phys. Chem. Chem. Phys. 2011, 13, 3873-3880.

Salts of 1,2,3-benzodithiazolium, 2,1,3-benzothiaselenazolium, and 1,2,3-benzodiselenazolium (Herz cations) were prepared from the corresponding chlorides. It was found that two of them spontaneously transform in MeCN solution. Five of them were structurally characterized by X-ray diffraction (XRD). In solution, eight of them were characterized by multinuclear nuclear magnetic resonance (NMR). The corresponding Herz radicals were obtained in toluene and DCM solutions by the reduction of the appropriate salts with triphenylstibine and characterized by EPR. The cations and radicals were investigated computationally at the density functional theory (DFT) and second-order Møller–Plesset (MP2) levels of theory. The B1B95/cc-pVTZ method was found to satisfactorily reproduce the experimental geometries; an increase in the basis set size to cc-pVQZ results in only minor changes. For the cations and the radicals, the Hirshfeld charges and bond orders, as well as the Hirshfeld spin densities for the radicals, were calculated using the B1B95/cc-pVQZ method. It was found for both the cations and the radicals that replacing S atoms with Se atoms leads to considerable changes in the atomic charges, bond lengths, and bond orders only at the involved and the neighboring sites. According to the calculations, 60% of the positive charge in the cations and 80% of the spin density in the radicals is localized on the heterocycles, with the spin density distributions being very similar for all radicals. For the cations, the NICS values (B3LYP/cc-pVTZ for B1B95/cc-pVTZ geometries) lie in the narrow range from −5.5 ppm to −6.6 ppm for the carbocycles, and from −14.4 ppm to −15.5 ppm for heterocycles, clearly indicating the aromaticity of the cations. Calculations on radical dimers revealed, with only one exception, positive dimerization energies, i.e., the dimers are inherently unstable in the gas phase.

Makarov, A.Yu.; Blockhuys, F.; Bagryanskaya, I.Yu.; Gatilov, Yu.V.; Shakirov, M.M.; Zibarev, A.V. Inorg. Chem. 2013, 52, 3699-3710.

The existence of the orbital interaction presented in the literature as being the cause for the stabilisation of the Z,Z configuration of Ph-S-N=S=N-S-Ph and its derivatives in the crystal phase, has been investigated. The results of theoretical calculations at the DFT/B3LYP/6-311+G* level of theory suggest that such a stabilising interaction might not exist or be extremely weak and that packing forces must be the main cause of the observed Z,Z configuration in the solid. To reach this conclusion structural and energetic parameters were combined to study the bonding in these -S-N=S=N-S- systems. For the analogous Ph-Se-N=S=N-Se-Ph in particular the isomeric equilibrium in solutions found in the variable-temperature Se NMR spectrum indicates that, in the gas phase phase or in solution, the observed Z,Z configuration is not stabilised to a greater extent than the Z,E configuration.

Tersago, K.; Mandado, M.; Van Alsenoy, C.; Bagryanskaya. I.Yu.; Kovalev, M.K.; Makarov, A.Yu.; Gatilov, Yu.V.; Shakirov, M.M.; Zibarev, A.V.; Blockhuys, F. Chem. Eur. J. 2005, 11, 4544-4551.

The molecular and crystal structures of three new derivatives of Ph-S-N=S=N-S-Ph, with 2,4,6-tri-tert-butylphenyl, pentafluorophenyl and 4-trifluoro-2,3,5,6-tetrafluorophenyl as peripheral rings, respectively, and one new derivative of Ph-Se-N=S=N-Se-Ph, with pentafluorophenyl as peripheral rings, are reported and discussed in connection with those of the two parent structures and those of the previously studied derivative of Ph-S-N=S=N-S-Ph with 4-chlorophenyl as peripheral rings. For these seven compounds the Z,Z configuration is the only one of the three theoretically possible configurations observed in the solid state and this configurational preference can not be explained by intramolecular stereoelectronic effects. Calculation of the packing energies and densities for the six most common space groups revealed that the crystal packing of the parent structure in the Z,Z configuration has a systematic preference over the corresponding packing of Ph-S-N=S=N-S-Ph in the Z,E configuration by 0.3–4.9 kJ/mol. As a result, packing forces are most likely responsible for the dominance of the Z,Z configuration of the title compounds in the crystal.

Tersago, K.; Bagryanskaya. I.Yu.; Gatilov, Yu.V.; Gromilov, S.A.; Makarov, A.Yu.; Mandado, M.; Van Alsenoy, C.; Zibarev, A.V.; Blockhuys, F. Eur. J. Inorg. Chem. 2007, 1958-1965.

New oligomeric analogues of poly(sulfur nitride) were synthesized and structurally characterized in the solid state using single-crystal XRD, in solution using variable-temperature NMR and in the gas phase using DFT/B3LYP calculations. In the crystal, three of the compounds display the well-known Z,Z configuration, whereas one is the first compound to display the E,Z configuration amongst twelve structurally defined Ph-X-N=S=N-X-Ph derivatives (X = S, Se) in the hydrocarbon and fluorocarbon series. Through a careful analysis of the packing schemes and the intermolecular interactions of the various compounds, an explanation of the abnormal behaviour of the latter compound is put forward.

Makarov, A.G.; Bagryanskaya, I.Yu.; Gatilov, Yu.V.; Kuratieva, N.V.; Makarov, A.Yu.; Shakirov, M.M.; Alexeyev, A.V.; Tersago, K.; Van Alsenoy, C.; Blockhuys, F.; Zibarev, A.V. Eur. J. Inorg. Chem. 2010, 4801-4810.

N-Sulfinylanilines

According to the results of quantum chemical calculations at various levels of theory, an isolated molecule of N,N'-disulfinyl-3,4,5,6-tetrafluoro-1,2-diaminobenzene prefers a non-planar Z,Z configuration, which is very similar to the configuration observed in the crystal. This is in contrast to its previously studied hydrocarbon analogue which features a planar Z,Z configuration, both in the crystal and as a calculated structure. Thus, the gas-phase molecular structures of these flexible compounds are resistant to the numerous intermolecular interactions in the solid state. The results obtained for the different molecular configurations and conformations of these compounds are in line with the qualitative bonding model suggested earlier for the isoelectronic [RNSN] anions, taking into account the anomeric interactions and the electron-acceptor strength of R. A number of additional factors operating on the molecular conformations of N,N'-disulfinyl-3,4,5,6-tetrafluoro-1,2-diaminobenzene and its hydrocarbon analogue, such as the van der Waals volume of the ortho-substituents X (X = H, F) and improper H...O hydrogen bonds, are also discussed.

Makarov, A.G.; Bagryanskaya, I.Yu.; Gatilov, Yu.V.; Makarov, A.Yu.; Tersago, K.; Van Alsenoy, C.; Blockhuys, F.; Zibarev, A.V. J. Mol. Struct. 2010, 978, 158-162.