In this review, we analyze and systematize our computational studies of the nucleic acid duplex formations and thermodynamic stability under the different factors of investigation. The proposed structural models of mini-helix contains N nucleobase pairs (N = 3-5); QM structural data suggest that the helical conformations of mini-helix adopt geometrical parameters comparable to those of natural A- and B-DNA forms under specific conditions as micro hydration and charge compensation. The gas-phase models adopt non regular conformations between the helical form and a ladder form.. The natural helical shape of DNA mini-helix is stabilized by the presence of counterions or by explicit micro-hydration of the major and minor groves. The presence of aqueous solution is shown as a minor factor for the helical shape formation. The studies are performed at the level of density functional theory.

In the mol-ecule of the title compound, C9H11N5O2, the oxime and hydrazide groups are situated in a cis-position in relation to the C-C bond linking the two functional groups. The CH3C(=NOH)C(O)NH fragment deviates from planarity because of a twist between the oxime and amide groups. In the crystal, mol-ecules are linked by O-H⋯O hydrogen bonds, forming zigzag chains in the [013] and [03] directions.

Aim. To study the rearrangement of Cookson’s diketone by the action of potassium halides under conditions of polyphosphoric acid catalysis. Results and discussion. Chemical behaviour of Cookson’s diketone (CS-trishomocubane-8,11-dione) in the reactions with potassium halides (KCl, KBr, KI) in the polyphosphoric acid (PPA) medium have been studied. When treated with the KI/PPA mixture Cookson’s diketone undergoes reduction leading to tetracyclo[6.3.0.0.4,11.05,9]undecane-2,7-dione. The use of KBr instead of KI leads to formal addition of HBr to the cyclobutane ring of CS-trishomocubane-8,11-dione and gives 3-bromotetracyclo[6.3.0.04,11.05,9]undecane-2,7-dione. The general scheme of the cycle opening mechanism has been proposed. In the case of using the KCl/PPA mixture the reaction does not occur. Experimental part. The structure and composition of compounds were proved by the methods of 1H and 13C NMR-spectroscopy, and also X-ray diffraction analysis. Elemental analysis was performed for the compounds obtained. Conclusions. It has been shown that hydrohalic acids generated in situ under the reaction conditions do not induce the rearrangement of Cookson’s diketone to the D3-trishomocubane system. The cyclobutane ring opening and reduction take place instead.

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Aromaticity and structural features of the isolated symm-triaminotrinitrobenzene (TATB) were examined using the nonempirical ab initio quantum chemical method and molecular dynamics at the Car-Parrinello level. Different criteria of the aromaticity were combined with the study of conformational flexibility of molecule and analysis of the electron density distribution. It was found that the cooperative effect of the resonance-assisted hydrogen bonds results in the ultimate decreasing aromaticity of the benzene ring in TATB. Values of the HOMA index indicate that it could be classified as low-aromatic in equilibrium state at zero temperature but completely nonaromatic at room temperature. An extremely high flexibility of the molecule is also not typical for aromatic rings. The electron delocalization in H-bonded O═N-C═C-N-H quasi-aromatic rings was found to be greater than that in the benzene ring of TATB.

Optimized synthesis of 1-methyltetrazolo[5,1-a]isoindole-derived amides and thioamides was elaborated. Based on 13C NMR spectroscopy and X-Ray diffraction studies data, it was proposed that zwitterionic resonance structures contributed significantly to the structure of these compounds. Geometry optimization was performed in vacuo using m06-2x/cc-pvtz method taking into account polarizing effect of environment (PCM model) and specific intermolecular interactions. Electronic density distribution in these molecules was analyzed using NBO method. Using Δ(HOMOdiene–LUMOdienophile) for amides and thioamides in vacuo and in a protic solvent, possibility of Diels–Alder reaction was evaluated. Energies of π-π conjugation and n→σ* hyperconjugation for the amide derivative were estimated in vacuo, aprotic and protic solvents.

Some fused aziridines are highly sensitive photochromes due to the presence of sterically strained three membered ring. The study of photoinduced transformations of several such compounds in solutions, crystalline state, and polymeric and liquid crystal matrices using UV-vis and ESR spectrometry in combination with quantum chemical calculations revealed stepwise character of the transformations. The first deep-colored product was proven to be a new type of stable triplet biradical species while the second one was poor-colored azomethine ylide which had been previously considered as the species responsible for photochromism in crystalline state. (C) 2017 Elsevier B.V. All rights reserved.

Background: Studies of transition metal complexes containing cubane core were inspired by the discovery of single-molecule magnetism in this family of compound. β-diketonates are quite often used for creation of cubane complexes. β-Ketosulfones, compounds containing S(O)2CH2C(O) fragment, to certain extent can be considered as analogues of β-diketones. It was intriguing to study the difference and similarities between the coordination behavior of β-diketones and β-ketosulfones, as well as the difference between the properties of 3d metal complexes with these ligands. Objectives: The aim of this work was to study the structure, magnetic and spectral properties of NiII and CoII complexes with a representative of β-ketosulfone family - analog of well-known β-diketonates. Methods: Crystallographic data were collected using Xcalibur Sapphire3 diffractometer with Mo-Kα radiation. UV/vis spectra were obtained using a Cary 300 machine in 350-800 nm range. TG experiments were carried our using Q1500 instrument in air. Reflectance spectra were measured on Beckman UV 5240 instrument. 1HNMR spectra were measured at 300 MHz on Bruker WP 100 SY instrument. Magnetic susceptibility measurements were carried out with Quantum Design PPMS-9 magnetometer operating in the range 300-2 K using field of 5000 Oe. Measurements were performed on polycrystalline samples sealed in a polyethylene bag and cover with mineral oil in order to prevent field-induced torquing of the crystals. The magnetic data were corrected for the sample holder, the mineral oil and the diamagnetic contribution. Results: The reaction of potassium salt of 2-(p-tolylsulfonyl)acetophenone (KL) with CoII and NiII nitrates resulted in the formation of tetranuclear complexes [Ni4(µ3-OCH3)4(H2O)3(CH3OH)(L)4]·H2O (1·H2O) and [Co4(µ3-OCH3)4(CH3OH)4(L)4]·4CH3OH·H2O (2·4CH3OH·H2O). Single crystal X-ray structure analysis showed that both 1·H2O and 2·4CH3OH·H2O possessed [M4(µ3-OCH3)4] tetranuclear cubane cores. Exchange coupling parameters were calculated for both NiII and CoII complexes by the analysis of temperature dependence of magnetic susceptibility by full-matrix diagonalization using a model, which included zero-field splitting (ZFS) of spin levels of metal ions and two (for 1) or one (for 2) different J parameters. All exchange interactions in 1 were found to be ferromagnetic, while for 2 it was concluded that the contributions of ZFS and exchange interactions were comparable. Conclusion: It was shown that β-sulfoketonate formed NiII and CoII cubanes, similarly to β-diketonates. Two new cubane-like polynuclear complexes were synthesized and characterized. For nickel complex all exchange interactions were ferromagnetic. The values of J for NiII complex were consistent with the ones, expected from the J vs. Ni-O-Ni angle correlation previously proposed for Ni4 β-diketonate cubanes. Magnetic properties of CoII analogue could be fitted using a model, which took into account ZFS of CoII and one J value. It was found that the contributions of ZFS and exchange interactions were comparable. Keywords: Polynuclear complexes, nickel, cobalt, cubane, magnetic properties, diketonate, sulfonyl.

A systematic topological analysis of fluorinated pyridines and benzenes is reported. Fluorine and nitrogen atoms are considered to be isolobal with respect to the supramolecular architecture in the crystalline phase. The comparison of the intermolecular interaction energies demonstrates that nitrogen atom within the aromatic ring and fluorine as a substituent both induce the same type of molecular arrangement in the solid state. Based on this, we suggest a general isotypic transformation principle for molecular crystals.

Reaction of C-s-trishomocubane-8,11-diol with hydrohalic acids results in haloalcohols - 4,7-disubstituted derivatives of D-3-trishomocubane. The reaction involves the rearrangement of the trishomocubane skeleton and the stereoselective formation of 4,7-D-3-trishomocubanediol and 5-oxahexacyclo[5.4.1.0(2)(,6).0(3)(,10).0(4)(,8).0(9,12)]-dodecane as side products. The mechanism of the rearrangement was proposed. 7-Halo-D-3-trishomocuban-4-ols were oxidized to the corresponding haloketones. The structure of the major isomers of the haloketones was confirmed through X-ray analysis. [GRAPHICS] .

Hantzsch reaction has been successfully employed for a one-step assembling of pyranopyridine fragment to produce 5 Н ,9 Н -pyrano[2',3':5,6]- chromeno[4,3- b ]pyridine-5,9-diones which upon treatment with binucleophiles undergo chemoselective γ-pyrone ring opening with the concomitant recyclization to give five-membered cycles, providing a concise route to 6-pyrazolyl(isoxazolyl)-5 H -chromeno[4,3- b ]- pyridin-5-ones.

Among the fluorescein dyes, the behaviour of their nitro derivatives in solution is most unusual, and yet at the same time rarely studied. In this study, their 13C nuclear magnetic resonance and electrospray spectra are reported, which confirm, in concert with their ultraviolet‐visible spectra, the molecular structures of the neutral and ionic species of 2,4,5,7‐tetranitrofluorescein observed in different solvents and at various pH values. A peculiar property of this dye consists in its lactonisation of the double‐charged anion, contrary to the well‐known coloured and fluorescent dianions of fluorescein, eosin, etc. Also, this dianion‐lactone exhibits high ability for opening the pyran ring. This cleavage takes place at much lower pH values as compared with those for fluorescein and its halogen derivatives. The ruptured species can be formed as either lactone or carbinol; the latter appears as a result of the nucleophilic attack of a HO− on the central carbon atom. The corresponding molecular structures are identified via the electrospray method and X‐ray analysis. The behaviour of some other nitrofluoresceins in alkaline media is also considered.

The use of DFT-calculated energy-vector diagrams (EVDs) featuring the topology of pairwise intermolecular interaction energies is applied to crystals of carbo-benzenes. A homogeneous set of six ideally centrosymmetric tetraphenyl-carbo-benzenes is selected, with various substituents R in para positions: R=4-anisyl, 1-ethyl-2-phenyl-1H-indol-3-yl, 2-chloro-2-(1-ethyl-2-phenyl-1H-indol-3-yl)ethenyl, tetradecyl, and 9,9-dihexyl-9H-fluoren-2-yl, 2-(9,9-dihexyl-9H-fluoren-2-yl)ethynyl. The basic structural motifs (BSMs) of the crystals vary from layers to columns, depending on the size and shape of the substituents R. The BSM cohesion is shown to rely on π-stacking, CH-π and dispersive interactions. Solvate molecules are shown to have a negligible role in the formation of the BSM, whereas they loosen the interaction between neighbouring BSMs.

The influence of substituents on the geometric parameters and acceptor properties of the amino group in the diaminobenzene analogues has been studied using quantum-chemical calculations and the study of crystal packing from the energetic viewpoint.

The "direct synthesis" approach, namely one-pot reaction of metal powders and ammonium salt with a methanol solution of a polydentate Schiff base (H2L) formed in situ from salicylaldehyde and ethanolamine, has been successfully used for the preparation of the new heterometallic compounds [Cu3Mn(L)4(CH3OH)3]I3 (1), [Cu3Mn(L)4(CH3OH)3(H2O)]NCS·H2O (2), [Cu3Mn(L)4(CH3OH)(H2O)2.55]Br·0.45H2O (3) and [Cu3Mn(L)4(H2O)3.4]BF4·0.6H2O (4). Crystallographic analysis revealed that 1-4 are based on the tetranuclear core {CuMnIII(μ3-O)4} where the metal centres are joined by the oxygen bridges of Schiff base ligands forming a cube-like arrangement. The novel heterometallic compound [Cu3Mn(L)4(CH3OH)3]2[Mn(NCS)4]·2CH3OH (5) has been obtained by the "building block" approach using the reaction of [Cu(HL)2] with manganese acetate and NH4NCS in methanol. The crystal structure of 5 revealed the {CuMnIII(μ-O)2(μ3-O)2} metal core which can be viewed as a double open cube. In spite of a similar {Cu3MnO4} atom set in the cores of 1-5, the complexes show rather different molecular structures and significantly differ by the number and combinations of coordinated CH3OH/H2O solvent molecules. Variable-temperature (2-300 K) magnetic susceptibility along with variable-field magnetization measurements of 1-5 showed a decrease of the effective magnetic moment value at low temperature, indicative of the antiferromagnetic coupling of medium size (-55 to -22 cm-1). For these systems resembling a compressed prism the coupling constant in walls J4 correlates with the averaged bonding angles in walls α: J4vs. α develops approximately according to a straight line.

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

The well-known aminoazoles, 3-amino-5-methylisoxazole and 5-amino-N-aryl-1H-pyrazole-4-carboxamides, were studied as an amine component in Ugi and Groebke–Blackburn–Bienaymé multicomponent reactions. The first example of an application of aminoazoles in an Ugi four-component reaction was discovered and novel features of a Groebke–Blackburn–Bienaymé cyclocondensation are established and discussed. The heterocycles obtained were evaluated for their antibacterial activity and several of them demonstrated a weak antimicrobial effect, but for most of the compounds a 30–50% increase in biomass of Gram-positive strains (mainly B. subtilis) compared to control was observed.