About the Aromaticity of symm-Triaminotrinitrobenzene.

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.

Supramolecular Architecture of Substituted Tetraphenyl-carbo-benzenes from the Energetic Viewpoint.

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.

New tricks of well-known aminoazoles in isocyanide-based multicomponent reactions and antibacterial activity of the compounds synthesized.

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.

Reactivity of C-Amino-1,2,4-triazoles toward Electrophiles: A Combined Computational and Experimental Study of Alkylation by Halogen Alkanes.

A combination of computational and experimental methods was used to examine the structure-reactivity relationships in the reactions of C-amino-1H-1,2,4-triazoles with electrophiles. The global nucleophilicity of 3-amino- and 3,5-diamino-1H-1,2,4-triazoles was predicted to be higher than that of 5-amino-1H-1,2,4-triazoles. Fukui functions and molecular electrostatic potential indicate that reactions involving an amino group should occur more easily for the 3-amino- than for the 5-amino-1H-1,2,4-triazoles. Increasing electrophile hardness should increase the probability of attack at the N-4 atom of the triazole ring, whereas increasing softness should enhance the probability of attack at the N-2 atom and 3-NH2 group. Calculated transition state energies of model SN2 reactions and experimental studies showed that quaternization of 1-substituted 3-amino- and 3,5-diamino-1H-1,2,4-triazoles by many alkyl halides proceeds with low selectivity and can involve the N-2 and N-4 atoms as well as the 3-NH2 group as reaction centers. A new method for the selective synthesis of 1,4-disubstituted 3-amino- and 3,5-diamino-1,2,4-triazoles based on quaternization of readily available 1-substituted 3-acetylamino-1,2,4-triazoles with subsequent removal of the acetyl protecting group by acid hydrolysis was developed.

Role of supramolecular synthons in the formation of the supramolecular architecture of molecular crystals revisited from an energetic viewpoint.

Analysis of the strengths and directionality of intermolecular interactions in the crystals containing only one type of supramolecular synthon allows the suggestion of a general classification of molecular crystals depending on type of their basic structural motifs. All crystals may be divided on four classes namely (I) crystals with isotropic packing of the building units; (II) columnar crystals where the basic structural motif (BSM) is a chain/column; (III) layered crystals with layers as the BSM; (IV) columnar-layered crystals containing chains/columns as the primary basic structural motif and layers as the secondary BSM. Taking into account the participation of different supramolecular synthons in the formation of different levels of the organization of molecular crystals, they may be considered as basic (responsible for the formation of molecular complexes as building units of crystals), primary, secondary and auxiliary, which are involved in the agglomeration of molecules in primary or secondary basic structural motifs or in the packing of these motifs, respectively. The ranking of supramolecular synthons depends on values of energies of intermolecular interactions and it is individual for each crystal.

Hydrazinolysis of 3-R-[1,2,4]triazino[2,3-c]quinazolin-2-ones. Synthetic and theoretical aspects.

It has been shown that heating of 3-R-[1,2,4]triazino[2,3-c]quinazolin-2-ones with 5-fold excess of hydrazine hydrate in propanol-2 gave the corresponding 3-(2-aminophenyl)-6-R-1,2,4-triazin-5-ones with high yields. The mechanism of the reaction has been proposed based on the results of theoretical investigation at B3LYP and MP2 levels of theory. According to calculations, an attack of the hydrazine molecule on the C6═N7 double bond leads to ring-opening with N5-C6 bond cleavage. The process continues by addition of the second nucleophile molecule and elimination of the formazan fragment through a series of transformations that yield the target product.

The unexpected influence of aryl substituents in N-aryl-3-oxobutanamides on the behavior of their multicomponent reactions with 5-amino-3-methylisoxazole and salicylaldehyde.

The switchable three-component reactions of 5-amino-3-methylisoxazole, salicylaldehyde and N-aryl-3-oxobutanamides under different conditions were studied and discussed. The unexpected influence of the aryl substituent in N-aryl-3-oxobutanamides on the behavior of the reaction was discovered. The key influence of ultrasonication and Lewis acid catalysts led to an established protocol to selectively obtain two or three types of heterocyclic scaffolds depending on the substituent in the N-aryl moiety.

The regioselective synthesis of spirooxindolo pyrrolidines and pyrrolizidines via three-component reactions of acrylamides and aroylacrylic acids with isatins and α-amino acids.

The regioselective three-component condensation of azomethine ylides derived from isatins and α-amino acids with acrylamides or aroylacrylic acids as dipolarophiles has been realized through a one-pot 1,3-dipolar cycloaddition protocol. Decarboxylation of 2'-aroyl-2-oxo-1,1',2,2',5',6',7',7a'-octahydrospiro[indole-3,3'-pyrrolizine]-1'-carboxylic acids is accompanied by cyclative rearrangement with formation of dihydropyrrolizinyl indolones.

Influence of deuteration and fluorination on the supramolecular architecture of pyridine N-oxide crystals.

To understand how deuterium and fluorine substituents influence the supramolecular architecture of pyridine N-oxide crystals, the crystal structure of 3-fluoropyridine N-oxide (PNO-3F) was determined and the crystal packing motives of non-deuterated pyridine-N-oxide (PNO), partial-deuterated pyridine-N-oxide (PNO-D) and PNO-3F were analyzed based on ab initio quantum-chemical calculations of the intermolecular interaction energy, using the MP2/6-311G(d,p) method. The appearance of the weak-directing substituents deuterium and fluorine leads to significant changes in the crystal organization of the isotropic packing of PNO molecules.

Conformational behaviour of peptides containing a 2-pyrrolidinemethanesulfonic acid (2PyMS) residue.

The conformational behaviour of model peptides containing a 2-pyrrolidinemethanesulfonic acid (2PyMS) residue was studied in both the crystalline state and in solution using X-ray, NMR and IR experiments. It was found that in crystals dipeptide PhC(O)-2PyMS-Phe-NHiPr adopted ß-turn conformation, which was not stabilized by an intramolecular hydrogen bond and could be classified as a type IV ß-turn. In the crystalline state tripeptide PhC(O)-Ala-2PyMS-Phe-NHiPr existed as an α-turn with uncommon cis-conformation of the amide bond formed by the pyrrolidine nitrogen atom of the 2PyMS residue, for which no close analogue can be envisaged among the tight turns identified so far. Although the tendency to adopt folded conformations was only partially retained in solution, 2-PyMS could be considered as a promising structural unit for the design of foldamers and peptidomimetics with unusual conformational properties.

B-DNA characteristics are preserved in double stranded d(A)3·d(T)3 and d(G)3·d(C)3 mini-helixes: conclusions from DFT/M06-2X study.

We report the results of the first comprehensive DFT study on the d(A)3·d(T)3 and d(G)3·d(C)3 nucleic acid duplexes. The ability of mini-helixes to preserve the conformation of B-DNA in the gas phase and under the influence of such factors as: solvent, uncompensated charge, and counter-ions was evaluated using M06-2X functional with 6-31G(d,p) basis set. The accuracy of the models was ascertained based on their ability to reproduce key structural features of natural B-DNA. Analysis of the helicity suggests that the helical conformations adopt geometrical parameters which are close to those of the B-DNA form. The torsion angles fall somewhere between the values observed for BI/BII conformational classes. The comparative analysis of parameters of isolated Watson-Crick base pairs versus B-DNA-like conformations indicates the same tendency of base-pair polarization and hydration. Specifically, effects of polarization of nucleobases in continuum type dielectric medium mimicking water are stronger than those caused by the presence of backbone. Polar environment as well as the presence of counterions stabilizes duplexes, facilitating helix formation. Substantial conformational changes of nucleotides upon duplex formation decrease the binding energy. In spite of structural and energetic changes, the placement of a mini-helix into the gas phase does not lead to significant disruption of the structure. On the contrary, the duplex preserves its helicity and the strands remain bound.

Tuning of character of the N-O bond in HONO from covalent to protocovalent by different types of intramolecular interactions.

Quantum-chemical calculations of the H-O-N=O molecule in the equilibrium and transition states and the complexes of the HONO with BH3, study of the intramolecular interactions using NBO theory, and investigation of the electron distribution on the basis of topological analysis of the ELF function clearly indicate the influence of the n-π* conjugation and n-σ* hyperconjugation interactions on a par with exchange repulsion of lone pairs the character of the N-O bond. It is shown that repulsion between lone pairs of oxygen and nitrogen atoms causes the elongation of the N-O bond only but character of this bond remains covalent. The interaction between lone pair of the terminal oxygen atom and antibonding orbital of the N-O bond (n-σ* hyperconjugation) coincides with influence of repulsion and reinforces it changing the character of the N-O bond from covalent to protocovalent. In contrary, the n-π* conjugation interaction between lone pairs of the bridged oxygen atom and π-orbital of the N=O double bond leads to the strengthening of the N-O bond making it more covalent.

The structure of DNA fragments: Quantum-chemical modelling.

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.

"Reported, but still unknown." A closer look into 3,4-bis- and 3,4,5-tris(trifluoromethyl)pyrazoles.

Straightforward practical synthetic approaches to 3,4-bis- and 3,4,5-tris(trifluoromethyl)pyrazoles have been developed. The key step of the both syntheses is a transformation of the carboxylic group in a pyrazole core into the trifluoromethyl group by sulfur tetrafluoride. The elaborated synthetic protocols allow gram-scale preparation of the target products. The obtained compounds are comprehensively characterized by means of crystallographic analysis, determination of pK(a) values and fluorescence measurements.

Tris(2,2'-bipyridine-κN,N')cobalt(III) tris-(oxalato-κO,O)ferrate(III) mono-hydrate.

The title compound, [Co(C(10)H(8)N(2))(3)][Fe(C(2)O(4))(3)]·H(2)O, con-sists of two discrete tris-(chelate) metal ions (Co(III)N(6) and Fe(III)O(6) chromophores) and a water mol-ecule. The structure is highly symmetrical; the Co(III) and Fe(III) ions occupy positions with site symmetry 3.2. The coordination polyhedra of the metal atoms have a nearly octa-hedral geometry with noticeable trigonal distortions. The Co-N and Fe-O bond lengths are equal by symmetry, viz. 1.981 (2) and 1.998 (4) Å, respectively. The cations and anions are arranged alternately along their threefold rotation axes parallel to [001], forming chains that are packed in a hexa-gonal manner. The water mol-ecules occupy voids between the chains. The crystal under investigation was an inversion twin.

Tetra-kis(µ(2)-cyanido-κ(2)C:N)dicyanido-tetra-kis-[tris-(2-amino-eth-yl)amine-κ(3)N,N',N'',N''']tetra-copper(II)iron(II) bis[pentacyanidonitrosoferrate(II)] hexahydrate.

The asymmetric unit of the title complex, [Cu(4)Fe(CN)(6)(C(6)H(18)N(4))(4)][Fe(CN)(5)(NO)](2)·6H(2)O, comprises a complex [{Cu(tren)CN}(4)Fe(CN)(2)](4+) [tren is tris-(2-amino-eth-yl)amine] cation, which exhibits -1 symmetry with the terminal cyanide ligands oriented trans to each other, and two [Fe(CN)(5)(NO)](2-) nitroprussiate counter-anions. In the crystal, N-H⋯N hydrogen-bonding inter-actions are observed between H atoms on the primary amine groups of the tren ligand and the terminal cyanide groups of the nitro-prussiate counter-ions. The N atom in the terminal CN ligand of the cation is equally disordered over two positions. The structure also contains disordered lattice water mol-ecules. Their contribution was elimin-ated from the refinement using the procedure described by van der Sluis & Spek (1990 ▶).

Bis(µ-4-nitro-2-{[2-(oxidometh-yl)phen-yl]imino-meth-yl}phenolato)bis-[chlorido(dimethyl sulfoxide)-iron(III)] dimethyl sulfoxide disolvate.

In the centrosymmetric dimeric title complex, [Fe(2)(C(14)H(10)N(2)O(4))(2)Cl(2)(C(2)H(6)OS)(2)]·2C(2)H(6)OS, two {Fe(L)Cl(DMSO)} units (L is the tridentate ligand 4-nitro-2-{[2-(oxidometh-yl)phen-yl]imino-meth-yl}phenolate; DMSO is dimethyl sulfoxide) are bridged by two O atoms, with an Fe⋯Fe separation of 3.1838 (8) Å. The coordination polyhedron of the Fe(III) atoms can be described as distorted octa-hedral, with four Fe-O, one Fe-N and one Fe-Cl coordination bonds. The L ligand is not planar, the dihedral angle between the 2-(oxidometh-yl)phen-yl]imino and 4-nitro-2-(imino-meth-yl)phenolate planes being 48.54 (9)°. The solvent DMSO molecule is disordered over two orientations with equal occupancy.

Tetra-methyl-ammonium dimethyl (phenyl-sulfonyl-amido)phosphate(1-).

The title compound, C(4)H(12)N(+)·C(8)H(11)NO(5)PS(-), was obtained from tetra-methyl-ammonium hydroxide and dimeth-yl(phenyl-sulfon-yl)amido-phosphate. The tetra-methyl-ammonium cation has a slightly distorted tetra-hedral configuration and the N-C bond lengths lie in the range 1.457 (3)-1.492 (3) Å. In the crystal, no classical hydrogen bonds are observed between the cation and the anion.

Hexa-kis-(dimethyl-formamide-κO)manganese(II) (dimethyl-formamide-κO)pentakis(-thio-cyanato--κN)chromate(III).

The title compound, [Mn(C(3)H(7)NO)(6)][Cr(NCS)(5)(C(3)H(7)NO)], was obtained unintentionally as a product of an attempted synthesis of heterometallic complexes based on Reineckes anion using manganese powder, Reineckes salt and 1-(2-hy-droxy-eth-yl)tetra-zole as starting materials. The crystal structure of the complex consists of an [Mn(dmf)(6)](2+) cation and a [Cr(NCS)(5)(dmf)](2-) anion (dmf = dimethyl-formamide). The Mn(II) and Cr(III) atoms show a slightly distorted octa-hedral MnO(6) and CrN(5)O coordination geometries with adjacent angles in the range 85.29 (13)-95.96 (14)°.

Crystal structure, Hirshfeld surface analysis and geometry optimization of 2-hy-droxy-imino-N-[1-(pyrazin-2-yl)ethyl-idene]propano-hydrazide.

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.