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.

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

In the mol-ecule of the title compound, CHNO, the oxime and hydrazide groups are situated in a -position in relation to the C-C bond linking the two functional groups. The CHC(=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.

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.

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.

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--aryl-1-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 ) compared to control was observed.

Details make the difference: a family of tetranuclear CuMn complexes with cube-like and double open cube-like cores.

The "direct synthesis" approach, namely one-pot reaction of metal powders and ammonium salt with a methanol solution of a polydentate Schiff base (HL) formed in situ from salicylaldehyde and ethanolamine, has been successfully used for the preparation of the new heterometallic compounds [CuMn(L)(CHOH)]I (1), [CuMn(L)(CHOH)(HO)]NCS·HO (2), [CuMn(L)(CHOH)(HO)]Br·0.45HO (3) and [CuMn(L)(HO)]BF·0.6HO (4).

Crystal structure of aqua-1κO-{μ-2-[(2-hydroxy-ethyl)methylamino]ethanolato-2:1κ(4) O (1),N,O (2):O (1)}[μ-2,2'-(methylimino)diethanolato-1:2κ(4) O,N,O':O]dithiocyanato-1κN,2κN-chromium(III)copper(II).

The title compound, [CrCu(C5H11NO2)(C5H12NO2)(NCS)2(H2O)] or [Cr(μ-mdea)Cu(μ-Hmdea)(NCS)2H2O], (where mdeaH2 is N-methylethanolamine, C5H13NO2) is formed as a neutral heterometal Cu(II)/Cr(III) complex. The mol-ecular structure of the complex is based on a binuclear {CuCr(μ-O)2} core. The coordination environment of each metal atom involves the N,O,O atoms of the tridentate ligand, one bridging O atom of the ligand and the N atom of the thio-cyanato ligands.

Lanthanide mixed-ligand complexes of the [Ln(CAPh)3(Phen)] and [LaxEu1-x(CAPh)3(Phen)] (CAPh = carbacylamidophosphate) type. A comparative study of their spectral properties.

A series of complexes Ln(Pip)3(Phen) (Ln(iii) = La, Ce-Nd, Sm-Lu, Y; HPip (CAPh type ligand) = 2,2,2-trichloro-N-(dipiperidin-1-yl-phosphoryl)acetamide, Phen = 1,10-phenanthroline) has been synthesized. The lanthanum(iii) doped europium(iii) complexes ([LaxEu1-x(Pip)3(Phen)], x = 0.99, 0.

A self-assembled octanuclear complex bearing the uncommon close-packed {Fe4Mn4(μ4-O)4(μ-O)4} molecular core.

A one-pot open-air reaction of manganese powder with iron(ii) chloride in DMF solution of the Schiff base (H2L) formed in situ from salicylaldehyde and hydroxylamine hydrochloride yields the heterometallic complex [Fe4(μ4-O)4Mn4(L)8(DMF)4]·2DMF (). Single crystal X-ray analysis shows that its molecular structure is based on the octanuclear core {Fe4Mn4(μ4-O)4(μ-O)4} with a quite rare molecular structure type {M8(μ4-X)4(μ-X)4}, where the central cube-like iron motif is modified with four terminal manganese fragments, the whole core being presented as the {Fe4(μ4-O)4} + 4{Mn(μ-O)} combination. Using the data from the Cambridge Structural Database (CSD), an analysis of the octanuclear structures with similar central {M4(μ4-X)4} fragments was performed.

Ionization and tautomerism of methyl fluorescein and related dyes.

The protolytic equilibrium of methyl ether of fluorescein is studied in water, aqueous ethanol, and in other solvents. The constants of the two-step dissociation are determined by spectrophotometry. In water, the fractions of the zwitterionic, quinonoid, and lactonic tautomes are correspondingly 11%, 6%, and 83%, as deduced from the UV-visible spectra.

Direct synthesis of a {Co₆(III)Fe₆(III)} dodecanuclear complex, revealing an unprecedented molecular structure type.

A novel heterometallic Co6Fe6 Schiff base complex, possessing an unprecedented {M12(μ-X)22} branched structure (according to the search via the Cambridge Structural Database), has been prepared using the "direct synthesis" approach and characterized by single crystal X-ray diffraction and magnetometry.

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.

Structural waters in the minor and major grooves of DNA--a major factor governing structural adjustments of the A-T mini-helix.

The role of microhydration in structural adjustments of the AT-tract in B-DNA was studied at the B97-D/def2-SV(P) level. The (dA:dT)5 complexes with 10 water molecules in minor and 15 water molecules in major grooves were studied. The obtained network of hydrogen bonds revealed the dependence between the groove width and the types of water patterns.

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.

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.

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 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.

Magnetic, high-field EPR studies and catalytic activity of Schiff base tetranuclear CuII2FeIII2 complexes obtained by direct synthesis.

Two novel heterometallic complexes [Cu2Fe2(HL(1))2(H2L(1))2]·10DMSO (1) and [Cu2Fe2(HL(2))2(H2L(2))2]·2DMF (2) have been prepared using the open-air reaction of copper powder, iron(II) chloride and DMSO (1) or DMF (2) solutions of the polydentate Schiff base (H4L(1), 1; H4L(2), 2) formed in situ from salicylaldehyde (1) or 5-bromo-salicylaldehyde (2) and tris(hydroxymethyl)aminomethane. Crystallographic analysis revealed that both compounds are based on the centrosymmetric tetranuclear core {Cu(II)2Fe(III)2(μ-O)6} where metal centres are joined by μ-O bridges from the deprotonated ligands forming a nonlinear chain-like arrangement. Variable-temperature (1.

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.

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.

Nucleic acid bases in anionic 2'-deoxyribonucleotides: a DFT/B3LYP study of structures, relative stability, and proton affinities.

Protonation of nucleobases in anions of canonical 2'-deoxyribonucleotides has been investigated by the DFT computational study at the B3LYP/aug-cc-pvdz level of theory. It is demonstrated that the protonation leads to a significant decrease of conformational space of purine nucleotides while almost all conformers found for non-protonated molecules correspond to minima of the potential energy surface for protonated mdTMP and mdCMP. However, in all nucleotides, only one conformer is populated.

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 β-turn conformation, which was not stabilized by an intramolecular hydrogen bond and could be classified as a type IV β-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.

Entropy versus aromaticity in the conformational dynamics of aromatic rings.

Comparison of the results of Car-Parrinello molecular dynamics simulations of isolated benzene, pyrimidine and 1,2,4-triazine molecules reveals that the unusually low population of planar geometry of the benzene ring is caused by entropy effects despite its high aromaticity. The decrease in symmetry of the molecule results in smaller changes in entropy and Gibbs free energy due to out-of-plane deformations of the ring, leading to an increase in the population of planar geometry of the ring. This leads to differences in the topology of potential energy and Gibbs free energy surfaces.

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.

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.