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.

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.

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.

Details make the difference: a family of tetranuclear CuIIMnIII 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 (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.

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. The Cu(II) ion adopts a distorted square-pyramidal coordination while the Cr(III) ion has a distorted octa-hedral coordination geometry completed by the aqua ligand. In the crystal, the binuclear complexes are linked via two pairs of O-H⋯O hydrogen bonds to form inversion dimers, which are arranged in columns parallel to the a axis. In the µ-mdea ligand two -CH2 groups and the methyl group were refined as disordered over two sets of sites with equal occupancies. The structure was refined as a two-component twin with a twin scale factor of 0.242 (1).

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, 0.95, 0.50) have been obtained by the co-crystallization method. The complexes have been characterized by means of X-ray diffraction, IR, (1)H and (31)P-NMR and absorption spectroscopy. Emission and excitation luminescence spectra were recorded at 295 and 77 K. The lifetime values (τ) for the emission of all europium complexes were determined. The (5)D0 luminescence quantum efficiency is 73-89%. The symmetries of the nearest europium surrounding in pure and doped complexes were evaluated from the Stark splitting of (5)D0-(7)FJ transitions. Crystal structures of [Ln(Pip)3(Phen)] (Ln = Nd (1), Eu (2) and Tb (3)) have been determined. Lattice parameters of the [Ln(Pip)3(Phen)] (Ln = Tb, Yb) and the doped [LaxEu1-x(Pip)3(Phen)] (x = 0.99, 0.95, 0.50) complexes have been measured. The presence of four polymorphs within a number of rare earth elements has been estimated: two in triclinic (Ln1 = La, Nd; Ln2 = Eu), one in the monoclinic (Ln3 = Tb) and one in the rhombic (Ln4 = Tb, Yb) symmetry. Complex 3 can be obtained in two crystal modifications: monoclinic and orthorhombic ones.

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. The hierarchical order of molecular structure types with the general formula M8Xn for such compounds was proposed and the topological features as well as the factors that influence the molecular type formation are discussed. Variable-temperature (1.8-300 K) magnetic susceptibility measurements reveal an antiferromagnetic coupling among the magnetic centres in .

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. Corresponding study of the ionization of the methyl ether ester of fluorescein, fluorescein ethyl ester, and sulfonefluorescein allows testing the correction of the attribution of the microscopic dissociation constants of methoxy fluorescein. The results of nuclear magnetic resonance and infrared spectroscopy, as well as the X-ray analysis confirm the predomination of the lactonic structure of the molecular species in solid state and in DMSO. Contrary to it, the spectroscopic studies in both hydrogen-donor bond (HDB) and non-HBD solvents confirm that the presence of lactonic monoanion is atypical for the dye under study and, with high probability, also for the mother compound fluorescein.

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.

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 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.

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.

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.

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 (1.8-300 K) magnetic susceptibility measurements of 1 and 2 showed a decrease of the effective magnetic moment value at low temperature, indicative of antiferromagnetic coupling (JCu-Fe/hc = -10.2 cm(-1), JFe-Fe/hc = -10.5 cm(-1) in 1, JCu-Fe/hc = -10.5 cm(-1), JFe-Fe/hc = -8.93 cm(-1) in 2) between the magnetic centres in both compounds. They reveal an exceptionally high catalytic activity in the oxidation of cyclohexane with hydrogen peroxide under mild conditions, with the best observed yield/TON combined values of 36%/596 and 44%/1.1 × 10(3) for 1 and 2, respectively.

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.

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. This applies to all tautomers of protonated molecules except the mdTMP and mdCMP with the proton attached to the carbonyl group where a minor population of second conformer is observed. Protonation of nucleobase leads to significant elongation of the N-glycosidic bond. These findings agree well with suggestions that protonation of nucleobase is a first step in cleavage of the glycosidic bond. The oxygen atoms of both carbonyl groups of thymine and the N3 atom of the pyrimidine ring of cytosine, guanine, and adenine represent the most preferable sites for protonation of anions of 2'-deoxyrobonucleotides. The highest proton affinity is observed for the base in mdGMP and the lowest for the thymine moiety in mdTMP. It should be noted that calculated values of the proton affinities in anionic nucleotides are significantly higher (by 2-3 eV) than for nucleosides and neutral nucleotides. This allows assuming that the proton affinity of the base in DNA macromolecule may be tuned by changing the extent of shielding or neutralization of negative charge of the phosphate group.