Crystal structure of bis-(ethyl-enedi-thio)-tetra-thia-fulvalenium μ2-acetato-bis-[tri-bromido-rhenate(III)] 1,1,2-tri-chloro-ethane hemisolvate.

The asymmetric unit of the title salt, (C10H8S8)[Re2Br6(CH3COO)]·0.5C2H3Cl3, contains one bis-(ethyl-enedi-thio)-tetra-thia-fulvalene (ET) radical cation, one μ2-acetato-bis-[tri-bromido-rhenate(III)] anion and a 1,1,2-tri-chloro-ethane mol-ecule with half-occupancy disordered about a twofold rotation axis. The tetra-thia-fulvalene fragment adopts an almost planar configuration typical of the ET radical cation.

Simple Instrumental and Visual Tests for Nonlaboratory Environmental Control.

Proposed are simple and available techniques that can be used for rapid and reliable environmental control specifically of natural water by means of instrumental and visual tests in outdoor conditions. Developed are the chemical colorimetric modes for fast detection of socially dangerous trace impurities in water such as Co(II), Pd(II), and Rh(III) as well as NO2 (-)-ions and Fe(III) serving as model impurities. Application of portable digital devices and scanner allows estimating the color coordinates and increasing the accuracy and sensitivity of the tests.

Two pseudo-enantiomeric forms of N-benzyl-4-hydroxy-1-methyl-2,2-dioxo-1H-2λ(6),1-benzothiazine-3-carboxamide and their analgesic properties.

The fact that molecular crystals exist as different polymorphic modifications and the identification of as many polymorphs as possible are important considerations for the pharmaceutic industry. The molecule of N-benzyl-4-hydroxy-1-methyl-2,2-dioxo-1H-2λ(6),1-benzothiazine-3-carboxamide, C17H16N2O4S, does not contain a stereogenic atom, but intramolecular hydrogen-bonding interactions engender enantiomeric chiral conformations as a labile racemic mixture. The title compound crystallized in a solvent-dependent single chiral conformation within one of two conformationally polymorphic P212121 orthorhombic chiral crystals (denoted forms A and B).

Crystal structure of N-hy-droxy-picolinamide monohydrate.

The crystal structure of the title compound, C6H6N2O2·H2O, consists of N-hy-droxy-picolinamide and water mol-ecules connected through O-H⋯O and N-H⋯N hydrogen bonds. The O-H⋯O inter-actions and π-π stacking inter-actions between the pyridine rings [centroid-centroid distance = 3.427 (1) Å] organize the components into columns extending along the b axis and the N-H⋯N hydrogen bonds link these columns into a two-dimensional framework parallel to (100).

Structure and Binding Energy of Double-Stranded A-DNA Mini-helices: Quantum-Chemical Study.

A-DNA is thought to play a significant biological role in gene expression due to its specific conformation and binding features. In this study, double-stranded mini-helices (dA:dT)3 and (dG:dC)3 in A-like DNA conformation were investigated. M06-2X/6-31G(d,p) method has been utilized to identify the optimal geometries and predict physicochemical parameters of these systems.

Crystal structure of 4-tert-butyl-2-{2-[N-(3,3-dimethyl-2-oxobut-yl)-N-iso-propyl-carbamo-yl]phen-yl}-1-isopropyl-1H-imidazol-3-ium perchlorate.

In the title salt, C26H40N3O2 (+)·ClO4 (-), the positive charge of the organic cation is delocalized between the two N atoms of the imidazole ring. The C N bond distances are 1.338 (2) and 1.

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.

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.

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.

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.

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.

Aromaticity in heterocyclic analogues of benzene: comprehensive analysis of structural aspects, electron delocalization and magnetic characteristics.

The degree of aromaticity of six-membered monoheterocycles with IV-VI group heteroatoms (C(6)H(5)X, where X = SiH, GeH, N, P, As, O(+), S(+), Se(+)) was analyzed using the results of ab initio calculations at the MP2/cc-pvtz level. Values of common aromaticity indices including those based on electronic delocalization properties, structural-dynamic features and magnetic properties all indicate high aromaticity of all considered heterocycles. A decrease in aromaticity is observed with increasing atomic number of the heteroatom, except in the case of the pyrylium cation.

Intra- and intermolecular interactions in the crystals of 3,4-diamino-1,2,4-triazole and its 5-methyl derivative. Experimental and theoretical investigations of charge density distribution.

In this paper intra- and intermolecular interactions in crystals of 3,4-diamino-1,2,4-triazole (DAT) and its 5-methyl derivative (DAMT) were investigated in details by experimental (high-resolution X-ray diffraction) and theoretical (ab initio quantum chemistry (MP2/aug-cc-pvdz), AIM, and NBO) methods. Influence of n-π conjugation and n→σ* hyperconjugation on the geometry of DAT and DAMT molecules was shown. All intermolecular interactions in crystals of the DAT and DAMT including weak X-H···π and mixed X-H···N/X-H···π hydrogen bonds were considered.

Seta-633 - a NIR fluorescence lifetime label for low-molecular-weight analytes.

We describe the photophysical properties of Seta-633, a commercially available near-infrared (NIR) dye, and its use as a fluorescent label to study the interaction between low-molecular-weight analytes and proteins using fluorescence lifetime as the readout parameter. In a model assay, we demonstrate that a biotinylated Seta-633 tracer binds to antibiotin with high specificity. Importantly, the lifetime of Seta-633-biotin increases about 1.

Diversification of a thieno[2,3-d]pyrimidin-4-one scaffold via regioselective alkylation reactions.

The 2-aryl-2,3,5,6,7,8-hexahydro[1]benzothieno[2,3-d]pyrimidin-4(1H)-ones and 2-aryl-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-ones have been diversified by alkylation reactions, applying benzylchlorides and N-substituted 2-chloroacetamides as alkylating agents. Under the found uniform conditions the substitution direction does not depend on the structure of the alkylating agent and gives monoalkylated products in high yields with simple workup. The alkylation of the 2,3-dihydropyrimidin-4(1H)-one derivatives proceeds onto the N1-position; however, in the case of pyrimidin-4(3H)-ones the O-alkylated products are formed selectively.

Near-infrared, dual-ratiometric fluorescent label for measurement of pH.

We describe the spectral properties of an amine-reactive, pH-sensitive, long-wavelength ratiometric fluorescent label having a pK(a) in the physiological pH range. The label exhibits its main absorption and emission in the near-infrared (NIR) region. On deprotonation, a blue shift of the excitation maximum is observed.

Dependence of deformability of geometries and characteristics of intramolecular hydrogen bonds in canonical 2'-deoxyribonucleotides on DNA conformations.

The molecular structure and deformability (with respect to average geometry) of methyl ethers of canonical 2'-deoxyribonucleotides thymidine-5'-phosphate (mTMP), 2-deoxycytidine-5'-phosphate (mCMP), 2-deoxyadenosine-5'-phosphate (mAMP) and 2'-deoxyguanosine-5'-phosphate (mGMP) in different types of DNA have been calculated using B3LYP/cc-pvdz method. Comparison of energy at equilibrium conformations of nucleotides and conformations with torsion angles of backbone fixed to average values for different types of DNA reveals that incorporation of nucleotides to A-DNA macromolecules requires the minimum amount of deformation energy. Therefore, this type of DNA should be the least strained from viewpoint of intramolecular deformations of monomers.

Rapid three-step one-pot microwave-assisted synthesis of 2,5-dioxo-1,2,5,6,7,8-hexahydro-3-quinolinecarbonitrile library.

Many well-known drugs contain 2-pyridone and 2-quinolone scaffolds. In the current paper, a one-pot three-step microwave-assisted method for the synthesis of N1-substituted 2,5-dioxo-1,2,5,6,7,8-hexahydro-3-quinolinecarbonitrile derivatives was developed. Employing this protocol, we quickly generated 105 compounds library from 1,3-cyclohexanediones, dimethylformamide dimethylacetal, and various cyanacetamides.

Synthesis of water-soluble, ring-substituted squaraine dyes and their evaluation as fluorescent probes and labels.

A series of ring-substituted squaraines absorbing and emitting in the red and NIR spectral region was synthesized and their spectral and photophysical properties (quantum yields, fluorescence lifetimes) and photostabilities were measured and compared to Cy5, a commonly used fluorescent label. The absorption maxima in aqueous media were found to be between 628 and 667 nm and the emission maxima are between 642 and 685 nm. Squaraine dyes exhibit high extinction coefficients (163,000-265,000 M(-1) cm(-1)) and lower quantum yields (2-7%) in aqueous buffer but high quantum yields (up to 45%) and long fluorescence lifetimes (up to 3.