Spectroscopic characterization, crystal structure determination and interaction with DNA of novel cyano substituted benzimidazole derivative

Novel cyano-substituted benzimidazole derivatives 3 and 4 were synthesized from 4-N,N-dimethylamino-benzaldehyde and 2-cyanomethyl-benzimidazole. 2-(1H-benzimidazol-2-yl)-3-(4-N,N-dimethylamino-phenyl)-acrylonitrile hydrochloride monohydrate 4 has been studied by ¹H and ¹³C NMR, IR, MS, UV/Vis and fluorescence spectroscopy and confirmed by X-ray crystal structure analysis. The interaction of 4 with ct-DNA has also been investigated by fluorescence spectroscopy and melting temperature determination experiment. According to the emission spectra recorded in the absence and presence of ct-DNA at different ratios r ([compound]/[polynucleotide]), 4 showed marked decrease in the fluorescence intensity and very strong hypochromic effect. Melting temperature experiment showed weak stabilization of double helix. To determine binding mode of 4, other additional experiments are necessary. The molecules of 4 are almost planar with the dihedral angle between benzimidazole and phenyl rings of 6.99(6)°. The protonation of nitrogen atom of benzimidazole ring is followed by π-electrons delocalization in the region resulting in C–N bond distances equality [1.341(2) and 1.337(2) Å]. Both NH groups of benzimidazole ring form intermolecular hydrogen bonds, one with the oxygen atom of water molecule [N···O 2.689(2) Å] and the other with Cl^? ion (N···Cl^? 3.051(1) Å). Except proton acceptor, water molecule acts as double proton donor in the formation of intermolecular hydrogen bonds with Cl^? ion [O···Cl^? 3.126(2) and 3.169(2) Å]. In that way, infinite chains along [110] direction are formed.     

Semi-Preparative Isolation of Crocins from Saffron (Crocus sativus L.)

Two-step, low-pressure liquid chromatography has been used to isolate crocins, the most abundant compounds in the hydroalcoholic extract of saffron. A mixture of styrene–divinylbenzene copolymer and modified starch polymers was used as stationary phase. A 600 mm × 15 mm i.d. column was used in the first step; the best resolution was achieved by gradient elution with an aqueous methanol gradient with the methanol content changing from 50 to 95%. The highest yield of crocins from this step was achieved by use of 20 mL of 300 mg mL^?1 saffron extract. Under these conditions the yellow pigments of the saffron extract were separated into twenty fractions. In the second step use of a 700 mm × 8 mm i.d. column resulted in crocin-1 [crocetin (di- -D-gentobisyl) ester], crocin-2 [crocetin (mono- -D-gentobisyl-mono- -D-glycoside) ester], and crocin-3 [crocetin ( -D-gentobisyl)-ester] with purity as high as 99.04%, 97.40%, and 96.70%, respectively.     

Structure and hydrogen bonding in polyhydrated complexes of guanine

Abstract Molecular structure of complexes of guanine with 12, 13, 16, and 17 water molecules were calculated using B3LYP/6-311G(d,p) level of theory. Interaction with water results in some deformation of geometrical parameters of guanine, which can be described as contribution of zwitter-ionic resonant form into the structure of DNA base. Saturation of water binding sites within guanine creates possibilities for the formation of the N···H–O hydrogen bond where the nitrogen atom of amino group acts as proton acceptor. The NBO analysis of guanine–water interactions reveals that hydrogen bonds involving the N(3) and N(7) atoms of guanine represent a case of mixed N···H–O/π···H–O hydrogen bonds where contribution of π-system into total energy of interaction varies from 3% to 41%. This contribution significantly depends on orientation of the hydrogen atom of water molecule with respect to plane of purine bicycle and influence of neighboring water molecules. Graphical Abstract      

Narcissistic reaction pathways: an example of Maxwell’s theorem of geometrical optics applied to the intrinsic reaction coordinate model

Maxwell’s theorem and the concept of stigmatic transformations that appear in the theory of geometrical optics are extended to the intrinsic reaction coordinate model when it is applied to the specific case of narcissistic reactions.      

Supramolecular amide and thioamide synthons in hydrogen bonding patterns of N-aryl-furamides and N-aryl-thiofuramides

The supramolecular synthon of amide group in the primary and secondary amides is well recognized to be infinite chains of the C(4) type formed by the intermolecular hydrogen bond of the type N–HO=C. On the other hand, there is a lack of structural data for the thioamides. Three compounds belonging to the class of N-aryl-fura-mides (N-(4-bromophenyl)-5-bromo-2-furancarboxamide, N-(4-chlorophenyl)-5-bromo-2-furancarboxamide) and to the class of N-aryl-thiofuramide (N-(4-methoxyphenyl)-2-furanthiocarboxamide) are prepared and characterized by the NMR spectroscopy in solution; molecular and crystal structures in the solid state have been determined by X-ray single crystal diffractometry and the structures in the gas phase by DFT and AM1 calculations. The investigation is carried out in order to establish supramolecular amide and thioamide synthons of hydrogen bonding patterns in these crystal structures. The geometry of the N–HO=C and the N–HS=C type of hydrogen bonds are compared due to the possibility of the N–H amide group to form intramolecular hydrogen bond with the furan oxygen atom, thus, commonly, leading to the three-center hydrogen bond pattern. The competition between the S=C proton acceptor of thioamides and the other proton acceptors (such as methoxy group) for the amide N–H proton donor group has been investigated. In that context, the above-mentioned compounds are correlated with the others of this class, structurally determined, so far.     

The first synthesis of 3-deoxyoripavine and its utilization in the preparation of 10-deoxyaporphines and cyprodime

The synthesis of 3-deoxyoripavine (7) was realized as a novel and promising intermediate towards the synthesis of the important class of dopaminergic and/or serotonergic 10-deoxyaporphines and the special pharmacological tool µ opioid antagonist cyprodime. Generally, the preparation of these valuable biologically active compounds was achieved in remarkable yields.      

Acylated benzothiazinesulfoneamides: Synthesis and molecular structure

1,2,3,4,4a,10b-Hexahydro-1,4-methano-6H-dibenzo[c,e]-5,6-thiazine-5,5-dioxide has been converted into the corresponding N-acyl derivatives via the reaction with acid chlorides and anhydrides. X-Ray diffraction data have revealed the presence of an intramolecular С–H···O=S hydrogen bond in the molecules of the obtained compounds.     

Six coordinate Ni(II) complexes of ONN donor aroylhydrazone ligands: synthesis,spectral studies,and crystal structures

A new ligand N′-(pyridin-2-ylmethylene)nicotinohydrazide (HL²) and two Ni(II) complexes of stoichiometry NiL¹·H₂O [L¹-2-benzoylpyridine nicotinoylhydrazone] and NiL²·H₂O have been synthesized and characterized by elemental analyses, IR and UV–Vis spectral studies. Structures of HL² and Ni(II) compounds have been determined by single crystal X-ray diffraction studies which reveal a distorted octahedral geometry around the two Ni(II) centers.

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Graphical abstract A new ligand N￠-(pyridin-2-ylmethylene)nicotinohydrazide (HL2) and two Ni(II) complexes of stoichiometry NiL1·H2O [L1-2-benzoylpyridine nicotinoylhydrazone] and NiL2·H2O have been synthesized and characterized by elemental analyses, IR, UV–Vis spectral studies and single crystal X-ray analysis.

     

P-Triazinylphosphonium chlorides as a new group of coupling reagents

Tertiary phosphines in reaction with 2-chloro-4,6-dialkoxy-1,3,5-triazines gave unstable quaternary P-triazinylphosphonium chlorides, which readily decomposed with a departure of the alkyl group of the triazine ring substituent. Stable quaternary P-triazinylphosphonium chlorides were obtained only in reaction of 2-chloro-4,6-diphenoxy-1,3,5-triazine. Both, stable quaternary P-triazinylphosphonium chlorides as well unstable analogues prepared in situ activated carboxylic acid yielding “superactive” triazine esters, useful as highly efficient reagents in peptide bond synthesis.      

The effect of aluminium oxide on the reduction of cobalt oxide and thermostabillity of cobalt and cobalt oxide

During precipitation and calcination at 200°C nanocrystalline Co₃O₄ was obtained with average size crystallites of 13 nm and a well developed specific surface area of 44 m² g^?1. A small addition of a structural promoter, e.g. Al₂O₃, increases the specific surface area of the cobalt oxide (54 m² g^?1) and decreases the average size of crystallites (7 nm). Al₂O₃ inhibits the reduction process of Co₃O₄ by hydrogen. Reduction of cobalt oxide with aluminium oxide addition runs by equilibrium state at all the respective temperatures. The apparent activation energy of the recrystallization process of the nanocrystalline cobalt promoted by the aluminium oxide is 85 kJ mol^?1. Aluminium oxide improves the thermostability of both cobalt oxide and the cobalt obtained as a result of oxide phase reduction.      

Properties of sodium phosphate-hydroxy ethanolamide gemini surfactant synthesized from the seed oil of Luffa cylindrical

The production of surfactant from biological and renewable sources is important as this reduces environmental hazards since the products are highly biodegradable. Oil extracted from the seed of Luffa cylindrica using hexane in a soxhlet extractor was used in the synthesis of sodium phosphate-hydroxy ethanolamide via a simple reaction mechanism. The progress of the reaction was monitored and confirmed by FTIR, ¹HNMR and ¹³CNMR. The process used gave a yield of 88.46% of sodium phosphate-hydroxy ethanolamide. The properties of this compound were compared with those of sodium dodecyl sulphate (SDS) used as a known reference surfactant. Important properties of sodium phosphate-hydroxy ethanolamide such as foam stability, wetting power and surface tension turned out superior to those of the known reference surfactant (SDS).      

Mechanical, thermal and surface properties of polyacrylamide/dextran semi-interpenetrating network hydrogels tuned by the synthesis temperature

The mechanical, rheological, thermal, and surface behaviors of three polyacrylamide/dextran (PAAm/Dx) semi-interpenetrating polymer network (semi-IPN) hydrogels, prepared at 22°C, 5°C and ?18°C, were investigated. The results were compared with those obtained on cross-linked PAAm without Dx synthesized under the same conditions. Hydrogels prepared at the lowest temperature were the most mechanically stable. The thermal stability of the semi-IPN hydrogels is slightly lower than the corresponding PAAm gels, irrespective of preparation temperature. The water vapor sorption capacity depended on the presence of Dx as well as preparation temperature, which determines the network morphology.      

157 nm Photodissociation of a Complete Set of Dipeptide Ions Containing C-Terminal Arginine

Twenty singly-charged dipeptide ions with C-terminal arginine were photodissociated with 157 nm light and their tandem mass spectra recorded. Many of the small product ions that were observed are standard peptide fragments that have been commonly seen in VUV photodissociation studies. However, the study of a library of dipeptides containing all 20 N-terminal amino acids enabled the recognition of trends associated with the occurrence of w-, v-, and immonium ions, the observation of competition between forming N- and C-terminal fragments in dipeptide RR, and the identification of some unusual fragment ions appearing at masses of 183, 187, 196, and 197 Da. A highly accurate internal calibration of the photodissociation TOF-TOF data enabled molecular formulae for these four product ions to be derived. Their proposed structures reflect the rather high-energy nature of this fragmentation phenomenon.      

Rhodium catalysts build into the structure of a silicate support in the hydroformylation of alkenes

Rhodium is build into a nano-structured calcium silicate during the synthesis of the silicate. Thereby, it was desired to create a robust heterogeneous catalyst, which does not suffer from catalyst leaching like rhodium impregnated on a pre-formed silicate. While this was achieved, the silicate structure was adversely affected by the incorporation of rhodium — the surface area and pore volume of the material were found to be comparatively low. Alcohol and acid washing were tested to address this issue. The alcohol treatment proved detrimental as catalytic material was leached from the silicate. The acid washed rhodium containing calcium silicate was quite active in the hydroformylation of alkenes and did not suffer loss of catalyst into the product phase. Acid treated rhodium containing silicates were more active than their untreated counterparts but less selective due to access to the rhodium centers being opened.      

Benzamidinium acetylsalicylate: crystal structure of the first salt with acetylsalicylate anion

The first crystal structure of a non-coordinating acetylsalicylate anion containing salt was determined by X-ray crystallography. Benzamidinium acetylsalicylate crystallizes in the triclinic space group $ P\bar{1} The first crystal structure of a non-coordinating acetylsalicylate anion containing salt was determined by X-ray crystallography. Benzamidinium acetylsalicylate crystallizes in the triclinic space group (a = 9.8885(5), b = 10.2769(5), c = 15.2656(7) ?, α = 87.219(4), β = 78.261(4) and γ = 72.589(4) Z = 4, V = 1449.17(12) ?³, R1 = 0.0346 and wR2 = 0.0697). The structure comprises pairs of hydrogen bonded benzamidinium cations and acetylsalicylate anions connected into infinite chains through further N–H···O hydrogen bonds.     

The first C(O)NHP(O)-based phosphoric triamide structure with an N‒H···π hydrogen bonding: A combination of X-ray crystallography and theoretical study to evaluate the strength of hydrogen bonds

The hydrogen bond pattern of N-(4-methoxybenzoyl)-N′,N″-bis(4-methylbenzyl)-phosphoric triamide, C₂₄H₂₈N₃O₃P, (I), was investigated. In the crystal structure, the molecules are aggregated through N_CP―H···O═P and N_P―H···O═C hydrogen bonds in a one-dimensional arrangement parallel to the c axis (N_CP is the nitrogen atom in the C(O)NHP(O) segment and N_P stands for the two other nitrogen atoms bonded to the P atom). There is also a novel N_P?H···π hydrogen bond in the crystal which extends the aggregation of the molecules to a two-dimensional array parallel to the bc plane. A Cambridge Structural Database (CSD, version 5.37, Feb 2016) analysis shows that the N―H···π hydrogen bond was not observed in any of 156 [RC(O)NH]P(O)[NR¹R² Allen, F. H.; Taylor, R. Chem. Soc. Rev. 2004, 33, 463-475.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]₂ (R¹ ≠ H, R² = H or ≠ H) phosphoric triamide structures reported so far. The theoretical calculations at the B3LYP/6-311G^** level of theory (DFT, AIM, and NBO) were performed to evaluate the strengths of N_CP―H···O═P, N_P―H···O═C and N_P―H···π hydrogen bonds, considering two-aggregate molecular assemblies containing these hydrogen bonds. The calculations on the title compound suggest that the intermolecular N_CP―H···O═P hydrogen bond is stronger than N_P―H···O═C and N_P―H···π interactions. The hydrogen bond strength was investigated by NBO, topological analysis, geometry calculation, Hirshfeld surface analysis and experimental spectroscopic results, which are in agreement with each other.     

Crystallographic and conformational analysis of two novel trans-azo benzene compounds

The molecular and crystal structure of (E)-2-Acetyl-4-(2-bromophenyldiazenyl)phenol (1) and (E)-2-Methyl-4-(o-tolyldiazenyl)phenol (2) were characterized and determined by single crystal X-ray diffraction method besides spectroscopic means. The periodic organization of 1 is stabilized by C–H···O type weak H-bond and Br···O type weak halogen bonding and thus, a two dimensional puckered network is established almost parallel to () the plane. Molecules of 2 are linked into C(7) chains generated by translation along the [1 0 1] direction with the aid of O–H···N type H-bonds, and these chains are strengthened by C–H···π interactions involving o-tolylphenol ring. Quantum chemical studies at B3LYP/6-311 ++G(d,p) level reveal that potential barrier of the compounds around Ar–N torsions is of double minimum character unless it is defected by the presence of o-substituent groups in the vicinity of the azo bridge. The results from crystallographic and quantum chemical studies suggest that azo benzene compounds may adapt non-planar geometry apart from the most stable planar conformation, which is located on the secondary minima of double potential barrier regarding rotational motion around Ar–N bonds.     

Research on thermal decomposition of trinitrophloroglucinol salts by DSC, TG and DVST

The thermal decomposition of the four nitrogen-rich salts of ammonia (NH₄), aminoguanidine (AG), carbohydrazide (CHZ) and 5-aminotetrazo (ATZ) based on trinitrophloroglucinol (H₃TNPG) was investigated using the differential scanning calorimetry (DSC), thermogravity (TG), and dynamic vacuum stability test (DVST). DSC and TG methods research the complete decomposition, while DVST method researches the very early reaction stage. The peak temperatures of DSC curves are consistent with the temperatures of maximum mass loss rates of TG curves. The apparent activation energies of these H₃TNPG-based salts obtained by DSC and DVST have the same regularity, i.e., (ATZ)(H₂TNPG)·2H₂O < (CHZ)(HTNPG)·0.5H₂O < NH₄(H₂TNPG) < (AG)(H₂TNPG). The thermal stability order is (ATZ)(H₂TNPG)·2H₂O < (CHZ)(HTNPG)·0.5H₂O < (AG)(H₂TNPG) < NH₄(H₂TNPG), which was evaluated by DVST according to the evolved gas amount of thermal decomposition. DVST can monitor the real-time temperature and pressure changes caused by thermal decomposition, dehydration, phase transition and secondary reaction, and also evaluate the thermal stability and kinetics.      

Reinvestigation of intramolecular hydrogen bond in malonaldehyde derivatives: An ab initio,AIM and NBO study

The RAHB systems in malonaldehyde and its derivatives at MP2/ 6‐311++G(d,p) level of theory were studied and their intramolecular hydrogen bond energies by using the related rotamers method was obtained. The topological properties of electron density distribution in O? H···O intramolecular hydrogen bond have been analyzed in term of quantum theory of atoms in molecules (QTAIM). Correlations between the H‐bond strength and topological parameters are probed. The results of QTAIM clearly showed that the linear correlation between the electron density distribution at HB critical point and RAHB ring critical point with the corresponding hydrogen bond energies was obtained. Moreover, it was found a linear correlation between the electronic potential energy density, V(r_cp), and hydrogen bond energy which can be used as a simple equation for evaluation of HB energy in complex RAHB systems. Finally, the similar linear treatment between the geometrical parameters, such as O···O or O? H distance, and Lp(O)→σ*_OH charge transfer energy with the intramolecular hydrogen bond energy is observed. © 2010 Wiley Periodicals, Inc., Int J Quantum Chem, 2011     

Fabrication of superhydrophobic surface of stearic acid grafted zinc by using an aqueous plasma etching technique

A stable superhydrophobic surface of stearic acid grafted zinc was fabricated with two steps, that is, the zinc surface was firstly treated with glow discharge electrolysis plasma (GDEP) and then followed by a grafted reaction of stearic acid onto the treated zinc surface. Results indicated that the wettability of zinc substrate changed from superhydrophily to superhyphodrobicity with a water contact angle (CA) up to 158° and a water sliding angle (SA) less than 5°. The surface morphology and composition were characterized by scanning electron microscopy (SEM) and X-ray diffraction (XRD), respectively.