How strong can the bend be on a DNA helix from cisplatin? DFT and MP2 quantum chemical calculations of cisplatin-bridged DNA purine bases

The B3LYP/6-31G(d) level of theory was used for the optimization of [Pt(NH(3))(4)](2+), [Pt(NH(3))(3)(H(2)O)](2+), cis-[Pt(NH(3))(2)(H(2)O)(2)](2+), and related platinum complexes. In addition, water or ammonium ligands were replaced by DNA purine bases so that finally cis-diammineplatinum with two bases (Pt-bridged complexes) is obtained. Single point calculations using the MP2/6-31+G(d) method were performed on the obtained reference geometries and were utilized for estimating bond dissociation energies (BDEs) and stabilization energies, and for electron density analyses. After reoptimization, IR spectra were determined from HF second derivatives. It was found that replacement of both water and ammonium by the DNA base is an exothermic process (20-50 kcal/mol depending on the ligands present in the complex). Asymmetric structures with one interbase H-bond were obtained for cis-diammine[bond](N(7),N(7)'-diadenine)[bond]platinum and mixed cis-diammine[bond](N(7)-adenine)[bond](N(7)-guanine)[bond]platinum complexes. In the case of the diguanine Pt-bridge, a symmetrical complex with two ammonium...O(6) H-bonds was found. The higher stabilization energy of the di-guanine complex is linked to a larger component of the Coulombic interaction. However, the BDE of Pt[bond]N(7)(G) is smaller in this complex than the BDE of Pt[bond]N(7)(G) from the mixed Pt[bond]AG complex. Also, steric repulsion of the ligands is about 10 kcal/mol smaller for the asymmetrical Pt[bond]AA and Pt[bond]AG bridges. The influence of the trans effect on DBE can be clearly seen. Adenine exhibits the largest trans effect, followed by guanine, ammonium, and water. The strength of the H-bond can be determined from the IR spectra. The strongest H-bond is the interbase H-bridge between adenine and guanine in the mixed Pt[bond]AG complex; otherwise, the H-bonds of adenine complexes are weaker than in guanine complexes. BDE can be traced in the guanine-containing complexes. The nature of the covalent bonding is analyzed in terms of partial charges and MO. A general explanation of the lower affinity of transition metals to oxygen than nitrogen can be partially seen in the less favorable geometrical orientation of lone electron pairs of oxygen.     

Synthesis and study of new rod-like mesogens containing 2-aminothiophene unit

We present a synthesis and mesomorphic properties of a new series of rod-like mesogens. All the compounds possess a substituted 2-aminothiophene unit as a main element in the structure attached to a stilbene moiety with a terminal alkyloxy chain (OR¹, OR² where R¹=C_nH_2n+1, R²=C_mH_2m+1; n, m ranging from 6 to 12). The synthesis of alkyloxybiphenyl substituted 2-aminothiophenes was carried out by the Gewald reaction and the appropriate reaction conditions were investigated. The liquid–crystalline properties were studied via polarizing optical microscopy, differential scanning calorimetry and X-ray diffraction. These materials exhibit nematic and/or smectic A phases. The influence of structural changes (variation in alkyloxy chain length and symmetry of the molecule) on mesogenic behaviour is discussed. Evaluation of UV–vis, fluorescent and electrochemical properties are also included.     

Synthesis,molecular characterisation,and in vivo study of platinum(IV) coordination compounds against B16 mouse melanoma tumours

A novel platinum(IV) coordination compound with 6-mercaptopurine (6-Hmp) has been synthesised and characterised by IR and NMR spectroscopy. Spectroscopic parameters indicate the presence of two chelate (S-6, N-7) monodeprotonated ligands and two chloride ions in the coordination sphere of [PtCl₂(6-mp)₂] · H₂O (I). Two Pt(IV) coordination compounds, [PtCl₂(6-mp)₂] · H₂O (I) and [PtCl₄(dbtp)₂] (II), were used in the in vivo test against B16 mouse melanoma tumours. Cytotoxic activity of compound II against the tumour cells was found to be high (LC₁₀ = 2.6 μM, LC₅₀ = 17.0 μM, LC₉₀ = 58.0 μM) compared to that of cisplatin.     

Quantitative EPR study on free radicals in the natural polyphenols interacting with metal ions and other environmental pollutants

Quantitative electron paramagnetic resonance (EPR) method was applied to characterise radicals stabilised in polyphenolic matrices of various biogenic materials: lichens, mosses, composts, soils, peats, brown coals and sewage sludge sediments. The investigations were carried out on raw materials and extracted fractions of humic acids (HA). General trends of g value and spin concentration changes were found. These parameters in lichens strongly depend on lichen species and air pollution. Determination of the g value and semiquinone spin concentration allows to assess degree of transformation of organic matter in compost, soil, peat and lignite. Application of gaseous ammonia as a base penetrating the organic matrices extends the possibilities and usefulness of the method. Interaction of metal ions with humic materials is illustrated by interaction of VO2+ ion with peat and lignite HA as well as demineralised (raw and carbonised) brown coal. Our investigations demonstrate that quantitative EPR is a rapid and effective monitoring method to study the influence of various environmental factors on substances containing polyphenolic matrices.     

Über den sterischen Verlauf der Umsetzung von Enaminen aus offenkettigen Aldehyden und Ketonen mit Nitroolefinen zu 2,3-disubstituierten 4-Nitroketonen

On the Steric Course of the Reaction of Enamines Derived from Open-Chain Aldehydes and Ketones with Nitro-olefins Yielding 2,3-Disubstituted 4-Nitroketones The relative configuration of the nitro-ketone 12 obtained by the title reaction has been proved by a Baeyer-Villiger degradation and subsequent reduction to the amino-alcohol (±)-(u)- 20 , the relative configuration of which is identical with a sample prepared from 2-methyl-3-hydroxybutyrate of known configuration (Scheme 1). The stereochemical course of the title reaction is thus as predicted by our topological rule. It is assumed that the other nitro-ketones 13–18 described here are also formed by (lk)-combination of the trigonal centers of the educts (diastereoselectivity > 90%, see Formulae and Fig. 1). It is not possible to reverse this relative topicity by employing (Z)- instead of (E)-components of the starting materials, due to the reversibility of the primary step of these Michael additions (Schemes 2 and 3, and Fig. 2).     

Past and Present of Sol-Gel Science and Technology

In the last twenty years sol-gel science has undergone a spectacular development. The various stages of the sol-gel process have been scrutinised in considerable detail and a sound basis for future technological developments established. In the beginning the studies centred mainly on silica and silicate glasses and were progressively extended to many ceramics and composites. A turning point was reached with the emergence of ormosils and of organic-inorganic nanocomposites. This opened the gateway to whole classes of new materials. The present studies show a definite tendency towards very specialised high-tech applications.     

Structures and energies of seleno derivatives of biuret.Ab Initio comparative studies of diselenobiuret, selenobiuret, and selenothiobiuret

Ab initio studies (LCAO-MO method) on conformers of three seleno derivatives of the biuret molecules diselenobiuret [I], selenobiuret [II], and selenothiobiuret [III] were carried out at the Hartree-Fock (HF) and MP2 levels. The molecular geometries of these species were fully optimized at the HF level and characterized by analysis of the harmonic vibrational frequencies using a split-valence triple-zeta basis set augmented by a set ofd polarization functions on heavy atoms andp polarization functions on hydrogen atoms [TZP(d, p)]. The total energies of the HF-optimized structures were calculated at the MP2 (frozen core) level using a larger TZP (2df, 2pd) basis set. The potential energy searches revealed a total of 11 minimum-energy conformers (assigned astrans-trans, trans-cis, cis-trans, andcis-cis) and seven transition-state species for the title molecules. The two predicted conformers for diselenobiuret (Ia=trans-trans andIc=cis-cis) are characterized byC ₂ and the third byC _s symmetry. For selenothiobiuret two forms (IIIa=trans-trans andIIId=cis-cis) possessC ₁ and two (IIIb=trans-cis andIIIc=cis-trans) possessC _s symmetries, respectively. For selenobiuret, four formsIIa=trans-trans (C₁),IIb=trans-cis (C _s),IIc=cis-trans (C ₁), andIId=cis-cis (C₁), were obtained as a result of gradient optimization. Comparison of the relative energies for the considered species indicated that thecis-trans forms are the most stable conformations for all three systems at both the HF and MP2 levels of theory.     

Bicyclic [b]-heteroannulated pyridazine derivatives. 4. Cyclization reactions of 4-aryltetrahydropyridazine-3,6-dione 3-hydrazones with some keto esters

Ethoxycarbonylalkylidene derivatives 2 and 6 of the title hydrazones were obtained in the reaction with ethyl pyruvate or ethyl aroylformate and ethyl acetoacetate, respectively, in methanol. Both compounds were mixtures of geometric isomers with high predominance of one of them. Nmr spectroscopy revealed an unexpected magnetic non-equivalence of the CH₂ protons in the ester ethyl group of the major isomer of 6 . On heating (?200°) in an inert medium or on refluxing in ethanolic sodium ethoxide 2 cyclized to the corresponding pyridazino[6,1-c]-triazines 4 , whereas 6 formed pyrazolylpyridazines 7 . The structure of the latter was unambigously established by X-ray analysis. Alkylation of 4a with benzyl bromide in the presence of tetrabutylammonium bromide occurred selectively on the pyridazine N atom.     

On-surface cyclodehydrogenation reaction pathway determined by selective molecular deuterations

Understanding the reaction mechanisms of dehydrogenative C_aryl–C_aryl coupling is the key to directed formation of π-extended polycyclic aromatic hydrocarbons. Here we utilize isotopic labeling to identify the exact pathway of cyclodehydrogenation reaction in the on-surface synthesis of model atomically precise graphene nanoribbons (GNRs). Using selectively deuterated molecular precursors, we grow seven-atom-wide armchair GNRs on a Au(111) surface that display a specific hydrogen/deuterium (H/D) pattern with characteristic Raman modes. A distinct hydrogen shift across the fjord of C_aryl–C_aryl coupling is revealed by monitoring the ratios of gas-phase by-products of H₂, HD, and D₂ with in situ mass spectrometry. The identified reaction pathway consists of a conrotatory electrocyclization and a distinct [1,9]-sigmatropic D shift followed by H/D eliminations, which is further substantiated by nudged elastic band simulations. Our results not only clarify the cyclodehydrogenation process in GNR synthesis but also present a rational strategy for designing on-surface reactions towards nanographene structures with precise hydrogen/deuterium isotope labeling patterns.

Selective deuterations were exploited to synthesize graphene nanoribbons on Au(111) surface with a specific H/D pattern on edges, allowing the determination of cyclodehydrogenation reaction pathway within the framework of pericyclic reactions.     

The Properties of Cu Ions in Zeolites CuY Studied by IR Spectroscopy

The properties of both Cu²⁺ and Cu⁺ ions in zeolite CuY were followed with NO and CO as probe molecules. Cu²⁺ was found to be located in S_II, S_II*, and S_III sites, whereas Cu⁺ was found in S_II and S_II* sites. The fine analysis of the spectra of Cu²⁺-NO and Cu⁺-CO adducts suggests that both in S_II and in S_II* sites two kinds of Cu cations exist. They differ in the positive charge, which may be related to the varying numbers of AlO₄⁻ in close proximity. The experiments of NO and CO adsorption and desorption evidenced that both Cu²⁺ and Cu⁺ sites of highest positive charge bind probe molecules most strongly but activate them to a lesser extent than the Cu sites of lowest positive charge. The experiments of reduction with hydrogen evidenced that the Cu ions of higher positive charge are first reduced by hydrogen. On the other hand, Cu sites of the lowest positive charge are first oxidized by oxygen. The experiments with CuNaY zeolites of various Cu contents suggest that the first introduced Cu (at low Cu contents) created Cu⁺, which was the most neutralized by framework oxygens. Such Cu cations are the most stabilized by framework oxygens.