Binding of cationic and neutral phenanthridine intercalators to a DNA oligomer is controlled by dispersion energy: quantum chemical calculations and molecular mechanics simulations

Correlated ab initio as well as semiempirical quantum chemical calculations and molecular dynamics simulations were used to study the intercalation of cationic ethidium, cationic 5-ethyl-6-phenylphenanthridinium and uncharged 3,8-diamino-6-phenylphenanthridine to DNA. The stabilization energy of the cationic intercalators is considerably larger than that of the uncharged one. The dominant energy contribution with all intercalators is represented by dispersion energy. In the case of the cationic intercalators, the electrostatic and charge-transfer terms are also important. The DeltaG of ethidium intercalation to DNA was estimated at -4.5 kcal mol(-1) and this value agrees well with the experimental result. Of six contributions to the final free energy, the interaction energy value is crucial. The intercalation process is governed by the non-covalent stacking (including charge-transfer) interaction while the hydrogen bonding between the ethidium amino groups and the DNA backbone is less important. This is confirmed by the evaluation of the interaction energy as well as by the calculation of the free energy change. The intercalation affects the macroscopic properties of DNA in terms of its flexibility. This explains the easier entry of another intercalator molecule in the vicinity of an existing intercalation site.     

Oxidation behavior of Ru/TiO2 and metallic Ru fine particles on heating in air

Thermogravimetry (TG) and differential thermal analysis (DTA) were used to investigate the oxidation behavior of Ru/TiO2 and metallic Ru fine particles during heating in air in the range 20-1000 degrees C. Temperature ranges of the oxidation for two samples of Ru/TiO2 with the compositions (92 wt% Ru, 8 wt% TiO2) and (75 wt% Ru, 25 wt% TiO2) and for pure metallic Ru fine particle agglomerates were determined. It was assumed that after the partial oxidation of Ru in the sample containing 75 wt% Ru and 25 wt% TiO2 and in the pure metallic Ru a diffusion barrier was formed, preventing further oxidation of Ru in Ru/RuO2 and Ru/RuO2/TiO2 matrices. XRD and TEM were used for the sample characterization.     

Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase,in a microhydrated environment and in aqueous solution. guanine: surprising stabilization of rare tautomers in aqueous solution

Altogether eight keto and enol tautomers of guanine were studied theoretically in the gas phase, in a microhydrated environment (1 and 2 water molecules) and in bulk water. The structures of isolated, as well as mono- and dihydrated tautomers were determined by means of the RI-MP2 method using the extended TZVPP (5s3p2d1f/3s2p1d) basis set. The relative energies of isolated tautomers included the correction to higher correlation energy terms evaluated at the CCSD(T)/aug-cc-pVDZ level. The relative enthalpies at 0 K and relative free energies at 298 K were based on the above-mentioned relative energies and zero-point vibration energies, temperature-dependent enthalpy terms and entropies evaluated at the MP2/6-31G level. The keto form having hydrogen atom at N7 is the global minimum while the canonical form having hydrogen atom at N9 represents the first local minimum at all theoretical levels in vacuo and in the presence of 1 and 2 water molecules. All three unusual rare tautomers having hydrogens at N3 and N7, at N3 and N9, and also at N9 and N7 are systematically considerably less stable and can be hardly detected in the gas phase. The theoretical predictions fully agree with existing theoretical as well as experimental results. The effect of bulk solvent on the relative stability of guanine tautomers was studied by self-consistent reaction field and molecular dynamics free energy calculations using the thermodynamic integration method. Bulk solvent, surprisingly, strongly favored these three rare tautomers over all remaining low-energy tautomers and probably only these forms can exist in water phase. The global minimum (tautomer with hydrogens at N3 and N7) is by 13 kcal/mol more stable than the canonical form (3rd local minimum). Addition of one or two water molecules does not change the relative stability order of isolated guanine tautomers but the respective trend clearly supports the surprising stabilization of three rare forms.     

Molecular recognition of cyclic-nucleotides and current sensors for their detection

This work briefly describes available sensors for cAMP and cGMP. Many sensors are based on derivatization of naturally occurring products such as immunoglobulins, protein kinases, etc. Only a few published works deal with chemosensors, which are built up by "total" chemical synthesis. This field stays opened for combinatorial chemist. The best sensors are protein kinases genetically modified with mutants of green fluorescent protein, which allow screening of entire cell cultures.     

The synthesis and characterization of a bis-oxime functionalized binucleating macrocycle and its polynuclear complexes

Summary A novel tetraoxime containing a substituted twofold macrocycle, 6,6-spirobi[1,12-di(hydroxyimino)-2,39,10-dibenzo-1, 11-diaza-4,8-dithiacyclotridecane] (5), has been synthesized from 6,6-bis(5-amino-3,4-benzo-2-thiapentyl)-1, 11-diamino-2, 39, 10-dibenzo-4,8-dithiaundecane (3), which was itself prepared from the potassium salt of 2-aminothiophenol (2), pentaerythrityltetrabromide (1) and cyanogendi-N-oxide (4). A polymeric Co^III complex of (5) containing a 11 metalligand ratio has been isolated. The template synthesis of a new Co^III complex containing bridging BF₂ groups was achieved using the hydrogen-bridged Co^III complex. The hetero-polynuclear complex of (5) was prepared by reacting the BF _inf2 ^sup– -capped polymeric Co^III complex with bis(benzonitrile)Pd^IIchloride. The structure of the ligand and its complexes are in accord to elemental analyses, ¹H- and ¹³C-n.m.r., i.r. and mass spectral data.     

Computational study of structures and properties of metallaboranes: cobalt bis(dicarbollide)

A density functional study at the BP86/AE1 level is presented for the cobalt bis(dicarbollide) ion [3-Co-(1,2-C2B9H11)2]- (1) and selected isomers and rotamers thereof. Rotation of the two dicarbollide moieties with respect to each other is facile, as judged by the small energetic separation of the three rotamers located (within 11 kJ mol(-1)) and by the low barriers for their interconversion (at most 41 kJ mol(-1)). Among the isomers differing in carbon atom positions that contain two equivalent dicarbollide ligands, the 1,7 ("carbon apart") form [2-Co-(1,7-C2B9H11)2]- is the most stable, 121 kJ mol(-1) below 1. The electronic structure of 1 is characterized in terms of molecular orbitals, population analysis, and excitation energies from time-dependent density functional theory, relevant to UV/Vis spectroscopy. Experimental 11B NMR chemical shifts of 1 are reproduced to better than 5 ppm at the GIAO-B3LYP/II' level, and the computed delta(11B) values are only little affected by rotational averaging or the presence of a polarizable continuum. Larger such effects are found for the as-yet unknown 59Co chemical shift, for which a value in the range between -1800 and -2400 ppm is predicted. Even though the accuracy achieved for the theoretical delta(11B) values is somewhat lower than that for heteroboranes at conventional ab initio levels, the level of density functional employed can afford qualitatively reliable chemical shifts, which can be useful in assignments and structural refinements of heteroboranes containing transition metal.     

Determination of the absolute configurations of natural products via density functional theory calculations of vibrational circular dichroism, electronic circular dichroism and optical rotation: the schizozygane alkaloid schizozygine

The development of density functional theory (DFT) methods for the calculation of vibrational circular dichroism (VCD), electronic circular dichroism (ECD), and transparent spectral region optical rotation (OR) has revolutionized the determination of the absolute configurations (ACs) of chiral molecules using these chiroptical properties. We report the first concerted application of DFT calculations of VCD, ECD, and OR to the determination of the AC of a natural product whose AC was previously undetermined. The natural product is the alkaloid schizozygine, isolated from Schizozygia caffaeoides. Comparison of DFT calculations of the VCD, ECD, and OR of schizozygine to experimental data leads, for each chiroptical technique, to the AC 2R,7S,20S,21S for the naturally occurring (+)-schizozygine. Three other alkaloids, schizogaline, schizogamine, and 6,7-dehydro-19beta-hydroxyschizozygine, have also been isolated from S. caffaeoides and shown to have structures closely related to schizozygine. Assuming a common biosynthetic pathway, their ACs are defined by that of schizozygine.     

Photodissociation of hydrogen halide molecules on free ice nanoparticles

Photodissociation of water clusters doped with HX(X=Br,Cl), molecules has been studied in a molecular beam experiment. The HX(H2O)n clusters are dissociated with 193 nm laser pulses, and the H fragments are ionized at 243.07 nm and their time-of-flight distributions are measured. Experiments with deuterated species DBr(H2O)n and HBr(D2O)n suggest that the photodissociation signal originates from the presence of the HX molecule on the water cluster, but does not come directly from a photolysis of the HX molecule. The H fragment is proposed to originate from the hydronium molecule H3O. Possible mechanisms of the H3O production are discussed. Experimental evidence suggests that acidic dissociation takes place in the cluster, but the H3O+ ion remains rather immobile.     

Correlation effects in R-matrix calculations of electron-F2 elastic scattering cross sections

Correlation effects are studied in electron scattering off the fluorine molecule. Fixed-nuclei approximation R-matrix calculations of the elastic collision cross sections are presented for a set of internuclear distances at three levels of correlation. The aim of this work is to study the role of electronic correlation on the properties of the 2Sigmau resonance. The Feshbach-Fano R-matrix method of resonance-background separation is used to study the effect of inclusion of various levels of correlation on the energy and width of the 2Sigmau resonance. Data required for construction of the nonlocal resonance model (construction of a discrete state and its coupling to the continuum) which allows the calculation of inelastic processes such as dissociative electron attachment and vibrational excitation [W. Domcke, Phys. Rep. 208, 97 (1991)] including the correlation are presented.     

Tetraphenylporphyrin-cobalt(III) bis(1,2-dicarbollide) conjugates: from the solution characteristics to inhibition of HIV protease

Tetraphenylporphyrin conjugates with one (PB1) and four (PB4) cobalt(III) bis(1,2-dicarbollide) substituents were synthesized and the physicochemical and photophysical properties as well as inhibition of HIV-1 protease were described. In methanol, both PB1 and PB4 were monomeric producing the triplet states and singlet oxygen after excitation. The triplet states of PB4 were quickly protonated. Porphyrins exhibited a small decrease of the quantum yields of the singlet oxygen formation (17% for PB4 and 13% for PB1) as compared with 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin. On the contrary, no singlet oxygen was detected in aqueous solutions because of strong aggregation. Light scattering and atomic force microscopy (AFM) measurements documented that the behavior of aggregates in aqueous solutions is fairly complex and depends on pH, concentration, and aging. The aggregation started from spherical particles in neutral solutions. In acidic solutions, extended aggregation occurred because of slow protonation of the porphyrin pyrrole nitrogen atoms. Both PB1 and PB4 are new representatives of nonpeptide HIV-1 protease inhibitors. Their activity increased with the increasing number of the cobalt(III) bis(1,2-dicarbollide) substituents and was characterized with the IC50 values of 290+/-44 nM for PB1 and 77+/-13 nM for PB4.