Note on the application of the reduced graph model in conjunction with search trees to the enumeration ofKekulé structures

The reduced graph model, when used in conjunction with the search trees method, provides a novel combinatorial procedure for the enumeration and generation ofKekulé structures. The procedure is suited for large benzenoid hydrocarbons consisting of cata- and thin peri-condensed parts.

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Zur Anwendung des Reduced Graph Model im Zusammenhang mit Search Trees zur Ermittlung der Anzahl möglicherKekulé-Strukturen

Zusammenfassung Das Modell erlaubt mit der im Titel genannten Kombination eine neuartige Methode zur Ermittlung und Generierung vonKekulé-Strukturen. Das Verfahren ist für große benzoide Kohlenwasserstoffe geeignet, die aus cata- und (dünnen) peri-kondensierten Teilstrukturen bestehen.

     

Secondary kinetic isotope effects: Deuterium abstraction by chlorine atoms from the CD3 group in CD3CH2Cl,CD3CHDCl,and CD3CD2Cl

The occurrence and magnitude of secondary kinetic isotope effects in the gas phase has been determined for deuterium abstraction from the CD₃ group in CD₃CH₂Cl, CD₃CHDCl, and CD₃CD₂Cl by photochemically generated ground-state chlorine atoms. Over the temperature range 10–94°C a discernible “inverse” kinetic isotope effect is observed. Both the pre-exponential factors and activation energies decrease with deuterium substitution in the vicinal chloromethyl group. The opposing trends result in a net effect close to unity.     

Discrimination between peptide 3(10)- and alpha-helices. Theoretical analysis of the impact of alpha-methyl substitution on experimental spectra

Detailed spectral simulations based on ab initio density functional theory computations of the amide I and II infrared (IR) and vibrational circular dichroism (VCD) spectra for Ac-(Ala)(4)-NH(2), Ac-(Aib-Ala)(2)-NH(2), and Ac-(Aib)(4)-NH(2) constrained to 3(10)- and alpha-helical conformations are presented. Parameters from these ab initio calculations are transferred onto corresponding larger oligopeptides to simulate the spectra for dodecamers. The differences between conformations and for different Aib substitution patterns within a conformation are reflected in observable spectral patterns where data are available. Simulated IR spectra show small frequency shifts in the amide I maxima between 3(10)- and alpha-helices, but the same magnitude shifts occur within one conformation upon Aib substitution. Thus, from a computational basis, the frequency of the amide I maximum does not discriminate between the 3(10)- or alpha-helical conformations. Calculated VCD band shapes for 3(10)-helices showed more significant changes in amplitude, with change in the fraction of Aib, than those for alpha-helices. Generally, with increasing Aib content, the overall amide I VCD intensity becomes weaker and the amide I couplet becomes more conservative, while the amide II VCD is less affected. Although the detailed band shape is shown to be sensitive to alpha-Me substitution, the basic pattern of amide I and II relative VCD intensities still differs between alpha- and 3(10)-helices and, as a consequence, successfully discriminates between them. These predictions are all borne out in experimental spectra of Aib, mixed Aib-Ala, and Ala-based helical peptides, where available.     

Amperometric urea biosensor based on urease and electropolymerized toluidine blue dye as a pH-sensitive redox probe

The electropolymerized toluidine blue film deposited on the glassy carbon electrode show amperometrically detectable pH sensitivity. This feature of polytoluidine blue (PTOB) film was used for a construction of an amperometric urea biosensor. We have observed a linear shift of the formal redox potential with increasing pH value between 4 and 8 giving the slope of 81 mV(Delta) pH(-1). Polytoluidine blue film has had a significantly increased stability and higher electrochemical activity compared to the adsorbed monomeric dye. The polytoluidine blue urea biosensor has been operating at a working potential of -200 mV vs. SCE. The sensitivity of the biosensor was 980 nA mM(-1) cm(-2). The biosensor showed linearity in concentration range up to 0.8 mM with the detection limit of 0.02 mM (S/N=3).     

Group ib organometallic chemistry : XXXIV. Thermal behaviour and chemical reactivity of tetranuclear Me2N-substituted diarypropenylcopper-copper anion (Vi2Cu4X2) and mixed diarylpropenyl/organocopper (Vi2Cu4R2) compounds

Thermal decomposition of configurationally pure 1,2-diarylpropenylcopper compounds Z-Vi₂CU₄Br₂ and Z-Vi₂Cu₄R₂ [Vi  (2-Me₂NC₆H₄)CC(Me)-(C₆H₄Me-4), R  2-Me₂NC₆H₄ or 4-MeC₆H₄CC] predominantly results in the formation of ViH. In contrast, only dimers (ViVi) were formed on thermolysis of (Z-ViCu₂OTf)_η which is a further illustration of the influence of the counter anion on the reactivity of organocopper cluster compounds. However, in both cases partial inversion of configuration, giving mixtures of isomers, was observed. The thermolysis of (Z-ViCu₂OTf)_η is discussed in terms of OTf-enhanced intraaggregate electron-transfer processes. The formation of incipient vinyl cations which are η²-coordinated to the copper cluster can explain the observed isomerization.Also in the hydrolysis reaction of Z-Vi₂Cu₄Br₂ mixtures of isomeric ViH compounds were obtained, the E/Z ratio being dependent on the type of reagent used. Mixtures of isomeric ViX compounds (X  Br, Cl, I) were formed in the reaction of Z-Vi₂Cu₄Br₂ with I₂ and CuCl₂. An explanation for the occurrence of isomerization is presented.Dimers (ViVi) were almost absent in the product mixture resulting from the reaction of Z-Vi₂Cu₄Br₂ with CuCl₂. In contrast, ViVi is obtained in about 50% yield from the reaction of ViLi with CuCl₂ which is in accord with earlier observations for the reaction of aryllithium compounds with cupric halides.Highly selective E-ViBr formation was observed in the reaction of E-ViLi with AgBr. This reaction probably proceeds via a thermally unstable Z-ViAg₂Br intermediate.     

Transfection mediated by gemini surfactants: engineered escape from the endosomal compartment

The structure of the lipoplex formed from DNA and the sugar-based cationic gemini surfactant 1, which exhibits excellent transfection efficiency, has been investigated in the pH range 8.8-3.0 utilizing small-angle X-ray scattering (SAXS) and cryo-electron microscopy (cryo-TEM). Uniquely, three well-defined morphologies of the lipoplex were observed upon gradual acidification: a lamellar phase, a condensed lamellar phase, and an inverted hexagonal (H(II)) columnar phase. Using molecular modeling, we link the observed lipoplex morphologies and physical behavior to specific structural features in the individual surfactant, illuminating key factors in future surfactant design, viz., a spacer of six methylene groups, the presence of two nitrogens that can be protonated in the physiological pH range, two unsaturated alkyl tails, and hydrophilic sugar headgroups. Assuming that the mechanism of transfection by synthetic cationic surfactants involves endocytosis, we contend that the efficacy of gemini surfactant 1 as a gene delivery vehicle can be explained by the unprecedented observation of a pH-induced formation of the inverted hexagonal phase of the lipoplex in the endosomal pH range. This change in morphology leads to destabilization of the endosome through fusion of the lipoplex with the endosomal wall, resulting in release of DNA into the cytoplasm.     

Dissociative recombination of the weakly bound NO-dimer cation: cross sections and three-body dynamics

Dissociative recombination (DR) of the dimer ion (NO)(2) (+) has been studied at the heavy-ion storage ring CRYRING at the Manne Siegbahn Laboratory, Stockholm. The experiments were aimed at determining details on the strongly enhanced thermal rate coefficient for the dimer, interpreting the dissociation dynamics of the dimer ion, and studying the degree of similarity to the behavior in the monomer. The DR rate reveals that the very large efficiency of the dimer rate with respect to the monomer is limited to electron energies below 0.2 eV. The fragmentation products reveal that the breakup into the three-body channel NO+O+N dominates with a probability of 0.69+/-0.02. The second most important channel yields NO+NO fragments with a probability of 0.23+/-0.03. Furthermore, the dominant three-body breakup yields electronic and vibrational ground-state products, NO(upsilon=0)+N((4)S)+O((3)P), in about 45% of the cases. The internal product-state distribution of the NO fragment shows a similarity with the product-state distribution as predicted by the Franck-Condon overlap between a NO moiety of the dimer ion and a free NO. The dissociation dynamics seem to be independent of the NO internal energy. Finally, the dissociation dynamics reveal a correlation between the kinetic energy of the NO fragment and the degree of conservation of linear momentum between the O and N product atoms. The observations support a mechanism in which the recoil takes place along one of the NO bonds in the dimer.     

The fluorescence quenching rate constant for the distance-dependent quenching processes in the presence of diffusion

It is shown that the fluorescence quenching constant is given by the Laplace transform of the time-dependent bimolecular rate constant k(t). The dependence of the quenching rate constant on the transformation parameter can be obtained from measurements of the fluorescence decay functions and a Stern-Volmer-type analysis in the Laplace domain. The advantages of this type of investigation of the quenching rate function are demonstrated by a numerical calculation for the distance-dependentquenching process in     

Quantitative analysis of the farnesyl transferase inhibitor lonafarnib (Sarasartrade mark, SCH66336) in human plasma using high-performance liquid chromatography coupled with tandem mass spectrometry

Lonafarnib is a novel anticancer drug that inhibits farnesyl transferase. To assess its pharmacokinetic properties, we developed a sensitive and quantitative assay using liquid chromatography coupled with tandem mass spectrometry for the determination of lonafarnib levels in human plasma. Sample pretreatment consisted of the addition of an isotopically labeled internal standard and protein precipitation with acetonitrile using 100 microL plasma. Chromatographic separation was performed on an Inertsil ODS-3 analytical column (50 x 2.1 mm i.d., particle size 5 microm) with acetonitrile/water/formic acid (50:50:0.05, v/v/v) as the mobile phase, at a flow rate of 0.2 mL/min. The analytical run time was 8 min. An API365 triple quadrupole mass spectrometer was used for specific and sensitive detection. It was operated in the positive ion mode and multiple reaction monitoring was used for drug quantification. The method was validated using a concentration range of 2.5 to 2500 ng/mL lonafarnib. Validation of the assay was performed according to the most recent FDA guidelines for bioanalytical method validation and all results were within the requirements. The described method was successfully applied to support a clinical phase I trial with lonafarnib.