Quantitative surface characterization using X-ray photoelectron spectroscopy

Use of X-ray Photoelectron Spectroscopy (XPS) for quantitative surface analysis is reviewed. Examples chosen are from our research on heterogeneous catalysts. XPS is useful for measuring distributions of oxidation states because of significant chemical shifts for many elements. However, linewidths complicate analysis of mixtures, necessitating the use of data analysis methodology. Use of factor analysis or deconvolution with non-linear least squares curve fitting gives useful protocols. Five important questions are posed, and some examples of solutions are presented: 1) How many components are present? 2) Where are they located? 3) What do they look like? 4) How much of each component is present? 5) How good is the answer?     

Acidities in cyclohexanediols enhanced by intramolecular hydrogen bonds

Equilibrium gas-phase acidities of the six isomeric cyclohexanediols were measured in a Fourier transform ion cyclotron resonance mass spectrometer. Although all six cyclohexanediols have the same functional groups and similar structures, the acidities vary over 11 kcal/mol. This large difference is due mostly to the balance between hydrogen bonding and geometric strain. To understand the origins of the acidity differences in more detail, the conformations and energetics of the cyclohexanediols were studied using density functional theory, which gave good agreement with the experimental acidities. Finally, methanol-methoxide and methanol-methanol interactions were used as a model for the hydrogen bonding.     

Two unusual, competitive mechanisms for (2-ethynylphenyl)triazene cyclization: pseudocoarctate versus pericyclic reactivity

The cyclization of (2-ethynylphenyl)triazenes in ODCB at 200 degrees C gives exclusively cinnolines, whereas addition of CuCl to 1,2-dichloroethane solutions of the triazenes at 50 degrees C results in the sole formation of isoindazoles. DFT calculations and deuterium labeling studies suggest the intermediacy of a 3-dehydrocinnolinium ion, produced through a pericyclic transition state. Calculations and trapping studies strongly implicate a carbene intermediate in isoindazole formation, which proceeds through a pseudocoarctate transition state.     

Metal salt catalyzed carbenoid—XIII: On the mechanisms of cyclopropanation and allylic CH insertions by diazo esters in the presence of olefins and homogeneous copper catalysts

Evidence is presented demonstrating the existence of two paths to the title processes which arise from a common intermediate. A rationale involving catalyzed addition of the diazo compound to the olefin and carbenoid addition to the olefin is proposed. The penultimate intermediate has one new CC bond formed. It is partitioned between products by forming the second CC bond or formation of a hydrocarbenoid allyl complex which collapses to the allylic CH insertion products. Cyclopropanation occurs stereospecifically. The proposed mechanism accounts for the stereospecificity of cyclopropanation, the variance of syn/anti ratios with catalyst concentration when diazoacetic ester is employed and optical inductions with chiral catalysts. The question of whether the alleged carbenoid and/or the penultimate intermediate contain N₂ is not answered although it is felt that a cupro-cyclobutane intermediate is the most probable intermediate before product partitioning.     

Kinetic study of anhydride formation during thermal degradation of isotactic and atactic polymethacrylic acid

A kinetic study of anhydride formation in isotactic and atactic polymethacrylic acids (PMA) has been performed at about 200° using a vacuum thermobalance. The results obey first order kinetics and show that the rate of water loss is about four times higher for the isotactic PMA than for the atactic isomer. The activation energies are almost identical (42 ± 1 kcal per mole); it is concluded that the arrangement of neighbouring carboxyl groups is more favourable for the formation of a cyclic anhydride by intramolecular reaction in the case of the isotactic PMA.     

Mass spectral study of ring E of taraxasterol and compounds with similar ring substitution

The origin of the [M–69]⁺ and [M–111]⁺ signals in the mass spectrum of taraxasterol was studied through the use of C(18), (19), (21), (22) and/or (30) deuteriated derivatives. The generality of these signals for ring systems with an exocyclic methylene group and a methyl moiety on an adjacent carbon was verified with 2-methylmethylenecyclohexane, 1-methyl-2-methylene-trans-decalin, 1,10-dimethyl-2-methylene-trans-decalin and some of their deuteriated derivatives. The most plausible mechanism for the formation of the [M–69]⁺ ion appears to involve cleavage of both bonds allylic to the exocyclic methylene group with a 1,3-hydrogen transfer from the adjacent ring. Genesis of the [M–111]⁺ ion is more complicated but a five-membered allylic ion generated from ring D is proposed.     

Proton and deuteron position preferences in water clusters: an ab initio study

In order to explore the effect of H-to-D substitution on the zero-point energy (ZPE) of water clusters, Hessians were computed for a database of 53 optimized (H2O)n clusters, 5 < or = n < or = 21, at the B3LYP6-311 + + G** level. The 53 clusters contained 1524 protons, which were sorted into 18 categories according to the type of their donor O and (if not free) acceptor O. Letting deltaZPE[H]* denote the change in ZPE when the proton H* is replaced by D, mean values for deltaZPE[H*] for the H-bonded categories ranged from -2172 cal mol(-1) for H* in a DDAA-DDAA bond to -2118 for H* in a DAA-DDA bond. Mean value for H* free on DAA (respectively, DA) was -2018 (respectively, -1969). For DAA-DDA bonds, and for short H bonds in general, there was a strong inverse correlation between /deltaZPE[H*]/ and the O-H* distance. deltaZPE for multiple H-to-D substitutions was additive, except for a cooperativity effect of -13.7 to -19.7 cal mol(-1) when two substituted protons were in the same H2O unit and a much smaller cooperativity when one proton's donor was the other's acceptor. Implications of these data include a relative preference for D to occupy H bonded rather than free positions in finite water clusters, a value of 3.82 for the disproportionation equilibrium constant of mixed ice at 150 K, increased occupation by H at surface positions of mixed ice, and a larger average coordination number for liquid D2O than for liquid H2O.     

THE USE OF TETRAZOLIUM SALTS TO DETERMINE SITES OF DAMAGE TO THE MITOCHONDRIAL ELECTRON TRANSPORT CHAIN IN INTACT CELLS FOLLOWING in vitro: PHOTODYNAMIC THERAPY WITH PHOTOFRIN II

Abstract: A method is described utilizing the tetrazolium salts neotetrazolium chloride (NTC), triphenyltetrazolium chloride (TTC), C, N -diphenyl- N' -4,5-dimethylthiazol-2-yrtetrazolium bromide (MTT) and various substrates to elucidate damage to the mitochondrial electron transport chain of intact cells following in vitro photodynamic therapy (PDT). Using this methodology, a portion of the dark toxicity manifested by Photofrin II (PII) was found to occur prior to entry of electrons into the transport chain through Complex I, as evidenced by the fact that the inhibition of MTT reduction was reversible by the addition of malic acid to the culture media. A second site of dark toxicity was found to be Complex IV (cytochrome oxidase). After photoirradiation of the cells, Complex I was found to be affected since malic acid could no longer reverse the inhibition of MTT reduction but it could be reversed by the addition of succinic acid, whose electrons enter the transport chain at Complex II. A second and more sensitive site of photoirradiation damage was found to be Complex IV. A region near cytochrome C was also affected by photoirradiation but appreciably less so than noted for Complexes I and IV. A kinetic analysis of MTT and TTC reduction following photoirradiation indicated that MTT reduction was sustained at a normal rate for 1 h after which it slowed down and eventually plateaued. In contrast, TTC reduction was found to be inhibited almost immediately indicating Complex IV is extremely susceptible to photoirradiation damage. Compared to other assays of mitochondrial function requiring subcellular fractionation, the use of tetrazolium salts is simpler to perform and can be done using physiologically relevant conditions.     

Hyper-Rayleigh scattering spectrum of liquid nitromethane

The vertical vertical (VV), horizontal vertical (HV), and vertical horizontal (VH) hyper-Rayleigh scattering (HRS) spectra were measured for liquid CH3NO2 at T= 300 K. The main HRS spectral component has a width upsilon1=1.28 +/- 0.04 cm(-1), which gives an orientation relaxation time pi=4.1 +/- 0.1 ps in good agreement with other experiments. However, the VH spectrum also contains a previously unobserved strong narrow peak at zero-frequency shift, absent from the VV and HV spectra, which is due to a slowly relaxing longitudinal orientation mode. The upper bound on the width of this peak is 5 MHz, which corresponds to a relaxation time pi > 30 ns.     

Eutectic phase polymerization of activated ribonucleotide mixtures yields quasi-equimolar incorporation of purine and pyrimidine nucleobases

The RNA world hypothesis requires a plausible mechanism by which RNA itself (or precursor RNA-like polymers) can be synthesized nonenzymatically from the corresponding building blocks. Simulation experiments have exploited chemically reactive mononucleotides as monomers. Solutions of such monomers in the prebiotic environment were likely to be very dilute, but in experimental simulations of polymerization reactions dilute solutions of activated mononucleotides in the millimolar range hydrolyze extensively, and only trace amounts of dimers and trimers are formed. We report here that random medium-size RNA analogues with mixed sequences (5- to 17-mers with traces of longer products) can be synthesized in ice eutectic phases that are produced when dilute solutions of activated monomers and catalysts (Mg(II) and Pb(II)) are frozen and maintained at -18 degrees C for periods up to 38 days. Under these conditions, the monomers are concentrated as eutectics in an ice matrix. Hydrolysis of the activated mononucleotides was suppressed at low-temperature ranges, and polymerization was enhanced with yields up to 90%. Analysis of the mixed oligomers established that incorporation of both purine and pyrimidine bases proceeded at comparable rates and yields. These results suggest that ice deposits on the early Earth could have facilitated the synthesis of short- and medium-size random sequence RNA analogues and thereby provided a microenvironment suitable for the formation of biopolymers or their precursors.