Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer

Benchmark calculations of proton affinities and gas-phase basicities of molecules most relevant to biological phosphoryl transfer reactions are presented and compared with available experimental results. The accuracy of proton affinity and gas-phase basicity results obtained from several multi-level model chemistries (CBS-QB3, G3B3, and G3MP2B3) and density-functional quantum models (PBE0, B1B95, and B3LYP) are assessed and compared. From these data, a set of empirical bond enthalpy, entropy, and free energy corrections are introduced that considerably improve the accuracy and predictive capability of the methods. These corrections are applied to the prediction of proton affinity and gas-phase basicity values of important biological phosphates and phosphoranes for which experimental data does not currently exist. Comparison is made with results from semiempirical quantum models that are commonly employed in hybrid quantum mechanical/molecular mechanical simulations. Data suggest that the design of improved semiempirical quantum models with increased accuracy for relative proton affinity values is necessary to obtain quantitative accuracy for phosphoryl transfer reactions in solution, enzymes, and ribozymes.     

The role of weakly bound on-top oxygen in the catalytic CO oxidation reaction over RuO2(110)

RuO(2)-based catalysts are much more active in the oxidation of CO than related metallic Ru catalysts. This high catalytic activity (or low activation barrier) is attributed to the weak oxygen surface bonding of bridging O atoms on RuO(2)(110) in comparison with the strongly chemisorbed oxygen on Ru(0001). Since the RuO(2)(110) surface is able to stabilize an even more weakly bound on-top oxygen species, one would anticipate that the catalytic activity will increase further under oxidizing conditions. We will show that this view is far too simple to explain our temperature-programmed reaction experiments, employing isotope labeling of the potentially active surface oxygen species on RuO(2)(110). Rather, both surface O species on RuO(2)(110) reveal similar activities in oxidizing CO.     

Soluble monolayers of n-decyl glucopyranoside and n-decyl maltopyranoside. Phase changes in the gaseous to the liquid-expanded range

To examine the transition from the gaseous to the liquid-expanded monolayer state, surface tension data were recorded for n-decyl beta-d-glucopyranoside (Glu) and n-decyl beta-d-maltopyranoside (Mal) solutions at low concentrations and at different temperatures. Comparisons were also made with n-decyl beta-d-thiomaltopyranoside (S-Mal) solutions at room temperature. The transitions observed occur at very low concentrations and surface pressures, about 0.5% of the critical micelle concentration (cmc) and between 0.8 and 1 mN/m for Glu and Mal at 22 degrees C. For S-Mal the transition is recorded for a concentration of 0.5% of the cmc as well, but the surface pressure is lower, about 0.4 mN/m. The gradual change in molecular area about the transition is from about 500 to 200 A(2) and 400 to 150 A(2) for Mal and Glu, respectively, and from about 800 to 250 A(2) for S-Mal. The comparatively large molecular areas after the transitions are incompatible with the notion that a coherent hydrocarbon film would cover the entire surface already at this stage. Standard surface thermodynamics was applied to elucidate the nature of these transitions in combination with two model concepts: The formation of an infinite network of surfactant molecules and, second, the formation of surface micelles. Hard-disk simulation results were employed to quantify the additional surface pressure after the transition attributed to the formation of surface micelles. In conclusion the formation of surface micelles is plausible as the hard-disk model is capable of accounting for the additional surface pressure increase with acceptable accuracy. Further, vibrational sum frequency spectroscopy was used to investigate the transition for Mal. Using the distinct feature of the non-hydrogen-bonded OH ("free OH") at 3700 cm(-)(1) for probing the surface water state, it could be determined that the surface holds a sizable fraction of unperturbed surface water even after the transition from the Henry range. The decrease in the free OH signal was found to correlate with the increase in surface density of surface micelles.     

Protein resistance of titanium oxide surfaces modified by biologically inspired mPEG-DOPA

In the present study, we have utilized X-ray photoelectron spectroscopy (XPS), spectroscopic ellipsometry (ELM), and optical waveguide lightmode spectroscopy (OWLS) to examine the surface adsorption and protein resistance behavior of bio-inspired polymers consisting of poly(ethylene glycol) (PEG) conjugated to peptide mimics of mussel adhesive proteins. Peptides containing up to three residues of 3,4-dihydroxyphenylalanine (DOPA), a key component of mussel adhesive proteins, were conjugated to monomethoxy-terminated PEG polymers. These mPEG-DOPA polymers were found to be highly adhesive to TiO2 surfaces, with quantitative XPS analysis providing useful insight into the binding mechanism. Additionally, the antifouling properties of immobilized PEG were reflected in the excellent resistance of mPEG-DOPA-modified TiO2 surfaces to protein adsorption. Measurements of mPEG-DOPA and human serum adsorption were related in terms of ethylene glycol (EG) surface density and serum mass adsorbed and demonstrated a threshold of approximately 15-20 EG/nm2, above which substantially little protein adsorbs. With respect to surface density of adsorbed PEG and the associated nonfouling behavior of the adlayers, strong parallels exist between the nonfouling properties of the surface-bound mPEG-DOPA polymers and PEG polymers immobilized to surfaces using other approaches. Peptide anchors containing three DOPA residues resulted in PEG surface densities higher than those achieved using several existing PEG immobilization strategies, suggesting that peptide mimics of mussel adhesive proteins may be useful for achieving high densities of protein-resistant polymers on surfaces.     

Radical substitution with azide: TMSN3-PhI(OAc)2 as a substitute of IN3

TMSN3 and PhI(OAc)2 were found to promote high-yield azide substitution of ethers, aldehydes and benzal acetals. The reaction is fast and occurs at zero to ambient temperature in acetonitrile. However, it is essential for the reaction that TMSN3 is added subsequent to the mixture of PhI(OAc)2 and the substrate. A primary deuterium kinetic isotope effect was found for the azidonation of benzyl ethers both with TMSN3-PhI(OAc)2 and with IN3. Also a Hammett free energy relationship study of this reaction showed good correlation with sigma+ constants giving with rho-values of -0.47 for TMSN3-PhI(OAc)2 and -0.39 for IN3. On this basis a radical mechanism of the reaction was proposed.     

Calculation of free energy through successive umbrella sampling

We consider an implementation of umbrella sampling in which the pertinent range of states is subdivided into small windows that are sampled consecutively and linked together. This allows us to simulate without a weight function or to extrapolate the results to the neighboring window in order to estimate a weight function. Additionally, we present a detailed error analysis in which we demonstrate that the error in umbrella sampling is controlled and, in the absence of sampling difficulties, independent of the window sizes. In this case, the efficiency of our implementation is comparable to a multicanonical simulation with a very good weight function, which in our scheme does not need to be known ahead of time. The analysis also allows us to detect sampling difficulties such as correlations between adjacent windows and provides a test of equilibration. We exemplify the scheme by simulating the liquid-vapor coexistence in a Lennard-Jones system.     

A study of the acylation of 4-hydroxy-6-methyl-2-pyrone and 4 hy(lroxy-6-phenyl-2-pyrone

The acylation of 4-hydroxy-6-melhyl-2-pyrone (1) and 4-hydroxy-6-phenyl-2-pyrone (XXII) with aliphatic acid anhydrides, or with aliphatic acid chlorides in trifluoroacetic acid, has been found to product; first the corresponding ester, which then rearranges, partially or wholly, depending on the conditions and on the nature of the acyl moiety, to form the corresponding 3-acylpyrone. With aromatic acid chlorides in pyridine or in trichloroacetic acid only the corresponding ester was obtained. These esters, however, could be rearranged to the corresponding 3-acylpyrones with aluminum chloride. Acetoaeetylation of 1 and 4-hydroxycoumarin (XXIX) with diketene gave, in both cases, the C-acetoacetylated product.     

Tandem catalysis and self-assembly: a one-pot approach to functionalized polymers

[reaction: see text] Side-chain functionalized polymers possessing terminal palladated SCS pincer complexes at each repeat unit were synthesized via ring-opening metathesis polymerization. These palladium centers function as both well-defined Heck catalysts and recognition units capable of quantitative self-assembly of pyridine-containing molecules. Exploitation of both the catalytic and self-assembly properties has led to the development of a controlled, one-pot tandem catalysis/self-assembly sequence for the synthesis of functionalized polymers.     

Synthese und Kristallstruktur eines μ-Methylen-μ-hydrido-dialanats [R2Al(μ-CH2)(μ-H)AlR2]− (R = CH(SiMe3)2)

Synthesis and Crystal Structure of a μ-Methylene-μ-hydrido-dialanate [R₂Al(μ-CH₂)(μ-H)AlR₂]^? (R = CH(SiMe₃)₂) tert-Butyl lithium reacts with the recently synthesized methylene bridged dialuminium compound [(Me₃Si)₂CH]₂Al? CH₂? Al[CH(SiMe₃)₂]₂ 2 in the presence of TMEDA under β-elimination; the thereby formed hydride anion is bound in a chelating manner by both unsaturated aluminium atoms forming a 3c–2e–Al? H? Al bond. The crystal structure of the product shows two independent molecules differing only slightly in bond lengths and angles, but significantly in conformation. While one of the Al₂CH heterocycles deviates little from planarity with a rough C₂ symmetry for the whole anion, the other one is folded with an angle of 21.1° and the arrangement of the substituents is best described by C_s symmetry.     

RESONANCE FLUORESCENCE IN CHLOROPHYLL a SOLUTIONS

Abstract— Chlorophyll a in aqueous hexane solutions has two fluorescence peaks, two fluorescence excitation peaks in the blue, and two fluorescence excitation peaks in the red. One of these set of peaks (excitation 2.34_μ^-1 and 1.52_μ-1, fluorescence 1–50_μ^-1) is identical with those found in methanol solutions of chlorophyll a and is assigned to an unaggregated species, while the other set of peaks (excitation 2.44_μ-1 and 1.475_μ^-l, fluorescence 1.48_μ^-l) is assigned to a species aggregated in the presence of water. The spectral shifts occurring in the aggregate follow the selection rules obtained by McRae and Kasha for a linear stack of parallel dye molecules. The sharply increased overlap of absorption and fluorescence leads to resonance fluorescence in the aggregate. The resonance fluorescence is demonstrated experimentally.