TPD, HREELS and UPS study of the adsorption and reaction of methyl nitrite (CH3ONO) on Pt(111)

The adsorption and reaction of methyl nitrite (CH₃ONO, CD₃ONO) on Pt(111) was studied using HREELS, UPS, TPD, AES, and LEED. Adsorption of methyl nitrite on Pt(111) at 105 K forms a chemisorbed monolayer with a coverage of 0.25 ML, a physisorbed second layer with the same coverage that desorbs at 134 K, and a condensed multilayer that desorbs at 117 K. The Pt(111) surface is very reactive towards chemisorbed methyl nitrite; adsorption in the monolayer is completely irreversible. CH₃ONO dissociates to form NO and an intermediate which subsequently decomposes to yield CO and H₂ at low coverages and methanol for CH₃ONO coverages above one-half monolayer. We propose that a methoxy intermediate is formed. At least some C–O bond breaking occurs during decomposition to leave carbon on the surface after TPD. UPS and HREELS show that some methyl nitrite decomposition occurs below 110 K and all of the methyl nitrite in the monolayer is decomposed by 165 K. Intermediates from methyl nitrite decomposition are also relatively unstable on the Pt(111) surface since coadsorbed NO, CO and H are formed below 225 K.     

Synthesis and optical characterization of c-axis oriented GaN thin films on amorphous quartz glass via sol–gel process

c-Axis oriented GaN nanocrystalline thin films were fabricated by nitridation of three different thin films of -GaO(OH), -Ga₂O₃ or β-Ga₂O₃ obtained by sol–gel technique on amorphous quartz glass substrates. All these GaN thin films showed near band edge emission at 390 nm and yellow luminescence at 570 nm. The crystalline nature and c-axis orientation as well as luminescence properties of the GaN thin films increased by several times by using a buffer layer of GaN on the substrate.     

Mass Spectrometric Distinction of In-Source and In-Solution Pyroglutamate and Succinimide in Proteins: A Case Study on rhG-CSF

Formation of cyclic intermediates involving water or ammonia loss is a common occurrence in any reaction involving terminal amines or hydroxyl group containing species. Proteins that have both these functional groups in abundance are no exception, and presence of amino acids such as asparagine, glutamines, aspartic acids, and glutamic acids aid in formation of such intermediates. In the biopharma scenario, such intermediates lead to product- or process-related impurities that might be immunogenic. Mass spectroscopy is a powerful technique that is used to decipher the presence and physicochemical characteristics of such impurities. However, such intermediates can also form in situ during mass spectrometric analysis. We present here the detection of in-source and in-solution formation of succinimide and pyroglutamate in the protein granulocyte colony stimulating factor. We also propose an approach for quick differentiation of such in-situ species from the tangible impurities. We believe that this will not only reduce the time spent in unambiguous identification of succinimide- and/or pyroglutamate-related impurity in bio-pharmaceutics but also provide a platform for similar studies on other impurities that may form due to stabilized intermediates.      

IR Probes of Protein Microenvironments: Utility and Potential for Perturbation

A variety of IR‐active moieties with absorptions that are distinct from those of proteins have been developed as probes of local protein environments, including carbon‐deuterium bonds (C?D), cyano groups (CN), and azides (N₃); however, no systematic analysis of their utility in a protein has been published. Previously, we characterized the N‐terminal Src homology 3 domain of the murine adapter protein Crk‐II (nSH3) with C?D bonds site‐selectively incorporated throughout, and showed that it is relatively rigid and electrostatically heterogeneous and that it thermally unfolds under equilibrium conditions via a simple two‐state mechanism. We now report the synthesis and characterization of eight variants of nSH3 with CN and/or N₃ probes at five of the same positions. In agreement with previous studies, the position‐dependent spectra suggest that both probes are predominantly sensitive to hydration, and not to their local electrostatic environments. Importantly, both probes also tend to significantly perturb the protein if they are not incorporated at surface‐exposed positions. Thus, unlike C?D labels, which are both sensitive to their environment and non‐perturbative, CN and N₃ probes should be used with caution.     

Site‐Specifically Arraying Small Molecules or Proteins on DNA Using An Expanded Genetic Alphabet

A class of replicable unnatural DNA base pairs formed between d 5SICS and either d MMO2 , d DMO , or d NaM were developed. To explore the use of these pairs to produce site‐specifically labeled DNA, the synthesis of a variety of derivatives bearing propynyl groups, an analysis of their polymerase‐mediated replication, and subsequent site‐specific modification of the amplified DNA by Click chemistry is reported. With the d 5SICS scaffold a propynyl ether linker is accommodated better than its aliphatic analogue, but not as well as the protected propargyl amine linker explored previously. It was also found that with the d MMO2 and d DMO analogues, the d MMO2 position para to the glycosidic linkage is best suited for linker attachment and that although aliphatic and ether‐based linkers are similarly accommodated, the direct attachment of an ethynyl group to the nucleobase core is most well tolerated. To demonstrate the utility of these analogues, a variety of them were used to site‐selectively attach a biotin tag to the amplified DNA. Finally, we use d 5SICS^CO –d NaM to couple one or two proteins to amplified DNA, with the double labeled product visualized by atomic force microscopy. The ability to encode the spatial relationships of arrayed molecules in PCR amplifiable DNA should have important applications, ranging from SELEX with functionalities not naturally present in DNA to the production, and perhaps “evolution” of nanomaterials.     

A temperature programmed desorption study of the reaction of methylacetylene on Pt(111) and Sn/Pt(111) surface alloys

The adsorption and reaction of methylacetylene (H₃CC≡CH) on Pt(111) and the p(2×2) and

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surface alloys were investigated with temperature programmed desorption, Auger electron spectroscopy and low energy electron diffraction. Hydrogenation of methylacetylene to form propylene is the most favored reaction pathway on all three surfaces accounting for ca 20% of the adsorbed monolayer. Addition of Sn to the Pt(111) surface to form these two ordered surface alloys suppresses the decomposition of methylacetylene to surface carbon. The alloy surfaces also greatly increase the amount of reversibly adsorbed methylacetylene, from none on Pt(111) to 60% of the adsorbed layer on the

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surface alloy. Methylacetylene reaction also leads to a small amount of desorption of benzene, along with butane, butene, isobutylene and ethylene. There is some difference in the yield of these other reaction products depending the Sn concentration, with the (2×2)-Sn/Pt(111) surface alloy having the highest selectivity for these. Despite previous experiments showing cyclotrimerization of acetylene to form benzene on the Pt–Sn surface alloys, the analogous reaction of methylacetylene on the alloy surfaces was not observed, that is, cyclotrimerization of methylacetylene to form trimethylbenzene. It is proposed that this and the high yield of propylene is due to facile dehydrogenation of methylacetylene because of the relatively weak H–CH₂CCH bond compared to acetylene. The desorption of several C₄ hydrocarbon products at low (<170 K) temperature indicates that some minor pathway involving C–C bond breaking is possible on these surfaces.     

Quenching of nucleotide-derived radicals by bis benzimidazole derivative Hoechst-33258 in aqueous solution

The pulse radiolysis technique has been employed to investigate the reaction of DNA-minor-groove ligand bisbenzimidazole Hoechst 33258 with pyrimidine and purine nucleotide-derived radicals. Formation of an N-centred Hoechst-33258 radical is observed. Bimolecular rate constants and the yields of Hoechst-33258 radical have been evaluated. While the rate constant for the reaction of pyrimidine-derived radicals with Hoechst-33258 remained the same (1–2) × 10⁹ dm³ mol⁻¹ s⁻¹, the yields of the Hoechst-33258 radical varied from 25% (5′-cytidine monophosphate) to 75% (5′-guanosine monophosphate) under anoxic conditions. The rate constant values for the reaction of purine-derived radicals with Hoechst-33258, under oxic and anoxic conditions, remained the same whereas with pyrimidine-derived radicals, the rate constant value under oxic conditions was about two orders of magnitude lower than under anoxic conditions. The difference in the yields of Hoechst-33258 radical with various nucleotide-derived radicals suggest the formation of different types of radicals and that the reaction mainly occurs by electron transfer from Hoechst-33258 to the nucleotide radicals.     

A nitrate bridged one-dimensional copper(II) coordination polymer with a tridentate (NNO) Schiff base: synthesis,X-ray structure and catalytic efficacy

Transition Metal Chemistry - A one-dimensional Cu(II) coordination polymer of [Cu(L)(μ-ONO2)]n (1) (HL = 4-methoxy-2-[1-(methylaminoethylimino)methyl]-phenol) with bidentate...