Molecularly defined (L)‐lactic acid oligomers and polymers: Synthesis and characterization

The synthesis of (L )‐lactide oligomers from dimer to 64mer via an exponential growth strategy is described. By careful selection of orthogonal protective groups, the synthesis were conducted using a t‐butyldimethylsilyl (TBDMS) ether as the protective group of the hydroxyl group and benzyl (Bn) ester as the protective group of the carboxylic acid group. The yields of both the deprotection steps and coupling reactions using 1,3‐dicyclohexylcarbodiimide or 1‐[3‐(dimethylamino)propyl]‐3‐ethylcarbodiimide hydrochloride were high (70–100%) and the absence of a requirement for conducting the majority of reactions under an inert atmosphere permitted a robust and efficient synthetic strategy to be developed. This allowed monodisperse dimer, tetramer, octamer, 16mer, 32mer, and 64mer materials to be prepared in gram quantities and fully characterized using mass spectrometry and size exclusion chromatography. Evaluation of the thermal and physical properties using thermogravimetric analysis, differential scanning calorimetry, and small angle X‐ray scattering demonstrated a close correlation between the molecular structure of the well‐defined Poly(lactide) oligomers and their physical properties. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 5977–5990, 2008     

The elastic net algorithm and protein structure prediction

Predicting protein structures from their amino acid sequences is a problem of global optimization. Global optima (native structures) are often sought using stochastic sampling methods such as Monte Carlo or molecular dynamics, but these methods are slow. In contrast, there are fast deterministic methods that find near-optimal solutions of well-known global optimization problems such as the traveling salesman problem (TSP). But fast TSP strategies have yet to be applied to protein folding, because of fundamental differences in the two types of problems. Here, we show how protein folding can be framed in terms of the TSP, to which we apply a variation of the Durbin-Willshaw elastic net optimization strategy. We illustrate using a simple model of proteins with database-derived statistical potentials and predicted secondary structure restraints. This optimization strategy can be applied to many different models and potential functions, and can readily incorporate experimental restraint information. It is also fast; with the simple model used here, the method finds structures that are within 5-6 A all-Calpha-atom RMSD of the known native structures for 40-mers in about 8 s on a PC; 100-mers take about 20 s. The computer time tau scales as tau approximately n, where n is the number of amino acids. This method may prove to be useful for structure refinement and prediction.     

Interactions of bovine serum albumin with aluminum polyoxocations and aluminum hydroxide

Interactions of aqueous solutions of aluminum polyoxocations (Al13-mers and Al30-mers) and aluminum hydroxide suspensions of varying particle sizes (26, 55, and 82 nm) with a model protein, bovine serum albumin (BSA), have been investigated using potentiometry, conductometry, viscometry, 27Al solution NMR, UV-vis spectroscopy, dynamic light scattering, zeta-potential measurements, thermogravimetry, X-ray diffraction, and scanning electron microscopy. Increasing amounts of BSA partially convert Al13-mers and, to a larger extent, Al30-mers into amorphous Al hydroxide without gel formation. At the same time, BSA molecules can form unstable aggregates in the Al polyoxocation solutions which redisperse easily upon standing. In the case of Al hydroxide sols, BSA addition causes substantial gelation, the extent of which is proportional to the amount of BSA added and inversely related to the Al hydroxide particle size. Upon freeze-drying or centrifugation of Al species-BSA solutions, an interesting sheetlike morphology with 150-200 nm wide nanoribbons is observed for pure Al hydroxide nanoparticles and for solutions of Al polyoxocations with the highest amount of BSA studied. On the basis of the combined solution, colloidal and solid-state characterization of model Al species-BSA systems, a qualitative model of possible interactions in the Al polyoxocation-BSA and Al hydroxide-BSA systems is proposed wherein core-shell hybrid nanoparticles are formed from protein "core" and Al polyoxocation "shell" or Al hydroxide "core" and protein "shell".     

Fragmentation mechanisms of oligodeoxynucleotides: Effects of replacing phosphates with methylphosphonates and thymines with other bases in T-rich sequences

This article reports another step in an ongoing effort to understand the fragmentation of T-rich oligodeoxynucleotides. We extended an earlier investigation of T-rich 4-mers to T-rich 6-mers, 8-mers and 10-mers by using four different tandem mass spectrometric methods. The methods include low-energy collisionally activated decomposition (CAD) of electrospray ionization (ESI)-produced ions, source-CAD of ESI-produced ions, post-source decay (PSD), and CAD of matrix assisted laser desorption ionization (MALDI)-generated ions. The most abundant fragment ions produced from [M - 2H]2- precursors upon low-energy CAD in an ion trap are the [a - B]- and their complementary w ions. The predominant cleavage sites for T-rich oligodeoxynucleotides are always the 3' C-O bonds adjoining a non-T nucleobase (i.e., a base with a higher proton affinity (PA) than that of T). The relative abundance of [a - B]- correlates with the PAs of the nucleobases, underscoring the importance of proton transfer to the base. The propensity to form [a - B]- ions falls in the order of G > C approximately A > T. Structural isomers up to 10-mers can be readily sequenced and distinguished with each of the four tandem mass spectrometric methods applied. The fragmentation of oligodeoxynucleotides in which various phosphates were replaced with methylphosphonate is a measure of the participation of the phosphate proton in the formation of [a - B] ions. For 4 and 5-mers, transfer of an acidic proton from the 5'-phosphate to the departing base is the initiating step in the formation of [a - B]- ions.     

Mass spectrometry characterization of Escherichia coli K4 oligosaccharides from 2-mers to more than 20-mers

The separation and characterization of oligosaccharides obtained by hyaluronidase [E.C. 3.2.1.35] digestion of Escherichia coli K4 polysaccharide using online high-performance liquid chromatography/electrospray ionization mass spectrometry (HPLC/ESI-MS) are presented. Complete identification and structural information for oligosaccharides containing 2-24 monomers (from 2- to 24-mers) were obtained. In particular, smaller K4 species, from 2-mers to 4-mers, exhibited mainly [M-H](-1) anions, whereas the 6- to 8-mers existed predominantly at the charge state of -2. The K4 oligomers from 10-mers to 14-mers were mainly represented by [M-3H](-3) anions while species from 16- to 20-mers were characterized by a charge state of -4. K4 oligosaccharides from 22- to 24-mers existed as [M-4H](-4) and [M-5H](-5) anions and, for this latter species, ions having a charge state of -6 appeared. For smaller K4 species, in particular from 6-mers to 10-mers, ESI-MS revealed anions related to the loss of one monosaccharide unit from the oligomers due to apparent collisional activation and ion source fragmentation. However, no odd-numbered anions were produced for K4 2/4-mer species or for oligosaccharides greater than 12-mers, while for K4 species 8/10-mer, ESI-MS revealed odd-numbered anions generally in low relative abundance making the interpretation of the spectra easier. The ESI-MS spectra of oligosaccharides separated by online HPLC were applied to the evaluation of the K4 polymerization process, confirming that the addition of fructose units is not critical for chain elongation as variously fructosylated oligomer species were detected directly on the K4 carbohydrate backbone.     

Fluorous affinity purification of oligonucleotides

[structure: see text] Nucleoside phosphoramidites bearing a fluorous dimethoxytrityl (FDMT) group were used to synthesize fluorous-tagged oligonucleotides, which were subjected to solid-phase extraction using a pH-stable fluorinated adsorbent. On-column detritylation afforded the purified oligonucleotides. The fluorous affinity purification method offers one-pass loading without ammonia removal, high selectivity for the removal of failure sequences, high recoveries (typically 70-100%), and the ability to purify long oligonucleotides (e.g., 50-100-mers).     

Liquid triarylamines: the scope and limitations of Piers-Rubinsztajn conditions for obtaining triarylamine-siloxane hybrid materials

New liquid triarylamine-siloxane hybrid materials are produced using the Piers-Rubinsztajn reaction. Under mild conditions, liquid analogues of conventional and commonly crystalline triarylamines are easily synthesized from readily available or accessible intermediates. Using a diverse selection of triarylamines, we explored the effects of siloxane group and substitution pattern on the physical properties of these materials, and we have demonstrated that relatively large molecular liquids with desirable electrochemical properties can be produced. The interactions between the strongly Lewis acidic catalyst used for this transformation, tris(pentafluorophenyl)borane (BCF), and the Lewis basic triarylamine substrates were studied. Through UV-vis-NIR and (19)F NMR spectroscopy, we have proposed that the catalyst undergoes a reversible redox reaction with the substrates to produce a charge transfer complex. The formation of this charge transfer complex is sensitive to the oxidation potential of the triarylamine and can greatly affect the kinetics of the Piers-Rubinsztajn reaction.     

Monitoring oligomer formation from self-aggregating amylin peptides using ESI-IMS-MS

Amyloid diseases are a serious cause for concern world-wide. To understand the mechanism of formation of the fibrillar structures associated with such disorders, it is necessary to study the progression from soluble protein or peptide monomer through an array of oligomers to the final, insoluble, fibrils. The protein IAPP is found in vivo in the form of insoluble amyloid deposits in the pancreatic islets of diabetes type II sufferers. Here, we have studied the in vitro self-aggregation of three fibril-forming peptides from the amyloidogenic core of IAPP. Using electrospray ionization—mass spectrometry coupled with ion mobility spectrometry, the mass and cross-sectional area of each oligomer present in the heterogeneous assembly mixtures can be determined individually in a single, rapid experiment over time. For the three peptides studied, oligomers ≤20-mer were characterized. Conversely, no oligomers higher than a dimer were detected for a non-assembling peptide control. The rate in which the cross-sectional area of the oligomers increases with increasing number of peptide sub-units indicates that assembly for the amyloid-forming peptides proceeds in a linear fashion until an oligomer of a certain size is attained. After this, a step increase in cross-sectional area occurs for the next higher-order oligomer. This behaviour can be explained by molecular modelling of singly, doubly, triply and quadruply stacked β-stranded structures. Using one peptide as an example, the cross-sectional areas of the lower order oligomers (dimer to pentamer) were found to be consistent with a single β-sheet model, whereas the higher order oligomers were consistent with double-stranded (hexamer to decamer oligomers), triply-stranded (11-mers to 15-mers) and quadruply-stranded (16-mers to 20-mers) β-sheet models.     

微波辐射法制备Cu-SSZ-13催化剂及其对柴油车尾气NOx的脱除

采用微波辐射法和传统水热法分别制备了Cu-SSZ-13催化剂,用于柴油车尾气NO_x的脱除.用X射线衍射(XRD)、N₂物理吸脱附、H₂程序升温还原(H₂-TPR)、电子顺磁共振(EPR)、NH₃程序升温脱附(NH₃-TPD)、电感耦合等离子体质谱(ICP-MS)及X射线光电子能谱(XPS)等方法对样品进行表征.结果表明,微波辐射法大大缩短了SSZ-13分子筛的晶化时间,晶化9 h制得样品的结晶度与传统水热法晶化72 h制得样品的结晶度相近,同时孔结构参数也得到了一定程度的改善,微波辐射法制备样品的Brönsted(B)酸性位和Lewis(L)酸性位增多,活性组分铜的负载量也得到显著的提高,使得微波辐射法制备的催化剂呈现出优异的低温活性和水热稳定性.     

Nonperturbative chemical modification of graphene for protein micropatterning

Graphene's extraordinary physical properties and its planar geometry make it an ideal candidate for a wide array of applications, many of which require controlled chemical modification and the spatial organization of molecules on its surface. In particular, the ability to functionalize and micropattern graphene with proteins is relevant to bioscience applications such as biomolecular sensors, single-cell sensors, and tissue engineering. We report a general strategy for the noncovalent chemical modification of epitaxial graphene for protein immobilization and micropatterning. We show that bifunctional molecule pyrenebutanoic acid-succinimidyl ester (PYR-NHS), composed of the hydrophobic pyrene and the reactive succinimide ester group, binds to graphene noncovalently but irreversibly. We investigate whether the chemical treatment perturbs the electronic band structure of graphene using X-ray photoemission (XPS) and Raman spectroscopy. Our results show that the sp(2) hybridization remains intact and that the π band maintains its characteristic Lorentzian shape in the Raman spectra. The modified graphene surfaces, which bind specifically to amines in proteins, are micropatterned with arrays of fluorescently labeled proteins that are relevant to glucose sensors (glucose oxidase) and cell sensor and tissue engineering applications (laminin).     

Strategy for streamlined release identity testing of chromatography media

In accordance with the US Code of Federal Regulations 21CFR 211.84 (6)(d)(1), a specific identity test must be performed for the release of chromatography media (stationary phase) before use in production of human pharmaceuticals. Due to the complexity of the physical and chemical properties of these media, i.e., variable particle morphology, insolubility, and chemical inertness, the development of specific identity tests presents a challenge. In this paper we report a new strategy for media identification that uses a combination of three relatively simple techniques: Fourier transform infrared (FT-IR) and near infrared (NIR) spectroscopy in conjunction with search libraries, and particle size distribution analysis. The methods are well established and suitable for routine application in a quality control laboratory. A hierarchical selection procedure utilizing these methods permits assignment of a unique identity for each of the chromatography media in use at a given facility, and form the basis of release tests for the media. Although this strategy was developed using specific media, the generic nature of the technology and the selection strategy proposed would permit its application to other chromatography media as well.     

Fluoropolyether coatings: Relationships of electrochemical impedance spectroscopy measurements,barrier properties,and polymer structure

Ten model coatings, selected and obtained from a family of fluorinated resins synthesized by the reaction of perfluoroether oligomeric diols of different molecular weights with polyisocyanurates of hexamethylenediisocyanate (HDI) and isophoronediisocyanate (IPDI), were characterized with differential scanning calorimetry, mechanical testing, and electrochemical impedance spectroscopy measurements. The electrochemical and chemico‐physical measurements show that the glass‐transition temperature of the starting isocyanate trimers greatly influences the properties of the final urethane coatings; the IPDI trimer gives harder coatings with lower water permeabilities than the corresponding HDI‐based materials. Moreover, for each class of materials (from IPDI or HDI), the fluorine content plays a relevant role: the higher the fluorine percentage, the lower the water absorption into the coatings. Furthermore, the chain length of the polyols used for the synthesis of the prepolymers is a variable that exhibits great influence on the coating properties: coatings containing shorter perfluoropolyether segments show better barrier properties. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 40: 52–64, 2002     

三氟丙炔基类液晶的合成及性能

合成了16个三氟丙炔为端基的液晶化合物,以苯甲醛衍生物与1,1,1-三氯三氟乙烷的有机锌试剂进行加成脱水成烯,再通过Suzuki偶联反应后脱去HCl制得目标产物,总产率67%,气相色谱(GC)纯度99.5%,通过红外光谱(IR)、核磁共振谱(NMR)和质谱(MS)确定其结构。利用DSC和POM对该类化合物的热性能进行了测试,结果表明,联苯类的化合物不具有液晶相,而三联苯类的化合物具有近晶A相,且熔点随烷基链碳原子的增加呈下降趋势。物理性能测试结果表明,该类化合物的Δε值为12.61~21.94,末端三氟甲基基团和侧氟的引入可以有效的增加Δε值;Δn值0.19~0.29,随分子内苯环数目的增加而变大;γ1值为49.9~468.0 m Pa·s,随分子内苯环数量的增加而增加。化合物4n具有高Δε(19.2)、高ε_⊥(10.3)及低Δε/ε_⊥(1.9)。通过模拟计算讨论了炔键位置对此类液晶材料性质的影响。该类化合物在调节混合液晶介电各向异性和双折射率方面有很好的应用价值,同时通过分子结构的改进也可以很好地应用于FFS(fringe-field switching)显示模式。     

Synthesis,Properties, and Redox Behavior of 1,1,4,4‐Tetracyano‐2‐ferrocenyl‐1,3‐butadienes Connected by Aryl,Biaryl, and Teraryl Spacers

Aryl‐substituted 1,1,4,4‐tetracyano‐1,3‐butadienes (FcTCBDs) and bis(1,1,4,4‐tetracyanobutadiene)s (bis‐FcTCBDs), possessing a ferrocenyl group on each terminal, were prepared by the reaction of a variety of alkynes with tetracyanoethylene (TCNE) in a [2+2] cycloaddition reaction, followed by retro‐electrocyclization of the initially formed [2+2] cycloadducts (i.e., cyclobutene derivatives). The characteristic intramolecular charge transfer (ICT) between the donor (ferrocene) and acceptor (TCBD) moieties were investigated by using UV/Vis spectroscopy. The redox behaviors of FcTCBDs and bis‐FcTCBDs were examined by cyclic voltammetry (CV) and differential pulse voltammetry (DPV), which revealed their properties of multi‐electron transfer depending on the number of ferrocene and TCBD moieties. Moreover, significant color changes were observed by visible spectroscopy under the electrochemical reduction conditions.     

Solid-phase synthesis of DOTA-peptides

A general synthetic route to two DOTA-linked N-Fmoc amino acids (DOTA-F and DOTA-K) is described that allows insertion of DOTA at any endo-position within a peptide sequence. Three model pentapeptides were prepared to test the general utility of these derivatives in solid-phase peptide synthesis. Both DOTA derivatives reacted smoothly by means of standard HBTU activation chemistry to the point of insertion of the DOTA amino acid, but extension of the peptide chain beyond the DOTA-amino acid insertion required the use of pre-activated C-pentafluorophenyl ester N-alpha-Fmoc amino acids. Three Gal-80 binding peptides (12-mers) were then prepared by using this methodology with DOTA positioned either at the N terminus or at one of two different internal positions;the binding of the resulting GdDOTA-12-mers to Gal-80 were compared. The methodology described here allows versatile, controlled introduction of DOTA into any location within a peptide sequence. This provides a potential method for the screening of libraries of DOTA-linked peptides for optimal targeting properties.     

Cyclodextrin chemistry. Selective modification of all primary hydroxyl groups of α- and β-cyclodextrins

Two efficient methods are described for the selective modification of all six primary hydroxyl groups of α-cyclodextrin (α-CD, 1 1 ). One, using an indirect strategy, involves protection of all 18 hydroxyl functions as benzoate esters, followed by selective deprotection of the six primary alcohol groups. The other, using a direct strategy, involves selective activation of the primary hydroxyl groups via a bulky triphenylphosphonium salt, which is then substituted by azide anion as the reaction proceeds. A number of modified α-cyclodextrin derivatives have been prepared and fully characterized, among which are: the useful intermediate α-cyclodextrin-dodeca (2, 3) benzoate ( 3 ); hexakis (6-amino-6-deoxy)-α-cyclodextrin hexahydrochloride ( 7 ); hexakis (6-amino-6-deoxy)-dodeca (2, 3)-O-methyl-α-cyclodextrin hexahydrochloride ( 9 ), hexa (6)-O-methyl-α-cyclodextrin ( 13 ). The direct substitution is shown to be even more efficient for β-cyclodextrin ( 16 ), giving the heptakis (6-azido-6-deoxy)-β-CD-tetradeca (2, 3)acetate ( 17 ), while the indirect strategy fails. The compounds are characterized by extensive use of ¹³C- and ¹H-NMR. spectroscopy. The steric and statistical problems of selective polysubstitution reactions for the cyclodextrins are discussed, and possible reasons for the observed differences in reactivity between α- and β-cyclodextrins are examined. The dodecabenzoate 3 presents a very marked solvent effect on physical properties (IR. and NMR. spectra, optical rotation); the effects observed may be ascribed to an unusually strong intramolecular network of hydrogen bonds which severely distorts the α-cyclodextrin ring and lowers the symmetry from six-fold to three-fold.     

Spectroscopy and electronic structure of electron deficient zinc phthalocyanines

The effect of introduction of perfluoro alkyl groups into phthalocyanines, as evidenced by the spectroscopic properties of 1,4,8,11,15,18,22,25-octa-fluoro-2,3,9,10,16,17,23,24-octa-perfluoro isopropyl zinc phthalocyanine, ZnF(64)Pc(-2) and its ring-reduced radical anion species, [ZnF(64)Pc(-3)](-), are reported. A combination of UV-visible absorption and magnetic circular dichroism (MCD) spectroscopy, ESI and MALDI-TOF mass spectrometry, cyclic and differential pulse voltammetry, and complete theoretical calculations using INDO/S and DFT techniques reveals that the substitution of all sixteen hydrogen atoms in protio ZnPc(-2) by eight F and eight i-C(3)F(7) groups red shifts the Q and pi --> pi transitions and narrows the HOMO-LUMO gap while simultaneously preventing ring photooxidation and stabilizing the radical anion. The [ZnF(64)Pc(-3)](-) species, which is in equilibrium in solution with the neutral complex when a reducing agent is present, is unusually stable. The above effects are attributed to the strong electron withdrawing properties of the peripheral substituents, which render ZnF(64)Pc extremely electron deficient.     

Ga2O3 and GaN nanocrystalline film: reverse micelle assisted solvothermal synthesis and characterization

Gallium oxide (beta-Ga2O3) nanoparticles were successfully deposited on quartz glass substrates using sodium bis(2-ethylhexyl) sulfosuccinate (AOT)/n-hexane/ethylene glycol monomethyl ether (EGME) reverse micelle-mediated solvothermal process with different omega values. The mean diameter of Ga2O3 particles was approximately 2-3 nm and found to be approximately independent of omega values of the reverse micelles. However, when the Ga2O3 nanocrystalline films were nitrided at 900 degrees C under flowing NH3 atmosphere for 1 h, the mean diameter of the resulted gallium nitride (wurtzite-GaN) nanoparticles varied from 3-9 nm. Both nanocrystalline films of Ga2O3 and GaN were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), Fourier transform infrared (FTIR) spectroscopy, UV-vis spectroscopy and photoluminescence in order to study their chemical and physical properties explicitly.     

Synthesis and pairing properties of alpha-tricyclo-DNA

We describe the synthesis of the phosphoramidite building blocks of alpha-tricyclo-DNA (alpha-tc-DNA) covering all four natural bases, starting from the already known corresponding alpha-tc-nucleosides. These building blocks were used for the preparation of three alpha-tc-oligonucleotide 10-mers representing a homopurine, a homopyrimidine, and a mixed purine/pyrimidine base sequence. The base-pairing properties with complementary parallel and antiparallel oriented DNA and RNA were studied by UV-melting analysis and CD spectroscopy. We found that alpha-tc-DNA binds preferentially to parallel nucleic acid complements through Watson-Crick duplex formation, with a preference for RNA over DNA. In comparison with natural DNA, alpha-tc-DNA shows equal to enhanced affinity to RNA and also pairs to antiparallel DNA or RNA complements, although with much lower affinity. In the mixed-base sequence these antiparallel duplexes are of the reversed Watson-Crick type, while in the homopurine/homopyrimidine sequences Hoogsteen and/or reversed Hoogsteen pairing is observed. Antiparallel duplex formation of two alpha-tc-oligonucleotides was also observed, although the thermal stability of this duplex was surprisingly low. The base-pairing properties of alpha-tc-DNA are discussed in the context of alpha-DNA, alpha-RNA, and alpha-LNA.     

Preparation, characterization, and optical properties of gold, silver, and gold-silver alloy nanoshells having silica cores

This report describes the structural and optical properties of a series of spherical shell/core nanoparticles in which the shell is comprised of a thin layer of gold, silver, or gold-silver alloy, and the core is comprised of a monodispersed silica nanoparticle. The silica core particles were prepared using the St?ber method, functionalized with terminal amine groups, and then seeded with small gold nanoparticles (approximately 2 nm in diameter). The gold-seeded silica particles were coated with a layer of gold, silver, or gold-silver alloy via solution-phase reduction of an appropriate metal ion or mixture of metal ions. The size, morphology, and elemental composition of the composite nanoparticles were characterized by field emission scanning electron microscopy (FE-SEM), energy-dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy, thermal gravimetric analysis (TGA), dynamic light scattering (DLS), and transmission electron microscopy (TEM). The optical properties of the nanoparticles were analyzed by UV-vis spectroscopy, which showed strong absorptions ranging from 400 nm into the near-IR region, where the position of the plasmon band reflected not only the thickness of the metal shell, but also the nature of the metal comprising the shell. Importantly, the results demonstrate a new strategy for tuning the position of the plasmon resonance without having to vary the core diameter or the shell thickness.