79 results on '"Marek, M."'
Search Results
2. An affinity probe for isolation of abscisic acid-binding proteins
- Author
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Marek M. Galka, Cindy M Graham, David C. Taylor, Yuanzhu Gai, A. S. Jadhav, Adrian J. Cutler, Ken M. Nelson, James M. Nyangulu, Gary M Banowetz, and Suzanne R. Abrams
- Subjects
Molecular Sequence Data ,Receptors, Cell Surface ,Plasma protein binding ,Brassica ,Biochemistry ,Catalysis ,Mixed Function Oxygenases ,chemistry.chemical_compound ,Structure-Activity Relationship ,Colloid and Surface Chemistry ,Affinity chromatography ,Cytochrome P-450 Enzyme System ,Amino Acid Sequence ,Receptor ,Abscisic acid ,Peptide sequence ,Plant Proteins ,organic chemicals ,Binding protein ,fungi ,food and beverages ,General Chemistry ,Abscisic acid binding ,Membrane protein ,chemistry ,Abscisic Acid ,Protein Binding - Abstract
An affinity probe has been developed for isolation of receptor proteins that bind the plant hormone abscisic acid (ABA). The structural features required for biological activity have been preserved, and the probe has been demonstrated to bind to known ABA-binding proteins.
- Published
- 2005
3. Choreographing Oscillatory Hydrodynamics with DNA-Coated Gold Nanoparticles.
- Author
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Rao A, Iglesias AS, and Grzelczak M
- Subjects
- Nucleic Acid Hybridization, Gold chemistry, Metal Nanoparticles chemistry, Hydrodynamics, DNA chemistry
- Abstract
Periodic responses to nonperiodic energy inputs, such as oscillations, are hallmarks of living systems. Nanoparticle-based systems have largely remained unexplored in the generation of oscillatory features. Here, we demonstrate a nanosystem featuring hierarchical response to light, where thermoplasmonic effects and reversible DNA-hybridization generate thermal convective forces and ultimately, oscillatory hydrodynamic flows. The slow aggregation of gold nanoparticles (AuNPs) serves as a positive feedback, while fast photothermal disassembly acts as negative feedback. These asymmetric feedback loops, combined with thermal hysteresis for time-delay, are essential ingredients for orchestrating an oscillating response.
- Published
- 2024
- Full Text
- View/download PDF
4. Single-Crystal-to-Single-Crystal Photosynthesis of Supramolecular Organoboron Polymers with Dynamic Effects.
- Author
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Bhandary S, Beliš M, Shukla R, Bourda L, Kaczmarek AM, and Van Hecke K
- Abstract
The solid-state synthesis of single-crystalline organic polymers, having functional properties, remains an attractive and developing research area in polymer chemistry and materials science. However, light-triggered topochemical synthesis of crystalline polymers comprising an organoboron backbone has not yet been reported. Here, we describe an intriguing example of single-crystal-to-single-crystal (SCSC) rapid photosynthesis (occurs on a seconds-scale) of two structurally different linear organoboron polymers, driven by environmentally sustainable visible/sun light, obtained from the same monomer molecule. A newly designed Lewis acid-base type molecular B ← N organoboron adduct (consisting of an organoboron core and naphthylvinylpyridine ligands) crystallizes in two solid-state forms featuring the same chemical structure but different 3D structural topologies, namely, monomers 1 and 2 . The solvate molecule-free crystals of 1 undergo topochemical photopolymerization via an unusual olefin-naphthyl ring [2 + 2] cyclization to yield the single crystalline [3]-ladderane polymer 1P growing along the B ← N linkages, accompanied by instantaneous and violent macroscopic mechanical motions or photosalient effects (such as bending-reshaping and jumping motions). In contrast, visible light-harvesting single crystals of 2 quantitatively polymerize to a B ← N bond-stabilized polymer 2P in a SCSC fashion owing to the rapid [2 + 2] cycloaddition reaction among olefin double bonds. Such olefin bonds in the crystals of 2 are suitably preorganized for photoreaction due to the presence of solvate molecules in the crystal packing. Single crystals of 2 also show photodynamic jumping motions - in response to visible light but in a relatively slower fashion than the crystals of 1 . In addition to SCSC topochemical polymerization and dynamic motions, both monomer crystals and their single-crystalline polymers feature green emissive and short-lived room-temperature phosphorescence properties upon excitation with visible-light wavelength.
- Published
- 2024
- Full Text
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5. Mechanistic Insights into S -Depalmitolyse Activity of Cln5 Protein Linked to Neurodegeneration and Batten Disease: A QM/MM Study.
- Author
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Dangat Y, Freindorf M, and Kraka E
- Subjects
- Humans, Child, Mutation, Membrane Proteins metabolism, Neuronal Ceroid-Lipofuscinoses genetics, Neuronal Ceroid-Lipofuscinoses metabolism
- Abstract
Ceroid lipofuscinosis neuronal protein 5 (Cln5) is encoded by the CLN5 gene. The genetic variants of this gene are associated with the CLN5 form of Batten disease. Recently, the first crystal structure of Cln5 was reported. Cln5 shows cysteine palmitoyl thioesterase S -depalmitoylation activity, which was explored via fluorescent emission spectroscopy utilizing the fluorescent probe DDP-5. In this work, the mechanism of the reaction between Cln5 and DDP-5 was studied computationally by applying a QM/MM methodology at the ωB97X-D/6-31G(d,p):AMBER level. The results of our study clearly demonstrate the critical role of the catalytic triad Cys
280 -His166 -Glu183 in S -depalmitoylation activity. This is evidenced through a comparison of the pathways catalyzed by the Cys280 -His166 -Glu183 triad and those with only Cys280 involved. The computed reaction barriers are in agreement with the catalytic efficiency. The calculated Gibb's free-energy profile suggests that S -depalmitoylation is a rate-limiting step compared to the preceding S -palmitoylation, with barriers of 26.1 and 25.3 kcal/mol, respectively. The energetics were complemented by monitoring the fluctuations in the electron density distribution through NBO charges and bond strength alterations via local mode stretching force constants during the catalytic pathways. This comprehensive protocol led to a more holistic picture of the reaction mechanism at the atomic level. It forms the foundation for future studies on the effects of gene mutations on both the S -palmitoylation and S -depalmitoylation steps, providing valuable data for the further development of enzyme replacement therapy, which is currently the only FDA-approved therapy for childhood neurodegenerative diseases, including Batten disease.- Published
- 2024
- Full Text
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6. Fully Automated Characterization of Protein-Peptide Binding by Microfluidic 2D NMR.
- Author
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Plata M, Sharma M, Utz M, and Werner JM
- Subjects
- Ligands, Magnetic Resonance Spectroscopy methods, Nuclear Magnetic Resonance, Biomolecular methods, Peptides, Microfluidics, Proteins chemistry
- Abstract
We demonstrate an automated microfluidic nuclear magnetic resonance (NMR) system that quantitatively characterizes protein-ligand interactions without user intervention and with minimal sample needs through protein-detected heteronuclear 2D NMR spectroscopy. Quantitation of protein-ligand interactions is of fundamental importance to the understanding of signaling and other life processes. As is well-known, NMR provides rich information both on the thermodynamics of binding and on the binding site. However, the required titrations are laborious and tend to require large amounts of sample, which are not always available. The present work shows how the analytical power of NMR detection can be brought in line with the trend of miniaturization and automation in life science workflows.
- Published
- 2023
- Full Text
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7. Photomechanical Motions in Organoboron-Based Phosphorescent Molecular Crystals Driven by a Crystal-State [2 + 2] Cycloaddition Reaction.
- Author
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Bhandary S, Beliš M, Kaczmarek AM, and Van Hecke K
- Subjects
- Cycloaddition Reaction
- Abstract
Photoluminescent molecular crystals integrated with the ability to transform light energy into macroscopic mechanical motions are a promising choice of materials for both actuating and photonic devices. However, such dynamic photomechanical effects, based on molecular organoboron compounds as well as phosphorescent crystalline materials, are not yet known. Here we present an intriguing example of photomechanical molecular single crystals of a newly synthesized organoboron containing Lewis acid-base molecular adduct (BN1, substituted triphenylboroxine and 1,2-di(4-pyridyl)ethylene) having a capsule shape molecular geometry. The single crystals of BN1 under UV light exhibit controllable rapid bending-shape recovery, delamination, violent splitting-jumping, and expanding features. The detailed structural investigation by single-crystal X-ray diffraction and
1 H NMR spectroscopy reveals that the photosalient behavior of the BN1 single crystals is driven by a crystal-to-crystal [2 + 2] cycloaddition reaction, supported by four donor-acceptor type B←N bonds. The instant photomechanical reaction in the BN1 crystals occurs under UV on account of sudden release of stress associated with the strained molecular geometry, significant solid-state molecular movements (supramolecular change), and cleavage of half intermolecular B←N linkages to result in a complete photodimerized single-crystalline product via the existence of two other intermediate photoproducts. In addition, the BN1 crystals display short-lived room temperature phosphorescence, and the photodynamic events are accompanied by the enhancement of their phosphorescence intensity to yield the photoproduct. Interestingly, the molecular crystals of the final photoproduct polymerize at ambient conditions when recrystallized from the solution forming a 2D supramolecular crystalline polymer stabilized by the retention of all B←N coordination modes.- Published
- 2022
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8. Mechanochemical Conversion of Aromatic Amines to Aryl Trifluoromethyl Ethers.
- Author
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Jakubczyk M, Mkrtchyan S, Shkoor M, Lanka S, Budzák Š, Iliaš M, Skoršepa M, and Iaroshenko VO
- Subjects
- Amides, Aniline Compounds chemistry, Catalysis, Amines chemistry, Ethers chemistry
- Abstract
Increased interest in the trifluoromethoxy group in organic synthesis and medicinal chemistry has induced a demand for new, selective, general, and faster methods applicable to natural products and highly functionalized compounds at a later stage of hit-to-lead campaigns. Applying pyrylium tetrafluoroborate, we have developed a mechanochemical protocol to selectively substitute the aromatic amino group with the OCF
3 functionality. The scope of our method includes 31 examples of ring-substituted anilines, including amides and sulfonamides. Expected SN Ar products were obtained in excellent yields. The presented concise method opens a pathway to new chemical spaces for the pharmaceutical industry.- Published
- 2022
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9. Atomically Dispersed Copper Sites in a Metal-Organic Framework for Reduction of Nitrogen Dioxide.
- Author
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Ma Y, Han X, Xu S, Wang Z, Li W, da Silva I, Chansai S, Lee D, Zou Y, Nikiel M, Manuel P, Sheveleva AM, Tuna F, McInnes EJL, Cheng Y, Rudić S, Ramirez-Cuesta AJ, Haigh SJ, Hardacre C, Schröder M, and Yang S
- Abstract
Metal-organic framework (MOF) materials provide an excellent platform to fabricate single-atom catalysts due to their structural diversity, intrinsic porosity, and designable functionality. However, the unambiguous identification of atomically dispersed metal sites and the elucidation of their role in catalysis are challenging due to limited methods of characterization and lack of direct structural information. Here, we report a comprehensive investigation of the structure and the role of atomically dispersed copper sites in UiO-66 for the catalytic reduction of NO
2 at ambient temperature. The atomic dispersion of copper sites on UiO-66 is confirmed by high-angle annular dark-field scanning transmission electron microscopy, electron paramagnetic resonance spectroscopy, and inelastic neutron scattering, and their location is identified by neutron powder diffraction and solid-state nuclear magnetic resonance spectroscopy. The Cu/UiO-66 catalyst exhibits superior catalytic performance for the reduction of NO2 at 25 °C without the use of reductants. A selectivity of 88% for the formation of N2 at a 97% conversion of NO2 with a lifetime of >50 h and an unprecedented turnover frequency of 6.1 h-1 is achieved under nonthermal plasma activation. In situ and operando infrared, solid-state NMR, and EPR spectroscopy reveal the critical role of copper sites in the adsorption and activation of NO2 molecules, with the formation of {Cu(I)···NO} and {Cu···NO2 } adducts promoting the conversion of NO2 to N2 . This study will inspire the further design and study of new efficient single-atom catalysts for NO2 abatement via detailed unravelling of their role in catalysis.- Published
- 2021
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10. Single Molecule Investigation of Nanoconfinement Hydrophobicity in Heterogeneous Catalysis.
- Author
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Dong B, Mansour N, Pei Y, Wang Z, Huang T, Filbrun SL, Chen M, Cheng X, Pruski M, Huang W, and Fang N
- Abstract
Nanoconfinement imposes physical constraints and chemical effects on reactivity in nanoporous catalyst systems. In the present study, we lay the groundwork for quantitative single-molecule measurements of the effects of chemical environment on heterogeneous catalysis in nanoconfinement. Choosing hydrophobicity as an exemplary chemical environmental factor, we compared a range of essential parameters for an oxidation reaction on platinum nanoparticles (NPs) confined in hydrophilic and hydrophobic nanopores. Single-molecule experimental measurements at the single particle level showed higher catalytic activity, stronger adsorption strength, and higher activation energy in hydrophobic nanopores than those in hydrophilic nanopores. Interestingly, different dissociation kinetic behaviors of the product molecules in the two types of nanopores were deduced from the single-molecule imaging data.
- Published
- 2020
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11. Stereocontrolled Synthesis of (-)-Bactobolin A.
- Author
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Vojáčková P, Michalska L, Nečas M, Shcherbakov D, Böttger EC, Šponer J, Šponer JE, and Švenda J
- Subjects
- Benzopyrans chemical synthesis, Catalysis, Stereoisomerism
- Abstract
A stereoselective synthesis of the ribosome-binding antitumor antibiotic (-)-bactobolin A is reported. The presented approach makes effective use of (-)-quinic acid as a chiral pool starting material and substrate stereocontrol to establish the five contiguous stereocenters of (-)-bactobolin A. The key steps of the synthesis include a stereoselective vinylogous aldol reaction to introduce the unusual dichloromethyl substituent, a completely diastereoselective rhodium(II)-catalyzed C-H amination reaction to set the configuration of the axial amine, and an intramolecular alkoxycarbonylation to build the bicyclic lactone framework. The developed synthetic route was used to prepare 90 mg of (-)-bactobolin A trifluoroacetate in 10% overall yield.
- Published
- 2020
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12. Different Reaction Specificities of F 420 H 2 -Dependent Reductases Facilitate Pyrrolobenzodiazepines and Lincomycin To Fit Their Biological Targets.
- Author
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Steiningerova L, Kamenik Z, Gazak R, Kadlcik S, Bashiri G, Man P, Kuzma M, Pavlikova M, and Janata J
- Subjects
- Benzodiazepines chemistry, Benzodiazepines pharmacology, Catalysis, Depsipeptides biosynthesis, Depsipeptides chemistry, Depsipeptides pharmacology, Lincomycin chemistry, Lincomycin pharmacology, Models, Molecular, Oxidoreductases chemistry, Peptides, Cyclic biosynthesis, Peptides, Cyclic chemistry, Peptides, Cyclic pharmacology, Proline analogs & derivatives, Proline metabolism, Pyrroles chemistry, Pyrroles pharmacology, Riboflavin analogs & derivatives, Riboflavin chemistry, Riboflavin metabolism, Substrate Specificity, Tyrosine analogs & derivatives, Tyrosine metabolism, Benzodiazepines metabolism, Lincomycin biosynthesis, Oxidoreductases metabolism, Pyrroles metabolism
- Abstract
Antitumor pyrrolobenzodiazepines (PBDs), lincosamide antibiotics, quorum-sensing molecule hormaomycin, and antimicrobial griselimycin are structurally and functionally diverse groups of actinobacterial metabolites. The common feature of these compounds is the incorporation of l-tyrosine- or l-leucine-derived 4-alkyl-l-proline derivatives (APDs) in their structures. Here, we report that the last reaction in the biosynthetic pathway of APDs, catalyzed by F
420 H2 -dependent Apd6 reductases, contributes to the structural diversity of APD precursors. Specifically, the heterologous overproduction of six Apd6 enzymes demonstrated that Apd6 from the biosynthesis of PBDs and hormaomycin can reduce only an endocyclic imine double bond, whereas Apd6 LmbY and partially GriH from the biosyntheses of lincomycin and griselimycin, respectively, also reduce the more inert exocyclic double bond of the same 4-substituted Δ1-pyrroline-2-carboxylic acid substrate, making LmbY and GriH unusual, if not unique, among reductases. Furthermore, the differences in the reaction specificity of the Apd6 reductases determine the formation of the fully saturated APD moiety of lincomycin versus the unsaturated APD moiety of PBDs, providing molecules with optimal shapes to bind their distinct biological targets. Moreover, the Apd6 reductases establish the first F420 H2 -dependent enzymes from the luciferase-like hydride transferase protein superfamily in the biosynthesis of bioactive molecules. Finally, our bioinformatics analysis demonstrates that Apd6 and their homologues, widely distributed within several bacterial phyla, play a role in the formation of novel yet unknown natural products with incorporated l-proline-like precursors and likely in the microbial central metabolism.- Published
- 2020
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13. Silica-Supported Organolanthanum Catalysts for C-O Bond Cleavage in Epoxides.
- Author
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Wang Z, Patnaik S, Eedugurala N, Manzano JS, Slowing II, Kobayashi T, Sadow AD, and Pruski M
- Abstract
Single-site organolanthanum complexes supported on mesoporous silica nanoparticles, La{C(SiHMe
2 )3 }n @MSNs, catalyze the ring-opening hydroboration reaction of aliphatic and styrenic epoxides with pinacolborane (HBpin). The surface-bound complexes, synthesized by reaction of the homoleptic tris(alkyl)lanthanum La{C(SiHMe2 )3 }3 and SBA-type MSN treated at 700 °C (MSN700 ), are mostly monopodal ≡SiO-La{C(SiHMe2 )3 }2 and contain an average of one bridging La↼H-Si per alkyl ligand. This structure was established through a combination of solid-state NMR (SSNMR) experiments, including J -resolved SiH coupling and quantitative29 Si measurements, diffuse reflectance IR, and elemental analysis. These rigorous analyses also established that grafting reactions in pentane provide a preponderance of ≡SiO-La{C(SiHMe2 )3 }2 sites and are superior to those in benzene and THF, and that grafting onto MSN treated at 550 °C (MSN550 ) results in a mixture of surface species. The single-site supported catalysts are more selective and in most cases more active than the homogeneous analogue, allow easy purification of products from the catalyst, are strongly resistant to leaching into solution phase, and may be recycled for reuse at least five times. After reaction of La{C(SiHMe2 )3 }n @MSN and HBpin, species including ≡SiO-La{C(SiHMe2 )3 }(H2 Bpin) and ≡SiO-La{C(SiHMe2 )3 }{κ2 -pinB-O(CMe2 )2 OBH3 } are identified by detailed 1D and 2D11 B SSNMR experiments.- Published
- 2020
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14. Electrophilic Organoiridium(III) Pincer Complexes on Sulfated Zirconia for Hydrocarbon Activation and Functionalization.
- Author
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Syed ZH, Kaphan DM, Perras FA, Pruski M, Ferrandon MS, Wegener EC, Celik G, Wen J, Liu C, Dogan F, Goldberg KI, and Delferro M
- Abstract
Single-site supported organometallic catalysts bring together the favorable aspects of homogeneous and heterogeneous catalysis while offering opportunities to investigate the impact of metal-support interactions on reactivity. We report a (
dm Phebox)Ir(III) (dm Phebox = 2,6-bis(4,4-dimethyloxazolinyl)-3,5-dimethylphenyl) complex chemisorbed on sulfated zirconia, the molecular precursor for which was previously applied to hydrocarbon functionalization. Spectroscopic methods such as diffuse reflectance infrared Fourier transformation spectroscopy (DRIFTS), dynamic nuclear polarization (DNP)-enhanced solid-state nuclear magnetic resonance (SSNMR) spectroscopy, and X-ray absorption spectroscopy (XAS) were used to characterize the supported species. Tetrabutylammonium acetate was found to remove the organometallic species from the surface, enabling solution-phase analytical techniques in conjunction with traditional surface methods. Cationic character was imparted to the iridium center by its grafting onto sulfated zirconia, imbuing high levels of activity in electrophilic C-H bond functionalization reactions such as the stoichiometric dehydrogenation of alkanes, with density functional theory (DFT) calculations showing a lower barrier for β-H elimination. Catalytic hydrogenation of olefins was also facilitated by the sulfated zirconia-supported (dm Phebox)Ir(III) complex, while the homologous complex on silica was inactive under comparable conditions.- Published
- 2019
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15. Evidence for Redox Mechanisms in Organometallic Chemisorption and Reactivity on Sulfated Metal Oxides.
- Author
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Klet RC, Kaphan DM, Liu C, Yang C, Kropf AJ, Perras FA, Pruski M, Hock AS, and Delferro M
- Abstract
The chemical and electronic interactions of organometallic species with metal oxide support materials are of fundamental importance for the development of new classes of catalytic materials. Chemisorption of Cp*(PMe
3 )IrMe2 on sulfated alumina (SA) and sulfated zirconia (SZ) led to an unexpected redox mechanism for deuteration of the ancillary Cp* ligand. Evidence for this oxidative mechanism was provided by studying the analogous homogeneous reactivity of the organometallic precursors toward trityl cation ([Ph3 C]+ ), a Lewis acid known to effect formal hydride abstraction by one-electron oxidation followed by hydrogen abstraction. Organometallic deuterium incorporation was found to be correlated with surface sulfate concentration as well as the extent of dehydration under thermal activation conditions of SA and SZ supports. Surface sulfate concentration dependence, in conjunction with a computational study of surface electron affinity, indicates an electron-deficient pyrosulfate species as the redox-active moiety. These results provide further evidence for the ability of sulfated metal oxides to participate in redox chemistry not only toward organometallic complexes but also in the larger context of their application as catalysts for the transformation of light alkanes.- Published
- 2018
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16. Excitation Modulation of Upconversion Nanoparticles for Switch-like Control of Ultraviolet Luminescence.
- Author
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Dawson P and Romanowski M
- Subjects
- Anthracenes chemistry, Energy Transfer, Luminescent Measurements, Luminescence, Nanoparticles chemistry, Ultraviolet Rays, Ytterbium chemistry
- Abstract
The ability to control ultraviolet (UV) luminescence intensity in a switch-like manner is demonstrated through the use of 980 nm excitation pulse-width modulation in NaYF
4 :Yb3+ ,Tm3+ upconversion nanoparticles (UNPs). Varying the ytterbium doping resulted in a single order of magnitude improvement of UV luminescence intensity. The excitation pulse-width modulation technique applied to these optimized UNPs enables 3 orders of magnitude control over UV luminescence intensity while maintaining NIR luminescence emission at 800 nm. Controlled in the switch-like manner, these UNPs can transfer their UV energy to 9,10-diphenylanthracene (DPA). Independent control of NIR luminescence and UV energy transfer through NIR excitation modulation may find applications in the development of multifunctional theranostic systems.- Published
- 2018
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17. Chemoselective Hydrogenation with Supported Organoplatinum(IV) Catalyst on Zn(II)-Modified Silica.
- Author
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Camacho-Bunquin J, Ferrandon M, Sohn H, Yang D, Liu C, Ignacio-de Leon PA, Perras FA, Pruski M, Stair PC, and Delferro M
- Abstract
Well-defined organoplatinum(IV) sites were grafted on a Zn(II)-modified SiO
2 support via surface organometallic chemistry in toluene at room temperature. Solid-state spectroscopies including XAS, DRIFTS, DRUV-vis, and solid-state (SS) NMR enhanced by dynamic nuclear polarization (DNP), as well as TPR-H2 and TEM techniques revealed highly dispersed (methylcyclopentadienyl)methylplatinum(IV) sites on the surface ((MeCp)PtMe/Zn/SiO2 , 1). In addition, computational modeling suggests that the surface reaction of (MeCp)PtMe3 with Zn(II)-modified SiO2 support is thermodynamically favorable (Δ G = -12.4 kcal/mol), likely due to the increased acidity of the hydroxyl group, as indicated by NH3 -TPD and DNP-enhanced17 O{1 H} SSNMR. In situ DRIFTS and XAS hydrogenation experiments reveal the probable formation of a surface Pt(IV)-H upon hydrogenolysis of Pt-Me groups. The heterogenized organoplatinum(IV)-hydride sites catalyze the selective partial hydrogenation of 1,3-butadiene to butenes (up to 95%) and the reduction of nitrobenzene derivatives to anilines (up to 99%) with excellent tolerance of reduction-sensitive functional groups (olefin, carbonyl, nitrile, halogens) under mild reaction conditions.- Published
- 2018
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18. Total Syntheses of Disorazoles A₁ and B₁ and Full Structural Elucidation of Disorazole B₁.
- Author
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Nicolaou KC, Bellavance G, Buchman M, and Pulukuri KK
- Subjects
- Antineoplastic Agents chemistry, Chemistry Techniques, Synthetic methods, Oxazoles chemistry, Stereoisomerism, Tin Compounds chemical synthesis, Tin Compounds chemistry, Antineoplastic Agents chemical synthesis, Oxazoles chemical synthesis
- Abstract
Described herein are the first total syntheses of naturally occurring antitumor agents disorazoles A
1 and B1 and the full structural assignment of the latter. The syntheses were achieved through convergent strategies employing enantioselective constructions of the required building blocks, including a novel Sharpless epoxidation/enzymatic kinetic resolution of stannane-containing substrates that led selectively to both enantiomeric forms of an epoxy vinyl stannane, and a series of coupling reactions, including a Wittig reaction, a Suzuki coupling, a Stille coupling, a Yamaguchi esterification and a Yamaguchi macrolactonization.- Published
- 2017
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19. Enantioselective Total Synthesis of Antibiotic CJ-16,264, Synthesis and Biological Evaluation of Designed Analogues, and Discovery of Highly Potent and Simpler Antibacterial Agents.
- Author
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Nicolaou KC, Pulukuri KK, Rigol S, Buchman M, Shah AA, Cen N, McCurry MD, Beabout K, and Shamoo Y
- Subjects
- Anti-Bacterial Agents chemistry, Chemistry Techniques, Synthetic methods, Gram-Positive Bacteria drug effects, Gram-Positive Bacterial Infections drug therapy, Humans, Lactones chemistry, Microbial Sensitivity Tests, Pyrazoles chemistry, Stereoisomerism, Structure-Activity Relationship, Anti-Bacterial Agents chemical synthesis, Anti-Bacterial Agents pharmacology, Lactones chemical synthesis, Lactones pharmacology, Pyrazoles chemical synthesis, Pyrazoles pharmacology
- Abstract
An improved and enantioselective total synthesis of antibiotic CJ-16,264 through a practical kinetic resolution and an iodolactonization reaction to form the iodo pyrrolizidinone fragment of the molecule is described. A series of racemic and enantiopure analogues of CJ-16,264 was designed and synthesized through the developed synthetic technologies and tested against drug-resistant bacterial strains. These studies led to interesting structure-activity relationships and the identification of a number of simpler, and yet equipotent, or even more potent, antibacterial agents than the natural product, thereby setting the foundation for further investigations in the quest for new anti-infective drugs.
- Published
- 2017
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20. Attenuation of London Dispersion in Dichloromethane Solutions.
- Author
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Pollice R, Bot M, Kobylianskii IJ, Shenderovich I, and Chen P
- Abstract
London dispersion constitutes one of the fundamental interaction forces between atoms and between molecules. While modern computational methods have been developed to describe the strength of dispersive interactions in the gas phase properly, the importance of inter- and intramolecular dispersion in solution remains yet to be fully understood because experimental data are still sparse in that regard. We herein report a detailed experimental and computational study of the contribution of London dispersion to the bond dissociation of proton-bound dimers, both in the gas phase and in dichloromethane solution, showing that attenuation of inter- and intramolecular dispersive interaction by solvent is large (about 70% in dichloromethane), but not complete, and that current state-of-the-art implicit solvent models employed in quantum-mechanical computational studies treat London dispersion poorly, at least for this model system.
- Published
- 2017
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21. Fingerprints of Through-Bond and Through-Space Exciton and Charge π-Electron Delocalization in Linearly Extended [2.2]Paracyclophanes.
- Author
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Zafra JL, Molina Ontoria A, Mayorga Burrezo P, Peña-Alvarez M, Samoc M, Szeremeta J, Ramírez FJ, Lovander MD, Droske CJ, Pappenfus TM, Echegoyen L, López Navarrete JT, Martín N, and Casado J
- Abstract
New stilbenoid and thiophenic compounds terminally functionalized with donor-donor, acceptor-acceptor, or donor-acceptor moieties and possessing a central [2.2]paracyclophane unit have been prepared, and their properties interpreted in terms of through-bond and through space π-electron delocalization (i.e., π-conjugations). Based on photophysical data, their excited-state properties have been described with a focus on the participation of the central [2.2]paracyclophane in competition with through-bond conjugation in the side arms. To this end, two-photon and one-photon absorption and emission spectroscopy, as a function of temperature, solvent polarity, and pressure in the solid state have been recorded. Furthermore, charge delocalization through the [2.2]paracyclophane in the neutral state and in the oxidized species (radical cations, dications and radical trications) has been investigated, allowing the elucidation of the vibrational Raman fingerprint of through-space charge delocalization. Thus, a complementary approach to both "intermolecular" excitation and charge delocalizations in [2.2]paracyclophane molecules is shown which can serve as models of charge and exciton migration in organic semiconductors.
- Published
- 2017
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22. Bambusuril as a One-Electron Donor for Photoinduced Electron Transfer to Methyl Viologen in Mixed Crystals.
- Author
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Fiala T, Ludvíková L, Heger D, Švec J, Slanina T, Vetráková L, Babiak M, Nečas M, Kulhánek P, Klán P, and Sindelar V
- Abstract
Methyl viologen hexafluorophosphate (MV
2+ ·2PF6 - ) and dodecamethylbambus[6]uril (BU6) form crystals in which the layers of viologen dications alternate with those of a 1:2 supramolecular complex of BU6 and PF6 - . This arrangement allows for a one-electron reduction of MV2+ ions upon UV irradiation to form MV+• radical cations within the crystal structure with half-lives of several hours in air. The mechanism of this photoinduced electron transfer in the solid state and the origin of the long-lived charge-separated state were studied by steady-state and transient spectroscopies, cyclic voltammetry, and electron paramagnetic resonance spectroscopy. Our experiments are supported by quantum-chemical calculations showing that BU6 acts as a reductant. In addition, analogous photochemical behavior is also demonstrated on other MV2+ /BU6 crystals containing either BF4 - or Br- counterions.- Published
- 2017
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23. Characterizing Substrate-Surface Interactions on Alumina-Supported Metal Catalysts by Dynamic Nuclear Polarization-Enhanced Double-Resonance NMR Spectroscopy.
- Author
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Perras FA, Padmos JD, Johnson RL, Wang LL, Schwartz TJ, Kobayashi T, Horton JH, Dumesic JA, Shanks BH, Johnson DD, and Pruski M
- Abstract
The characterization of nanometer-scale interactions between carbon-containing substrates and alumina surfaces is of paramount importance to industrial and academic catalysis applications, but it is also very challenging. Here, we demonstrate that dynamic nuclear polarization surface-enhanced NMR spectroscopy (DNP SENS) allows the unambiguous description of the coordination geometries and conformations of the substrates at the alumina surface through high-resolution measurements of
13 C-27 Al distances. We apply this new technique to elucidate the molecular-level geometry of13 C-enriched methionine and natural abundance poly(vinyl alcohol) adsorbed on γ-Al2 O3 -supported Pd catalysts, and we support these results with element-specific X-ray absorption near-edge measurements. This work clearly demonstrates a surprising bimodal coordination of methionine at the Pd-Al2 O3 interface.- Published
- 2017
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24. High-Yield Seeded Growth of Monodisperse Pentatwinned Gold Nanoparticles through Thermally Induced Seed Twinning.
- Author
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Sánchez-Iglesias A, Winckelmans N, Altantzis T, Bals S, Grzelczak M, and Liz-Marzán LM
- Abstract
We show that thermal treatment of small Au seeds results in extensive twinning and a subsequent drastic improvement in the yield (>85%) of formation of pentatwinned nanoparticles (NPs), with preselected morphology (nanorods, bipyramids, and decahedra) and aspect ratio. The "quality" of the seeds thus defines the yield of the obtained NPs, which in the case of nanorods avoids the need for additives such as Ag
+ ions. This modified seeded growth method also improves reproducibility, as the seeds can be stored for extended periods of time without compromising the quality of the final NPs. Additionally, minor modification of the seeds with Pd allows their localization within the final particles, which opens new avenues toward mechanistic studies. Together, these results represent a paradigm shift in anisotropic gold NP synthesis.- Published
- 2017
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25. Ribosomal Peptide Syntheses from Activated Substrates Reveal Rate Limitation by an Unexpected Step at the Peptidyl Site.
- Author
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Wang J, Kwiatkowski M, and Forster AC
- Subjects
- Hydrogen-Ion Concentration, Kinetics, Molecular Structure, Peptide Synthases chemistry, Peptides chemistry, RNA, Transfer chemistry, Substrate Specificity, Peptide Synthases metabolism, Peptides metabolism, Protein Biosynthesis, RNA, Transfer metabolism, Ribosomes enzymology
- Abstract
Protein synthesis (translation) is central to cellular function and antibiotic development. Interestingly, the key chemical step of translation, peptide bond formation, is among the slower enzymatic reactions. The reason for this remains controversial because of reliance on studies using highly modified, severely minimized, or unreactive substrate analogues. Here, we investigated this problem by fast kinetics using full-length aminoacyl-tRNA substrates with atomic substitutions that activated the ester electrophile. While trifluoro substitution of hydrogens in nonconserved positions of the peptidyl-site substrate dramatically increased the ester reactivity in solution assays, a large hastening of the combined rates of ribosomal accommodation and peptidyl transfer was observed only with a slowly reacting aminoacyl-site nucleophile, proline. With a fast-reacting A-site nucleophile, phenylalanine, effects did not correlate at all with electrophilicities. As effects were observed using the same, natural, aminoacyl-tRNA at the A site and all rates of accommodation/peptidyl transfer were pH dependent, we concluded that rate limitation was not by A-site accommodation but rather by peptidyl transfer and a hitherto unexpected step at the P site. This new slow step, which we term P-site accommodation, has implications for the activation or inhibition of ribosome function in vitro and in vivo.
- Published
- 2016
- Full Text
- View/download PDF
26. Pnictogen-Silicon Analogues of Benzene.
- Author
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Seitz AE, Eckhardt M, Erlebach A, Peresypkina EV, Sierka M, and Scheer M
- Abstract
Since the discovery of the first "inorganic benzene" (borazine, B3N3H6), the synthesis of other noncarbon derivatives is an ongoing challenge in Inorganic Chemistry. Here we report on the synthesis of the first pnictogen-silicon congeners of benzene, the triarsa- and the triphospha-trisilabenzene [(PhC(NtBu)2)3Si3E3] (E = P (1a), As (1b)) by a simple metathesis reaction. These compounds are formed by the reaction of [Cp″2Zr(η(1:1)-E4)] (E = P, As; Cp″ = C5H3tBu2) with [PhC(NtBu)2SiCl] in toluene at room temperature along with the silicon pnictogen congeners of the cyclobutadiene, [(PhC(NtBu)2)2Si2E2] (E = P (2a), As (2b)), which is unprecedented for the arsenic system 2b. All compounds were comprehensively characterized, and density functional theory calculations were performed to verify the stability and the aromatic character of the triarsa- and the triphospha-trisilabenzene.
- Published
- 2016
- Full Text
- View/download PDF
27. Interpreting the Paramagnetic NMR Spectra of Potential Ru(III) Metallodrugs: Synergy between Experiment and Relativistic DFT Calculations.
- Author
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Novotný J, Sojka M, Komorovsky S, Nečas M, and Marek R
- Abstract
Ruthenium-based compounds are potential candidates for use as anticancer metallodrugs. The central ruthenium atom can be in the oxidation state +2 (e.g., RAPTA, RAED) or +3 (e.g., NAMI, KP). In this study we focus on paramagnetic NAMI analogs of a general structure [4-R-pyH](+)trans-[Ru(III)Cl4(DMSO)(4-R-py)](-), where 4-R-py stands for a 4-substituted pyridine. As paramagnetic systems are generally considered difficult to characterize in detail by NMR spectroscopy, we performed a systematic structural and methodological NMR study of complexes containing variously substituted pyridines. The effect of the paramagnetic nature of these complexes on the (1)H and (13)C NMR chemical shifts was systematically investigated by temperature-dependent NMR experiments and density-functional theory (DFT) calculations. To understand the electronic factors influencing the orbital (δ(orb), temperature-independent) and paramagnetic (δ(para), temperature-dependent) contributions to the total NMR chemical shifts, a relativistic two-component DFT approach was used. The paramagnetic contributions to the (13)C NMR chemical shifts are correlated with the distribution of spin density in the ligand moiety and the (13)C isotropic hyperfine coupling constants, Aiso((13)C), for the individual carbon atoms. To analyze the mechanism of spin distribution in the ligand, the contributions of molecular spin-orbitals (MSOs) to the hyperfine coupling constants and the spatial distribution of the z-component of the spin density in the MSOs calculated at the relativistic four-component DFT level are discussed and rationalized. The significant effects of the substituent and the solvent on δ(para), particularly the contact contribution, are demonstrated. This work should contribute to further understanding of the link between the electronic structure and the NMR chemical shifts in open-shell systems, including the ruthenium-based metallodrugs investigated in this account.
- Published
- 2016
- Full Text
- View/download PDF
28. Natural Abundance (17)O DNP Two-Dimensional and Surface-Enhanced NMR Spectroscopy.
- Author
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Perras FA, Kobayashi T, and Pruski M
- Abstract
Due to its extremely low natural abundance and quadrupolar nature, the (17)O nuclide is very rarely used for spectroscopic investigation of solids by NMR without isotope enrichment. Additionally, the applicability of dynamic nuclear polarization (DNP), which leads to sensitivity enhancements of 2 orders of magnitude, to (17)O is wrought with challenges due to the lack of spin diffusion and low polarization transfer efficiency from (1)H. Here, we demonstrate new DNP-based measurements that extend (17)O solid-state NMR beyond its current capabilities. The use of the PRESTO technique instead of conventional (1)H-(17)O cross-polarization greatly improves the sensitivity and enables the facile measurement of undistorted line shapes and two-dimensional (1)H-(17)O HETCOR NMR spectra as well as accurate internuclear distance measurements at natural abundance. This was applied for distinguishing hydrogen-bonded and lone (17)O sites on the surface of silica gel; the one-dimensional spectrum of which could not be used to extract such detail. Lastly, this greatly enhanced sensitivity has enabled, for the first time, the detection of surface hydroxyl sites on mesoporous silica at natural abundance, thereby extending the concept of DNP surface-enhanced NMR spectroscopy to the (17)O nuclide.
- Published
- 2015
- Full Text
- View/download PDF
29. Benzene selectivity in competitive arene hydrogenation: effects of single-site catalyst···acidic oxide surface binding geometry.
- Author
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Gu W, Stalzer MM, Nicholas CP, Bhattacharyya A, Motta A, Gallagher JR, Zhang G, Miller JT, Kobayashi T, Pruski M, Delferro M, and Marks TJ
- Abstract
Organozirconium complexes are chemisorbed on Brønsted acidic sulfated ZrO2 (ZrS), sulfated Al2O3 (AlS), and ZrO2-WO3 (ZrW). Under mild conditions (25 °C, 1 atm H2), the supported Cp*ZrMe3, Cp*ZrBz3, and Cp*ZrPh3 catalysts are very active for benzene hydrogenation with activities declining with decreasing acidity, ZrS ≫ AlS ≈ ZrW, arguing that more Brønsted acidic oxides (those having weaker corresponding conjugate bases) yield stronger surface organometallic electrophiles and for this reason have higher benzene hydrogenation activity. Benzene selective hydrogenation, a potential approach for carcinogenic benzene removal from gasoline, is probed using benzene/toluene mixtures, and selectivities for benzene hydrogenation vary with catalyst as ZrBz3(+)/ZrS(-), 83% > Cp*ZrMe2(+)/ZrS(-), 80% > Cp*ZrBz2(+)/ZrS(-), 67% > Cp*ZrPh2(+)/ZrS(-), 57%. For Cp*ZrBz2(+)/ZrS(-), which displays the highest benzene hydrogenation activity with moderate selectivity in benzene/toluene mixtures. Other benzene/arene mixtures are examined, and benzene selectivities vary with arene as mesitylene, 99%, > ethylbenzene, 86% > toluene, 67%. Structural and computational studies by solid-state NMR spectroscopy, XAS, and periodic DFT methods applied to supported Cp*ZrMe3 and Cp*ZrBz3 indicate that larger Zr···surface distances are present in more sterically encumbered Cp*ZrBz2(+)/AlS(-) vs Cp*ZrMe2(+)/AlS(-). The combined XAS, solid state NMR, and DFT data argue that the bulky catalyst benzyl groups expand the "cationic" metal center-anionic sulfated oxide surface distances, and this separation/weakened ion-pairing enables the activation/insertion of more sterically encumbered arenes and influences hydrogenation rates and selectivity patterns.
- Published
- 2015
- Full Text
- View/download PDF
30. Glycans as biofunctional ligands for gold nanorods: stability and targeting in protein-rich media.
- Author
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García I, Sánchez-Iglesias A, Henriksen-Lacey M, Grzelczak M, Penadés S, and Liz-Marzán LM
- Subjects
- Adsorption, Animals, Biocompatible Materials metabolism, Biocompatible Materials pharmacology, Carbohydrate Conformation, Cell Line, Drug Stability, Humans, Lectins metabolism, Ligands, Metal Nanoparticles chemistry, Mice, Models, Molecular, Molecular Weight, Phagocytosis drug effects, Polysaccharides metabolism, Polysaccharides pharmacology, Biocompatible Materials chemistry, Gold chemistry, Nanotubes chemistry, Polysaccharides chemistry, Proteins chemistry
- Abstract
Poly(ethylene glycol) (PEG) has become the gold standard for stabilization of plasmonic nanoparticles (NPs) in biofluids, because it prevents aggregation while minimizing unspecific interactions with proteins. Application of Au NPs in biological environments requires the use of ligands that can target selected receptors, even in the presence of protein-rich media. We demonstrate here the stabilizing effect of low-molecular-weight glycans on both spherical and rod-like plasmonic NPs under physiological conditions, as bench-marked against the well-established PEG ligands. Glycan-coated NPs are resistant to adsorption of proteins from serum-containing media and avoid phagocytosis by macrophage-like cells, but retain selectivity toward carbohydrate-binding proteins in protein-rich biological media. These results open the way toward the design of efficient therapeutic/diagnostic glycan-decorated plasmonic nanotools for specific biological applications.
- Published
- 2015
- Full Text
- View/download PDF
31. Hydrogen-bonded organic semiconductor micro- and nanocrystals: from colloidal syntheses to (opto-)electronic devices.
- Author
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Sytnyk M, Głowacki ED, Yakunin S, Voss G, Schöfberger W, Kriegner D, Stangl J, Trotta R, Gollner C, Tollabimazraehno S, Romanazzi G, Bozkurt Z, Havlicek M, Sariciftci NS, and Heiss W
- Abstract
Organic pigments such as indigos, quinacridones, and phthalocyanines are widely produced industrially as colorants for everyday products as various as cosmetics and printing inks. Herein we introduce a general procedure to transform commercially available insoluble microcrystalline pigment powders into colloidal solutions of variously sized and shaped semiconductor micro- and nanocrystals. The synthesis is based on the transformation of the pigments into soluble dyes by introducing transient protecting groups on the secondary amine moieties, followed by controlled deprotection in solution. Three deprotection methods are demonstrated: thermal cleavage, acid-catalyzed deprotection, and amine-induced deprotection. During these processes, ligands are introduced to afford colloidal stability and to provide dedicated surface functionality and for size and shape control. The resulting micro- and nanocrystals exhibit a wide range of optical absorption and photoluminescence over spectral regions from the visible to the near-infrared. Due to excellent colloidal solubility offered by the ligands, the achieved organic nanocrystals are suitable for solution processing of (opto)electronic devices. As examples, phthalocyanine nanowire transistors as well as quinacridone nanocrystal photodetectors, with photoresponsivity values by far outperforming those of vacuum deposited reference samples, are demonstrated. The high responsivity is enabled by photoinduced charge transfer between the nanocrystals and the directly attached electron-accepting vitamin B2 ligands. The semiconducting nanocrystals described here offer a cheap, nontoxic, and environmentally friendly alternative to inorganic nanocrystals as well as a new paradigm for obtaining organic semiconductor materials from commercial colorants.
- Published
- 2014
- Full Text
- View/download PDF
32. Decarboxylative polymerization of 2,6-naphthalenedicarboxylic acid at surfaces.
- Author
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Gao HY, Held PA, Knor M, Mück-Lichtenfeld C, Neugebauer J, Studer A, and Fuchs H
- Abstract
Metal-catalyzed polymerization of 2,6-naphthalenedicarboxylic acid (NDCA) to form poly-2,6-naphthalenes at various surfaces is reported. Polymerizations occur via initial formal dehydrogenation of self-assembled diacids with subsequent decarboxylation to give polymeric bisnaphthyl-Cu species at elevated temperature as intermediate structures (<160 °C). Further temperature increase eventually leads to poly-naphthalenes via reductive elimination. It is demonstrated that the Cu(111) surface works most efficiently to conduct such polymerizations as compared to the Au(111), Ag(111), Cu(100), and Cu(110) surfaces. Poly-2,6-naphthalene with a chain length of over 50 nm is obtained by using this approach. The decarboxylative coupling of aromatic diacids is a very promising tool which further enlarges the portfolio of reactions allowing for on-surface polymerizations and novel organometallic systems preparations.
- Published
- 2014
- Full Text
- View/download PDF
33. Inefficient delivery but fast peptide bond formation of unnatural L-aminoacyl-tRNAs in translation.
- Author
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Ieong KW, Pavlov MY, Kwiatkowski M, Forster AC, and Ehrenberg M
- Subjects
- Kinetics, Peptides chemical synthesis, Peptides chemistry, RNA, Transfer, Amino Acyl chemistry, Peptides metabolism, RNA, Transfer, Amino Acyl metabolism
- Abstract
Translations with unnatural amino acids (AAs) are generally inefficient, and kinetic studies of their incorporations from transfer ribonucleic acids (tRNAs) are few. Here, the incorporations of small and large, non-N-alkylated, unnatural l-AAs into dipeptides were compared with those of natural AAs using quench-flow techniques. Surprisingly, all incorporations occurred in two phases: fast then slow, and the incorporations of unnatural AA-tRNAs proceeded with rates of fast and slow phases similar to those for natural Phe-tRNA(Phe). The slow phases were much more pronounced with unnatural AA-tRNAs, correlating with their known inefficient incorporations. Importantly, even for unnatural AA-tRNAs the fast phases could be made dominant by using high EF-Tu concentrations and/or lower reaction temperature, which may be generally useful for improving incorporations. Also, our observed effects of EF-Tu concentration on the fraction of the fast phase of incorporation enabled direct assay of the affinities of the AA-tRNAs for EF-Tu during translation. Our unmodified tRNA(Phe) derivative adaptor charged with a large unnatural AA, biotinyl-lysine, had a very low affinity for EF-Tu:GTP, while the small unnatural AAs on the same tRNA body had essentially the same affinities to EF-Tu:GTP as natural AAs on this tRNA, but still 2-fold less than natural Phe-tRNA(Phe). We conclude that the inefficiencies of unnatural AA-tRNA incorporations were caused by inefficient delivery to the ribosome by EF-Tu, not slow peptide bond formation on the ribosome.
- Published
- 2012
- Full Text
- View/download PDF
34. A simple road for the transformation of few-layer graphene into MWNTs.
- Author
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Quintana M, Grzelczak M, Spyrou K, Calvaresi M, Bals S, Kooi B, Van Tendeloo G, Rudolf P, Zerbetto F, and Prato M
- Abstract
We report the direct formation of multiwalled carbon nanotubes (MWNT) by ultrasonication of graphite in dimethylformamide (DMF) upon addition of ferrocene aldehyde (Fc-CHO). The tubular structures appear exclusively at the edges of graphene layers and contain Fe clusters. Fc in conjunction with benzyl aldehyde, or other Fc derivatives, does not induce formation of NT. Higher amounts of Fc-CHO added to the dispersion do not increase significantly MWNT formation. Increasing the temperature reduces the amount of formation of MWNTs and shows the key role of ultrasound-induced cavitation energy. It is concluded that Fc-CHO first reduces the concentration of radical reactive species that slice graphene into small moieties, localizes itself at the edges of graphene, templates the rolling up of a sheet to form a nanoscroll, where it remains trapped, and finally accepts and donates unpaired electron to the graphene edges and converts the less stable scroll into a MWNT. This new methodology matches the long held notion that CNTs are rolled up graphene layers. The proposed mechanism is general and will lead to control the production of carbon nanostructures by simple ultrasonication treatments.
- Published
- 2012
- Full Text
- View/download PDF
35. Multiwalled carbon nanotubes drive the activity of metal@oxide core-shell catalysts in modular nanocomposites.
- Author
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Cargnello M, Grzelczak M, Rodríguez-González B, Syrgiannis Z, Bakhmutsky K, La Parola V, Liz-Marzán LM, Gorte RJ, Prato M, and Fornasiero P
- Abstract
Rational nanostructure manipulation has been used to prepare nanocomposites in which multiwalled carbon nanotubes (MWCNTs) were embedded inside mesoporous layers of oxides (TiO(2), ZrO(2), or CeO(2)), which in turn contained dispersed metal nanoparticles (Pd or Pt). We show that the MWCNTs induce the crystallization of the oxide layer at room temperature and that the mesoporous oxide shell allows the particles to be accessible for catalytic reactions. In contrast to samples prepared in the absence of MWCNTs, both the activity and the stability of core-shell catalysts is largely enhanced, resulting in nanocomposites with remarkable performance for the water-gas-shift reaction, photocatalytic reforming of methanol, and Suzuki coupling. The modular approach shown here demonstrates that high-performance catalytic materials can be obtained through the precise organization of nanoscale building blocks.
- Published
- 2012
- Full Text
- View/download PDF
36. Molecular recognition principles and stationary-phase characteristics of topoisomer-selective chemoaffinity materials for chromatographic separation of circular plasmid DNA topoisomers.
- Author
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Mahut M, Lindner W, and Lämmerhofer M
- Subjects
- Chromatography, Molecular Structure, Silicon Dioxide, DNA, Circular chemistry
- Abstract
We recently discovered the molecular recognition capability of a quinine carbamate ligand attached to silica as a powerful chemoaffinity material for the chromatographic separation of circular plasmid topoisomers of different linking numbers. In this paper we develop structure-selectivity relationship studies to figure out the essential structural features for topoisomer recognition. By varying different moieties of the original cinchonan-derived selector, it was shown that intercalation by the quinoline moiety of the ligand as assumed initially as the working hypothesis is not an essential feature for topoisomer recognition during chromatography. We found that the key elements for topoisomer selectivity are the presence of a rigid weak anion-exchange site and a H-donor site separated from each other in a defined distance by a 4-atom spacer. Additionally, incorporation of the weak anion-exchange site into a cyclic ring structure provides greater rigidity of the ligand molecule and turned out to be advantageous, if not mandatory, for (close to) baseline separation., (© 2011 American Chemical Society)
- Published
- 2012
- Full Text
- View/download PDF
37. Mechanical unfolding of the beet western yellow virus -1 frameshift signal.
- Author
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White KH, Orzechowski M, Fourmy D, and Visscher K
- Subjects
- Base Sequence, Beta vulgaris virology, Crystallography, X-Ray, Frameshift Mutation, Magnesium, Nucleic Acid Conformation, Frameshifting, Ribosomal genetics, Luteovirus genetics, RNA, Viral genetics
- Abstract
Using mechanical unfolding by optical tweezers (OT) and steered molecular dynamics (SMD) simulations, we have demonstrated the critical role of Mg(2+) ions for the resistance of the Beet Western Yellow Virus (BWYV) pseudoknot (PK) to unfolding. The two techniques were found to be complementary, providing information at different levels of molecular scale. Findings from the OT experiments indicated a critical role of stem 1 for unfolding of the PK, which was confirmed in the SMD simulations. The unfolding pathways of wild type and mutant appeared to depend upon pH and nucleotide sequence. SMD simulations support the notion that the stability of stem 1 is critical for -1 frameshifting. The all-atom scale nature of the SMD enabled clarification of the precise role of two Mg(2+) ions, Mg45 and Mg52, as identified in the BWYV X-ray crystallography structure, in -1 frameshifting. On the basis of simulations with "partially" and "fully" hydrated Mg(2+) ions, two possible mechanisms of stabilizing stem 1 are proposed. In both these cases Mg(2+) ions play a critical role in stabilizing stem 1, either by directly forming a salt bridge between the strands of stem 1 or by stabilizing parallel orientation of the strands in stem 1, respectively. These findings explain the unexpected drop in frameshifting efficiency to null levels of the C8U mutant in a manner consistent with experimental observations.
- Published
- 2011
- Full Text
- View/download PDF
38. Twisted π-system chromophores for all-optical switching.
- Author
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He GS, Zhu J, Baev A, Samoć M, Frattarelli DL, Watanabe N, Facchetti A, Ågren H, Marks TJ, and Prasad PN
- Abstract
Molecular chromophores with twisted π-electron systems have been shown to possess unprecedented values of the quadratic hyperpolarizability, β, with very large real parts and much smaller imaginary parts. We report here an experimental and theoretical study which shows that these twisted chromophores also possess very large values of the real part of the cubic hyperpolarizability, γ, which is responsible for nonlinear refraction. Thus, for the two-ring twisted chromophore TMC-2 at 775 nm, relatively close to one-photon resonance, n(2) extrapolated to neat substance is large and positive (1.87 × 10(-13) cm(2)/W), leading to self-focusing. Furthermore, the third-order response includes a remarkably low two-photon absorption coefficient, which means minimal nonlinear optical losses: the T factor, α(2)λ/n(2), is 0.308. These characteristics are attributed to closely spaced singlet biradical and zwitterionic states and offer promise for applications in all-optical switching., (© 2011 American Chemical Society)
- Published
- 2011
- Full Text
- View/download PDF
39. Water-soluble J-type rosette nanotubes with giant molar ellipticity.
- Author
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Borzsonyi G, Beingessner RL, Yamazaki T, Cho JY, Myles AJ, Malac M, Egerton R, Kawasaki M, Ishizuka K, Kovalenko A, and Fenniri H
- Abstract
A new self-assembling tricyclic module (×K1) featuring the Watson-Crick H-bonding arrays of guanine and cytosine fused to an internal pyridine ring was synthesized. When dissolved in water at room temperature, this module rapidly self-assembles into hexameric rosettes, which then stack to form J-type rosette nanotubes (RNTs) with increased inner/outer diameters and the largest molar ellipticity ever reported (4 × 10(6) deg·M(-1)·m(-1)). Using a combination of imaging and spectroscopic techniques we established the structure of ×K1-RNT and have shown that the extended π system of the self-assembling module resulted in a new family of J-type RNTs with enhanced intermodular electronic communication.
- Published
- 2010
- Full Text
- View/download PDF
40. Untying knots in proteins.
- Author
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Sułkowska JI, Sułkowski P, Szymczak P, and Cieplak M
- Subjects
- Amino Acids chemistry, Protein Conformation, Proteins chemistry
- Abstract
A shoelace can be readily untied by pulling its ends rather than its loops. Attempting to untie a native knot in a protein can also succeed or fail depending on where one pulls. However, thermal fluctuations induced by the surrounding water affect conformations stochastically and may add to the uncertainty of the outcome. When the protein is pulled by the termini, the knot can only get tightened, and any attempt at untying results in failure. We show that, by pulling specific amino acids, one may easily retract a terminal segment of the backbone from the knotting loop and untangle the knot. At still other amino acids, the outcome of pulling can go either way. We study the dependence of the untying probability on the way the protein is grasped, the pulling speed, and the temperature. Elucidation of the mechanisms underlying this dependence is critical for a successful experimental realization of protein knot untying.
- Published
- 2010
- Full Text
- View/download PDF
41. Unusual, solvent viscosity-controlled tautomerism and photophysics: meso-alkylated porphycenes.
- Author
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Gil M, Dobkowski J, Wiosna-Sałyga G, Urbańska N, Fita P, Radzewicz C, Pietraszkiewicz M, Borowicz P, Marks D, Glasbeek M, and Waluk J
- Abstract
Stationary and time-resolved studies of 9,10,19,20-tetramethylporphycene and 9,10,19,20-tetra-n-propylporphycene in condensed phases reveal the coexistence of trans and cis tautomeric forms. Two cis configurations, cis-1 and cis-2, play a crucial role in understanding the excited-state deactivation and tautomer conversion dynamics. The trans-trans tautomerization, involving intramolecular transfer of two hydrogen atoms, is extremely rapid (k ≥ 10(13) s(-1)), both in the ground and lowest electronically excited states. The cis-1-trans conversion rate, even though the process is thermodynamically more favorable, is much slower and solvent-dependent. This is explained by the coupling of alkyl group rotation with the hydrogen motion. Excited-state deactivation is controlled by solvent viscosity: the S(1) depopulation rate decreases by more than 2 orders of magnitude when the chromophore is transferred from a low-viscosity solution to a polymer film. Such behavior confirms a model for excited state deactivation in porphycene, which postulates that a conical intersection exists along the single hydrogen transfer path leading from the trans to a high energy cis-2 tautomeric form. For this process, the tautomerization coordinate includes not only hydrogen translocation but also large-amplitude twisting of the two protonated pyrrole moieties attached to the opposite sides of the ethylene bridge.
- Published
- 2010
- Full Text
- View/download PDF
42. Conformations of silica-bound (pentafluorophenyl)propyl groups determined by solid-state NMR spectroscopy and theoretical calculations.
- Author
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Mao K, Kobayashi T, Wiench JW, Chen HT, Tsai CH, Lin VS, and Pruski M
- Subjects
- Magnetic Resonance Spectroscopy, Molecular Conformation, Surface Properties, Hydrocarbons, Fluorinated chemistry, Molecular Dynamics Simulation, Silicon Dioxide chemistry
- Abstract
The conformations of (pentafluorophenyl)propyl groups (-CH(2)-CH(2)-CH(2)-C(6)F(5), abbreviated as PFP), covalently bound to the surface of mesoporous silica nanoparticles (MSNs), were determined by solid-state NMR spectroscopy and further refined by theoretical modeling. Two types of PFP groups were described, including molecules in the prone position with the perfluorinated aromatic rings located above the siloxane bridges (PFP-p) and the PFP groups denoted as upright (PFP-u), whose aromatic rings do not interact with the silica surface. Two-dimensional (2D) (13)C-(1)H, (13)C-(19)F and (19)F-(29)Si heteronuclear correlation (HETCOR) spectra were obtained with high sensitivity on natural abundance samples using fast magic angle spinning (MAS), indirect detection of low-gamma nuclei and signal enhancement by Carr-Purcell-Meiboom-Gill (CPMG) spin-echo sequence. 2D double-quantum (DQ) (19)F MAS NMR spectra and spin-echo measurements provided additional information about the structure and mobility of the pentafluorophenyl rings. Optimization of the PFP geometry, as well as calculations of the interaction energies and (19)F chemical shifts, proved very useful in refining the structural features of PFP-p and PFP-u functional groups on the silica surface. The prospects of using the PFP-functionalized surface to modify its properties (e.g., the interaction with solvents, especially water) and design new types of the heterogeneous catalytic system are discussed.
- Published
- 2010
- Full Text
- View/download PDF
43. Combining very large quadratic and cubic nonlinear optical responses in extended, tris-chelate metallochromophores with six pi-conjugated pyridinium substituents.
- Author
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Coe BJ, Fielden J, Foxon SP, Brunschwig BS, Asselberghs I, Clays K, Samoc A, and Samoc M
- Subjects
- 2,2'-Dipyridyl chemistry, Chelating Agents chemical synthesis, Crystallography, X-Ray, Electrochemistry, Magnetic Resonance Spectroscopy methods, Models, Molecular, Nonlinear Dynamics, Organometallic Compounds chemical synthesis, Pyridinium Compounds chemical synthesis, Scattering, Radiation, Spectrophotometry, Ultraviolet methods, 2,2'-Dipyridyl analogs & derivatives, Chelating Agents chemistry, Ferrous Compounds chemistry, Organometallic Compounds chemistry, Pyridinium Compounds chemistry, Ruthenium chemistry
- Abstract
We describe a series of nine new complex salts in which electron-rich Ru(II) or Fe(II) centers are connected via pi-conjugated bridges to six electron-accepting N-methyl-/N-arylpyridinium groups. This work builds upon our previous preliminary studies (Coe , B. J. J. Am. Chem. Soc. 2005, 127, 13399-13410; J. Phys. Chem. A 2007, 111, 472-478), with the aims of achieving greatly enhanced NLO properties and also combining large quadratic and cubic effects in potentially redox-switchable molecules. Characterization has involved various techniques, including electronic absorption spectroscopy and cyclic voltammetry. The complexes display intense, visible d --> pi* metal-to-ligand charge-transfer (MLCT) bands, and their pi --> pi* intraligand charge-transfer (ILCT) absorptions in the near-UV region show molar extinction coefficients as high as ca. 3.5 x 10(5) M(-1) cm(-1). Molecular quadratic nonlinear optical (NLO) responses beta have been determined by using hyper-Rayleigh scattering at 800 and 1064 nm and also via Stark (electroabsorption) spectroscopic studies. The directly and indirectly derived beta values are very large, with the Stark-based static first hyperpolarizabilities beta(0) reaching as high as ca. 10(-27) esu, and generally increase on extending the pi-conjugation and enhancing the electron-accepting strength of the ligands. Cubic NLO properties have also been measured by using the Z-scan technique, revealing relatively high two-photon absorption cross sections of up to 2500 GM at 750 nm.
- Published
- 2010
- Full Text
- View/download PDF
44. Solid-state NMR investigations of the immobilization of a BF4(-) salt of a palladium(II) complex on silica.
- Author
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Wiench JW, Michon C, Ellern A, Hazendonk P, Iuga A, Angelici RJ, and Pruski M
- Abstract
The structure of the silica supported palladium(II) complex [Pd(dppp)(S2C-NEt2)]BF4 (abbreviated as [Pd(dppp)(dtc)]BF4, where dppp is Ph2P(CH2)3PPh2) and interactions between the [Pd(dppp)(dtc)]+ cation, the BF4(-) anion, and the silica surface are studied using solid-state NMR spectroscopy. The unsupported, crystalline form of [Pd(dppp)(dtc)]BF4 is also investigated, both by X-ray diffraction and NMR. The structures of the cation and anion are found to be essentially the same in both unsupported and supported complex. The [Pd(dppp)(dtc)]BF4 loading has been determined by quantitative measurements of 11B, 19F, and 31P intensities, whereas the arrangement of anions and cations on the surface of silica has been established by two-dimensional heteronuclear correlation experiments involving 1H, 11B, 13C, 19F, 29Si, and 31P nuclei. At low coverages, the [Pd(dppp)(dtc)]+ cations are located near the BF4(-) anions, which in turn are immobilized directly on the surface near the Q4 sites. At higher loadings, which in this study corresponded to 0.06-0.15 mmol/g, the complexes stack on top of each other, despite the fact that the directly adsorbed molecules take up less than 10% of the silica surface. The relevance of these findings to heterogeneous catalysis is discussed.
- Published
- 2009
- Full Text
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45. Length-dependent convergence and saturation behavior of electrochemical, linear optical, quadratic nonlinear optical, and cubic nonlinear optical properties of dipolar alkynylruthenium complexes with oligo(phenyleneethynylene) bridges.
- Author
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Babgi B, Rigamonti L, Cifuentes MP, Corkery TC, Randles MD, Schwich T, Petrie S, Stranger R, Teshome A, Asselberghs I, Clays K, Samoc M, and Humphrey MG
- Abstract
The syntheses of trans-[Ru{4,4'-C[triple bond]CC(6)H(2)[2,5-(OEt)(2)]C[triple bond]CC(6)H(4)NO(2)}Cl(dppm)(2)] (19), trans-[Ru{4,4',4''-C[triple bond]CC(6)H(4)C[triple bond]CC(6)H(2)[2,5-(OEt)(2)]C[triple bond]CC(6)H(4)NO(2)}Cl(dppm)(2)] (20), trans-[Ru{4,4',4'',4'''-C[triple bond]CC(6)H(4)C[triple bond]CC(6)H(2)[2,5-(OEt)(2)]C[triple bond]CC(6)H(2)[2,5-(OEt)(2)]C[triple bond]CC(6)H(4)NO(2)}Cl(dppe)(2)] (21), trans-[Ru{4,4',4'',4'''-C[triple bond]CC(6)H(4)C[triple bond]CC(6)H(2)[2,5-(OEt)(2)]C[triple bond]CC(6)H(2)[2,5-(OEt)(2)]C[triple bond]CC(6)H(4)NO(2)}Cl(dppm)(2)] (22), trans-[Ru{4,4',4'',4'''-C[triple bond]CC(6)H(4)C[triple bond]CC(6)H(4)C[triple bond]CC(6)H(2)[2,5-(OEt)(2)]C[triple bond]CC(6)H(4)NO(2)}Cl(dppm)(2)] (23), and trans-[Ru{4,4',4'',4''',4''''-C[triple bond]CC(6)H(4)C[triple bond]CC(6)H(4)C[triple bond]CC(6)H(2)[2,5-(OEt)(2)]C[triple bond]CC(6)H(2)[2,5-(OEt)(2)]C[triple bond]CC(6)H(4)NO(2)}Cl(dppm)(2)] (24) are reported, together with those of precursor alkynes, complexes with the donor-pi-bridge-acceptor formulation that affords efficient quadratic and cubic NLO compounds; the identity of 19 was confirmed by a structural study. The electrochemical properties of 19-24 and related complexes with shorter pi-bridge ligands were assessed by cyclic voltammetry, and the linear optical, quadratic nonlinear optical, and cubic nonlinear optical properties were assayed by UV-vis-NIR spectroscopy, hyper-Rayleigh scattering studies at 1064 and 1300 nm, and broad spectral range femtosecond Z-scan studies, respectively. The Ru(II/III) oxidation potentials and wavelengths of the optical absorption maxima decrease on pi-bridge lengthening, until the tri(phenyleneethynylene) complex is reached, further chain lengthening leaving these parameters invariant; theoretical studies employing time-dependent density functional theory have shed light on this behavior. The quadratic nonlinearity beta(1064) and two-photon absorption cross-section reach maximal values at this same pi-bridge length, a similar saturation behavior that may reflect a common importance of ruthenium-to-alkynyl ligand charge transfer in electronic and optical behavior in these molecules.
- Published
- 2009
- Full Text
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46. Carbohydrate dependent targeting of cancer cells by bleomycin-microbubble conjugates.
- Author
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Chapuis JC, Schmaltz RM, Tsosie KS, Belohlavek M, and Hecht SM
- Subjects
- Antibiotics, Antineoplastic chemistry, Biotin chemistry, Bleomycin administration & dosage, Bleomycin chemistry, Bleomycin pharmacokinetics, Breast Neoplasms drug therapy, Cell Line, Tumor, Humans, Microbubbles, Streptavidin administration & dosage, Streptavidin chemistry, Antibiotics, Antineoplastic administration & dosage, Antibiotics, Antineoplastic pharmacokinetics, Biotin analogs & derivatives, Bleomycin analogs & derivatives, Breast Neoplasms metabolism, Drug Delivery Systems methods
- Abstract
Biotinylated bleomycin A(5) was attached to streptavidin-derivatized microbubbles, and a solution containing the conjugate was passed over a monolayer of cultured MCF-7 cells. The bleomycin-derivatized microbubbles adhered to the MCF-7 cells, and the association could be monitored by the use of a microscope. Three other cancer cell lines gave similar results. The bleomycin-microbubble conjugate did not bind to a normal breast cell line (MCF-10A) or to the matched noncancer cell lines corresponding to the other cancer cell lines targeted by bleomycin. No binding to any tested cell line was observed when the microbubbles lacked conjugated bleomycin A(5) or when the microbubble contained a bleomycin A(5) analogue lacking the carbohydrate moiety.
- Published
- 2009
- Full Text
- View/download PDF
47. Identification of conical structures in small aluminum oxide clusters: infrared spectroscopy of (Al2O3)1-4(AlO)+.
- Author
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Santambrogio G, Janssens E, Li S, Siebert T, Meijer G, Asmis KR, Döbler J, Sierka M, and Sauer J
- Abstract
The vibrational spectroscopy of the electronically closed-shell (Al 2O 3) n (AlO) (+) cations with n = 1-4 is studied in the 530-1200 cm (-1) range by infrared predissociation spectroscopy of the corresponding ion-He atom complexes in combination with quantum chemical calculations. In all cases we find, assisted by a genetic algorithm, global minimum structures that differ considerably from those derived from known modifications of bulk alumina. The n = 1 and n = 4 clusters exhibit an exceptionally stable conical structure of C 3 v symmetry, whereas for n = 2 and n = 3, multiple isomers of lower symmetry and similar energy may contribute to the recorded spectra. A blue shift of the highest energy absorption band is observed with increasing cluster size and attributed to a shortening of Al-O bonds in the larger clusters. This intense band is assigned to vibrational modes localized on the rim of the conical structures for n = 1 and n = 4 and may aid in identifying similar, highly symmetric structures in larger ions.
- Published
- 2008
- Full Text
- View/download PDF
48. Surface structure of metal-organic framework grown on self-assembled monolayers revealed by high-resolution atomic force microscopy.
- Author
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Szelagowska-Kunstman K, Cyganik P, Goryl M, Zacher D, Puterova Z, Fischer RA, and Szymonski M
- Subjects
- Crystallization, Microscopy, Atomic Force, Microscopy, Electron, Transmission, Nanoparticles chemistry, Surface Properties, Copper chemistry, Organometallic Compounds chemistry, Silicon chemistry, Silicon Dioxide chemistry, Tricarboxylic Acids chemistry
- Abstract
The surface structure of an individual metal-organic framework (MOF) microcrystal grown on a functionalized surface has been successfully investigated for the first time in air and vacuum using high-resolution atomic force microscopy. Moreover, this detailed surface analysis has been utilized to optimize the MOF formation procedure to obtain a defect-free surface structure. Comparison of obtained data with recent microscopic studies performed on the same MOF crystal but grown by a conventional procedure clearly shows a much higher quality of crystals produced by surface oriented growth. Importantly, this method of preparing crystals suitable for microscopic analysis is also much faster (3 days compared to 2 years) and, in contrast to the conventional method, produces material suitable for in situ study. These results thus demonstrate for the first time the possibility of nanoscale investigation/modification of MOF surface structure.
- Published
- 2008
- Full Text
- View/download PDF
49. The photo-Favorskii reaction of p-hydroxyphenacyl compounds is initiated by water-assisted, adiabatic extrusion of a triplet biradical.
- Author
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Givens RS, Heger D, Hellrung B, Kamdzhilov Y, Mac M, Conrad PG 2nd, Cope E, Lee JI, Mata-Segreda JF, Schowen RL, and Wirz J
- Subjects
- Benzyl Alcohols chemical synthesis, Benzyl Alcohols chemistry, Free Radicals chemistry, Free Radicals radiation effects, Molecular Structure, Phenylacetates chemical synthesis, Phenylacetates radiation effects, Photochemistry, Quantum Theory, Ultraviolet Rays, Water chemistry, Phenylacetates chemistry
- Published
- 2008
- Full Text
- View/download PDF
50. Chemical shift correlation NMR spectroscopy with indirect detection in fast rotating solids: studies of organically functionalized mesoporous silicas.
- Author
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Wiench JW, Bronnimann CE, Lin VS, and Pruski M
- Published
- 2007
- Full Text
- View/download PDF
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