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Intermediate Structures (intermediate + structure)
Selected AbstractsSolid,Solid Phase Transitions: Interface Controlled Reactivity and Formation of Intermediate StructuresCHEMISTRY - A EUROPEAN JOURNAL, Issue 36 2007Stefano Leoni Dr. Abstract Finding new pathways to novel materials is an open challenge in modern solid-state chemistry. Among the reasons that still prevent a rational planning of synthetic routes is the lack of an atomistic understanding at the moment of phase formation. Metastable phases are, in this respect, powerful points of access to new materials. For the synthetic efforts to fully take advantage of such peculiar intermediates, a precise atomistic understanding of critical processes in the solid state in its many facets, that is, nucleation patterns, formation and propagation of interfaces, intermediate structures, and phase growth, is mandatory. Recently we have started a systematic theoretical study of phase transitions, especially of processes with first-order thermodynamics, to reach a firm understanding of the atomistic mechanisms governing polymorphism in the solid state. A clear picture is emerging of the interplay between nucleation patterns, the evolution of domain interfaces and final material morphology. Therein intermediate metastable structural motifs with distinct atomic patterns are identified, which become exciting targets for chemical synthesis. Accordingly, a new way of implementing simulation strategies as a powerful support to the chemical intuition is emerging. Simulations of real materials under conditions corresponding to the experiments are shedding light onto yet elusive aspects of solid,solid transformations. Particularly, sharp insights into local nucleation and growth events allow the formulation of new concepts for rationalizing interfaces formed during phase nucleation and growth. Structurally different and confined in space, metastable interfaces occurring during polymorph transformations bring about distinct diffusion behavior of the chemical species involved. More generally, stable structures emerge as a result of the concurrence of the transformation mechanism and of chemical reactions within the phase-growth fronts. [source] Reactions of platinum cluster ions with benzeneRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 12 2006Hongtao Liu In this work, the cation and anion products of the reactions between platinum clusters produced by laser ablation and the benzene molecules seeded in argon have been studied using a high-resolution reflectron time-of-flight mass spectrometer (RTOFMS). The dominant cation products are [C6nH6n,,,k]+ and [Ptm(C6H6)n]+ complexes, while the dominant anion products are dehydrogenated species, [C6H5PtH],, [PtC12Hk], and [PtmC6H4,·,·,·,(C6H6)n],, etc. Some important intermediate structures ([PtC6H6]+, [Pt(C6H6)2]+, [Pt2(C6H6)3]+, [C6H5PtH],, [Pt2C6H4],, [Pt3C6H4], and [Pt4C6H4],) have been analyzed using density functional theory (DFT) calculations. Different reaction mechanisms are proposed for platinum cluster cations and anions with benzene, respectively. Copyright © 2006 John Wiley & Sons, Ltd. [source] Fibrillation of ,-lactalbumin: Effect of crocin and safranal, two natural small molecules from Crocus sativus,BIOPOLYMERS, Issue 10 2010Mohammad-Bagher Ebrahim-Habibi Abstract Formation of toxic amyloid structures is believed to be associated with various late-onset neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. The fact that many proteins in addition to those that are associated with clinical conditions have the potential to form amyloid fibrils in vitro provides opportunities for studying the fundamentals of protein aggregation and amyloid formation in model systems. Accordingly, considerable interest and effort has been directed toward developing small molecules to inhibit the formation of fibrillar assemblies and their associated toxicities. In the present study, we investigated the inhibitory effect of crocin and safranal, two principal components of saffron, on fibrillation of apo-,-lactalbumin (a-,-LA), used as a model protein, under amyloidogenic conditions. In the absence of any ligand, formation of soluble oligomers became evident after 18 h of incubation, followed by subsequent appearance of mature fibrils. Upon incubation with crocin or safranal, while transition phase to monomeric beta structures was not significantly affected, formation of soluble oligomers and following fibrillar assemblies were inhibited. While both safranal and crocin had the ability to bind to hydrophobic patches provided in the intermediate structures, and thereby inhibit protein aggregation, crocin was found more effective, possibly due to its simultaneous hydrophobic and hydrophilic character. Cell viability assay indicated that crocin could diminish toxicity while safranal act in reverse order. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 854,865, 2010. [source] Limited proteolysis analysis of the ribosome is affected by subunit associationBIOPOLYMERS, Issue 6 2009Daisy-Malloy Hamburg Abstract Our understanding of the structural organization of ribosome assembly intermediates, in particular those intermediates that result from misfolding leading to their eventual degradation within the cell, is limited because of the lack of methods available to characterize assembly intermediate structures. Because conventional structural approaches, such as NMR, X-ray crystallography, and cryo-EM, are not ideally suited to characterize the structural organization of these flexible and sometimes heterogeneous assembly intermediates, we have set out to develop an approach combining limited proteolysis with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) that might be applicable to ribonucleoprotein complexes as large as the ribosome. This study focuses on the limited proteolysis behavior of appropriately assembled ribosome subunits. Isolated subunits were analyzed using limited proteolysis and MALDI-MS and the results were compared with previous data obtained from 70S ribosomes. Generally, ribosomal proteins were found to be more stable in 70S ribosomes than in their isolated subunits, consistent with a reduction in conformational flexibility on subunit assembly. This approach demonstrates that limited proteolysis combined with MALDI-MS can reveal structural changes to ribosomes on subunit assembly or disassembly, and provides the appropriate benchmark data from 30S, 50S, and 70S proteins to enable studies of ribosome assembly intermediates. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 410,422, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Early Structural Evolution of Native Cytochrome c after Solvent RemovalCHEMBIOCHEM, Issue 15 2008Michal Z. Steinberg Abstract Electrospray ionization transfers thermally labile biomolecules, such as proteins, from solution into the gas phase, where they can be studied by mass spectrometry. Covalent bonds are generally preserved during and after the phase transition, but it is less clear to what extent noncovalent interactions are affected by the new gaseous environment. Here, we present atomic-level computational data on the structural rearrangement of native cytochrome c immediately after solvent removal. The first structural changes after desolvation occur surprisingly early, on a timescale of picoseconds. For the time segment of up to 4.2 ns investigated here, we observed no significant breaking of native noncovalent bonds; instead, we found formation of new noncovalent bonds. This generally involves charged residues on the protein surface, resulting in transiently stabilized intermediate structures with a global fold that is essentially the same as that in solution. Comparison with data from native electron capture dissociation experiments corroborates both its mechanistic postulations and our computational predictions, and suggests that global structural changes take place on a millisecond timescale not covered by our simulations. [source] Solid,Solid Phase Transitions: Interface Controlled Reactivity and Formation of Intermediate StructuresCHEMISTRY - A EUROPEAN JOURNAL, Issue 36 2007Stefano Leoni Dr. Abstract Finding new pathways to novel materials is an open challenge in modern solid-state chemistry. Among the reasons that still prevent a rational planning of synthetic routes is the lack of an atomistic understanding at the moment of phase formation. Metastable phases are, in this respect, powerful points of access to new materials. For the synthetic efforts to fully take advantage of such peculiar intermediates, a precise atomistic understanding of critical processes in the solid state in its many facets, that is, nucleation patterns, formation and propagation of interfaces, intermediate structures, and phase growth, is mandatory. Recently we have started a systematic theoretical study of phase transitions, especially of processes with first-order thermodynamics, to reach a firm understanding of the atomistic mechanisms governing polymorphism in the solid state. A clear picture is emerging of the interplay between nucleation patterns, the evolution of domain interfaces and final material morphology. Therein intermediate metastable structural motifs with distinct atomic patterns are identified, which become exciting targets for chemical synthesis. Accordingly, a new way of implementing simulation strategies as a powerful support to the chemical intuition is emerging. Simulations of real materials under conditions corresponding to the experiments are shedding light onto yet elusive aspects of solid,solid transformations. Particularly, sharp insights into local nucleation and growth events allow the formulation of new concepts for rationalizing interfaces formed during phase nucleation and growth. Structurally different and confined in space, metastable interfaces occurring during polymorph transformations bring about distinct diffusion behavior of the chemical species involved. More generally, stable structures emerge as a result of the concurrence of the transformation mechanism and of chemical reactions within the phase-growth fronts. [source] | ||||||||||