Search

A single-domain protein catenane refers to two mechanically interlocked polypeptide rings that fold synergistically into a compact and integrated structure, which is extremely rare in nature. Herein, we report a single-domain protein catenane of dihydrofolate reductase (cat-DHFR). The design was achieved by rewiring the connectivity between secondary motifs to introduce artificial entanglement and the synthesis was readily accomplished by a series of programmed streamlined post-translational processing events in cells without any additional in vitro reactions. The target molecule contains few exogenous motifs and has been thoroughly characterized by combined techniques of LC-MS, SDS-PAGE, protease cleavage experiment, and ion mobility mass spectrometry. Compared to the linear control, cat-DHFR retains the catalytic capability and exhibits enhanced stability against thermal or chemical denaturation due to conformational restriction. The results suggest that linear proteins may be converted into concatenated single-domain counterparts with almost identical chemical composition, well-preserved function, and elevated stability, which represents an entirely new horizon in protein science.

Ni(COD)2-catalyzed cycloaddition reactions to access pyridines have been extensively studied. However, this catalyst typically requires drying procedures and inert-atmosphere techniques for the reactions. Herein, we report operationally simple nickel(0) catalysis to access substituted pyridines from various nitriles and 1,6-diynes without the aid of air-free techniques. The Ni-Xantphos-based catalytic manifold is tolerant to air, moisture, and heat while promoting the [2 + 2 + 2] cycloaddition reactions with high reaction yields and broad substrate scope. In addition, we disclose that not only the steric effect but also the frontier molecular orbital interactions can play a critical role in determining the regiochemical outcome of nickel-catalyzed [2 + 2 + 2] cycloaddition for the synthesis of substituted pyridines.

Entangled proteins have attracted significant research interest. Herein, we report the first rationally designed lasso proteins, or protein [1]rotaxanes, by using a p53dim-entwined dimer for intramolecular entanglement and a SpyTag-SpyCatcher reaction for side-chain ring closure. The lasso structures were confirmed by proteolytic digestion, mutation, NMR spectrometry, and controlled ligation. Their dynamic properties were probed by experiments such as end-capping, proteolytic digestion, and heating/cooling. As a versatile topological intermediate, a lasso protein could be converted to a rotaxane, a heterocatenane, and a "slide-ring" network. Being entirely genetically encoded, this robust and modular lasso-protein motif is a valuable addition to the topological protein repertoire and a promising candidate for protein-based biomaterials.

A rationally designed supramolecular FRET pair consisting of cyanine3-cucurbit[7]uril (Cy3-CB[7]) and boron-dipyrromethene 630/650-adamantylammonium (BDP-AdA) can be used to visualize organelle-specific autophagy events. The intracellular accumulations of Cy3-CB[7] in lysosomes and BDP-AdA in lipid droplets (LDs) and the formation of an intracellular host-guest complex between Cy3-CB[7] and BDP-AdA resulting in FRET signals allow us to visualize the fusion of LDs with lysosomes, namely, lipophagy. This study demonstrates the potential of supramolecular imaging based on bio-orthogonal host-guest interactions in the investigation of selective autophagy events.

Hierarchical self-assembly of building blocks over multiple length scales is ubiquitous in living organisms. Microtubules are one of the principal cellular components formed by hierarchical self-assembly of nanometer-sized tubulin heterodimers into protofilaments, which then associate to form micron-length-scale, multi-stranded tubes. This peculiar biological process is now mimicked with a fully synthetic molecule, which forms a 1:1 host-guest complex with cucurbit[7]uril as a globular building block, and then polymerizes into linear poly-pseudorotaxanes that associate laterally with each other in a self-shape-complementary manner to form a tubular structure with a length over tens of micrometers. Molecular dynamic simulations suggest that the tubular assembly consists of eight poly-pseudorotaxanes that wind together to form a 4.5 nm wide multi-stranded tubule.

Herein we report a facile transformation of hydroxylated cucurbit[n]uril (CB[n], n = 6 and 7) to other functionality-conjugated CB[n]s by nucleophilic substitution of the hydroxyl group with a wide...

Es existieren über 100 Hydrophobieskalen für Aminosäuren, die auf unterschiedlichen Ansätzen basieren und einheitlich in kondensierter Phase ermittelt werden. Ein Vergleich der Hydrophobiewerte aus verschiedenen Methoden und die Ermittlung ihrer relativen Rangfolge sind jedoch anspruchsvoll, da die Wechselwirkungen zwischen der Umgebung und der Aminosäure in jeder Methode spezifisch sind. Hier überwinden wir diese Einschränkung, indem wir die Eigenschaften von Aminosäuren in der Reinraumumgebung der Gasphase untersuchen. In der Gasphase bleiben standardmäßig entropische Beiträge des hydrophoben Effektes aus, und nur die Polarität der Seitenkette ist für die Selbstorganisation entscheidend. Dies ermöglicht die Ableitung einer neuartigen Hydrophobieskala, die ausschließlich auf der Interaktion einzelner Aminosäureeinheiten innerhalb des Clusters basiert und somit die Eigenschaften der Seitenketten besser abbildet. Dieses Prinzip kann für die Klassifizierung von nicht‐natürlichen Derivaten angewendet werden, wie hier für fluorierte Aminosäurevarianten gezeigt ist.

The protonated basic side chains in tryptic peptide ions can form intramolecular hydrogen bonds with backbone amide carbonyls, which inhibit the backbone cleavage and hinder the peptide sequencing using mass spectrometry. To study the strength of intramolecular hydrogen bonds and its effect on the backbone cleavage, we carried out the energy-dependent collision-induced dissociation (CID) of tryptic peptides and their modified ones. The N-acylation of lysine-terminated peptides was used to convert the primary amines at both lysine and the N-terminus into amides in order to block the primary protonation sites. The guanidination was employed to transform lysine into homoarginine in order to imitate arginine-terminated peptides. Then, N-acylation was applied to the guanidinated peptides to prepare N-acylated, homoarginine-terminated peptides. Singly charged peptide ions were generated by electrospray ionization in a Q-TOF instrument and their CID spectra were obtained as a function of collision energy under nearly single-collision conditions with Xe as the target gas. The energy-dependent survival yield of the precursor ion provided information on the change in dissociation energy of peptides after chemical modifications. We also identified possible sites and numbers of hydrogen bonds that stabilized a charge-solvated structure by comparing the variation in product yields with the location of backbone cleavage. By taking these data together, we estimated the relative strength of intramolecular hydrogen bonds formed in lysine- and homoarginine-terminated peptides before and after N-acylation. Our results demonstrate that N-acylation lowers the dissociation energy of tryptic peptides and facilitates the backbone cleavage by preventing the formation of intramolecular hydrogen bonds, enabling accurate identification of peptides.

Polyoxometalate clusters possess unique catalytic and electromagnetic properties. The structure and function of polyoxometalates is dictated by complex oligomerization processes, which in turn depend on the solution conditions. In this work, small gas-phase polyoxomolybdate nanoclusters HMonO3n+11-, n = 1--8, and MonO3n+12-, n = 2--8 were investigated after nanoelectrospray of an acidified solution of ammonium heptamolybdate heptahydrate by ion-mobility spectrometry--mass spectrometry (IMS--MS), infrared multiple photon dissociation (IRMPD) spectroscopy, and infrared action spectroscopy in helium nanodroplets. The spectra and collision cross-sections obtained were matched to predictions from density-functional theory (DFT) to unravel the structural progression of nanoclusters with increasing size. For doubly charged clusters, a transition between chain (n = 2--3), ring (n = 4--5), and compact (n ≥ 6) structures is observed in IM--MS and IR spectroscopy experiments, in agreement with low-energy structures from DFT calculations. For singly charged clusters, reduced Coulombic repulsion and hydrogen bonding interactions are found to strongly influence the most stable cluster structure. Notably, a noncovalent ring structure is observed for HMo3O101-, stabilized by a strong intramolecular hydrogen bond, and a compact structure is observed for HMo5O161-, in contrast to the ring structure favored for Mo5O162-.

A protonated amino acid can interact in several ways with another uncharged amino acid molecule to form a protonated dimer. In case of amino acids that do not have basic or acidic side chains, the most likely protonation site is the amino group and the then protonated amine can be involved in a pairwise interaction with a neutral amine, a carboxylic acid, a carboxylate group and/or the sidechain of the partner amino acid. Here, we employ gas-phase infrared spectroscopy and density functional theory to identify these pairwise interactions in protonated homodimers of serine, isoleucine, phenylalanine and tyrosine. The results show the influence of the different side-chains on the respective interactions. A charge-solvated structure with pairwise interaction between a protonated amine and a neutral amine is preferred if the side chain can provide additional stabilizing interaction with the positive charge. In contrast, for amino acids where the side chain only interacts weakly with the protonated amine group, a protonated dimer is formed by an interaction between the protonated amine and the neutral carboxylic acid of the second amino acid.

Annulative π-extension chemistry provides a concise synthetic route to polycyclic arenes. Herein, we disclose a nondirected annulation approach of unactivated simple arenes. The palladium-catalyzed 2-fold C–H arylation event facilitates tandem C–C linkage relays to furnish fully benzenoid triphenylene frameworks using cyclic diaryliodonium salts. The inseparable regioisomeric mixture of 1- and 2-methyltriphenylenes is identified by the combined analysis of ion mobility-mass spectrometry, gas-phase infrared spectroscopy, and molecular simulation studies.

Amyloidogenic peptides and proteins play a crucial role in a variety of neurodegenerative disorders such as Alzheimer's and Parkinson's disease. These proteins undergo a spontaneous transition from a soluble, often partially folded form, into insoluble amyloid fibrils that are rich in β-sheets. Increasing evidence suggests that highly dynamic, polydisperse folding intermediates, which occur during fibril formation, are the toxic species in the amyloid-related diseases. Traditional condensed-phase methods are of limited use for characterizing these states because they typically only provide ensemble averages rather than information about individual oligomers. Here we report the first direct secondary-structure analysis of individual amyloid intermediates using a combination of ion mobility spectrometry-mass spectrometry and gas-phase infrared spectroscopy. Our data reveal that oligomers of the fibril-forming peptide segments VEALYL and YVEALL, which consist of 4-9 peptide strands, can contain a significant amount of β-sheet. In addition, our data show that the more-extended variants of each oligomer generally exhibit increased β-sheet content.

Ion mobility mass spectrometry (IM-MS) has been broadly utilized in the structural characterization of noncovalent, supramolecular complexes. In this chapter, we discuss three types of supramolecular complexes, and their structural dynamics observed in IM-MS studies. Firstly, host–guest chemistry of cucurbituril, crown ether, and cyclodextrin is discussed. Secondly, self-assembly mechanisms of amino acids and peptides are introduced. Finally, structural studies of protein–protein complexes are presented. We mainly focus on insights into the physicochemical properties of supramolecular complexes (e.g. molecular interactions, role of water molecules in complexation and structural features).

The classification of amino acids according to their intrinsic properties, such as the physico‐chemical properties and structure, yields fundamental insights into their role in interactions in biological processes. More than 100 hydrophobicity scales have been introduced, with each being based on a distinct condensed‐phase approach. However, a comparison of the hydrophobicity values gained from different techniques, and their relative ranking is not straightforward, as the interactions between the environment and amino acid are unique to each method. Here, we overcome this limitation by studying the properties of amino acids in the clean‐room environment of the gas phase. In the gas phase, entropic contributions from the hydrophobic effect are by default absent and only the side‐chain´s polarity dictates self‐assembly. This allows for the derivation of a novel hydrophobicity scale, which is solely based on the interaction between individual amino acid units within the cluster and thus more accurately reflects the intrinsic nature of a side‐chain. This principle can be further applied to classify non‐natural derivatives, as shown here for fluorinated amino acid variants.

Polyalanine based peptides that carry a lysine at the C-terminus ([Ac-AlanLys + H](+)) are known to form α-helices in the gas phase. Three factors contribute to the stability of these helices: (i) the interaction between the helix macro dipole and the charge, (ii) the capping of dangling C[double bond, length as m-dash]O groups by lysine and (iii) the cooperative hydrogen bond network. In previous studies, the influence of the interaction between the helix dipole and the charge as well as the impact of the capping was studied intensively. Here, we complement these findings by systematically assessing the third parameter, the H-bond network. In order to selectively remove one H-bond along the backbone, we use amide-to-ester substitutions. The resulting depsi peptides were analyzed by ion-mobility and m/z-selective infrared spectroscopy as well as theoretical calculations. Our results indicate that peptides which contain only one ester bond still maintain the helical conformation. We conclude that the interaction between the charge and the helix macro-dipole is most crucial for the formation of the α-helical conformation and a single backbone H-bond has only little influence on the overall stability.

The immediate environment of a molecule can have a profound influence on its properties. Benzocaine, the ethyl ester of para-aminobenzoic acid, which finds an application as a local anesthetic (LA), is found to adopt in its protonated form at least two populations of distinct structures in the gas phase and their relative intensities strongly depend on the properties of the solvent used in the electrospray ionization (ESI) process. Here we combine IR-vibrational spectroscopy with ion mobility-mass spectrometry (IM-MS) to yield gas-phase IR spectra of simultaneously m/z and drift-time resolved species of benzocaine. The results allow for an unambiguous identification of two protomeric species - the N- and O-protonated form. Density functional theory (DFT) calculations link these structures to the most stable solution and gas-phase structures, respectively, with the electric properties of the surrounding medium being the main determinant for the preferred protonation site. The fact that the N-protonated form of benzocaine can be found in the gas phase is owed to kinetic trapping of the solution phase structure during transfer into the experimental setup. These observations confirm earlier studies on similar molecules where N- and O-protonation has been suggested.

The amino acid serine is known to form a very stable octamer that has properties that set it apart from serine complexes of different sizes or from complexes composed of other amino acids. For example, both singly protonated serine octamers and anionic octamers complexed with two halogen ions strongly prefer homochirality, even when assembled from racemic D,L mixtures. Consequently, the structures of these complexes are of great interest, but no acceptable candidates have so far been identified. Here, we investigate anionic serine octamers coordinated with two chloride ions using a novel technique coupling ion mobility spectrometry–mass spectrometry with infrared spectroscopy, in combination with theoretical calculations. The results allow the identification of a unique structure for (Ser8Cl2)2− that is highly symmetric, very stable and homochiral and whose calculated properties match those observed in experiments. Octameric complexes of serine are long known for their special properties, such as their enhanced stability and preference for homochirality. Yet, there is no consensus on their structures. Now, experimental data on the serine octamer–dichloride complex is presented that supports a highly symmetrical, highly stable structure.

In the gas phase, protein ions can adopt a broad range of structures, which have been investigated extensively in the past using ion mobility-mass spectrometry (IM-MS)-based methods. Compact ions with low number of charges undergo a Coulomb-driven transition to partially folded species when the charge increases, and finally form extended structures with presumably little or no defined structure when the charge state is high. However, with respect to the secondary structure, IM-MS methods are essentially blind. Infrared (IR) spectroscopy, on the other hand, is sensitive to such structural details and there is increasing evidence that helices as well as β-sheet-like structures can exist in the gas phase, especially for ions in low charge states. Very recently, we showed that also the fully extended form of highly charged protein ions can adopt a distinct type of secondary structure that features a characteristic C5-type hydrogen bond pattern. Here we use a combination of IM-MS and IR spectroscopy to further investigate the influence of the initial, native conformation on the formation of these structures. Our results indicate that when intramolecular Coulomb-repulsion is large enough to overcome the stabilization energies of the genuine secondary structure, all proteins, regardless of their sequence or native conformation, form C5-type hydrogen bond structures. Furthermore, our results suggest that in highly charged proteins the positioning of charges along the sequence is only marginally influenced by the basicity of individual residues.

Triacylglycerol (TAG) lipases hydrolyze ester bonds in TAG and release diacylglycerol (DAG), monoacylglycerol (MAG), and FA. We present a one-step chemical derivatization method for label-free quantification of a mixture of TAG, DAG, and MAG following lipase assay by ESI-MS. Because the ionization efficiencies of TAG, DAG, and MAG are not identical, lipase reaction products, DAG and MAG, are derivatized to TAG species by esterifying their hydroxyl groups using acyl chloride, whose acyl chain contains one less (or one more) -CH2 group than that of substrate TAG. This resulted in three TAG species that were separated by 14 Da from one another and exhibited similar ion responses representing their molar amounts in the mass spectra. A good linear correlation was observed between peak intensity ratios and molar ratios in calibration curve. This method enables simultaneous quantification of TAG, DAG, and MAG in lipase assay and, in turn, allows stoichiometric determination of the concentrations of FAs released from TAG and DAG separately. By applying this strategy to measure both TAG and DAG lipolytic activities of the yeast Tgl2 lipase, we demonstrated its usefulness in studying enzymatic catalysis, as lipase enzymes often show dissimilar activities toward these lipids.

The energy- and time-dependent branching to the competing dissociation paths are studied by theory for coupled unimolecular dissociations of the o-, m-, and p-chlorotoluene radical cations to C7H7 + (benzylium and tropylium). There are four different paths to C7H7 + , three to the benzylium ion and one to the tropylium ion, and all of them are coupled together. The branching to the multiple paths leads to the multiexponential decay of reactant with the branching ratio depending on both internal energy and time. To gain insights into the multipath branching, we study the detailed kinetics as a function of time and internal energy on the basis of ab inito/RRKM calculations. The number of reaction steps to C7H7 + is counted for each path. Of the three isomers, the meta mostly goes through the coupling, whereas the para proceeds with little or no coupling. In the beginning, some reactants with high internal energy decay fast to the benzylium ion without any coupling and others rearrange to the other isomers. Later on all three isomers dissociate to the products via long-lived intermediates. Thus, the reactant shows a multiexponential decay and the branching ratio varies with time as the average internal energy decreases with time. The reciprocal of the effective lifetime is taken as the rate constant. The resulting rate-energy curves are in line with experiments. The present results suggest that the coupling between the stable isomers is thermodynamically controlled, whereas the branching to the product is kinetically controlled.

In the management of alien invasive plants in coastal dunes, plot-based approaches have generally been adopted: researchers establish a set of experimental (often topographically homogeneous) plots of a given size where the plants are removed, and recovery patterns are monitored for a period of time. Therefore, the literature still lacks a detailed understanding of where (i.e., under what topographic circumstances) native and invasive species are likely to recolonize after clearance of a large dunefield. In this study, we report on an unprecedented case from the Sindu dunefield in western Korea in which both native and invasive plants had been thoroughly removed to bare sand over a vast area (ca. 11.0 ha), followed by in situ exhaustive mapping of regeneration patterns throughout the entire cleared zone twelve times within four years. The results showed that, after removal, natives and invaders increased to occupy larger (>50%) areas than those in the pre-removal state. Furthermore, Ecological-Niche Factor Analysis revealed that these two vegetation types exhibited markedly and significantly contrasting regeneration hotspots: invasive plants expanded primarily in low-lying sites that were close to trails. These findings indicate that the recolonization of invasive species was not a spatially random process but rather concentrated along the trails through which local employees transported removed plant material, inadvertently dropping invader propagules. We conclude that removal is often costly, and if executed without a careful plan for the movement of workers, equipment, and plant debris, these efforts may even increase the extent of invasions beyond the initial state.

Kann die Struktur kleinerer bis mittelgroser Proteine beim Ubergang aus der Losung in die Gasphase bewahrt werden? Zwar haben sich eine Vielzahl von Studien dieser Frage gewidmet, jedoch steht eine eindeutige Antwort noch aus. Die Klarung dieses Problems ist gleichwohl wichtig, denn davon hangt es ab, ob die empfindlichen Methoden der nativen Massenspektrometrie Probleme der Strukturbiologie adressieren konnen. Mithilfe einer Kombination aus Ionenmobilitats-Massenspektrometrie und Infrarotspektroskopie untersuchen wir sowohl Sekundar- als auch Tertiarstruktur von Proteinen, die unter milden Bedingungen aus der Losung in die Gasphase gebracht werden. In dieser Studie wurden die Molekule Myoglobin und β-Lactoglobulin untersucht, die prototypische Beispiele fur helikale bzw. β-Faltblatt-reiche Proteine sind. Unsere Ergebnisse zeigen, dass fur niedrige Ladungszustande und unter sanften Bedingungen Aspekte der nativen Sekundar- und Tertiarstuktur bewahrt werden konnen.

Can the structures of small to medium‐sized proteins be conserved after transfer from the solution phase to the gas phase? A large number of studies have been devoted to this topic, however the answer has not been unambiguously determined to date. A clarification of this problem is important since it would allow very sensitive native mass spectrometry techniques to be used to address problems relevant to structural biology. A combination of ion‐mobility mass spectrometry with infrared spectroscopy was used to investigate the secondary and tertiary structure of proteins carefully transferred from solution to the gas phase. The two proteins investigated are myoglobin and β‐lactoglobulin, which are prototypical examples of helical and β‐sheet proteins, respectively. The results show that for low charge states under gentle conditions, aspects of the native secondary and tertiary structure can be conserved.

The charge distribution in a molecule is crucial in determining its physical and chemical properties. Aminobenzoic acid derivatives are biologically active small molecules, which have two possible protonation sites: the amine (N-protonation) and the carbonyl oxygen (O-protonation). Here, we employ gas-phase infrared spectroscopy in combination with ion mobility-mass spectrometry and density functional theory calculations to unambiguously determine the preferred protonation sites of p-, m-, and o-isomers of aminobenzoic acids as well as their ethyl esters. The results show that the site of protonation does not only depend on the intrinsic molecular properties such as resonance effects, but also critically on the environment of the molecules. In an aqueous environment, N-protonation is expected to be lowest in energy for all species investigated here. In the gas phase, O-protonation can be preferred, and in those cases, both N- and O-protonated species are observed. To shed light on a possible proton migration pathway, the protonated molecule-solvent complex as well as proton-bound dimers are investigated.

So-called super-secondary structures such as the beta-hairpin, studied here, form an intermediate hierarchy between secondary and tertiary structures of proteins. Their sequence-derived 'pure' peptide backbone conformation is combined with 'remote' interstrand or interresidue contacts reminiscent of the 3D-structure of full-length proteins. This renders them ideally suited for studying potential nucleation sites of protein folding reactions as well as intermolecular interactions. But beta-hairpins do not merely serve as model systems; their unique structure characteristics warrant a central role in structural studies on their own. In this study we applied photo cross-linking in combination with high-resolution mass spectrometry and computational modeling as well as with ion mobility-mass spectrometry to elucidate these structural properties. Using variants of a known beta-hairpin representative, the so-called trpzip peptide and its ligands, we found evidence for a conformational transition of the beta-hairpin and its impact on ligand binding.

Specific and nonspecific bindings of alkaline-earth metal ions to the thrombin-binding aptamer (TBA) DNA d(GGTTGGTGTGGTTGG) were studied using electrospray ionization (ESI) mass spectrometry (MS). A single-stranded DNA d(AATTAATGTAATTAA) was used as a control for nonspecific binding. Both 1:1 and 2:1 metal–DNA complexes formed in 3:1 water/isopropanol were detected with ESI-MS and their binding constants were determined by the titration method. The 1:1 binding constant (K1) of Sr2+ or Ba2+ for TBA was three orders of magnitude greater than their K1 for the control DNA, whereas K1 of Mg2+ or Ca2+ for TBA was comparable to their K1 for the control DNA. To the contrary, the second binding constant (K2) was nearly the same independent of the metal ion and DNA. To see if addition of metal ion led to a structural change in DNA, the circular dichroism (CD) spectra of DNA in ESI solvent were obtained in the presence and absence of metal ion. TBA showed characteristic bands of the chair-type guanine-quadruplex (G4) structure. Significantly, addition of Sr2+ or Ba2+ enhanced the G4 bands of TBA, but neither Mg2+ nor Ca2+ induced a change, indicating that Sr2+ and Ba2+ interact strongly with G4 TBA and stabilize it. Control DNA showed no special motif and none of the four metal ions affected its CD spectra. Binding constants and CD results suggest that only the first binding of Sr2+ and Ba2+ to G4 TBA is specific and the first binding of Mg2+ and Ca2+ as well as the second binding of all four metal ions are nonspecific. The specific and nonspecific bindings of alkaline-earth metal ions to G4 TBA are further rationalized in terms of ionic radius, coordination number, and Gibbs free energy of dehydration of the metal ion.

Currently, Building Information Modeling (BIM) has been recognized as one of the main processes and technologies that can enhance design and construction quality by simulating and optimizing busine...

The size and shape of CdSe nanorods, CdSe tetrapods, and CdS nanowires were tailored by chemical and photochemical etchings in chloromethane solvents. Nanocrystals were synthesized by colloidal growth, and their sizes and shapes were visualized by transmission electron microscopy before and after etching. Crystal structures were confirmed by X-ray diffraction, and optical properties were monitored during etching. Chemical etching with tributylphosphine preferentially shortens the length of nanocrystals, whereas photochemical etching with both primary alkylamine and tributylphosphine reduces the diameter more than the length. The surface of etched nanocrystals was characterized by X-ray photoelectron spectroscopy, and the etching products dissolved in solvent were analyzed by matrix-free laser desorption ionization mass spectrometry. Spectroscopic results suggest that the chloride ion is the active species: Chloride ions are generated either by chemical activation of chloromethane solvents with tributylpho...

With the rapid development of computer technology and ongoing destruction of traditional buildings, more and more attention is paid to digital methods for the design and preservation of traditional buildings. Unlike 2D methods, Building Information Modeling (BIM) provides an object-oriented and parametric digital representation way for traditional building components. However, one of the main limitations currently is that parametric information cannot be exchanged between BIM software packages. Therefore each kind of software must have their own parametric library which causes extensive works. In this research, the authors developed an open BIM-based library using an XML parametric approach to solve the above problems, represented traditional components according to an XML schema, and parametrically implemented these XML files in a browser which can be accessed by users for their easy component edit and selection. And then based on the XML file of one component, implemented an Add-on in ArchiCAD for users to parametrically edit and directly utilize. Thus based on these XML files, a browser for users' view and selection purpose and an add-on for users' application purpose were developed. Future research will focus on implementing these XML files in other BIM tools like Revit and Digital Project. If the whole library was to be completed based on this XML approach, an open BIM-based library would be established that all kinds of BIM software users could apply this parametric library for easy modeling of traditional houses.

The design process in architecture includes sequential workflows such as planning, feasibility study, schematic design, design development, and construction document phase. The design process depends on design information generated through cooperation after the initial phases of design. As design information generated during the initial phases of a project is interpreted during later phases, errors committed during the initial phase are constantly discovered. Consequently, incorrect initial design information may constitute a significant problem that reduces the quality of design products generated during the life cycle of buildings; in particular, planning information such as design objectives, requirements, and constraint conditions has a significant influence on subsequent phases of the design process. Therefore, it is important that design projects allow for collaboration and adjustment by participants in their initial phases. Moreover, the planning information should be continuously shared, managed, and used during the design process. However, general projects in design offices remain time-consuming and laborious. Problems that arise in design projects include the following.

Focused electrospray (FES) deposition method is presented for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. FES ion optics consists of two cylindrical focusing electrodes capped with a truncated conical electrode through which an electrospray emitter passes along the cylindrical axis. A spray of charged droplets is focused onto a sample well on a MALDI target plate under atmospheric pressure. The shape and size distributions of matrix crystals are visualized by scanning electron microscope and the mass spectra are obtained by time-of-flight mass spectrometry. Angiotensin II, bradykinin, and substance P are used as test samples, while α-cyano-4-hydroxycinnamic acid and dihydroxybenzoic acid are employed as matrices. FES of a sample/matrix mixture produces fine crystal grains on a 1‒3 mm spot and reproducibly yields the mass spectra with little shot-to-shot and spot-to-spot variations. Although FES greatly stabilizes the signals, the space charge due to matrix ions limits the detection sensitivity of peptides. To avoid the space charge problem, we adopted a dual FES/FES mode, which separately deposits matrix and sample by FES in sequence. The dual FES/FES mode reaches the detection sensitivity of 0.88 amol, enabling ultrasensitive detection of peptides by homogeneously depositing matrix and sample under atmospheric pressure.

Architectural design work depends on information created from the initial phase and this information has great influence on various parts of the design process. Despite this, the poor management and use of initial information still is one of the major problems in design. Design tools with planning information created in the initial phase do not address the need for data interoperability. This study aims to develop the Industry Foundation Classes (IFC) extension model for the management and use of planning information through integration of design models and planning information in design work. This paper introduces the scope, rationale, method, implementation, and verification of study. The validity of the proposed method is also demonstrated.

Collisional activation of ions in the ion cyclotron resonance (ICR) cell by short off-resonance burst irradiation (ORBI) was studied by time-resolved photodissociation of the meta-bromotoluene radical cation. Off-resonance chirp or single-frequency burst was applied for 2 ms to the probe ion in the presence of Ar buffer gas. The amount of internal energy imparted to the probe ion by collision under ORBI was precisely determined by time-resolved photodissociation spectroscopy. The rate of unimolecular dissociation of the probe ion following the photolysis at 532 nm was measured by monitoring the real-time appearance of the C7H7+ product ion. The internal energy of the probe ion was extracted from the known rate-energy curve. To help understand the collisional activation of an ion under ORBI, we simulated the radial trajectory of the ion using Green's method. The calculated radial kinetic energy was converted to the collision energy in the center-of-mass frame, and the collision frequency was estimated by using a reactive hard-sphere collision model with an ion-induced dipole potential. Both experiments and trajectory simulations suggest that chirp irradiation leads to less collisional activation of ions than other waveforms.

The unimolecular dissociations of o-, m-, and p-bromotoluene radical cations to C7H7(+) (benzylium and tropylium) are examined by considering the coupling of the three isomers in the dissociation pathways. The potential energy surface obtained from ab initio calculations suggests the interconversion of isomers through methylene and hydrogen migrations on the ring. The rate equations for each isomer are combined together to form a rate matrix for coupled reactions. The rate matrix contains the microcanonical rate constants for all elementary steps, which are calculated using Rice-Ramsperger-Kassel-Marcus theory based on the molecular parameters obtained from density functional theory. The unimolecular dissociation rates for coupled reactions are determined by numerically solving the matrix equation. As a result of reaction coupling, the product branching ratio becomes time-dependent and the reaction rates of three isomers become parallel to one another as the energy increases, although their initial rates differently vary with energy. The calculated rate-energy curves fall below the time-resolved photodissociation data in the energy range 2.2-2.7 eV but are in line with the photoelectron photoion coincidence data in the energy range 2.7-3.5 eV. The discrepancy between experiment and theory in the low-energy region is ascribed to the uncertainties of the potential energy surface as well as the contribution of the radiative relaxation rate that has not been taken into account in the theoretical calculations. The rate-energy curves are then used to calculate the thermal reaction rate constants, and the Arrhenius parameters are determined in the temperature range 700-1300 K. Comparison of the activation energy and entropy obtained from the Arrhenius plot with the calculated enthalpy and entropy changes between the reactant and the highest-lying transition state suggests that a series of [1,2] H-atom migrations occurring near the entrance comprise the rate-determining steps and the subsequent [1,2] H-atom migrations play an important role in increasing the activation energy and decreasing the entropy by reducing the net flux to the exit.

An investigation of the host-guest chemistry of cucurbit[n]uril (CB[n], n = 6 and 7) with α,ω-alkyldiammonium guests (H2N(CH2)xNH2, x = 4, 6, 8, 10, and 12) both in solution and in the gas phase elucidates their intrinsic host-guest properties and the contribution of solvent water. Isothermal titration calorimetry and nuclear magnetic resonance measurements indicate that all alkyldiammonium cations have inclusion interactions with CB[n] except for the CB[7]-tetramethylenediamine complex in aqueous solution. The electrospray ionization of mixtures of CB[n] and the alkyldiammonium guests reflects their solution phase binding constants. Low-energy collision-induced dissociations indicate that, after the transfer of the CB[n]-alkyldiammonium complex to the gas phase, its stability is no longer correlated with the binding properties in solution. Gas phase structures obtained from density functional theory calculations, which support the results from the ion mobility measurements, and molecular dynamics simulated structures in water provide a detailed understanding of the solvated complexes. In the gas phase, the binding properties of complexation mostly depend on the ion-dipole interactions. However, the ion-dipole integrity is strongly affected by hydrogen bonding with water molecules in the aqueous condition. Upon the inclusion of water molecules, the intrinsic characteristics of the host-guest binding are dominated by entropic-driven thermodynamics.