Flexible Clusters Research Articles

Stochastic structure determination for conformationally flexible heterogenous molecular clusters: Application to ionic liquids

We present a novel method that enables accurate and efficient computational determination of conformationally flexible clusters, "Kick(3)" This method uses stochastically generated structures in combination with fast quantum mechanical methods. We demonstrate the power of this method by elucidating the structure of ionic liquid (IL) ([xMIM(+)][NO3(-)])n clusters (x = E, B, D, n = 1-10,15). Dispersion-corrected, third-order self-consistent-charge density-functional tight-binding (DFTB3) is shown to be a computationally efficient, yet reliable approximation to density functional theory for predicting and understanding IL structure and stability. The presented approach, therefore, enables the accurate and efficient screening of ILs with high potential toward practical applications, without recourse to more expensive quantum chemical methods.

Overdamped Dynamics of Folded Protein Domains within a Locally Harmonic Basin Using Coarse Graining Based on a Partition of Compact Flexible Clusters

A coarse-graining method based on the partitioning of atoms into compact flexible clusters is used to formulate the dynamics of the nonequilibrium response of a protein to ligand dissociation. The α-carbon positions are used as the degrees of freedom. The net stiffness between each pair of neighboring α-carbons is calculated for the quasi-static, overdamped regime within the harmonic (quadratic potential energy surface) using the equivalent stiffness matrix of the network of atoms occupying the intervening space within the locally interacting region. This localized approach realizes a divide and conquer strategy that results in a substantial reduction in computational complexity while accurately predicting relaxations under general loading conditions. A close correlation between the shapes and time scales of the relaxation curves of the coarse-grained and all-atom instances of two medium-sized proteins, T4 lysozyme and ferric binding protein (each of which having known apo and holo structures), was observed for the holo to the apo transitions. Furthermore, for both proteins the dominant modes of motion and the decay rates of the temporal relaxation profiles monitoring the separation distance between select amino acid pairs were found to be nearly identical when calculated on the coarse-grained and all-atom scales.

Conservation of Flexible Residue Clusters among Structural and Functional Enzyme Homologues

Conformational flexibility between structural ensembles is an essential component of enzyme function. Although the broad dynamical landscape of proteins is known to promote a number of functional events on multiple time scales, it is yet unknown whether structural and functional enzyme homologues rely on the same concerted residue motions to perform their catalytic function. It is hypothesized that networks of contiguous and flexible residue motions occurring on the biologically relevant millisecond time scale evolved to promote and/or preserve optimal enzyme catalysis. In this study, we use a combination of NMR relaxation dispersion, model-free analysis, and ligand titration experiments to successfully capture and compare the role of conformational flexibility between two structural homologues of the pancreatic ribonuclease family: RNase A and eosinophil cationic protein (or RNase 3). In addition to conserving the same catalytic residues and structural fold, both homologues show similar yet functionally distinct clusters of millisecond dynamics, suggesting that conformational flexibility can be conserved among analogous protein folds displaying low sequence identity. Our work shows that the reduced conformational flexibility of eosinophil cationic protein can be dynamically and functionally reproduced in the RNase A scaffold upon creation of a chimeric hybrid between the two proteins. These results support the hypothesis that conformational flexibility is partly required for catalytic function in homologous enzyme folds, further highlighting the importance of dynamic residue sectors in the structural organization of proteins.

Synthetic Control to Achieve Lanthanide(III)/Pyrimidine-4,6-dicarboxylate Compounds by Preventing Oxalate Formation: Structural, Magnetic, and Luminescent Properties

Control over the synthetic conditions in many metal/diazinedicarboxylato systems is crucial to prevent oxalate formation, since dicarboxylato ligands easily undergo degradation in the presence of metal salts. We report here an efficient route to obtain oxalato-free compounds for the lanthanide/pyrimidine-4,6-dicarboxylato (pmdc) system on the basis of the reaction temperature and nonacidic pH or oxygen free atmosphere. Two different crystal architectures have been obtained: {[Ln(μ-pmdc)(1.5)(H(2)O)(3)]·xH(2)O}(n) (1-Ln) and {[Ln(2)(μ(4)-pmdc)(2)(μ-pmdc)(H(2)O)(2)]·H(2)O}(n) (2-Ln) with Ln(III) = La-Yb, except Pm. Both crystal structures are built from distorted two-dimensional honeycomb networks based on the recurrent double chelating mode established by the pmdc. In compounds 1-Ln, the tricapped trigonal prismatic coordination environment of the lanthanides is completed by three water molecules, precluding a further increase in the dimensionality. Crystallization water molecules are arranged in the interlamellar space, giving rise to highly flexible supramolecular clusters that are responsible for the modulation found in compound 1-Gd. Two of the coordinated water molecules are replaced by nonchelating carboxylate oxygen atoms of pmdc ligands in compounds 2-Ln, joining the metal-organic layers together and thus providing a compact three-dimensional network. The crystal structure of the compounds is governed by the competition between two opposing factors: the ionic size and the reaction temperature. The lanthanide contraction rejects the sterically hindered coordination geometries whereas high-temperature entropy driven desolvation pathway favors the release of solvent molecules leading to more compact frameworks. The characteristic luminescence of the Nd, Eu, and Tb centers is improved when moving from 1-Ln to 2-Ln compounds as a consequence of the decrease of the O-H oscillators. The magnetic properties of the compounds are dominated by the spin-orbit coupling and the ligand field perturbation, the exchange coupling being almost negligible.

How Amelogenin Orchestrates the Organization of Hierarchical Elongated Microstructures of Apatite

Amelogenin (Amel) accelerates the nucleation of hydroxyapatite (HAP) in supersaturated solutions of calcium phosphate (Ca-P), shortening the induction time (delay period), under near-physiological conditions of pH, temperature, and ionic strength. Hierarchically organized Amel and amorphous calcium phosphate (ACP) nanorod microstructures are formed involving a coassembly of Amel-ACP particles at low supersaturations and low protein concentrations in a slow, well-controlled, constant composition (CC) crystallization system. At the earliest nucleation stages, the CC method allows the capture of prenucleation clusters and intermediate nanoclusers, spherical nanoparticles, and nanochains prior to enamel-like nanorod microstructure formations at later maturation stages. Amel-ACP nanoscaled building blocks are formed spontaneously by synergistic interactions between flexible Amel protein molecules and Ca-P prenucleation clusters, and these spherical nanoparticles evolve by orientated aggregation to form nanochains. Our results suggest that, in vivo, Amel may determine the structure of enamel by controlling prenucleation cluster aggregation at the earliest stages by forming stable Amel-ACP microstructures prior to subsequent crystal growth and mineral maturation.

FLEXIBLE AND SECURE ACCESS TO COMPUTING CLUSTERS

The investigation presented in this paper was prompted by the need to provide a manageable solution for secure access to computing clusters with a federated authentication framework. This requirement is especially important for scientists who need direct access to computing nodes in order to run their applications (e.g. chemical or medical simulations) with proprietary, open-source or custom-developed software packages. Our existing software, which enables non-Web clients to use Shibboleth-secured services, has been extended to provide direct SSH access to cluster nodes using the Linux Pluggable Authentication Modules mechanism. This allows Shibboleth users to run the required software on clusters. Validation and performance comparison with existing SSH authentication mechanisms confirm that the presented tools satisfy the stated requirements.

PANDA: a virtual breeding environment for SMEs in the ERP/CRM industry using a service oriented approach

PANDA is a European Union co-funded Information Society Technologies project examining innovative aspects of e-collaboration in the European enterprise resource planning/customer relationship management (ERP/CRM) industry of small and medium enterprises (SMEs). One outcome of PANDA is an advanced business-to-business (B2B) web-platform, dedicated to serving as a virtual breeding environment (VBE) for the ERP/CRM industry. PANDA introduces a system with a service-oriented architecture (SOA) approach, which includes request-based virtual organisations (RBVOs), i.e., flexible clusters reflecting international ERP/CRM value chains, comprised of ERP/CRM vendors, their national representatives, dealers and consultants. RBVOs are facilitated by a community of intelligent agents. The paper discusses the objectives of PANDA, illustrates its main concepts, briefly outlines the operations and explains the architecture of PANDA's system.

Preparation of thermally stable and optically active organosoluble aromatic polyamides containing l-leucine amino acid under green conditions

An optically active bulky dicarboxylic acid (2S)-4-[(4-methyl-2-phthalimidylpentanoylamino)benzoylamino]isophthalic acid (1), was synthesized in five step starting from l-leucine and phthalic anhydride. A set of new aromatic polyamides containing (N-phthaloyl-l-leucine) units was synthesized by the direct one-pot phosphorylation polycondensation of diacid 1 with various aromatic diamines in the presence of different imidazolium salts and triphenyl phosphite (TPP) without adding extra compounds (Method I). This method was compared with a classical method in a medium consisting of TPP, N-methyl-2-pyrrolidinone, pyridine, and calcium chloride (Method II) and the results are comparable. The polymers were produced with high yields and from moderate to high inherent viscosities (0.43–0.81 dL g−1). Amino acid existence in this backbone results in optically active polymers. The chemical structures of some of these polymers were characterized by 1H-NMR and elemental analysis, and all of them with FT-IR and specific rotation tools. By introduction of bulky and flexible clusters in these new polyamides pendent group; make them soluble in most polar aprotic solvents.

Onset of Double Helical Structure in Small-Sized Homoleptic Gold Thiolate Clusters

Low-lying isomers of homoleptic gold thiolate clusters (AuSR)(N) (N = 6-12) are studied by using a global-minimum search method. Besides previously known zigzag crown structures for (AuSR)(N) (N = 6-12) and catenane structures for (AuSR)(N) (N = 10, 12), onset of a new structural family of double helical structures in small-sized gold thiolate clusters and the separate-ring structures in larger clusters is revealed. At N = 6-9, the double helical structures are predicted to be the global minima. The onset of double helical structures suggests a new folding way for flexible gold thiolate clusters. The simulated UV-vis spectra and XRD patterns for all low-lying clusters are ready to compare with future experiments.

Electric deflection studies on lead clusters

The dielectric response to an inhomogeneous electric field has been investigated for Pb(N) clusters (N=7-38) within a molecular beam experiment. The experiments give clear evidence that lead clusters with 12, 14, and 18 atoms possess permanent dipole moments. For these cluster sizes, the permanent electric dipole moments strongly determine the response to the electric field, leading to a significantly increased apparent polarizability. An adiabatic polarization mechanism allows a semiquantitative explanation of the observed susceptibility anomalies. The beam profiles of most of the lead clusters with N not equal12, 14, and 18 also display a small broadening induced by the electric field, indicating permanent dipole moments of about (0.01-0.02) D/atom. Nearly constant dipole moments per atom for larger lead clusters (N>20) manifest in a linear increase in the polarizability per atom. Also, for lead clusters such as Pb(25), which do exhibit almost no measurable beam broadening, the polarizabilties are increased compared to the bulk value. This could be partially explained by the electronic structure of the lead clusters but might be also a consequence of quenched permanent dipole moments because for highly flexible clusters only an increased beam deflection, but no broadening, will be observed.

Room Temperature Ionic Liquids as Replacements for Organic Solvents: Direct Preparation of Wholly Aromatic Polyamides Containing Phthalimide and S-valine Moieties

Ionic liquids (IL)s are often considered as green solvents capable of replacing traditional organic solvents and have extensively studied in material chemistry and catalysis. In this work a new class of wholly aromatic and optically active polyamides (PAs) having phthalimide and S-valine pendent groups were prepared by the reaction of 5-(2-phthalimidyl-3-methylbutanoylamino)isophthalic acid as a diacid monomer with various aromatic diamines. ILs media in the presence of triphenyl phosphite was used as a condensing agent. The resulting novel optically active PAs with inherent viscosities ranging from 0.35–0.71 dLg−1, were obtained in excellent yields. This method of polymerization was also compared with direct polyamidation using conventional phosphorylation reaction. Introduction of bulky and flexible clusters in these polymers pendent group, make them readily soluble in most organic solvents. The resulting polymers show optical rotation, therefore, are optically active.

Divide to conquer? Limits to the adaptability of disintegrated, flexible specialization clusters

This article investigates the role of disintegration for the adaptability of clusters. It develops a simulation model to test when disintegrated flexible specialization clusters can be more adjustable than those with firm centred, quasi-integrated production networks. The benefits to flexible specialization are conditional on limited product complexity and greater firm numbers. Moreover, flexible specialization increases the risk of firm failure. For the viability of such clusters, strong start-up dynamics are therefore required. These results provide an explanation for the contrasting evidence on flexible specialization and adaptability in Italian districts and the Silicon Valley Boston 128 case.

Structure and Properties of Iron Oxide Nanoparticles Encapsulated by Phospholipids with Poly(ethylene glycol) Tails

Iron oxide nanoparticles with diameters of 20.1 and 8.5 nm coated with phospholipids containing poly(ethylene glycol) (PEG) tails were studied using small-angle X-ray scattering (SAXS), transmission electron microscopy, dynamic light scattering, and magnetometry. Novel SAXS data analysis methods are applied to build three-dimensional structural models of the nanoparticles coated with PEGylated phospholipids in aqueous solution. The SAXS data demonstrate that the density inside iron oxide nanoparticles is not uniform and depends on the nanoparticle size, which in turn is dependent on the reaction conditions. This heterogeneity is attributed to the presence of two crystalline phases, spinel and wustite, in the nanoparticles. Because of magnetic properties, the nanoparticles in solution associate in flexible dynamic clusters consisting on average of four individual cores. The magnetometry further supports the SAXS-based models.

Facile Syntheses of a Class of Supramolecular Gelator Following a Combinatorial Library Approach: Dynamic Light Scattering and Small-Angle Neutron Scattering Studies

Following a combinatorial library approach, 60 organic salts have been prepared by reacting 5 bile acids and 12 secondary amines. Gelation tests with various organic and aqueous solvents reveal that 16 salts are supramolecular gelators of which 6 salts are found to be ambidextrous displaying the ability to form gels with organic as well as aqueous solvents. The salt didodecylammonium cholate (1a7b) is the most versatile gelator, displaying gelation ability with a maximum number of solvents. AFM images of the xerogels of 1a7b in organic and aqueous solvents reveal the presence of fibrous aggregate including helical fibers. Dynamic and morphological behaviors of the aggregates in the gel state have been probed by dynamic light scattering (DLS) and small-angle neutron scattering (SANS) experiments on an aqueous gel (1:1 DMSO/H2O) of 1a7b. It is revealed that the gelation takes place via the formation of flexible fibrous clusters followed by physical cross-linking. DLS and SANS results also disclose that (1) ...

Dynamics of Nondilute Hairy-Rod Polymer Solutions in Simple Shear Flow

We investigate the shear response of nondilute solutions of a hairy-rod polyester using in-situ optical rheometry. The transition to the concentrated regime, c**, is characterized by a strong concentration dependence of the zero shear viscosity, a change in the sign of birefringence, and the emergence of linear conservative dichroism. These features indicate the presence of clusters which dominate the dynamics in this concentration regime, and as such they represent their identifying signature. The stress−optical rule is found to hold only in the concentration regime below c**, yielding stress−optical coefficients closer to those of flexible chains rather than rods, consistent with the wormlike character of the polyesters. At the highest concentrations these solutions can be viewed as nondilute solutions of flexible ellipsoidal clusters. The dynamics as well as the anomalous birefringence (change of sign) can be rationalized using the theoretical analysis of Cates, who considered a presmectic local orderi...

ChemInform Abstract: Tetrahedral Stars as Flexible Basis Clusters in sp‐Bonded Intermetallic Frameworks and the Compound BaLi7Al6 with the NaZn13 Structure.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Tetrahedral Stars as Flexible Basis Clusters in sp-Bonded Intermetallic Frameworks and the Compound BaLi7Al6 with the NaZn13 Structure

The cluster units obtained by the capping of all faces of a tetrahedron (tetrahedral star, TS) and a trigonal bipyramid (double tetrahedral star, DTS) are used as building units to describe and rationalize framework structures found in the intermetallic structure types NaBa, NaZn13, Th6Mn23, Ba2Li4.21Al4.79, BaHg11, BaCd11, Cr23C6, β-Mn, Ba3Li3Ga4.1, BaLi4, CaZn3, EuMg5.2, ErZn5, Sr3Mg13, and Sr9Li17.5Al25.5. The electronic requirements for optimum structural stability of these frameworks in the case of sp-bonding have been investigated with the simple tight-binding Huckel model. As a result the networks exhibit a pronounced maximum of stability in the range of 2.1−2.6 electrons per atom with the particular optimum values slightly depending on the kind of basis cluster and its connectivity. Considering the sp-bonded representatives of the above mentioned structure types, the frameworks described by the basis clusters TS and DTS are usually formed by the divalent metals Be, Mg, Zn, Cd, and Hg or a combinat...

On the foundations of generalized Taylor dispersion theory

Generalized Taylor dispersion theory extends the basic long-time, asymptotic scheme of Taylor and Aris greatly beyond the class of rectilinear duct and channel flow dispersion problems originally addressed by them. This feature has rendered it indispensable for studying flow and dispersion phenomena in porous media, chromatographic separation processes, heat transfer in cellular media, sedimentation of non-spherical Brownian particles, and transport of flexible clusters of interacting Brownian particles, to mention just a few examples of the broad class of non-unidirectional transport phenomena encompassed by this scheme. Moreover, generalized Taylor dispersion theory enjoys the attractive feature of conferring a unified paradigmatic structure upon the analysis of such apparently disparate physical problems. For each of the problems thus treated it provides an asymptotic, macroscale description of the original microscale transport process, being based upon a convective-diffusive ‘model’ problem characterized by a set of constant (position- and time-independent) phenomenological coefficients.The present contribution formally substantiates the scheme. This is accomplished by demonstrating that the coarse-grained (macroscale) transport ‘model’ equation leads to a solution which accords asymptotically with the leading-order behaviour of the comparable solution of the exact (microscale) convective–diffusive problem underlying the transport process. It is also shown, contrary to current belief, that no systematic improvement in the asymptotic order of approximation is possible through the incorporation of higher-order gradient terms into the model constitutive equation for the coarse-grained flux. Moreover, the inherent difference between the present rigorous asymptotic scheme and the dispersion models resulting from Gill–Subramanian moment-gradient expansions is illuminated, thereby conclusively resolving a long-standing puzzle in longitudinal dispersion theory.