Bond Network Research Articles

Time-Resolved Vibrational Fingerprints for Two Silver Cluster-DNA Fluorophores.

DNA-templated silver clusters are chromophores in which the nucleobases encode the cluster spectra and brightness. We describe the coordination environments of two nearly identical Ag106+ clusters that form with 18-nucleotide strands CCCCA CCCCT CCCX TTTT, with X = guanosine and inosine. For the first time, femtosecond time-resolved infrared (TRIR) spectroscopy with visible excitation and mid-infrared probing is used to correlate the response of nucleobase vibrational modes to electronic excitation of the metal cluster. A rich pattern of transient TRIR peaks in the 1400-1720 cm-1 range decays synchronously with the visible emission. Specific infrared signatures associated with the single guanosine/inosine along with a subset of cytidines, but not the thymidines, are observed. These fingerprints suggest that the network of bonds between a silver cluster adduct and its polydentate DNA ligands can be deciphered to rationally tune the coordination and thus spectra of molecular silver chromophores.

Paramagnetic Shifts and Guest Exchange Kinetics in ConFe4-n Metal-Organic Capsules.

We investigate the magnetic resonance properties and exchange kinetics of guest molecules in a series of hetero-bimetallic capsules, [ConFe4-nL6]4- (n = 1-3), where L2- = 4,4'-bis[(2-pyridinylmethylene)amino]-[1,1'-biphenyl]-2,2'-disulfonate. H bond networks between capsule sulfonates and guanidinium cations promote the crystallization of [ConFe4-nL6]4-. The following four isostructural crystals are reported: two guest-free forms, (C(NH2)3)4[Co1.8Fe2.2L6]·69H2O (1) and (C(NH2)3)4[Co2.7Fe1.3L6]·73H2O (2), and two Xe- and CFCl3-encapsulated forms, (C(NH2)3)4[(Xe)0.8Co1.8Fe2.2L6]·69H2O (3) and (C(NH2)3)4[(CFCl3)Co2.0Fe2.0L6]·73H2O (4), respectively. Structural analyses reveal that Xe induces negligible structural changes in 3, while the angles between neighboring phenyl groups expand by ca. 3° to accommodate the much larger guest, CFCl3, in 4. These guest-encapsulated [ConFe4-nL6]4- molecules reveal 129Xe and 19F chemical shift changes of ca. -22 and -10 ppm at 298 K, respectively, per substitution of low-spin FeII by high-spin CoII. Likewise, the temperature dependence of the 129Xe and 19F NMR resonances increases by 0.1 and 0.06 ppm/K, respectively, with each additional paramagnetic CoII center. The optimal temperature for hyperpolarized (hp) 129Xe chemical exchange saturation transfer (hyper-CEST) with [ConFe4-nL6]4- capsules was found to be inversely proportional to the number of CoII centers, n, which is consistent with the Xe chemical exchange accelerating as the portals expand. The systematic study was facilitated by the tunability of the [M4L6]4- capsules, further highlighting these metal-organic systems for developing responsive sensors with highly shifted 129Xe resonances.

Catalytic hydrotreatment of humins into cyclic hydrocarbons over solid acid supported metal catalysts in cyclohexane

Humins are common undesirable sideproducts during many acid-catalyzed reactions in renewable biomass platform conversion. However, few studies have been reported to the efficient utilization of humins. For the first time, the selective catalytic conversion of biomass-derived humins into cyclic hydrocarbons with high conversion rate and selectivity is presented using a home-made Ru/W-P-Si-O bifunctional catalyst. The multistage polymerization structure of humins was studied through controlled experiments. Results show that the CC bond network can be efficiently depolymerized at a mild reaction temperature of 340–380 °C, catalyzed by the cooperative catalysis of nano-Ru particles and porous strong Lewis solid acid. Particularly, 95.4% conversion of humins was achieved under the optimal condition with up to 88.3% yield of cyclic hydrocarbons. The detailed composition after liquefaction was also analyzed. This study paves the way for the efficient production of cyclic and aromatic hydrocarbons from furan-derived humin polymer through Lewis acid-catalyzed Diels–Alder reactions between furan rings.

Electret and Strength Properties of Polymeric Materials Based on Epoxy Oligomer and Amine Curing Agents

Electret properties of polymeric materials based on DER-331 epoxy oligomer and amine curing agents, produced in the course of synthesis of the polymer in a constant electric field, were examined. It was shown that the presence of certain polar functional groups and fragments in the structure of the curing agent can both raise the electret characteristics of polymers (by making larger the number of polar groups capable of orientation) and diminish these characteristics (due to steric factors). To obtain polymeric epoxy materials possessing good electret characteristics, it is preferable to use diethylenetriamine as the amine curing agent. The hardness of epoxy polymers is determined by parameters of the network of chemical bonds and by their structural organization. Using N-aminoethylpiperazine in manufacturing polymeric materials based on the epoxy oligomer makes it possible to obtain 3D structures providing a higher hardness owing to the presence of a heterocyclic fragment in the structure of the curing agent. Converting the network polymeric structures to the polarized state results in hardness increases. This is due to the orientation of polar groups, which gives rise to a denser network of physical bonds.

Hydrogen-Bonding in Liquid Water at Multikilobar Pressures.

High-precision THz (30 to 360 cm-1) spectra of bulk liquid water are presented from ambient conditions up to hydrostatic pressures of 10 kbar. In concert with ab initio simulations, this allows us to characterize the molecular-level changes of the H-bond network under solvent stress conditions. Both the experimental and theoretical THz spectra reveal a blue shift in the intermolecular translational mode at 180 cm-1 by 40 cm-1 at 10 kbar and a blue shift together with an intensity increase in the relaxation mode. These changes can be traced back to a pressure-induced increase of the population of so-called short H-bond double donor configurations at the expense of those with longer such intermolecular bonds. Distinct electronic polarization effects are critical to capture the characteristic intensity changes of the THz line shape function. These advances in high-pressure THz spectroscopy open the door to investigate the pressure response of solvation shells and solute-solvent couplings.

Persistence of perorally inoculated entomopoxvirus spindles in the midgut of Bombyx mori larvae

Abstract Peroral inoculation of entomopoxvirus (EV) spindles, microstructures composed of the protein fusolin, enhances the infectivity of some insect viruses by disrupting the physical barrier against microbe infection, the peritrophic matrix, in the insect midgut. Here, we examined the temporal persistence of spindles of Anomala cuprea EV (ACEV) that infect Coleopteran species in Bombyx mori larva midgut because spindle solubility over time in the midgut is closely associated with the degree of the enhancement of microbe infectivity by fusolin. A number of ACEV spindles fed to B. mori larvae were retained in the digestive systems even 20 h after the completion of feeding spindles, and a number of spindles were found to be excreted still almost intact in feces under a light microscope. In an in vitro experiment, most ACEV spindles remained intact in B. mori midgut juice 1 h after the start of incubation and some of spindles appeared even overnight in contrast to Bombyx mori nucleoplyhedrovirus polyhedra, which were immediately dissolved in midgut juice. These results suggest spindles are not generally dissolved readily in the midgut of many insects. The difficulty in solubility of ACEV spindles is considered to be mainly due to that fusolin contains many cysteine residues that form a 3D network of disulfide bonds between fusolin dimers. To use spindles at a low cost as additives in microbial insecticides, increasing the solubility of spindles by protein engineering is important to utilize full spindles inoculated.

Numerical simulation of creep fracture with internal time-dependent hyperelastic-Kelvin cohesive bonds

The macro brittle creep is closely related to the fracturing process on the micro scale. The virtual internal bond (VIB) is a microstructure-based continuum modeling method. It considers a solid as a bond network on the micro scale. The macro constitutive relation is directly derived from the micro bond potential, which intrinsically contains the micro fracture mechanisms. In this study, the VIB is firstly extended for modeling viscoelasticity, and then it is applied to creep fracture simulation. To reflect the time-dependence property of creep, a viscous bond is introduced to join a time-dependent hyperelastic bond in parallel to constitute a hybrid hyperelastic-Kelvin bond. Based on the hybrid bond potential, the macro viscohyperelastic constitutive relation is derived. The corresponding relationship between the micro bond parameters and the macro material constants is theoretically calibrated. Through this model, the typical three-stage feature of the brittle creep is well reproduced and the creep fracture is effectively simulated. The simulation results suggest that the fast and unstable fracture growth leads to the tertiary stage of creep. The viscosity mainly affects the deformation rate in the primary and tertiary stage of creep. The constitutive relation of the VIB stems from the 1D micro bond; thus, the rheology model derived from the cluster of rheological elements (e.g., spring, dashpot) is easily incorporated into the VIB framework, avoiding the 1D-to-3D generalization of the rheology law. For both the micro viscosity and fracture mechanisms that are incorporated into the macro constitutive relation, the present VIB can simulate complex creep fractures without a separate fracture criterion. It has great potential to simulate fracture propagation in a more extensive viscohyperelastic material.

Homology modeling and in vivo functional characterization of the zinc permeation pathway in a heavy metal P-type ATPase.

The P1B ATPase heavy metal ATPase 4 (HMA4) is responsible for zinc and cadmium translocation from roots to shoots in Arabidopsis thaliana. It couples ATP hydrolysis to cytosolic domain movements, enabling metal transport across the membrane. The detailed mechanism of metal permeation by HMA4 through the membrane remains elusive. Here, homology modeling of the HMA4 transmembrane region was conducted based on the crystal structure of a ZntA bacterial homolog. The analysis highlighted amino acids forming a metal permeation pathway, whose importance was subsequently investigated functionally through mutagenesis and complementation experiments in plants. Although the zinc pathway displayed overall conservation among the two proteins, significant differences were observed, especially in the entrance area with altered electronegativity and the presence of a ionic interaction/hydrogen bond network. The analysis also newly identified amino acids whose mutation results in total or partial loss of the protein function. In addition, comparison of zinc and cadmium accumulation in shoots of A. thaliana complemented lines revealed a number of HMA4 mutants exhibiting different abilities in zinc and cadmium translocation. These observations could be instrumental to design low cadmium-accumulating crops, hence decreasing human cadmium exposure.

Electrostatic potential in crystals of α-boron, γ-boron and boron carbide

Abstract An overview is given of the recently proposed method for computation of the electrostatic potential (ESP) of dynamic charge densities derived from multipole models [C. B. Hubschle, S. van Smaalen, J. Appl. Crystallogr. 2017, 50, 1627]. The dynamic ESP is presented for the multipole models of the boron polymorphs α-B12 and γ-B28, and stoichiometric boron carbide B13C2. Minimum values of the ESP are conspiciously equal at approximately −1 electron/Å. Regions with the ESP close to its minimum value form an extended network throughout the crystal structures at locations far away from atoms and bonds. Boron and boron carbide are extended solids containing an infinite network of strong chemical bonds. We have shown that for such solids, the ESP can usefully considered on Hirshfeld surfaces encompassing groups of atoms. Accordingly, we discuss bonding in boron and boron carbide with aid of the ESP on the Hirsfeld surface encompassing a B12 icosahedral cluster. The structure of the ESP corroborates the interpretation of the bonding characteristics previously proposed for α-B12, γ-B28 and B13C2.

Fabrication of composites via spouted bed granulation process and simulation of their micromechanical properties

In this contribution numerical simulation of Young’s modulus of copper-polymer composites is presented. For the simulation of the composites the Bonded-Particle-Model was applied. The model allows representing of the structure of composite materials realistically. The polymer matrix, which surrounds the particles, was represented as network of solid bonds connecting copper particles. Simulation results were validated based on mechanical determination of modulus of elasticity. The modulus of elasticity was approximated in experiments as well as in simulation by four-point-bending tests. It was observed, that obtained simulation results are in good agreement with experimental results.

Abstract IA18: Gut microbiota-host immunomodulatory interactions

Abstract Adaptive co-evolution has formed a complex network of inextricable bonds between the resident microbes and the mammalian host. These symbiotic microbes are now believed to have critical impacts on human health. One of the most common gut symbionts, Bacteroides fragilis, produces an outersurface polysaccharide (PSA) that possesses immunomodulatory effects on the host. We adapted a metabolic labeling approach to study the microbiota communication with the host in real-time. We labeled PSA and detected B. fragilis in vivo associated with immune cells and organs. We extended this labeling approach to commensals from diverse phyla in order to study their effects on the host. This method has the potential to enhance our understanding of microbiota colonization as well as to define a set of characteristics of protective cells whose stimulation by previously undiscovered commensal-derived molecules may represent an important new approach to the treatment and prevention of diseases. Citation Format: Naama Geva-Zatorsky, David Alvarez, Jason E. Hudak, Nicola C. Reading Mans, Deniz Erturk-Hasdemir, Suryasarathi Dasgupta, Ulrich von Andrian, Dennis Kasper. Gut microbiota-host immunomodulatory interactions [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr IA18.

Stability of one- and two-layers [TM(Benzene)m]±1, m ≤ 3; TM = Fe, Co, and Ni, complexes

The structural and energetic properties for neutral and charged complexes of transition metal atoms and benzene molecules, TM(C6H6)m ≤ 3, TM = Fe, Co, Ni, were studied using density functional theory. Including dispersion corrections all-electron calculations were done with the BPW91–D2 and M11L functionals. Basis sets of 6–311++G(2d,2p) and Def2TZVP quality were employed. Binding energies, D0, ionization energies, IE, and electron affinities, EA, were determined for the located ground states. Structural and electronic parameters accounting for the stability of TM(C6H6)m were also addressed. Metal-carbon (η2–η6) coordination occur in the neutral and positively charged TM(C6H6)1,2 species. But in the CoC6H6 and NiC6H6 ions the metal atom seats on two hydrogen atoms, η2H, of the benzene ring, with the peculiarity that the ground state geometries are planar. In the neutral and charged TM(C6H6)3, TM = Fe, Co and Ni species a benzene molecule lies in the external region and by means of CH–π and π–π stacking interactions it is bonded to the ligands lying in the first coordination layer. Although weak, some external molecules present direct interactions with the metal atom. The D0 for the molecules in the outer region is much smaller than the one for the ligands in the first layer. Therefore, solvent behavior is exhibited by the studied neutral and charged [TM(C6H6)3]±1 complexes. Experiment and theory agree that: D0(Fe+(C6H6)2) > D0(Co+(C6H6)2) > D0(Ni+C6H6)2) and D0(NiC6H6) > D0(CoC6H6). Reasonable accuracy was found for the D0 of each complex; other tendencies are not fully reproduced at these levels of theory. The small D0’s of CoC6H6 and NiC6H6 and those of the anions, complicate their determination. In general, the EA increases from m = 1 to 2 and from 2 to 3. The IE decreases from m = 1 to 3, being due to delocalization trough the Cδ–Hδ+⋯π network of bonds.

X-ray Absorption Spectroscopy Study of the Effect of Rh doping in Sr2IrO4.

We investigate the effect of Rh doping in Sr2IrO4 using X-ray absorption spectroscopy (XAS). We observed appearance of new electron-addition states with increasing Rh concentration (x in Sr2Ir1−xRhxO4) in accordance with the concept of hole doping. The intensity of the hole-induced state is however weak, suggesting weakness of charge transfer (CT) effect and Mott insulating ground states. Also, Ir Jeff = 1/2 upper Hubbard band shifts to lower energy as x increases up to x = 0.23. Combined with optical spectroscopy, these results suggest a hybridisation-related mechanism, in which Rh doping can weaken the (Ir Jeff = 1/2)–(O 2p) orbital hybridisation in the in-planar Rh-O-Ir bond networks.

Electronic origin of the dependence of hydrogen bond strengths on nearest-neighbor and next-nearest-neighbor hydrogen bonds in polyhedral water clusters (H2O)n, n = 8, 20 and 24.

The influence of the nearest neighbor and next-nearest neighbor water molecules on the strength of the hydrogen (H) bonds was examined for the polyhedral clusters of cubic (H2O)8, dodecahedral (H2O)20 and tetrakaidecahedral (H2O)24 cages. The relative stability and the characteristics of the H bond networks are also studied. The charge-transfer (CT) and dispersion interaction terms of every pair of H bonds are evaluated using perturbation theory based on the locally-projected molecular orbitals (LPMO PT). Every water molecule and every H-bonded pair in these polyhedral clusters are classified by the types of the neighbor molecules and H bonds. The relative binding energies among the polyhedral clusters are grouped by these classifications. The optimized OO distances, which are strongly correlated with the calculated pairwise CT terms, are dependent on the 49 sub-groups of the H bonds determined by the type of the neighbor molecules. The electronic origin of this dependence is analyzed using Mulliken's charge-transfer theory, and employing a few assumptions, the analytical formulas for the contribution of the CT terms to the H bond energy are derived.

Highly Dense Amorphous Si2BC3N Monoliths with Excellent Mechanical Properties Prepared by High Pressure Sintering

The fabrication of dense amorphous Si–B–C–N monoliths is a processing challenge given that it is hard to avoid crystallization at the sintering temperatures needed to attain full density up to 1900°C for conventional hot pressing and SPS methods. We report here successful densification of amorphous Si2BC3N monoliths achieved by heating at 1100°C and 5 GPa. The relationships between microstructure, types of chemical bonding, and mechanical properties were investigated. The strong amorphous 3‐D networks of Si–C, C–B, C‐N (sp3), N‐B (sp3), and C–B–N bonds provide high densities at high applied pressure and thus amorphous Si2BC3N monoliths show high hardness of 29.4 GPa and elastic modulus of 291 GPa. The amorphous structure is lost with crystallization of β‐SiC and BN(C) reducing contributions from Si–C, C‐N (sp3), and C–B–N bond networks thereby decreasing mechanical properties.

Thermoplastic deformation and structural evolutions in nanoimprinting metallic glasses using molecular dynamics analysis

We perform simulations on nanoimprinting metallic glasses to investigate the thermoplastic deformation and structural evolutions via molecular dynamics analysis. The atomic diffusion mechanisms, including single atomic and highly collective hopping, are observed in metallic glass block. Mold filling speed is significantly affected by the initial metallic glass film thickness, and the film with the thickness approaching the width of the pattern on mold is optimal to shorten mold filling time and save materials. With the support of a modified equation of plane Poiseuille flow, we analyze the resistance of boundary condition and capillary force, which have reasonably explained the thickness effect. We then show the structural evolutions to assess the impact of the mold filling process on the short-range and the middle-range orders in metallic glasses. Lower fractions of icosahedra and icosahedra-like clusters and smaller aggregated clusters have been detected in the processed structure than in the billets, showing that the processed metallic glasses are more symmetrical and have more disorder. The results further suggest that the mold filling process has broken the original structures in metallic glasses, resulting in less icosahedra and bond networks, which lead to a better plasticity in the processed metallic glasses.

52 Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico

Microtubules, the primary components of the chromosome segregation machinery, are stabilized by longitudinal and lateral noncovalent bonds between the tubulin subunits. However, the thermodynamics of these bonds and the microtubule physicochemical properties are poorly understood. Here, we explore the biomechanics of microtubule polymers using multiscale computational modeling and nanoindentations in silico of a contiguous microtubule fragment. A close match between the simulated and experimental force–deformation spectra enabled us to correlate the microtubule biomechanics with dynamic structural transitions at the nanoscale. Our mechanical testing revealed that the compressed MT behaves as a system of rigid elements interconnected through a network of lateral and longitudinal elastic bonds. The initial regime of continuous elastic deformation of the microtubule is followed by the transition regime, during which the microtubule lattice undergoes discrete structural changes, which include first the revers...

Systematic Flexibility and the History of the IUPAC Nomenclature of Organic Chemistry

For chemists and chemistry students around the world, “IUPAC” is synonymous with “nomenclature” – especially the nomenclature of organic chemistry. Generations of chemists have learned – sometimes grudgingly – to read and write systematic names for organic compounds using guidelines codified by the International Union of Pure and Applied Chemistry. [1,2,3] The prefixes, suffixes, numbers, and parentheses of IUPAC names put molecules in order: individually, by expressing the network of atoms and bonds that constitutes the structure of an organic compound, and collectively, by situating each compound among the tens of millions of known organic chemical substances. IUPAC names carry this order out of chemical journals and into such sites as patent records, customs lists, and environmental regulatory databases.

An investigation of the interconnection between topological characteristics of physical and chemical networks of anhydride adamantane-containing epoxy polymers

The interconnection between topological characteristics of chemical and physical networks of adamantane-containing epoxy polymers of anhydride curing is studied. It is shown that the introduction of adamantane fragments into the network of an epoxy polymer by different methods affects the glass-transition point and stress-strain properties. The changes in polymer properties depending on the concentration of modifying agents are analyzed during comparison of the frequency parameters of the networks of chemical bonds and engagements within a cluster model of the structure of the polymer amorphous state.

The Physical Origins of the Chemical Bond

The properties of the chemical bond are the same as those of the electrostatic flux that links the cores of two bonded atoms via their bonding electrons. Both the bond and the flux depend only on the number of electrons that form the bond, and significantly, neither depends on how the electron density is distributed. This allows the rules of chemical bonding to be developed using classical electrostatic theory without the need to know how the electron density is distributed. The magnitude of the flux is equal to the bond order (bond valence) and hence correlates with the bond length [1]. A network of bonds is equivalent to a capacitive electric circuit which allows one to predict the bond fluxes, hence also the bond lengths. Bond angles are determined by the spherical symmetry of the flux around each atom, and the resulting bonding geometry can be predicted using little more than a pocket calculator. The rules of all the predictive bond models: the VSEPR model, the ionic model, the covalent bond model and the bond valence model can be derived using classical electrostatics without introducing problematic concepts such as hypervalency, dative bonding, hybridization and the dichotomy between ionic and covalent bonding, thus eliminating the paradoxes created by the physically questionable Lewis and orbital models. Quantum effects are rarely important except in the transition metals where in some cases they perturb the bonding geometry.