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At least 379 records · Page 21

Enhanced active-site electric field accelerates enzyme catalysis

In this study, the design and improvement of enzymes based on physical principles remain challenging. Here we demonstrate that the principle of electrostatic catalysis can be leveraged to substantially improve a natural enzyme’s activity. We enhanced the active-site electric field in horse liver alcohol dehydrogenase by replacing the serine hydrogen-bond donor with threonine and replacing the catalytic Zn 2+ with Co 2+ . Based on the electric field enhancement, we make a quantitative prediction of rate acceleration—50-fold faster than the wild-type enzyme—which was in close agreement with experimental measurements. The effects of the hydrogen bonding and metal coordination, two distinct chemical forces, are described by a unified physical quantity—electric field, which is quantitative, and shown here to be additive and predictive. These results suggest a new design paradigm for both biological and non-biological catalysts.

59 BASIC BIOLOGICAL SCIENCES↗

Unit-cell-thick zeolitic imidazolate framework films for membrane application

Zeolitic imidazolate frameworks (ZIFs) are a subset of metal–organic frameworks with more than 200 characterized crystalline and amorphous networks made of divalent transition metal centres (for example, Zn 2+ and Co 2+ ) linked by imidazolate linkers. ZIF thin films have been intensively pursued, motivated by the desire to prepare membranes for selective gas and liquid separations. To achieve membranes with high throughput, as in ångström-scale biological channels with nanometre-scale path lengths, ZIF films with the minimum possible thickness—down to just one unit cell—are highly desired. However, the state-of-the-art methods yield membranes where ZIF films have thickness exceeding 50 nm. Here we report a crystallization method from ultradilute precursor mixtures, which exploits registry with the underlying crystalline substrate, yielding (within minutes) crystalline ZIF films with thickness down to that of a single structural building unit (2 nm). The film crystallized on graphene has a rigid aperture made of a six-membered zinc imidazolate coordination ring, enabling high-permselective H 2 separation performance. The method reported here will probably accelerate the development of two-dimensional metal–organic framework films for efficient membrane separation.

36 MATERIALS SCIENCE↗

Design of metal-mediated protein assemblies via hydroxamic acid functionalities

The self-assembly of proteins into sophisticated multicomponent assemblies is a hallmark of all living systems and has spawned extensive efforts in the construction of novel synthetic protein architectures with emergent functional properties. Protein assemblies in nature are formed via selective association of multiple protein surfaces through intricate noncovalent protein-protein interactions, a challenging task to accurately replicate in the de novo design of multiprotein systems. In this protocol, we describe the application of metal-coordinating hydroxamate (HA) motifs to direct the metal-mediated assembly of polyhedral protein architectures and 3D crystalline protein frameworks (protein-MOFs). This strategy has been implemented using an asymmetric cytochrome cb562 monomer through selective, concurrent association of Fe 3+ and Zn 2+ ions to form polyhedral cages. Furthermore, the use of ditopic HA linkers as bridging ligands with metal-binding protein nodes has allowed the construction of crystalline 3D protein-MOF lattices. The protocol is divided into two major sections: (1) the development of a Cys-reactive HA molecule for protein derivatization and self-assembly of protein-HA conjugates into polyhedral cages and (2) the synthesis of ditopic HA bridging ligands for the construction of ferritin-based protein-MOFs using symmetric metal-binding protein nodes. Furthermore, protein cages can be analyzed using analytical ultracentrifugation (AUC), transmission electron microscopy (TEM) and single-crystal X-ray diffraction (sc-XRD) techniques. HA-mediated protein-MOFs are formed in sitting-drop vapor diffusion crystallization trays and are probed via sc-XRD and multi-crystal small-angle X-ray scattering (SAXS) measurements. Ligand synthesis, construction of HA-mediated assemblies, and post-assembly analysis as described in this protocol can be performed by a graduate-level researcher within six weeks.

36 MATERIALS SCIENCE↗

Spectroscopic characterization of a new Re(i) tricarbonyl complex with a thiosemicarbazone derivative: towards sensing and electrocatalytic applications

This work describes the preparation of a new thiosemicarbazone derivative, (Z)- N -ethyl-2-(6-oxo-1,10-phenanthrolin-5(6 H )-ylidene)hydrazinecarbothioamide (phet) and its respective Re( I ) tricarbonyl chloro complex, fac -[ReCl(CO) 3 (phet)]. The spectroscopic, photophysical and electrochemical properties of the new complex were fully investigated through steady state and time-resolved techniques along with computational calculations. In fac -[ReCl(CO) 3 (phet)], the new ligand is coordinated to the metal center through the pyridyl rings of the phenanthroline moiety. The unbound electron pairs in the S atom of the bending thiosemicarbazone group induce new low energy lying electronic transitions. Consequently, enhanced visible light absorption up to 550 nm is observed in acetonitrile due to the overlap between MLCT Re→phet and IL phet(n→π*) transitions. The absorption bands and emission quantum yields of fac -[ReCl(CO) 3 (phet)] are sensitive to proton concentration due to an acid-basic equilibrium in the N atoms of the thiosemicarbazone. Proton dissociation constants of 10.0 ± 0.1 and 11.4 ± 0.2 were determined respectively for the ground and excited states of the new complex. Spectral changes could also be observed in the presence of Zn 2+ cations which can be further explored for sensing applications. The electrochemical behavior of the new complex was studied in detail, revealing up to four one electron reduction processes in the range from 0 to -2.4 V vs. Fc + /Fc. With support of DFT calculations, the first three processes are ascribed to the reduction of the coordinated phet ligand followed by the Re I/0 reduction and consequent Cl - release. Furthermore, the new complex was able to act as an electrocatalyst for CO 2 reduction into CO ( E onset = -1.92 V vs. Fc + /Fc), with a turnover frequency of 2.81 s -1 and turnover number of 24 ± 1 in anhydrous acetonitrile, being the first Re( I ) tricarbonyl complex with a thiosemicarbazone derivative described for this goal. The detailed characterization carried out here can drive the development of new Re( I )-thiosemicarbazone derivatives for different applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Alkyl decorated metal–organic frameworks for selective trapping of ethane from ethylene above ambient pressures

Here the trapping of paraffins is beneficial compared to selective olefin adsorption for adsorptive olefin purification from a process engineering point of view. Here we demonstrate the use of a series of Zn 2 (X-bdc) 2 (dabco) (where X-bdc 2- is bdc 2- = 1,4-benzenedicarboxylate with substituting groups X, DM-bdc 2- = 2,5-dimethyl-1,4-benzenedicarboxylate or TM-bdc 2- = 2,3,5,6-tetramethyl-1,4-benzenedicarboxylate and dabco = diazabicyclo[2.2.2.]octane) metal-organic frameworks (MOFs) for the adsorptive removal of ethane from ethylene streams. The best performing material from this series is Zn2(TM-bdc)2(dabco) (DMOF-TM), which shows a high ethane uptake of 5.31 mmol g -1 at 110 kPa, with a good IAST selectivity of 1.88 towards ethane over ethylene. Through breakthrough measurements a high productivity of 13.1 L/kg per breakthrough is revealed with good reproducibility over five consecutive cycles. Molecular simulations show that the methyl groups of DMOF-TM are forming a van der Waals trap with the methylene groups from dabco, snuggly fitting the ethane. Further, rarely used high pressure coadsorption measurements, in pressure regimes that most scientific studies on hydrocarbon separation on MOFs ignore, reveal an increase in ethane capacity and selectivity for binary mixtures with increased pressures. The coadsorption measurements reveal good selectivity of 1.96 at 1000 kPa, which is verified also through IAST calculations up to 3000 kPa. This study overall showcases the opportunities that pore engineering by alkyl group incorporation and pressure increase offer to improve hydrocarbon separation in reticular materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Generalizable, tunable control of divalent cation solvation structure via mixed anion contact ion pair formation

Multivalent batteries are a promising new technology for energy storage, but they face challenges to developing suitable electrolytes that can support reversible deposition/dissolution at the metal anode and enable compatibility with high voltage oxide cathode materials. Here, in this work, we investigate the solvation behavior of Zn 2+ , Mg 2+ , Ca 2+ and Cu 2+ in mixed anion electrolytes containing TFSI - and Cl - . Raman and nuclear magnetic resonance spectroscopies are utilized to probe the bulk solvation structure of these electrolytes and demonstrate that mixed anion contact ion pairs (CIPs) are formed in all four systems, indicating this behavior is likely general to divalent cations. Furthermore, the relative population of mixed anion CIPs can be tuned by controlling the relative ratio of TFSI : Cl, with significant CIP populations observed even at low relative fractions of Cl - . These findings imply that modifying the anion chemistry can easily adjust the solvation structure of bulk cations, which has important implications for the development of next-generation electrolytes. By understanding the factors that influence the formation of mixed anion CIPs, we can design systems that promote the formation of electrochemically-active solvation structures that can enable multivalent batteries with improved performance and lifetimes.

25 ENERGY STORAGE↗

Electronic and catalytic engineering in two-dimensional vdW metal–organic frameworks through alloying

Bimetallic metal-organic framework (MOF s ) alloys, in which heterogeneous metal clusters are incorporated into their backbone, are capable of highly selective separations and catalysis. Due to limitations in our fundamental understanding of their alloying, however, established methods result in phase-separated or amorphous two-dimensional (2D) MOF s or lack precise control over alloy ratios. Here, our results demonstrate 2D MOF alloys where metal cation ratios (M 1 and M 2 ) in M 1 xM 2 1-x BDC (M 1 or M 2 = Zn, Cu, Ni, Co, Fe, Mn) can be engineered on demand by controlling the metal salt dissociation constants. Resulting MOF alloys exhibit a highly 2D nature with excellent crystallinity and minute control over metal cation ratios. Overall, our experimental and theoretical results show that their electronic bandgaps and photoexcited carrier lifetimes can be engineered by metal cation alloying. Interestingly, 2D alloyed MOF s enable high-efficiency photo-catalytic water reduction performance in Co/Ni MOF alloys owing to the spatially separated metal clusters in 2D MOF alloys.

2D materials↗

Fermi–Löwdin orbital self-interaction correction of adsorption energies on transition metal ions

Density functional theory (DFT)-based descriptions of the adsorption of small molecules on transition metal ions are prone to self-interaction errors. Here, we show that such errors lead to a large over-estimation of adsorption energies of small molecules on Cu + , Zn + , Zn 2+ , and Mn + in local spin density approximation (LSDA) and Perdew, Burke, Ernzerhof (PBE) generalized gradient approximation calculations compared to reference values computed using the coupled-cluster with single, doubles, and perturbative triple excitations method. These errors are significantly reduced by removing self-interaction using the Perdew–Zunger self-interaction correction (PZ-SIC) in the Fermi–Löwdin Orbital (FLO) SIC framework. In the case of FLO-PBE, typical errors are reduced to less than 0.1 eV. Furthermore, analysis of the results using DFT energies evaluated on self-interaction-corrected densities [DFT(@FLO)] indicates that the density-driven contributions to the FLO-DFT adsorption energy corrections are roughly the same size in DFT = LSDA and PBE, but the total corrections due to removing self-interaction are larger in LSDA.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spectral widths and Stokes shifts in InP-based quantum dots

InP-based quantum dots (QDs) have Stokes shifts and photoluminescence (PL) line widths that are larger than in II–VI semiconductor QDs with comparable exciton energies. The mechanisms responsible for these spectral characteristics are investigated in this paper. Upon comparing different semiconductors, we find the Stokes shift decreases in the following order: InP > CdTe > CdSe. We also find that the Stokes shift decreases with core size and decreases upon deposition of a ZnSe shell. We suggest that the Stokes shift is largely due to different absorption and luminescent states in the angular momentum fine structure. The energy difference between the fine structure levels, and hence the Stokes shifts, are controlled by the electron–hole exchange interaction. Luminescence polarization results are reported and are consistent with this assignment. Spectral widths are controlled by the extent of homogeneous and inhomogeneous broadening. Here, we report PL and PL excitation (PLE) spectra that facilitate assessing the roles of homogeneous and different inhomogeneous broadening mechanisms in the spectra of zinc-treated InP and InP/ZnSe/ZnS particles. There are two distinct types of inhomogeneous broadening: size inhomogeneity and core–shell interface inhomogeneity. The latter results in a distribution of core–shell band offsets and is caused by interfacial dipoles associated with In–Se or P–Zn bonding. Quantitative modeling of the spectra shows that the offset inhomogeneity is comparable to but somewhat smaller than the size inhomogeneity. The combination of these two types of inhomogeneity also explains several aspects of reversible hole trapping dynamics involving localized In 3+ /V Zn 2– impurity states in the ZnSe shells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Photonuclear cross sections for 197 Au: An update on the gold standard

Cross sections for the 197 Au(γ, n) reaction are broadly used in nuclear physics as a standard for normalizing photonuclear reaction cross-section data at photon beam energies above approximately 8 MeV. In this paper, we report cross-section measurements for the 197 Au(γ, n) 196 Au g+m1 reaction at beam energies from 13 to 31 MeV. Our measurements provide the first cross-section data for this reaction at beam energies above 20 MeV, enabling the use of this reaction as a cross-section standard up to 30 MeV. Also, this work provides first cross-section measurements for the 197 Au(γ, n) 196 Au m2 reaction. In addition, we measured cross-section data for the 197 Au(γ, 3n) 194 Au reaction, which can be used as a cross-section standard above about 25 MeV. These measurements were performed using a new target activation method that is based on the angle-energy correlation of the laser Compton- scattered photon beams at the High Intensity Gamma-ray Source (HIγS). The technique enables measuring photonuclear reaction cross-sections at several discrete beam energies concurrently via a single irradiation on a stack of different targets. Measurements were carried out by irradiating a stack of concentric-ring targets consisting of Au, TiO 2 , Zn, Os, and Au (in order of the γ-ray beam direction). Our data for the 197 Au(γ,n) 196 Au g+m1 reaction in the energy range of 13 to 20 MeV are in good agreement with existing ones measured using monoenergetic γ-ray beams, but differ from data acquired using a bremsstrahlung γ-ray beam. Also, above 18 MeV, our data for the 197 Au(γ,n) 196 Au g+m1 and 197 Au(γ,n) 196 Au m2 reactions differ significantly from the most recent TENDL and JENDL evaluations, suggesting a need to update these data libraries. Furthermore, the TENDL evaluation and existing data are consistent with our data for the 197 Au(γ,3n) reaction, but differ significantly from the JENDL evaluation above 26 MeV.

190 ≤ A ≤ 219↗

Screening two-dimensional materials with topological flat bands

The topological flat band (TFB) has been proposed theoretically in various lattice models, to exhibit a rich spectrum of intriguing physical behaviors. However, the experimental demonstration of flat band (FB) properties has been severely hindered by the lack of materials realization. In this study, by screening materials from a first-principles materials database, we identify a group of two-dimensional materials with TFBs near the Fermi level, covering some simple line-graph and generalized line-graph FB lattice models. These include the kagome sublattice of O in Ti O 2 yielding a spin-unpolarized TFB, and that of V in ferromagnetic V 3 F 8 yielding a spin-polarized TFB. The monolayer Nb 3 Te Cl 7 and its counterparts from element substitution are found to be breathing-kagome-lattice crystals. The family of monolayer II I 2 V I 3 compounds exhibit a TFB representing the coloring-triangle lattice model. Re F 3 , Mn F 3 , and Mn Br 3 are all predicted to be diatomic-kagome-lattice crystals, with TFB transitions induced by atomic substitution. Finally, Hg F 2 , Cd F 2 , and Zn F 2 are discovered to host dual TFBs in the diamond-octagon lattice. Our findings pave the way to further experimental exploration of eluding FB materials and properties.

36 MATERIALS SCIENCE↗

The Transcription Factor Roc1 Is a Key Regulator of Cellulose Degradation in the Wood-Decaying Mushroom Schizophyllum commune

Wood-decaying fungi of the class Agaricomycetes (phylum Basidiomycota) are saprotrophs that break down lignocellulose and play an important role in nutrient recycling. They secrete a wide range of extracellular plant cell wall degrading enzymes that break down cellulose, hemicellulose, and lignin, the main building blocks of plant biomass. Although the production of these enzymes is regulated mainly at the transcriptional level, no activating regulators have been identified in any wood-decaying fungus in the class Agaricomycetes. We studied the regulation of cellulase expression in the wood-decaying fungus Schizophyllum commune. Comparative genomics and transcriptomics on two wild isolates revealed a Zn 2 Cys 6 -type transcription factor gene (roc1) that was highly upregulated during growth on cellulose, compared to glucose. It is only conserved in the class Agaricomycetes. A roc1 knockout strain showed an inability to grow on medium with cellulose as sole carbon source, and growth on cellobiose and xylan (other components of wood) was inhibited. Growth on non-wood-related carbon sources was not inhibited. Cellulase gene expression and enzyme activity were reduced in the Δroc1 strain. ChIP-Seq identified 1474 binding sites of the Roc1 transcription factor. Promoters of genes involved in lignocellulose degradation were enriched with these binding sites, especially those of LPMO (lytic polysaccharide monooxygenase) CAZymes, indicating that Roc1 directly regulates these genes. A conserved motif was identified as the binding site of Roc1, which was confirmed by a functional promoter analysis. Together, Roc1 is a key regulator of cellulose degradation and the first identified in wood-decaying fungi in the phylum Basidiomycota.

59 BASIC BIOLOGICAL SCIENCES↗

Materials Data on Zn3Fe2(CN)12 by Materials Project

(Fe)2(Zn(CN)4)3 is Corundum structured and crystallizes in the trigonal R-3c space group. The structure is zero-dimensional and consists of twelve iron molecules and eighteen Zn(CN)4 clusters. In each Zn(CN)4 cluster, Zn2+ is bonded in a tetrahedral geometry to four N3- atoms. There is two shorter (1.96 Å) and two longer (1.97 Å) Zn–N bond length. There are two inequivalent C2+ sites. In the first C2+ site, C2+ is bonded in a distorted single-bond geometry to one N3- atom. The C–N bond length is 1.17 Å. In the second C2+ site, C2+ is bonded in a distorted single-bond geometry to one N3- atom. The C–N bond length is 1.17 Å. There are two inequivalent N3- sites. In the first N3- site, N3- is bonded in a distorted linear geometry to one Zn2+ and one C2+ atom. In the second N3- site, N3- is bonded in a linear geometry to one Zn2+ and one C2+ atom.

36 MATERIALS SCIENCE↗

Molecular Scale Tuning of Covalent Organic Frameworks for Enhanced Properties

Covalent organic frameworks (COFs) are a type of porous, extended structure material which has demonstrated utility in numerous applications, including sensing and separations. Judicious choice of the linker and node not only fine tune the size of the framework, but also the functionality. We seek to tailor COF materials for applications in gas capture and electrochemical sensing. Herein, we demonstrate the material properties of COFs can be fine-tuned via post-synthetic metal cation doping of the parent structures. We have synthesized several COF structures with varying linkers which allow for the incorporation of metal cations. Structures incorporating Zn 2+ , Mn 2+ , and Cu 2+ have demonstrated utility in improving the CO 2 uptake properties of the COFs, while Ag + doped structures show potential as electrochemical sensors for chloride anions.

36 MATERIALS SCIENCE↗

Oligonucleotide synthesis catalyzed by the Zn/2+/ ion

Results of experiments are reported in which Zn(2+) ion catalyzed the formation of oligonucleotides from nucleoside phosphorimidazolides in aqueous solution, even in the absence of a template. Specifically, the imidazolides (ImpU or ImpA) polymerized to form ImpApA, and pApA, pApApA, and pApApApA, or the analogous uracil compounds. In addition, the expected hydrolysis products of the hydrolysis of ImpA were formed (pA, imidazole). Judging from the ratio of pA(n) over pA (with and without zinc ion), this ion increased the efficiency of phosphodiester-bond formation by up to 10 times. Possible mechanisms for the reaction are tentatively proposed.

Sawai, H.↗

Studies on precellular evolution - The encapsulation of polyribonucleotides by liposomes

Liposomes have been suggested as possible models of precellular systems formed in the early Archean earth from lipids of nonenzymatic origin. Since it is generally accepted that RNA molecules preceded double-stranded DNA molecules as genetic material, the encapsulation of polyribonucleotides within liposomes (made from dipalmitoyl phosphatidylcholine and from egg yolk phosphatidylcholine) was studied. Quantitative determinations show that approximately 50 percent of the available lipids form liposomes, and that up to 5 percent of the polyribonucleotides can be entrapped by them. Also studied was the encapsulation of polyribonucleotides in the presence of urea and cyanamide and of Zn(2+) and Pb(2+).

Baeza, I.↗

The binding energies of one and two water molecules to the first transition-row metal positive ions. II

The present investigation of H2O's binding energy to transition-metal ions proceeds from the D(2h) structure and bends the two water molecules out of plane. The molecule is constrained to have C(2v) symmetry, so that each water molecule and metal ion lies on a plane. The ground states are bent only for Mn(H2O)2(+) and Zn(H2O)2(+), where only 4s4p hybridization is energetically favorable; 4s4p hybridization reduces repulsion.

Rosi, Marzio↗

STRUCTURE AND PROPERTIES STUDY ON ENERGY MATERIALS: THERMOELECTRIC MATERIAL TETRAHEDRITE AND LITHIUM ION CONDUCTOR

Development of efficient energy materials is critical in order to ease the energy demand and reduce our dependence of fossil fuel. Thermoelectric materials are promising due to their capability of generating electrical power by recovering waste heat. The performance of thermoelectric materials is quantified by a dimensionless figure of merit zT, which depends on their properties such as electrical conductivity, Seebeck coefficient and thermal conductivity. Tetrahedrites, a copper antimony sulfosalt mineral, typified by Cu 12-x MxSb 4 S 13 , where M is a transition metal element such as Ni, Zn, Fe or Mn, have great potential for thermoelectric application due to their relatively high zT (close to 1 at 700 K), earth-abundance, environmental friendliness, favorable electrical properties, and most importantly intrinsic low lattice thermal conductivity (less than 1 W m -1 K -1 ) in wide temperature. In addition to energy recovery, reliable energy storage devices are also emerging to relieve the energy demand and improve the efficiency of consuming energy resources. Lithium-ion batteries are known to be reliable and successful electrochemical energy storage devices and appliable in various aspects, including laptops, smartphones and electrical vehicles. Lithium phosphorous oxynitride (LiPON) are widely used as thin-film solid-state electrolytes in Li-ion battery, which is the only demonstrated solid-state electrolyte that is quite stable in direct contact with Li metal at potentials from 0-5 V. However, the structure of LiPON, the effects of N doping, and the origin of its good electrochemical stability remains inconclusive. In this thesis, reliable modeling techniques accompanied with experimental tools, are applied to study the thermoelectric material tetrahedrite and the ionic conductor LiPON, in order to study their structural and dynamical properties. Accurate and efficient density-functional theory (DFT) and density-functional tight-binding (DFTB) methods, combined with molecular dynamics (MD) simulations are utilized in order to investigate the structures and properties of these energy materials. The incoherent and coherent atomic dynamics study of tetrahedrite Cu 10.5 NiZn 0.5 Sb 4 S 13 provides the origin of softening upon cooling by investigate the motion of Cu12e at different temperatures. The dynamic structure factors in the longitudinal and transverse direction will also be discussed. The Cu movement of Cu-rich tetrahedrite Cu 14 Sb 4 S 13 is revealed by Cu self-diffusivity, nuclear density map and “nudged elastic band” (NEB). Moreover, we investigate the effect of simulation cell size and basis sets on the DFT-based MD simulation results using tetrahedrite Cu1 0 Zn 2 Sb 4 S 13 thermoelectric as a model material, showing the advantage of larger cell by accessing smaller Q range. In addition, the low-temperature structural properties of Cu 12 Sb 4 S 13 is measured by neutron diffraction, which indicates that no cubic to tetragonal transition occurs at metal-semiconductor transition (MST) temperature. Thermoelectric properties such as Seebeck coefficient, electrical resistivity and electrical thermal conductivity will also be investigated. DFTB method is implemented to study the structure and transport properties of Li 3 PO 4 and LiPON, while the exploration of N doping effect is included. Lastly, the LiPON/Li interphase will be revealed in order to study the origin of electrochemical stability.

Li, Junchao↗