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At least 1,711 records · Page 95

Characterizing intracellular proteomes for microbes: An experimental approach using label-free protein quantitation

Genomic and transcriptomic studies generate a rich source of molecular information; however, neither a static genome nor the presence of a messenger RNA provides the most direct insight into the functional state of a microbial cell at any given time. Rather, it is the ensemble of proteins (i.e., proteome) that is the primary workhorse for most biological processes that are concurrent and coordinately active in a living cell. Currently, mass-spectrometry-based (MS) technologies provide unprecedented information into the composition of the proteome, shedding light on the numerous complex biological processes actively shaping observed phenotypes. Herein, we detail a protocol for the exploration of intracellular proteomes through the large-scale, unbiased identification of proteins and their relative abundances using liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS). In general, this protocol is applicable to both microbial and eukaryotic systems.

Abraham, Paul↗

Guest Editorial

Energy Systems Integration (ESI) is the process of coordinating the operation and planning of energy systems across multiple pathways and/or geographical scales to deliver reliable, cost-effective energy services with minimal impact on the environment. Energy systems have evolved from individual systems with little or no dependencies into a complex set of integrated systems at scales that include customers, cities, and regions. This evolution has been driven by political, economic, and environmental objectives. As we try to meet the globally recognized imperative to reduce carbon emissions through the deployment of large renewable energy capacities while also maintaining reliability and competitiveness, flexible energy systems are required. This flexibility can be attained through integrating various systems: by physically linking energy vectors, namely electricity, heat, and fuels; by coordinating these vectors across other infrastructures, namely water, data, and transport; by institutionally coordinating energy markets; and, spatially, by increasing market footprint with granularity all the way down to the customer level. Smart grids and ESI are related, in particular, the coupling between electricity, consumers, data and transport. This special section focuses on the aspects of ESI where electricity is coupled to water, heat and fuels and where this coupling brings challenges and/or opportunities.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Development of a dipodal Schiff base ligand with N-imine and O-naphtholate donors: A potential chelator towards Cu(II) metal ion established through potentiometric and spectrophotometric studies

A novel hydroxynaphthaldehyde derived Schiff base ligand N,N’-bis-[2-[(2-hydroxy-1-naphthyl)methyleneamino]ethyl]propanediamide (DOTA2HNAP) containing nitrogen and oxygen donor atoms has been developed. The lowest energy molecular structure of DOTA2HNAP and its complexes with Cu (II) metal ion were examined by molecular mechanics using MM+ force which later was re-optimized by semi-empirical method. The theoretical IR and UV spectra of the ligand were obtained using semi empirical/ZINDO/PM3 and were compared with the experimental ones. The coordinating ability of DOTA2HNAP with H{sup +} and Cu(II) ions was investigated in 1:99 (DMSO: water) binary solvent mixture at 25±1°C by potentiometric and spectrophotometric method. The electronic spectra of the ligand show three distinct peaks (253nm, 320nm and 360nm) implicating existence of the Schiff base in quinone form that was well supported by theoretical spectral studies. Out of various complex species forming in solution, all the metal ions show higher stability of complexes when in 1:1 metal-ligand stoichiometry, binding through two N-imine and two O-naphtholate groups.

36 MATERIALS SCIENCE↗

Pentavalent Curium, Berkelium, and Californium in Nitrate Complexes: Extending Actinide Chemistry and Oxidation States

Pentavalent actinyl nitrate complexes An V O 2 (NO 3 ) 2 - were produced by elimination of two NO 2 from An III (NO 3 ) 4 - for An = Pu, Am, Cm, Bk, and Cf. Density functional theory (B3LYP) and relativistic multireference (CASPT2) calculations confirmed the AnO 2 (NO 3 ) 2 - as AnVO 2 + actinyl moieties coordinated by nitrates. Computations of alternative An III O 2 (NO 3 ) 2 - and AnI V O 2 (NO 3 ) 2 - revealed significantly higher energies. Previous computations for bare AnO 2 + indicated AnVO 2 + for An = Pu, Am, Cf, and Bk, but Cm III O 2 + : electron donation from nitrate ligands has here stabilized the first Cm V complex, Cm V O 2 (NO 3 ) 2 - . Structural parameters and bonding analyses indicate increasing An-NO 3 bond covalency from Pu to Cf, in accordance with principles for actinide separations. Atomic ionization energies effectively predict relative stabilities of oxidation states; more reliable energies are needed for the actinides.

36 MATERIALS SCIENCE↗

Comparison of Mutual Awareness in Analog vs. Digital Control Rooms

Control rooms in nuclear power plants are complex, collaborative working environments rife with potential for human error. As control rooms evolve from analog to digital interface environments, crew communication strategies must change as well. Operators in the analog control room operate the plant and communicate with each other with the help of control boards with large control panels, meters, and switches. Reactor operators could choose a particular set of controls on the particular control board which corresponds to the part of the system of interest. Visual display units (VDU), which became a fixture in the control rooms with the shift to digital human-machine interfaces (HMI), bring benefits for safety and flexibility combining information from various sources. With the increase in automation and the use of digital HMIs operators received their personal sitting workstations where they are able to navigate and operate the plant. The amount of information increased as well as the complexity of monitoring and analyzing the system states. Also computerized systems cause operators to get absorbed by their personal screens and reduce interaction between the crew members. Therefore, the collaboration and coordination of task demands requires vigilance and mutual awareness. The level of automation has an influence on the level of mutual awareness experienced by operators in the control rooms. Teams function to carry out highly interdependent tasks, requiring synthesis and sharing of information to achieve common goals. Improving the performance of the team necessitates the operators to focus on the system, the surrounding environment, and situational awareness about the system states. Collaboration of team members is critical when employing the digital operating systems as the acute awareness of the overall progress of the group and individual activities of the operators drives the team to the desired end-states of the plant operations. Out-of-the loop (OOTL) performance problems can be referred to as the lack of supervisory control, system monitoring, and information processing in the digital HMIs. Under some circumstances Senior Reactor Operators (SRO) struggle to follow the actions of other Reactor Operators (RO) because with the new digital interfaces SROs lose track of how the procedures are carried out by ROs, which results in the loss of three way communication. Mutual awareness plays a significant role in keeping the SROs in the loop of plant operations. This paper will investigate, through literature review and expert interviews, the impact and human errors attributed to the increasing complexity of new digital main control rooms. Comparison of the new digital interfaces with the analog interfaces in nuclear power plants has the potential to shed light on increasing mutual awareness and three way communications between the SROs and ROs. Further, identification of the human errors and human actions can provide beneficial information, suggesting significant and critical improvements that can be implemented in the main control rooms to increase safety and reliability of new technology. Additionally, insights on mutual awareness for analog vs. digital control rooms can serve to improve human reliability.

99 GENERAL AND MISCELLANEOUS↗

Synthesis, structure, and properties of nickel complexes with nitrilotris(methylenephosphonic acid) [Ni(H{sub 2}O)3N(CH2PO{sub 3}H){sub 3}] and Na{sub 4}[Ni(H{sub 2}O)N(CH{sub 2}PO{sub 3}){sub 3}] ∙ 11H{sub 2}O

Nitrilotris(methylenephosphonato)triaquanickel and tetrasodium nitrilotris(methylenephosphonato) aquanickelate undecahydrate were synthesized and characterized. The crystal of [Ni(H{sub 2}O){sub 3}N(CH{sub 2}PO{sub 3}H){sub 3}] is composed of linear coordination polymers and belongs to sp. gr. P2{sub 1}/c, Z = 4, a = 9.17120(10) Å, b = 16.05700(10) Å, c = 9.70890(10) Å, β = 115.830(2)°. The Ni atom is in an octahedral coordination formed by two oxygen atoms of one phosphonate ligand, one oxygen atom of another ligand molecule, and three water molecules in a meridional configuration. The crystal of Na{sub 4}[Ni(H{sub 2}O)N(CH{sub 2}PO{sub 3}){sub 3}] ∙ 11H{sub 2}O has an island dimeric chelate structure and belongs to sp. gr. C2/c, Z = 8, a = 18.7152(2) Å, b = 12.05510(10) Å, c = 21.1266(2) Å, β = 104.4960(10)°. The Ni atom has a slightly distorted octahedral coordination involving one nitrogen atom and closes three five-membered N–C–P–O–Ni rings sharing the Ni–N bond.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Dilute Alloys Based on Au, Ag, or Cu for Efficient Catalysis: From Synthesis to Active Sites

The development of new catalyst materials for energy-efficient chemical synthesis is critical as over 80% of industrial processes rely on catalysts, with many of the most energy-intensive processes specifically using heterogeneous catalysis. Catalytic performance is a complex interplay of phenomena involving temperature, pressure, gas composition, surface composition and structure over multiple length and time scales. In response to this complexity, the integrated approach to heterogeneous dilute-alloy catalysis reviewed here brings together materials synthesis, mechanistic surface chemistry, reaction kinetics, in-situ and operando characterization, and theoretical calculations in a coordinated effort to develop design principles to predict and improve catalytic selectivity. Dilute alloy catalysts—in which isolated atoms or small ensembles of the minority metal on the host metal lead to enhanced reactivity while retaining selectivity—are particularly promising as selective catalysts. Several dilute alloy materials using Au, Ag and Cu as the majority host element, including more recently introduced support-free nanoporous metals and oxide-supported nanoparticle "raspberry colloid templated (RCT)" materials, are reviewed for selective oxidation and hydrogenation reactions. Progress in understanding how such dilute alloy catalysts can be used to enhance selectivity of key synthetic reactions is reviewed, including quantitative scaling from model studies to catalytic conditions. The dynamic evolution of catalyst structure and composition studied in surface science and catalytic conditions and their relationship to catalytic function are also discussed, followed by advanced characterization and theoretical modeling that have been developed to determine the distribution of minority metal atoms at or near the surface. Furthermore, the integrated approach demonstrates the success of bridging the divide between fundamental knowledge and design of catalytic processes in complex catalytic systems, which can accelerate the development of new and efficient catalytic processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Efficient Optimization of Large Wind Farms for Real-Time Control: Preprint

Wind turbines in a wind farm typically operate individually to maximize their own performance regardless of the impact of aerodynamic interactions on neighboring turbines. Properly coordinating turbines, by operating some turbines suboptimally, within a wind farm has the potential to improve overall wind farm performance. Computing the optimal control strategy under varying atmospheric conditions can be computationally intense for large wind farms. As wind power farms increase in size and related models become more complex, computationally efficient algorithms are needed to perform real-time optimization and control. This study proposes a distributed optimization framework and computationally efficient wake steering wind farm control strategy that uses the yaw angle of a turbine to alter the behavior of a turbine wake and minimize turbine interactions. This computational efficiency allows the strategy to be feasible for real-time control.

17 WIND ENERGY↗

Long noncoding RNA HOTTIP cooperates with CCCTC-binding factor to coordinate HOXA gene expression

Highlights: • HOTTIP is required for activation of distal HOXA genes but its role is restricted by CTCF boundary. • HOTTIP and CTCF coordinate to specify the pattern of histone modifications on HOXA genes in foreskin fibroblasts. • HOTTIP RNA acts as a new interaction partner of CTCF. The spatiotemporal control of HOX gene expression is dependent on positional identity and often correlated to their genomic location within each loci. Maintenance of HOX expression patterns is under complex transcriptional and epigenetic regulation, which is not well understood. Here we demonstrate that HOTTIP, a lincRNA transcribed from the 5′ edge of the HOXA locus, physically associates with the CCCTC-binding factor (CTCF) that serves as an insulator by organizing HOXA cluster into disjoint domains, to cooperatively maintain the chromatin modifications of HOXA genes and thus coordinate the transcriptional activation of distal HOXA genes in human foreskin fibroblasts. Our results reveal the functional connection of HOTTIP and CTCF, and shed light on lincRNAs in gene activation and CTCF mediated chromatin organization.

60 APPLIED LIFE SCIENCES↗

Partitioning of oxygen isotopes during the aqueous solvation of nitric acid

Mixtures of water and inorganic acids show differences in isotopic composition between the vapor and liquid phases, reportedly even at an azeotrope. A recent reactive azeotropy analysis rationalized this by allowing for differences in stable isotope composition between bound solvation complexes and the bulk liquid. In this study, a mixture of water and nitric acid was examined experimentally to determine whether or not significant differences in stable isotope composition exist between bound solvation complexes and the bulk solution. A Rayleigh distillation was conducted using a solution of nitric acid and water. During the distillation, it was expected that bulk water would be vaporized first while (bound) water involved with hydrating the acid would be vaporized at later times along with the acid. Samples of both distillate and residual liquid were collected over time intervals and analyzed to determine oxygen and nitrogen stable isotope composition using isotope ratio mass spectrometry. Comparative samples were collected from the distillation of water alone. The measured oxygen fractionation factors suggest that the acid is preferentially hydrated with 18 O-enriched water, compared to the unbound, or bulk, water. Preferential coordination of 18 O-enriched water with the dissolved acid is consistent with heavier water forming stronger bonds relative to light water. Here, the results imply that isotope-dependent partitioning between bulk solvent and dissolved complexes may prove necessary in developing accurate descriptions of isotope fractionation during vapor-liquid equilibrium.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Complexation and Solvent Extraction Studies of High Valency Actinides by Hard/Soft Donor Schiff Base Ligands

Successful separation of the mid actinides (U, Np, Pu, Am) from other elements is imperative for drastically lowering the long term radiotoxicity of SNF. Ubiquitous to these mid actinides is a wide range of oxidation states (+III, +IV, +V, +VI) where the +V and +VI oxidation states exist in a linear dioxo actinyl cation AnO{sub 2}{sup n+} (O=An=O){sup n+} guaranteeing unique ligand coordination about the equatorial plane. Multidentate Schiff base ligands which possess nitrogen and oxygen donor groups can accommodate the steric demands of the actinyl cations as well as providing selectivity for actinides in a separation process. Group extraction or retention of the mid actinides in a biphasic solvent extraction process can be achieved by complexation of their actinyl species by Schiff base ligands in one phase while all other non actinyl cations are complexed in the other phase. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Ultrafast Spectroscopic Signatures of Coherent Electron-Transfer Mechanisms in a Transition Metal Complex

The prevalence of ultrafast electron-transfer processes in light-harvesting materials has motivated a deeper understanding of coherent reaction mechanisms. Kinetic models based on the traditional (equilibrium) form of Fermi’s Golden Rule are commonly employed to understand photoinduced electron-transfer dynamics. These models fail in two ways when the electron-transfer process is fast compared to solvation dynamics and vibrational dephasing. First, electron-transfer dynamics may be accelerated if the photoexcited wavepacket traverses the point of degeneracy between donor and acceptor states in the solvent coordinate. Second, traditional kinetic models fail to describe electron-transfer transitions that yield products which undergo coherent nuclear motions. We address the second point in this work. Transient absorption spectroscopy and a numerical model are used to investigate coherent back-electron-transfer mechanisms in a transition metal complex composed of titanium and catechol, [Ti(cat) 3] 2– . The transient absorption experiments reveal coherent wavepacket motions initiated by the back-electron-transfer process. Model calculations suggest that the vibrationally coherent product states may originate in either vibrational populations or coherences of the reactant. That is, vibrational coherence may be produced even if the reactant does not undergo coherent nuclear motions. Lastly, the analysis raises a question of broader significance: can a vibrational population-to-coherence transition (i.e., a nonsecular transition) accelerate electron-transfer reactions even when the rate is slower than vibrational dephasing?

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A facile method to introduce iron secondary metal centers into metal–organic frameworks

In this report, we report the successful incorporation of iron (0) species into a 2, 2'-bipyridine functionalized metal–organic framework (MOF) (UiO-67-bpydc). Considering the limited window size of the MOF, a small molecule, iron pentacarbonyl, was used to introduce iron (0) to coordinate to the backbone of the MOF. The newly generated material contains the iron coordinated linker, Fe(CO) 3 (bpydc), which was supported by a series of characterization techniques. DFT calculation was also used to help understand the structure of the formed complex inside the MOF. The MOF structure remained unchanged after the post-synthetic modification, and the resulted material is a great precursor to generate MOF supported catalyst.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Redox-Mediator-Assisted Electrocatalytic Hydrogen Evolution from Water by a Molybdenum Sulfide-Functionalized Metal–Organic Framework

The Zr 6 -based metal–organic framework NU-1000 was successfully functionalized with candidate catalysts—MoS x units—via SIM (solvothermal deposition in MOFs) of molybdenum(VI), followed by reaction with H2S gas. The structure of the material, named MoS x - SIM, was characterized spectroscopically and through a single-crystal X-ray diffraction measurement. These measurements and others established that the catalyst is monometallic, with mixed oxygen and sulfur coordination, and that it forms from a MOF-node-supported molybdenum-based cluster featuring only oxy ligands. Notably, the formal potential for the MOF-grafted complex, like that for the metal–sulfur active site of hydrogenase, is nearly coincident with the formal potential for the hydrogen couple. Its effective concentration within the mesoporous MOF is several hundred millimolar, and its porous-framework-based immobilization/heterogenization obviates the need for aqueous solubility as a condition for use as a well-defined catalyst. MoS x - SIM was evaluated as an electrocatalyst for evolution of molecular hydrogen from aqueous acid. Although the MoS x - functionalized framework exhibits catalytic behavior, the highly insulating nature of the support inhibits high electrocatalytic performance. Introduction of an archetypal redox mediator (RM), methyl viologen (MV 2+ ), resulted in more than 20-fold enhancement in its catalytic performance on a turnover frequency basis, implying efficient RM-assisted electron transfer to otherwise electrochemically non-addressable MoS x moieties. Electrochemical kinetic studies with additional viologens as mediators reveal an unexpected square-root dependence of overall reaction rate on mediator concentration, as well as sensitivity to the strength of RM •+ as a reductant. These observations, together with observations of potential-dependent H/D isotope effects and potential-dependent pH effects, provide useful insights into the catalysis mechanism and help to explain how the MOF-affixed monometallic catalyst can effectively catalyze a two-electron reduction reaction, i.e., hydrogen evolution from acidified water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Rational design of efficient electrode–electrolyte interfaces for solid-state energy storage using ion soft landing

Here, the rational design of improved electrode-electrolyte interfaces (EEI) for energy storage is critically dependent on a molecular-level understanding of ionic interactions and nanoscale phenomena. The presence of non-redox active species at EEI has been shown to strongly influence Faradaic efficiency and long-term operational stability during energy storage processes. Herein, we achieve substantially higher performance and long-term stability of EEI prepared with highly-dispersed discrete redox-active cluster anions (50 ng of pure ~0.7 nm size molybdenum polyoxometalate anions (POM) anions on 25 mg (≈ 0.2 wt%) carbon nanotube (CNT) electrodes) by complete elimination of strongly coordinating non-redox species through ion soft-landing (SL). For the first time, electron microscopy provides atomically-resolved images of individual POM species directly on complex technologically relevant CNT electrodes. In this context, SL is established as a versatile approach for the controlled design of novel surfaces for both fundamental and applied research in energy storage.

25 ENERGY STORAGE↗

Ligand-coordinated Ir single-atom catalysts stabilized on oxide supports for ethylene hydrogenation and their evolution under a reductive atmosphere

In this work, we present a novel series of oxide-supported Ir-ligand single-atom catalysts (SACs) for ethylene hydrogenation. The SACs were created by a metal–ligand self-assembly strategy developed by our group, using one of two ligands, either 1,10-phenanthroline-5,6-dione (PDO) or 3,6-Di-2-pyridyl-1,2,4,5-tetrazine (DPTZ), on powder supports of either CeO 2 or MgO. Characterization by XAS, XPS, and CO adsorption proved that Ir exist principally as highly uniform, cationic single-atoms. Ir SACs show significantly higher durability and metal utilization efficiency than Ir nanoparticle (NP) catalysts during ethylene hydrogenation at 100 °C, as well as excellent stability, as no Ir aggregates were detected after >10 h reaction. The activity can be tuned by ligand and support effects: PDO and CeO 2 are superior to DPTZ and MgO, respectively. This tunability is attributed to differences in H 2 activation capability, which results from differences in support reducibility, electron density on Ir, and, potentially, the local coordination environment of Ir. The Ir SACs lose H 2 activation activity either under inert gas or under H 2 . Through XPS and in situ XAS studies, we attributed the former to the reversible loss of Ir hydride, which is the active species for H 2 activation, and the latter to irreversible over-hydrogenation and loss of Ir–O/N coordination. This work presents a new type of Ir hydrogenation SACs that are more durable, efficient, and tunable than supported Ir NPs, while more stable than homogeneous Ir complexes. It also offers fundamental understanding regarding ligand and support effects, as well as the evolution of Ir single-atoms under H 2 , instructing future design of stable, effective hydrogenation SACs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Derivative-free stochastic optimization via adaptive sampling strategies

In this paper, we present a novel derivative-free framework for solving unconstrained stochastic optimization problems. Many problems in fields ranging from simulation optimization to reinforcement learning to quantum computing involve settings where only stochastic function values are obtained via a zeroth-order oracle, which has no available gradient information and necessitates the usage of derivative-free optimization methodologies. Our approach includes estimating gradients using stochastic function evaluations and integrating adaptive sampling techniques to control the accuracy in these stochastic approximations. Our framework encapsulates several gradient estimation techniques, including standard finite-difference, Gaussian smoothing, sphere smoothing, randomized coordinate finite-difference, and randomized subspace finite-difference methods. We provide theoretical convergence guarantees for our framework and analyze the worst-case iteration and sample complexities associated with each gradient estimation method. Finally, we demonstrate the empirical performance of the methods on logistic regression and nonlinear least squares problems.

Adaptive sampling↗

Opportunities for fundamental physics research with radioactive molecules

Molecules containing short-lived, radioactive nuclei are uniquely positioned to enable a wide range of scientific discoveries in the areas of fundamental symmetries, astrophysics, nuclear structure, and chemistry. Recent advances in the ability to create, cool, and control complex molecules down to the quantum level, along with recent and upcoming advances in radioactive species production at several facilities around the world, create a compelling opportunity to coordinate and combine these efforts to bring precision measurement and control to molecules containing extreme nuclei. In this paper, we review the scientific case for studying radioactive molecules, discuss recent atomic, molecular, nuclear, astrophysical, and chemical advances which provide the foundation for their study, describe the facilities where these species are and will be produced, and provide an outlook for the future of this nascent field.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗