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Data Visualization Saliency Model: A Tool for Evaluating Abstract Data Visualizations.
Abstract not provided.
Ammonia Oxidation by Abstraction of Three Hydrogen Atoms from a Mo–NH 3 Complex
We report ammonia oxidation by homolytic cleavage of all three H atoms from a Mo৶ 15 NH 3 complex using the 2,4,6-tri-tert-butylphenoxyl radical to afford a Mo-alkylimido (Mo৶ 15 NR) complex (R = 2,4,6-tri-t-butylcyclohexa-2,5-dien-1-one). Reductive cleavage of Mo৶15NR generates a terminal Mo৶N nitride, and a [Mo৶ 15 NH] + complex is formed by protonation. Computational analysis describes the energetic profile for the stepwise removal of three H atoms from the Mo৶ 15 NH 3 complex and the formation of Mo৶ 15 NR. Acknowledgment. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Re-search Center funded by the U.S. Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences. EPR and mass spectrometry experiments were performed using EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at PNNL. The authors thank Dr. Eric D. Walter and Dr. Rosalie Chu for assistance in performing EPR and mass spectroscopy analysis, respectively. Computational resources provided by the National Energy Re-search Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Pacific North-west National Laboratory is operated by Battelle for the U.S. DOE.
Steric effects in light-induced solvent proton abstraction
The significance of solvent structural factors in the excited-state proton transfer (ESPT) reactions of Schiff bases with alcohols is reported here. In this work, we use the super photobase FR0-SB and a series of primary, secondary, and tertiary alcohol solvents to illustrate the steric issues associated with solvent to photobase proton transfer. Steady-state and time-resolved fluorescence data show that ESPT occurs readily for primary alcohols, with a probability proportional to the relative –OH concentration. For secondary alcohols, ESPT is greatly diminished, consistent with the barrier heights obtained using quantum chemistry calculations. ESPT is not observed in the tertiary alcohol. We explain ESPT using a model involving an intermediate hydrogen-bonded complex where the proton is “shared” by the Schiff base and the alcohol. The formation of this complex depends on the ability of the alcohol solvent to achieve spatial proximity to and alignment with the FR0-SB* imine lone pair stabilized by the solvent environment.
Rate constants for H abstraction from benzo(a)pyrene and chrysene: a theoretical study
Density functional B3LYP/6-31G(d) and ab initio G3(MP2,CC) calculations have been carried out to determine thermal rate constants of direct H abstraction reactions from four- and five-ring polycyclic aromatic hydrocarbons (PAH) chrysene and benzo[a]pyrene by various radicals abundant in combustion flames, such as H, CH 3 , C 3 H 3 , and OH, using transition state theory. The results show that the H abstraction reactions with OH have the lowest barriers of ~4 kcal mol -1 , followed by those with H and CH 3 with barriers of 16–17 kcal mol -1 , and then with propargyl radicals with barriers of 24–26 kcal mol -1 . Thus, the OH radical is predicted to be the fastest H abstractor from PAH. Even at 2500 K, the rate constant for H abstraction by H is still 34% lower than the rate constant for H abstraction by OH. The reaction with H is calculated to have rate constants 35–19 times higher than those for the reaction with CH 3 due to a more favorable entropic factor. The reactions of H abstraction by C 3 H 3 are predicted to be orders of magnitude slower than the other reactions considered and their equilibrium is strongly shifted toward the reactants, making propargyl an inefficient H abstractor from the aromatics. The calculations showed strong similarity of the reaction energetics in different H abstraction positions of benzo[a]pyrene and chrysene within armchair and zigzag edges in these molecules, but clear distinction between the armchair and zigzag sites. The zigzag sites appear to be more reactive, with H abstraction rate constants by H, CH 3 , and OH being respectively 37–42%, a factor of 2.1, and factors of 8–9 higher than the corresponding rate constants for the H abstraction reactions from armchair sites. Although the barrier heights for the two types of edges are similar, the entropic factor makes zigzag sites more favorable for H abstraction. Rate expressions have been generated for all studied reactions with the goal to rectify current combustion kinetics mechanisms.
Methods and Experiences for Developing Abstractions for Data-intensive, Scientific Applications
Developing software for scientific applications that require the integration of diverse types of computing, instruments, and data present challenges that are distinct from commercial software. These applications require scale, and the need to integrate various programming and computational models with evolving and heterogeneous infrastructure. Pervasive and effective abstractions for distributed infrastructures are thus critical; however, the process of developing abstractions for scientific applications and infrastructures is not well understood. While theory-based approaches for system development are suited for well-defined, closed environments, they have severe limitations for designing abstractions for scientific systems and applications. The design science research (DSR) method provides the basis for designing practical systems that can handle real-world complexities at all levels. In contrast to theory-centric approaches, DSR emphasizes both practical relevance and knowledge creation by building and rigorously evaluating all artifacts. In this work, we show how DSR provides a well-defined framework for developing abstractions and middleware systems for distributed systems. Specifically, we address the critical problem of distributed resource management on heterogeneous infrastructure over a dynamic range of scales, a challenge that currently limits many scientific applications. We use the pilot-abstraction, a widely used resource management abstraction for high-performance, high throughput, big data, and streaming applications, as a case study for evaluating the DSR activities. For this purpose, we analyze the research process and artifacts produced during the design and evaluation of the pilot-abstraction. We find DSR provides a concise framework for iteratively designing and evaluating systems. Finally, we capture our experiences and formulate different lessons learned.
Assessing the impacts of water abstractions on river ecosystem services: an eco-hydraulic modelling approach
The provision of important river ecosystem services (ES) is dependent on the flow regime. This requires methods to assess the impacts on ES caused by interventions on rivers that affect flow regime, such as water abstractions. This study proposes a method to i) quantify the provision of a set of river ES, ii) simulate the effects of water abstraction alternatives that differ in location and abstracted flow, and iii) assess the impact of water abstraction alternatives on the selected ES. The method is based on river modelling science, and integrates spatially distributed hydrological, hydraulic and habitat models at different spatial and temporal scales. The method is applied to the hydropeaked upper Noce River (Northern Italy), which is regulated by hydropower operations. We selected locally relevant river ES: habitat suitability for the adult marble trout, white-water rafting suitability, hydroelectricity production from run-of-river (RoR) plants. Our results quantify the seasonality of river ES response variables and their intrinsic non-linearity, which explains why the same abstracted flow can produce different effects on trout habitat and rafting suitability depending on the morphology of the abstracted reach. An economic valuation of the examined river ES suggests that incomes from RoR hydropower plants are of comparable magnitude to touristic revenue losses related to the decrease in rafting suitability.
Programming Abstractions for Managing Workflows on Tiered Storage Systems
Scientific workflows in High Performance Computing (HPC) environments are processing large amounts of data. The storage hierarchy on HPC systems is getting deeper, driven by new technologies (NVRAMs, SSDs, etc.) There is a need for new programming abstractions that allow users to seamlessly manage data at the workflow level on multi-tiered storage systems, and provide optimal workflow performance and use of storage resources. In previous work, we introduced a software architecture Managing Data on Tiered Storage for Scientific Workflows (MaDaTS) that used a Virtual Data Space (VDS) abstraction to hide the complexities of the underlying storage system while allowing users to control data management strategies. In this article, we detail the data-centric programming abstractions that allow users to manage a workflow around its data on the storage layer. The programming abstractions simplify data management for scientific workflows on multi-tiered storage systems, without affecting workflow performance or storage capacity. We measure the overheads and effectiveness introduced by the programming abstractions of MaDaTS. Our results show that these abstractions can optimally use the storage capacity in lesser capacity storage tiers, and simplify data management without adding any performance overheads.
From electronic structure to model application of key reactions for gasoline/alcohol combustion: Hydrogen-atom abstraction by $CH_3O\dot{O}$ radicals
Hydrogen atom abstraction by methyl peroxy ($CH_3O\dot{O}$) radicals can play an important role in gasoline/ethanol interacting chemistry for fuels that produce high concentrations of methyl radicals. Detailed kinetic reactions for hydrogen atom abstraction by $CH_3O\dot{O}$ radicals from the components of FGF-LLNL (a gasoline surrogate) including cyclopentane, toluene, 1-hexene, n -heptane, and isooctane have been systematically studied in this work. Here, the M06-2X/6-311 ++ G(d,p) level of theory was used to obtain the optimized structure and vibrational frequency for all stationary points and the low-frequency torsional modes. The 1-D hindered rotor treatment for low-frequency torsional modes was treated at M06-2X/6-31G level of theory. The UCCSD(T)-F12a/cc-pVDZ-F12 and QCISD(T)/CBS level of theory were used to calculate single point energies for all species. High pressure limiting rate constants for all hydrogen atom abstraction channels were performed using conventional transition state theory with unsymmetric tunneling corrections. Individual rate constants are reported in the temperature range from 298.15 to 2000 K. Our computed results show that the abstraction of allylic hydrogen atoms from 1-hexene is the fastest at low temperatures. When the temperature increases, the hydrogen atom abstraction reaction channel at the primary alkyl site gradually becomes dominant. Thermodynamics properties for all stable species and high-pressure limiting rate constants for each reaction pathway obtained in this work were incorporated into the latest gasoline surrogate/ethanol model to investigate the influence of the rate constants calculated here on model predicted ignition delay times.
Abstraction of Hydride from Alkanes and Dihydrogen by the Perfluorotrityl Cation
Abstract Lewis acids play a central role in a large variety of chemical transformations. The reactivity of the strongest Lewis acids is typically studied in the context of affinity towards hard bases, such as fluoride or oxygenous species. Carbocations can be viewed as soft Lewis acids, possessing significant affinity for softer bases, such as hydride. This work presents the ambient‐temperature isolation of salts of the perfluorotrityl cation ((C 6 F 5 ) 3 C + or F 15 Tr + ) in combination with halogenated carborane anions. The F 15 Tr + cation exhibits remarkable hydride affinity, illustrated by the observation of hydride abstraction from dihydrogen, and of the rapid abstraction of hydride from −CH 2 −groups in alkanes. Theoretical studies support the favorability of hydride abstraction from dihydrogen, and indicate that the hydride abstraction from alkanes proceeds via a concerted hydride transfer process that is sensitive to steric effects.
Abstraction of Hydride from Alkanes and Dihydrogen by the Perfluorotrityl Cation
Abstract Lewis acids play a central role in a large variety of chemical transformations. The reactivity of the strongest Lewis acids is typically studied in the context of affinity towards hard bases, such as fluoride or oxygenous species. Carbocations can be viewed as soft Lewis acids, possessing significant affinity for softer bases, such as hydride. This work presents the ambient‐temperature isolation of salts of the perfluorotrityl cation ((C 6 F 5 ) 3 C + or F 15 Tr + ) in combination with halogenated carborane anions. The F 15 Tr + cation exhibits remarkable hydride affinity, illustrated by the observation of hydride abstraction from dihydrogen, and of the rapid abstraction of hydride from −CH 2 −groups in alkanes. Theoretical studies support the favorability of hydride abstraction from dihydrogen, and indicate that the hydride abstraction from alkanes proceeds via a concerted hydride transfer process that is sensitive to steric effects.
Transformation of an Embedded Five-Membered Ring in Polycyclic Aromatic Hydrocarbons via the Hydrogen-Abstraction–Acetylene-Addition Mechanism: A Theoretical Study
Five-membered rings are constituents of many polycyclic aromatic hydrocarbons (PAHs) and their presence on the edges of large PAHs has been repeatedly observed experimentally. However, modern kinetic combustion models often do not consider the growth of PAHs through the transformation of the five-membered rings. Here, in connection with the above, we carried out a theoretical study of the mechanism of Hydrogen-Abstraction-aCetylene-Addition (HACA) transformation of an embedded five-membered ring on the armchair PAH edge to a six-membered ring, considering cyclopenta[d,e,f]phenanthrene (4,5-methylenephenanthrene) as a prototype system for this process. The potential energy surface for the reactions of cyclopenta[d,e,f]phenanthrenyl radicals produced by direct H abstractions from cyclopenta[d,e,f]phenanthrene with acetylene has been compiled at the G3(MP2,CC)//B3LYP/6-311G(d,p) level of theory including zero-point vibrational energy corrections. The computed energies and molecular parameters were then used to solve the Rice-Ramsperger-Kassel-Marcus Master Equation (RRKM-ME) in order to calculate reaction rate at various pressures and temperatures, which were fitted to modified Arrhenius equation for further kinetic modeling. The results show that the HACA transformation of the embedded five-membered ring to a six-membered ring is possible, albeit slow. The most viable reaction mechanism involves the R2 + C 2 H 2 reaction, where the acetylene molecules adds to a σ-radical in the six-membered ring adjacent to the five-membered ring via a low entrance barrier. The predominant product of R2 + C 2 H 2 is predicted to be 3 ethynyl 4H cyclopenta[def]phenanthrene Pr5 via immediate H elimination from the initial addition complex. Next, Pr5 undergoes H-assisted isomerization to 4aH-pentaleno[4,3,2,1-cdef]phenanthrene Pr4, and the latter adds an H atom eventually forming the 1-pyrenylmethyl radical Pr3: R2 + C 2 H 2 ⇌ 3 ethynyl 4H cyclopenta[def]phenanthrene (Pr5) + H ⇌ 4aH-pentaleno[4,3,2,1-cdef]phenanthrene (Pr4) + H Pr5 + H ⇌ Pr4 + H Pr4 + H → 1-pyrenylmethyl (Pr3) This HACA sequence may be competitive with the methyl radical addition to the R1 radical formed by H abstraction from the CH 2 group in the five-membered ring of cyclopenta[d,e,f]phenanthrene, which provides a pathway to pyrene following two H atom losses. Relative contributions of the two mechanisms of the five- to six-membered ring transformation would strongly depend on the branching ratios of the R1 and R2 radicals produced by the H abstractions and the available concentration of C 2 H 2 vs. CH 3 and hence differ in different flames.
A unifying modeling abstraction for infinite-dimensional optimization
Infinite-dimensional optimization (InfiniteOpt) problems involve modeling components (variables, objectives, and constraints) that are functions defined over infinite-dimensional domains. Examples include continuous-time dynamic optimization (time is an infinite domain and components are functions of time), PDE optimization problems (space and time are infinite domains and components are functions of space-time), as well as stochastic and semi-infinite optimization (random space is an infinite domain and components are a function of such random space). InfiniteOpt problems also arise from combinations of these problem classes (e.g., stochastic PDE optimization). Given the infinite-dimensional nature of objectives and constraints, one often needs to define appropriate quantities (measures) to properly pose the problem. Moreover, InfiniteOpt problems often need to be transformed into a finite dimensional representation so that they can be solved numerically. Here in this work, we present a unifying abstraction that facilitates the modeling, analysis, and solution of InfiniteOpt problems. The proposed abstraction enables a general treatment of infinite-dimensional domains and provides a measure-centric paradigm to handle associated variables, objectives, and constraints. This abstraction allows us to transfer techniques across disciplines and with this identify new, interesting, and useful modeling paradigms (e.g., event constraints and risk measures defined over time domains). Our abstraction serves as the backbone of an intuitive Julia-based modeling package that we call InfiniteOpt.jl. We demonstrate the developments using diverse case studies arising in engineering.
Con Connections: Detecting Fraud from Abstracts using Topological Data Analysis
In this paper we present a novel approach for identifying fraudulent papers from their titles and abstracts. The premise of the approach is that there are holes in the presentation of the approach and findings of fraudulent research papers. As an abstract is intended to highlight key features of the approach as well as important conclusions the authors seek to determine if the assumed existence of holes can be identified from analysis of abstracts alone. The data set considered is derived from papers sharing a single author with labels determined based on a formal linguistic analysis of the complete documents. To detect these logical and literary holes we utilize techniques from topological data analysis which summarizes data based on the presence of multi-dimensional, topological holes. We find that, in fact, topological features derived through a combination of techniques in natural language processing and time-series analysis allow for superior detection of the fraudulent papers than the natural language processing tools alone. Thus we conclude that the connections and holes present in the abstracts of research cons contributes to an ability to infer the scientific validity of the corresponding work.
SynopFrame: Multiscale time-dependent visual abstraction framework for analyzing DNA nanotechnology simulations
We present an open-source framework, SynopFrame, that allows DNA nanotechnology (DNA-nano) experts to analyze and understand molecular dynamics simulation trajectories of their designs. We use a multiscale multi-dimensional abstraction space, connect the representations to a projected conformational space plot of the structure’s temporal sequence, and thus enable experts to analyze the dynamics of their structural designs and, specifically, failure cases of the assembly. In addition, our time-dependent abstraction representation allows the biologists, for the first time in a smooth and structurally clear way, to identify and observe temporal transitions of a DNA-nano design from one configuration to another, and to highlight important periods of the simulation for further analysis. We realize SynopFrame as a dashboard of the different synchronized 3D spatial and 2D schematic visual representations, with a color overlay to show essential properties such as the status of hydrogen bonds. The linking of the spatial, schematic, and abstract views ensures that users can effectively analyze the high-frequency motion. We also categorize the status of the hydrogen bonds into a new format to allow us to color-encode it and overlay it on the representations. To demonstrate the utility of SynopFrame, we describe example usage scenarios and report user feedback.
Theory-Based Mechanism for Fluoromethane Combustion I: Thermochemistry and Abstraction Reactions
A new detailed chemical kinetic mechanism is presented for small fluorinated hydrocarbons. Ab initio electronic structure theory is used to provide heats of formation with subchemical accuracy. The ANL0 method is extended to include fluorine. The resulting heats of formation at 0 K are in excellent agreement with 36 benchmark species in the Active Thermochemical Tables, with a mean error of μ = –0.02 kJ/mol and a standard deviation of σ = 0.91 kJ/mol. The thermophysical properties for 92 small-molecule H/C/O/F species are computed. The rate coefficients for 40+ H-abstraction reactions involving H, O, F, OH, OF, HO 2 , and various methyl radicals with CH 4 , CH 3 F, CH 2 F 2 , CHF 3 , CH 2 O, and CHFO are discussed. Here, the computed rate constants are in excellent agreement with the available literature. Additionally, 30+ rate constants are provided for F abstraction, which are several orders of magnitude smaller than H abstraction. The thermophysical properties and rate constants are provided in a mechanism. This mechanism is the first in a series of theory-based investigations into the thermal destruction of per- and polyfluorinated species.
A Pd III Sulfate Dimer Initiates Rapid Methane Monofunctionalization by H Atom Abstraction
An electrogenerated Pd III 2 species in fuming sulfuric acid is competent for rapid and concurrent methane monohydroxylation to methyl bisulfate (CH 3 OSO 3 H) and methane sulfonation to methanesulfonic acid (CH 3 SO 3 H). In situ NMR at 50 °C is used to track methane transformation exclusively to CH 3 OSO 3 H and CH 3 SO 3 H at high conversions. Integrating a set of kinetic and computational studies, the mechanism of methane monofunctionalization by Pd III 2 is examined. Here, experimental rate laws and common kinetic isotope effects for CH 3 OSO 3 H and CH 3 SO 3 H formation suggest that both transformations proceed via a common rate-limiting C-H activation step. Introduction of O 2 or Pd II,III 2 suppresses CH 3 SO 3 H generation, indicating a radical chain sequence. Although the metal-metal bonded Pd III 2 complex is a net two-electron oxidant, our aggregate kinetic data point to a mechanistic model that features rate-limiting H atom abstraction by the Pd III 2 complex to generate a methyl radical intermediate. The CH 3 • intermediate then recombines with Pd II,III 2 to furnish a CH 3 Pd III 2 intermediate that reductively eliminates CH 3 OSO 3 H. Alternatively, the CH 3 intermediate can enter a chain reaction with SO 3 to generate CH 3 SO 3 H. DFT computations support the radical-based C-H activation by Pd III 2 and delineate H atom abstraction pathways with computed reaction barriers and kinetic isotope effects (KIEs) that are consistent with experimental data. These mechanistic investigations challenge the paradigm of electrophilic C-H activation and highlight H atom abstraction as a potent pathway for selective methane C-H oxidative functionalization at high reaction rates.
Weakening the N–H Bonds of NH 3 Ligands: Triple Hydrogen-Atom Abstraction to Form a Chromium(V) Nitride
Weakening and cleaving N-H bonds is crucial for improving molecular ammonia oxidation catalysts. In this work, we report the synthesis and hydrogen atom abstraction chemistry of bis(ammonia) Cr porphyrin complexes Cr(TPP)(NH 3 ) 2 and Cr(TMP)(NH 3 ) 2 (TPP = 5,10,15,20-tetraphenyl-meso-porphyrin and TMP = 5,10,15,20-tetramesityl-meso-porphyrin) using bulky aryloxyl radicals. The triple hydrogen atom abstraction reaction results in the formation of Cr V (por)(≡N), with the nitride deriving from ammonia, as indicated by UV-Vis and FT-IR spectroscopy, and a single crystal structural determination of Cr(TPP)(≡N). Subsequent oxidation of this chromium(V)-nitrido complex results in the formation of Cr III (por), with scission of the Cr≡N bond. A computational analysis illustrates the progression from Cr II to Cr V and evaluates the energetics of abstracting hydrogen atoms from Cr II -NH 3 to generate Cr V ≡N. The formation and isolation of Cr V (por)(≡N) illustrates the stability of these species and the need to chemically activate the nitride moiety for atom transfer or N-N coupling reactivity.