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NASA NTRS2014

Coordination Between Sectors in Shared Airspace Operations

Recent studies have shown that a more efficient use of airspace may involve shared airspace operations, i.e., temporal as well as spatial separation of arrival and departure flows [1][2]. Temporal separation would permit a departure aircraft to fly through an arrival flow, depending on an available gap. This would necessitate careful and precise coordination between controllers in different sectors. Three methods of coordination which permit the penetration of a controller's airspace by another controller's aircraft are described: point out, look-and-go, and prearranged coordination procedure. Requirements of each method are given, along with associated problems that have surfaced in the field as described by Aviation Safety and Reporting System (ASRS) and other reports. A Human-in-the-Loop simulation was designed to compare two of the methods: point out and prearranged coordination procedures. In prearranged coordination procedures (P-ACP), the controllers control an aircraft in another controller's airspace according to specified prearranged procedures, without coordinating each individual aircraft with another controller, as is done with point outs. In the simulation, three experienced controllers rotated through two arrival sectors and a non-involved arrival sector of a Terminal Radar Approach Control (TRACON) airspace. Results of eighteen one-hour simulation runs (nine in each of the two conditions) showed no impact of the coordination method on separation violations nor on arrival times for 208 departing aircraft crossing an arrival stream. Participant assessment indicated that although both coordination conditions were acceptable, the prearranged coordination procedure condition was slightly safer, more efficient, timely, and overall, worked better operationally. Problems arose in the point out condition regarding controllers noticing acceptance of point outs. Also, in about half of the point-out runs, time pressure was felt to have had an impact on when and if the departures could cross an arrival stream. An additional problem with point outs may be confusion in the field about which controller has responsibility for separating point-out aircraft from other aircraft.

Parke, Bonny↗

DOE OSTI2023

Review of Carbon Support Coordination Environments for Single Metal Atom Electrocatalysts (SACS)

This topical review focuses on the distinct role of carbon support coordination environment of single-atom catalysts (SACs) for electrocatalysis. The article begins with an overview of atomic coordination configurations in SACs, including a discussion of the advanced characterization techniques and simulation used for understanding the active sites. A summary of key electrocatalysis applications is then provided. These processes are oxygen reduction reaction (ORR), oxygen evolution reaction (OER), hydrogen evolution reaction (HER), nitrogen reduction reaction (NRR), and carbon dioxide reduction reaction (CO 2 RR). The review then shifts to modulation of the metal atom-carbon coordination environments, focusing on nitrogen and other non-metal coordination through modulation at the first coordination shell and modulation in the second and higher coordination shells. Representative case studies are provided, starting with the classic four-nitrogen-coordinated single metal atom (M$-$N 4 ) based SACs. Bimetallic coordination models including homo-paired and hetero-paired active sites are also discussed, being categorized as emerging approaches. The theme of the discussions is the correlation between synthesis methods for selective doping, the carbon structure–electron configuration changes associated with the doping, the analytical techniques used to ascertain these changes, and the resultant electrocatalysis performance. In conclusion, critical unanswered questions as well as promising underexplored research directions are identified.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Disordered interfaces of alkaline aluminate salt hydrates provide glimpses of Al 3+ coordination changes

Hypothesis: The precipitation and dissolution of aluminum-bearing mineral phases in aqueous systems often proceed via changes in both aluminum coordination number and connectivity, complicating molecular-scale interpretation of the transformation mechanism. Here, the thermally induced transformation of crystalline sodium aluminum salt hydrate, a phase comprised of monomeric octahedrally coordinated aluminate which is of relevance to industrial aluminum processing, has been studied. Because intermediate aluminum coordination states during melting have not previously been detected, it is hypothesized that the transition to lower coordinated aluminum ions occurs within a highly disordered quasi-two-dimensional phase at the solid-solution interface. Experiments and simulations: In this work, in situ X-ray diffraction (XRD), Raman and 27 Al nuclear magnetic resonance (NMR) spectroscopy were used to monitor the melting transition of nonasodium aluminate hydrate (NSA, Na 9 [Al(OH) 6 ] 2 ·3(OH)·6H 2 O). A mechanistic interpretation was developed based on complementary classical molecular dynamics (CMD) simulations including enhanced sampling. A reactive forcefield was developed to bridge speciation in the solution and in the solid phase. Findings: In contrast to classical dissolution, aluminum coordination change proceeds through a dynamically stabilized ensemble of intermediate states in a disordered layer at the solid-solution interface. In both melting and dissolution of NSA, octahedral, monomeric aluminum transition through an intermediate of pentahedral coordination. The intermediate dehydroxylates to form tetrahedral aluminate (Al(OH)$_4^–$) in the liquid phase. This coordination change is concomitant with a breaking of the ionic aluminate-sodium ion linkages. The solution phase Al(OH)$_4^–$ ions subsequently polymerize into polynuclear aluminate ions. However, there are some differences between bulk melting and interfacial dissolution, with the onset of the surface-controlled process occurring at a lower temperature (~30 °C) and the coordination change taking place more gradually as a function of temperature. This work to determine the local structure and dynamics of aluminum in the disordered layer provides a new basis to understand mechanisms controlling aluminum phase transformations in highly alkaline solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

New water soluble heterometallic complex showing unpredicted coordination modes of EDTA

A mesoporous 3D polymeric complex (I) having formula ([Zr(IV)O-μ{sup 3}-(EDTA)Fe(III)OH]·H{sub 2}O){sub n} has been crystallized and characterized by various techniques. Single-crystal X-ray diffraction analysis revealed that complex (I) crystallized in chiral monoclinic space group Cc (space group no. 9) with unexpected coordination modes of EDTA and mixture of two transition metal ions. In this complex, the coordination number of Zr(IV) ion is seven where four carboxylate oxygen atoms, two nitrogen atoms, one oxide atom are coordinating with Zr(IV). Fe(III) is four coordinated and its coordination environment is composed of three different carboxylic oxygen atoms from three different EDTA and one oxygen atom of –OH group. The structure consists of 4-c and 16-c (2-nodal) net with new topology and point symbol for net is (3{sup 36}·4{sup 54}·5{sup 30})·(3{sup 6}). TGA study and XRPD pattern showed that the coordination polymer is quite stable even after losing water molecule and –OH ion. Quenching behavior in fluorescence of ligand is observed by complexation with transition metal ions is due to n–π⁎ transition. The SEM micrograph shows the morphology of complex (I) exhibits spherical shape with size ranging from 50 to 280 nm. The minimum N{sub 2} (S{sub BET}=8.7693 m{sup 2}/g) and a maximum amount of H{sub 2} (high surface area=1044.86 m{sup 2}/g (STP)) could be adsorbed at 77 K. From DLS study, zeta potential is calculated i.e. −7.94 shows the negative charges on the surface of complex. Hirshfeld surface analysis and fingerprint plots revealed influence of weak or non bonding interactions in crystal packing of complex. - Graphical abstract: The complex (I) crystallized with unexpected coordination modes of EDTA having 4-c, 16-c net with new topology and point symbol is (3{sup 36}·4{sup 54}·5{sup 30})·(3{sup 6}). TGA study and XRPD pattern proved its stability with high preference of H{sub 2} uptake by complex. - Highlights: • 3D complex having unexpected coordination modes of EDTA with Zr(IV) and Fe(III). • The structure consists of 4-c and 16-c (2-nodal) net with new topology. • Reasonable S{sub BET} (8.7693 m{sup 2}/g) but high H{sub 2} uptake (1044.86 m{sup 2}/g) due to limited pore size. • Quenching behavior due to n–π⁎ transition by complexation with transition metal ions. • From DLS study, zeta potential value is −7.94.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Complexations of Ln(III) with SnS{sub 4}H and Sn{sub 2}S{sub 6}: Solvothermal syntheses and characterizations of lanthanide coordination polymers with thiostannate and polyamine mixed ligands

Polymeric lanthanide complexes with thiostannate and polyamine mixed ligands, [Ln(peha)(μ–SnS{sub 4}H)]{sub n} [Ln=La (1a), Nd (1b)] and [(Ln(tepa)(μ–OH)){sub 2}(μ–Sn{sub 2}S{sub 6})]{sub n}nH{sub 2}O [Ln=Nd (2a), Sm (2b), Gd (2c), Dy (2d)] (peha=pentaethylenehexamine, tepa=tetraethylenepentamine) were respectively prepared in peha and tepa coordinative solvents by the solvothermal methods. In 1a and 1b, the Ln{sup 3+} ions are coordinated by a hexadentate peha ligand forming [Ln(peha)]{sup 3+} units. The [SnS{sub 4}H]{sup 3−} anion chelates a [Ln(peha)]{sup 3+} unit via two S atoms and coordinates to another [Ln(peha)]{sup 3+} unit via the third S atom. As a result, the [Ln(peha)]{sup 3+} units are connected into coordination polymers [Ln(peha)(μ–SnS{sub 4}H)]{sub n} by an unprecedented tridentate μ–η{sup 1},η{sup 2}–SnS{sub 4}H bridging ligands. In 2a–2d, the Ln{sup 3+} ions are coordinated by a pentadentate tepa ligand, and two [Ln(tepa)]{sup 3+} units are joined by two μ–OH bridges to form a binuclear [(Ln(tepa)(μ–OH)){sub 2}]{sup 4+} unit. Behaving as a bidentate μ–η{sup 1}, η{sup 1}–Sn{sub 2}S{sub 6} bridging ligand, the Sn{sub 2}S{sub 6} unit connects [(Ln(tepa)(μ–OH)){sub 2}]{sup 4+} units into a neutral coordination polymer [(Ln(tepa)(μ–OH)){sub 2}(μ–Sn{sub 2}S{sub 6})]{sub n} via the trans S atoms. The Ln{sup 3+} ions are in distorted monocapped square antiprismatic and bicapped trigonal prismatic environments in [(Ln(peha)(μ–SnS{sub 4}H)]{sub n} and [(Ln(tepa)(μ–OH)){sub 2}(μ–Sn{sub 2}S{sub 6})]{sub n}, respectively. The denticities of ethylene polyamine play an important role on the formation and complexation of the thiostannate in the presence of lanthanide ions. Compounds 1a–2d show well-defined absorption edges with band gaps between 2.81 and 3.15 eV. - Graphical abstract: Lanthanide coordination polymers concerning thiostannate ligands were prepared by the solvothermal methods, and μ{sub 3}–SnS{sub 4}H and μ–Sn{sub 2}S{sub 6} ligands to Ln(III) centers were obtained. - Highlights: • Lanthanide coordination polymers were prepared in polyamines with higher denticity. • The μ–η{sup 1},η{sup 2}–SnS{sub 4}H and μ–η{sup 1},η{sup 1}–Sn{sub 2}S{sub 6} ligands to Ln(III) centers were obtained. • Effect of amine on the complexation of Ln(III) with thiostannate is observed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Stable, Efficient Iron Electrodeposition via Anion-Directed Control of Fe(II) Coordination

Traditional steelmaking processes consume about 7% of the world’s energy supply, with reduction of iron oxides into iron via blast furnaces representing the most energy-demanding and capital-intensive step. To economize and modularize iron reduction processes, we aim to develop an electrodeposition technique to reduce aqueous iron ions to metallic iron. However, the hydrogen reduction reaction (HER) occurs at a more positive standard reduction potential than the iron reduction reaction. In addition, aqueous Fe(II) cations easily precipitate at mildly acidic conditions (pH ≥ 3), which limits the deposition efficiency and degrades deposit quality. To address these challenges, we first search for anions that have intermediate coordination strength with Fe(II) based on the hard-soft acid-base theory, trading a slightly more negative Fe(II) reduction potential for a considerably broader pH stability range. We select citrate with predicted intermediate coordination strength, in combination with more weakly coordinating anions (e.g., SO 4 2- , Cl - ) to control the coordination structure of Fe 2+ for improved electrolyte stability and electrodeposition behavior. We find that citrate coordination stabilizes Fe 2+ -based electrolytes at higher pH conditions (4.8–5.5), significantly extending their shelf life while also suppressing HER during Fe electrodeposition by orders of magnitude. To measure Faradaic efficiencies (FE), we developed a straightforward, titration-based methodology to quantify the amount of deposited iron regardless of the rate of concurrent HER. Although coordination between citrate and Fe 2+ decreases the reduction potential of Fe(II), high FE (≥98%) was achieved at 10 mA cm -2 . FE and achievable deposition rates are tunable by both concentration and the ratio of Fe 2+ to citrate. In all cases, Raman spectroscopy and X-ray diffraction (XRD) reveal that iron deposition in citrate-containing electrolytes suppresses iron oxide/hydroxide precipitation, in contrast to deposits generated in citrate-free electrolytes. Altogether, this work demonstrates that citrate-mediated anion coordination enables high-purity iron electrodeposition with increased FE, high current density, and improved electrolyte stability. This multi-anion coordination strategy provides a versatile framework for designing stable electrolyte and efficient metal electrodeposition.

coordination↗

DOE OSTI2021

Coordinated Modeling of Electric Grid and Natural Gas Network Operations

Presentation based upon full report of a Colorado case study and coordination framework, which is available at https://www.nrel.gov/docs/fy20osti/77096.pdf. JISEA analysts Brian Sergi, Omar Guerra, and Bri-Mathias Hodge will present on recent JISEA work on coordination between the natural gas and electricity sectors. Power and gas are becoming increasingly interdependent but weren't designed to function together. How does greater coordination impact system operations with different levels of solar and wind penetrations? This free JISEA presentation will take place in a Webinar on Tuesday, May 11, 2021 at 12 p.m.: Learn how greater coordination between the natural gas and electricity sectors impacts system operations with different levels of solar and wind penetrations. Presentation information includes: Historical and projected data for natural gas consumption and power generation in the United States as demonstrated by 2014 East Coast Polar Vortex, 2021 Texas Winter Storm Uri. Showing coupling points, FERC identified need for better coordination, different levels of coordination (decision making and optimization control), coordination framework. Case study on Colorado Front Range, ramping requirements and gas nominations, real-time dispatch (June and December scenarios), results of analysis of impacts of coordination on unserved load. Total real-time gas offtakes by node, impacts on unserved gas, effect on CO2 emissions. Discussions on clusions drawn from Colorado Case study expanded co-simulation via HELICS, objectives of the HELICS+ natural gas use case, modeling of hydrogen blending, techno economic assessment of blending, and blending impacts on energy content and pressure.

analysis↗

DOE OSTI2026

Online task-space motion control for positioner-coordinated multi-robot manufacturing systems

Incorporating multiple robotic manipulators into large-scale manufacturing systems enhances production efficiency and expands manufacturing capabilities beyond those of single-robot systems. Workpiece positioners in robotic manufacturing have demonstrated significant benefits for process optimization, but coordination strategies for multi-robot systems with shared positioners have received limited attention. This work presents a task-space coordinated trajectory-tracking control framework for multi-robot manufacturing systems, in which robots coordinate their motions within a shared, dynamic workpiece positioning frame. A workpiece positioner actively adjusts the pose of the manufactured component to enable greater operational concurrency and improve overall production efficiency. The proposed motion-coordination scheme employs a distributed and scalable architecture, supporting coordination across heterogeneous multi-robot systems. Two optimization methodologies are introduced to manage kinematic redundancies and maintain continuous, near-optimal operation throughout the manufacturing process. The first strategy exploits a task-space dimensionality reduction to achieve locally optimal configurations by leveraging symmetry-axis rotations of the tool. The second strategy utilizes the workpiece positioner to drive the coordinated robots toward stable and kinematically favorable configurations. For both optimization strategies, multiple objectives are defined to improve key performance metrics, including manipulability, configuration consistency, proximity to mechanical limits, and motion efficiency. Addressing a key limitation of existing coordination approaches, the framework is designed around online setpoint modification, allowing coordinated robots to respond effectively to in-situ process feedback. The proposed control framework is validated using the Robot Operating System (ROS) middleware on a combination of physical and simulated multi-robot system hardware.

Arbogast, Alex [ORNL] (ORCID:0000000154740723)↗

DOE OSTI2014

Vibrational quasi-degenerate perturbation theory with optimized coordinates: Applications to ethylene and trans-1,3-butadiene

A perturbative extension to optimized coordinate vibrational self-consistent field (oc-VSCF) is proposed based on the quasi-degenerate perturbation theory (QDPT). A scheme to construct the degenerate space (P space) is developed, which incorporates degenerate configurations and alleviates the divergence of perturbative expansion due to localized coordinates in oc-VSCF (e.g., local O–H stretching modes of water). An efficient configuration selection scheme is also implemented, which screens out the Hamiltonian matrix element between the P space configuration (p) and the complementary Q space configuration (q) based on a difference in their quantum numbers (λ{sub pq} = ∑{sub s}|p{sub s} − q{sub s}|). It is demonstrated that the second-order vibrational QDPT based on optimized coordinates (oc-VQDPT2) smoothly converges with respect to the order of the mode coupling, and outperforms the conventional one based on normal coordinates. Furthermore, an improved, fast algorithm is developed for optimizing the coordinates. First, the minimization of the VSCF energy is conducted in a restricted parameter space, in which only a portion of pairs of coordinates is selectively transformed. A rational index is devised for this purpose, which identifies the important coordinate pairs to mix from others that may remain unchanged based on the magnitude of harmonic coupling induced by the transformation. Second, a cubic force field (CFF) is employed in place of a quartic force field, which bypasses intensive procedures that arise due to the presence of the fourth-order force constants. It is found that oc-VSCF based on CFF together with the pair selection scheme yields the coordinates similar in character to the conventional ones such that the final vibrational energy is affected very little while gaining an order of magnitude acceleration. The proposed method is applied to ethylene and trans-1,3-butadiene. An accurate, multi-resolution potential, which combines the MP2 and coupled-cluster with singles, doubles, and perturbative triples level of electronic structure theory, is generated and employed in the oc-VQDPT2 calculation to obtain the fundamental tones as well as selected overtones/combination tones coupled to the fundamentals through the Fermi resonance. The calculated frequencies of ethylene and trans-1,3-butadiene are found to be in excellent agreement with the experimental values with a mean absolute error of 8 and 9 cm{sup −1}, respectively.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2024

Spontaneous bodily coordination varies across affective and intellectual child-adult interactions

Research on child-adult interactions has identified that the morphology of bodily coordination seems to be sensitive to age and type of interaction. Mirror-like imitation emerges earlier in life and is more common during emotionally laden interactions, while anatomical imitation is acquired later and associated with cognitive tasks. However, it remains unclear whether these morphologies also vary with age and type of interaction during spontaneous coordination. Here we report a motion capture study comparing the spontaneous coordination patterns of thirty-five 3-year-old (20 girls; M age = 3.15 years) and forty 6-year-old children (20 girls; M age = 6.13 years) interacting with unacquainted adults during two storytelling sessions. The stories narrated the search of a character for her mother (Predominantly Affective Condition) or an object (Predominantly Intellectual Condition) inside a supermarket. Results show that children of both ages consistently coordinated their spontaneous movements towards adult storytellers, both in symmetric and asymmetric ways. However, symmetric coordination was more prominent in 3-year-old children and during predominantly emotional interactions, whereas asymmetric coordination prevailed in 6-year-old children and during predominantly intellectual interactions. These results add evidence from spontaneous interactions in favor of the hypothesis that symmetric coordination is associated with affective interactions and asymmetric coordination with intellectual ones.

Cornejo, Carlos↗

NASA NTRS2017

Time-Coordination Strategies and Control Laws for Multi-Agent Unmanned Systems

Time-critical coordination tools for unmanned systems can be employed to enforce the type of temporal constraints required in terminal control areas, ensure minimum distance requirements among vehicles are satisfied, and successfully perform coordinated missions. In comparison with previous literature, this paper presents an ampler spectrum of coordination and temporal specifications for unmanned systems, and proposes a general control law that can enforce this range of constraints. The constraint classification presented con- siders the nature of the desired arrival window and the permissible coordination errors to define six different types of time-coordination strategies. The resulting decentralized coordination control law allows the vehicles to negotiate their speeds along their paths in response to information exchanged over the communication network. This control law organizes the different members in the fleet hierarchically per their behavior and informational needs as reference agent, leaders, and followers. Examples and simulation results for all the coordination strategies presented demonstrate the applicability and efficacy of the coordination control law for multiple unmanned systems.

Puig-Navarro, Javier↗

DOE OSTI2023

Coordination Chemistry as a Universal Strategy for a Controlled Perovskite Crystallization

The most efficient and stable perovskite solar cells (PSCs) are made from complex mixture of precursors, which are practically always dissolved in combinations of the volatile (and toxic) N, N-Dimethylformamide (DMF), and the non-volatile (and green) dimethyl sulfoxide (DMSO) solvents. Typically, to then form a thin film, an extreme oversaturation of the perovskite precursor is initiated to trigger nucleation sites, e.g. by vacuum, an airstream or a so-called antisolvent. Unfortunately, most such oversaturation triggers do not expel the lingering (and highly coordinating) DMSO, which is highly coordinating, from the thin films; this detrimentally affects long-term stability. Here, for the first time, we introduce (the green) dimethyl sulfide (DMS) as a novel nucleation trigger for perovskite films combining, uniquely, high coordination and high vapor pressure. More precisely, DMS coordinates more strongly than all currently used solvents, hence replacing them, including DMSO, effectively during film formation. Crucially, DMS also has among the highest vapor pressures reported in literature, thus effectively leaving the thin film shortly after formation. This gives DMS a universal scope: DMS replaces other solvents by coordinating more strongly and removes itself once the film formation is finished. To demonstrate this novel coordination chemistry approach, we process MAPbI 3 PSCs, typically dissolved in hard-to-remove (and green) DMSO achieving 21.6% efficiency, among the highest reported efficiencies for this system. To confirm the universality of our strategy, we tested DMS for FAPbI 3 as another composition, which showed higher efficiency of 23.5% compared to 20.9% for fabricated device with CB. Finally, this work provides a universal strategy to control perovskite crystallization using coordination chemistry heralding the revival of perovskite compositions with pure DMSO, such as MAPbI 3 .

36 MATERIALS SCIENCE↗

DOE OSTI2023

Coordination Stoichiometry Effects on the Binding Hierarchy of Histamine and Imidazole–M 2+ Complexes

Histidine–M 2+ coordination bonds are a recognized bond motif in biogenic materials with high hardness and extensibility, which has led to growing interest in their use in soft materials for mechanical function. However, the effect of different metal ions on the stability of the coordination complex remains poorly understood, complicating their implementation in metal-coordinated polymer materials. Herein, rheology experiments and density functional theory calculations are used to characterize the stability of coordination complexes and establish the binding hierarchy of histamine and imidazole with Ni 2+ , Cu 2+ , and Zn 2+ . It is found that the binding hierarchy is driven by the specific affinity of the metal ions to different coordination states, which can be macroscopically tuned by changing the metal-to-ligand stoichiometry of the metal-coordinated network. These findings facilitate the rational selection of metal ions for optimizing the mechanical properties of metal-coordinated materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

An efficient and numerically stable procedure for generating sextic force fields in normal mode coordinates

In this paper, we outline a general, scalable, and black-box approach for calculating high-order strongly coupled force fields in rectilinear normal mode coordinates, based upon constructing low order expansions in curvilinear coordinates with naturally limited mode-mode coupling, and then transforming between coordinate sets analytically. The optimal balance between accuracy and efficiency is achieved by transforming from 3 mode representation quartic force fields in curvilinear normal mode coordinates to 4 mode representation sextic force fields in rectilinear normal modes. Using this reduced mode-representation strategy introduces an error of only 1 cm{sup −1} in fundamental frequencies, on average, across a sizable test set of molecules. We demonstrate that if it is feasible to generate an initial semi-quartic force field in curvilinear normal mode coordinates from ab initio data, then the subsequent coordinate transformation procedure will be relatively fast with modest memory demands. This procedure facilitates solving the nuclear vibrational problem, as all required integrals can be evaluated analytically. Our coordinate transformation code is implemented within the extensible PyPES library program package, at http://sourceforge.net/projects/pypes-lib-ext/.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2012

Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase

Two divalent metal ions are required for primer-extension catalyzed by DNA polymerases. One metal ion brings the 3'-hydroxyl of the primer terminus and the {alpha}-phosphorus atom of incoming dNTP together for bond formation so that the catalytically relevant conformation of the triphosphate tail of the dNTP is in an {alpha},{beta},{gamma}-tridentate coordination complex with the second metal ion required for proper substrate alignment. A probable base selectivity mechanism derived from structural studies on Dpo4 suggests that the inability of mispaired dNTPs to form a substrate-aligned, tridentate coordination complex could effectively cause the mispaired dNTPs to be rejected before catalysis. Nevertheless, we found that mispaired dNTPs can actually form a properly aligned tridentate coordination complex. However, complementary dNTPs occasionally form misaligned complexes with mutant RB69 DNA polymerases (RB69pols) that are not in a tridentate coordination state. Here, we report finding a {beta},{gamma}-bidentate coordination complex that contained the complementary dUpNpp opposite dA in the structure of a ternary complex formed by the wild type RB69pol at 1.88 {angstrom} resolution. Our observations suggest that several distinct metal-ion coordination states can exist at the ground state in the polymerase active site and that base selectivity is unlikely to be based on metal-ion coordination alone.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

The crystal and coordination chemistry of neptunium in all its oxidation states: An expanded structural hierarchy of neptunium compounds

We report structures of 388 neptunium-bearing crystal structures are sorted into an expanded structural hierarchy and examined. The majority of structures contain Np(V) (149), Np(VI) (99), or Np(IV) (91) whereas structures containing Np(II), Np(III), Np(VII), or more than one oxidation state are rare. Coordination geometry of Np(V) and Np(VI) compounds is dominated by the approximately linear neptunyl cation. Actinyl–actinyl interactions (AAIs) are most prevalent in Np(V) compounds and are observed in 48% of these extended structures. Prismatic coordination geometries are commonly observed in Np(IV) compounds. Np(III) organometallic complexes display a variety of coordination modes. Coordination chemistry of Np(VII) compounds is dominated by the tetra-oxido core. Updated average bond length values are provided for Np(IV), Np(V), Np(VI), and Np(VII) compounds and updated bond valence parameters for Np(IV) are reported. A graphical notation system for neptunyl structures coordinated by organic ligands was developed to facilitate discussion and identify similarities between neptunyl compounds coordinated by oxyanions and neptunyl compounds coordinated by organic ligands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Bound-preserving discontinuous Galerkin methods for conservative phase space advection in curvilinear coordinates

In this study, we extend the positivity-preserving method of Zhang & Shu to simulate the advection of neutral particles in phase space using curvilinear coordinates. The ability to utilize these coordinates is important for non-equilibrium transport problems in general relativity and also in science and engineering applications with specific geometries. The method achieves high-order accuracy using Discontinuous Galerkin (DG) discretization of phase space and strong stability-preserving, Runge-Kutta (SSP-RK) time integration. Special care in taken to ensure that the method preserves strict bounds for the phase space distribution function $f$; i.e., $f\in[0,1]$. The combination of suitable CFL conditions and the use of the high-order limiter proposed in Zhang & Shu (2010) is sufficient to ensure positivity of the distribution function. However, to ensure that the distribution function satisfies the upper bound, the discretization must, in addition, preserve the divergence-free property of the phase space flow. Proofs that highlight the necessary conditions are presented for general curvilinear coordinates, and the details of these conditions are worked out for some commonly used coordinate systems (i.e., spherical polar spatial coordinates in spherical symmetry and cylindrical spatial coordinates in axial symmetry, both with spherical momentum coordinates). Results from numerical experiments --- including one example in spherical symmetry adopting the Schwarzschild metric --- demonstrate that the method achieves high-order accuracy and that the distribution function satisfies the maximum principle.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Spectroscopic characterization of Mn 2+ and Cd 2+ coordination to phosphorothioates in the conserved A9 metal site of the hammerhead ribozyme

Phosphorothioate modifications have widespread use in the field of nucleic acids. As substitution of sulfur for oxygen can alter metal coordination preferences, the phosphorothioate metal-rescue experiment is a powerful method for identifying metal coordination sites that influence specific properties in a large RNAs. The A9/G10.1 metal binding site of the hammerhead ribozyme (HHRz) has previously been shown to be functionally important through phosphorothioate rescue experiments. While an A9-S Rp substitution is inhibitory in Mg 2+ , thiophilic Cd 2+ rescues HHRz activity. Mn 2+ is also often used in phosphorothioate metal-rescue studies but does not support activity for the A9-S Rp HHRz. Here, we use EPR, electron spin-echo envelope modulation (ESEEM), and X-ray absorption spectroscopic methods to directly probe the structural consequences of Mn 2+ and Cd 2+ coordination to R p and S p phosphorothioate modifications at the A9/G10.1 site in the truncated hammerhead ribozyme (tHHRz). The results demonstrate that while Cd 2+ does indeed bind to S in the thio-substituted ligand, Mn 2+ coordinates to the non–sulfur oxo group of this phosphorothioate, regardless of isomer. Computational models demonstrate the energetic preference of Mn—O over Mn—S coordination in metal-dimethylthiophosphate models. In the case of the tHHRz, the resulting Mn 2+ coordination preference of oxygen in either R p or S p A9 phosphorothioates differentially tunes catalytic activity, with Mn—O coordination in the A9-S Rp phosphorothioate enzyme being inhibitory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗