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At least 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Evidence of Atypical Structural Flexibility of the Active Site Surrounding of an [FeFe] Hydrogenase from Clostridium beijerinkii

[FeFe] hydrogenase from Clostridium beijerinkii (CbHydA1) is an unusual hydrogenase in that it can withstand prolonged exposure to O 2 by reversibly converting into an O 2 -protected, inactive state (Hinact). It has been indicated in the past that an atypical conformation of the “SC 367 CP” loop near the [2Fe] H portion of the six-iron active site (H-cluster) allows the Cys367 residue to adopt an “off-H + -pathway” orientation, promoting a facile transition of the cofactor to Hinact. Here, we investigated the electronic structure of the H-cluster in the oxidized state (H ox ) that directly converts to Hinact under oxidizing conditions and the related CO-inhibited state (H ox -CO). We demonstrate that both states exhibit two distinct forms in electron paramagnetic resonance (EPR) spectroscopy. The ratio between the two forms is pH-dependent but also sensitive to the buffer choice. Our IR and EPR analyses illustrate that the spectral heterogeneity is due to a perturbation of the coordination environment of the H-cluster’s [4Fe4S] H subcluster without affecting the [2Fe] H subcluster. Overall, we conclude that the observation of two spectral components per state is evidence of heterogeneity of the environment of the H-cluster likely associated with conformational mobility of the SCCP loop. Such flexibility may allow Cys367 to switch rapidly between off- and on-H + -pathway rotamers. Consequently, we believe such structural mobility may be the key to maintaining high enzymatic activity while allowing a facile transition to the O 2 -protected state.

08 HYDROGEN↗
DOE OSTI2024

Adsorption of Ag, Au, Cu, and Ni on MoS 2 : theory and experiment

Abstract Here, we present results of a computational and experimental study of adsorption of various metals on MoS2. In particular, we analyzed the binding mechanism of four metallic elements (Ag, Au, Cu, Ni) on MoS2. Among these elements, Ni exhibits the strongest binding and lowest mobility on the surface of MoS2. On the other hand, Au and Ag bond very weakly to the surface and have very high mobilities. Our calculations for Cu show that its bonding and surface mobility are between these two groups. Experimentally, Ni films exhibit a composition characterized by randomly oriented nanoscale clusters. This is consistent with the larger cohesive energy of Ni atoms as compared with their binding energy with MoS2, which is expected to result in 3D clusters. In contrast, Au and Ag tend to form atomically flat plateaued structures on MoS2, which is contrary to their larger cohesive energy as compared to their weak binding with MoS2. Cu displays a surface morphology somewhat similar to Ni, featuring larger nanoscale clusters. However, unlike Ni, in many cases Cu exhibits small plateaued surfaces on these clusters. This suggests that Cu likely has two competing mechanisms that cause it to span the behaviors seen in the Ni and Au/Ag film morphologies. These results indicate that calculations of the initial binding conditions could be useful for predicting film morphologies. In addition, out calculations show that the adsorption of adatoms with odd electron number like Ag, Au, and Cu results in 100% spin-polarization and integer magnetic moment of the system. Adsorption of Ni adatoms, with even electron number, does not induce a magnetic transition.

Harms, Haley↗
DOE OSTI2020

Materials Data on Al12W by Materials Project

Al12W is Tungsten structured and crystallizes in the cubic Im-3 space group. The structure is zero-dimensional and consists of two Al12W clusters. W is bonded in a cuboctahedral geometry to twelve equivalent Al atoms. All W–Al bond lengths are 2.74 Å. Al is bonded in a distorted single-bond geometry to one W atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on YAl3 by Materials Project

Al3Y crystallizes in the hexagonal P6_3/mmc space group. The structure is zero-dimensional and consists of two Al3Y clusters. Y is bonded in a trigonal planar geometry to three equivalent Al atoms. All Y–Al bond lengths are 2.95 Å. Al is bonded in a distorted single-bond geometry to one Y atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on AsIF12 by Materials Project

AsF6IF6 is Halite, Rock Salt structured and crystallizes in the cubic Pa-3 space group. The structure is zero-dimensional and consists of four AsF6 clusters and four IF6 clusters. In each AsF6 cluster, As is bonded in an octahedral geometry to six equivalent F atoms. All As–F bond lengths are 1.78 Å. F is bonded in a single-bond geometry to one As atom. In each IF6 cluster, I is bonded in an octahedral geometry to six equivalent F atoms. All I–F bond lengths are 1.83 Å. F is bonded in a single-bond geometry to one I atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on NiSn(ClO)6 by Materials Project

NiO6SnCl6 crystallizes in the trigonal R-3 space group. The structure is zero-dimensional and consists of three NiO6 clusters and three SnCl6 clusters. In each NiO6 cluster, Ni is bonded in an octahedral geometry to six equivalent O atoms. All Ni–O bond lengths are 1.95 Å. O is bonded in a single-bond geometry to one Ni atom. In each SnCl6 cluster, Sn is bonded in an octahedral geometry to six equivalent Cl atoms. All Sn–Cl bond lengths are 2.47 Å. Cl is bonded in a single-bond geometry to one Sn atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on H3S by Materials Project

SH3 is High-temperature superconductor structured and crystallizes in the monoclinic Cm space group. The structure is zero-dimensional and consists of two SH3 clusters. H+0.33+ is bonded in a single-bond geometry to one S1- atom. The H–S bond length is 1.45 Å. S1- is bonded in a distorted T-shaped geometry to three equivalent H+0.33+ atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on MgTe(ClO)6 by Materials Project

MgO6TeCl6 is Modderite-like structured and crystallizes in the trigonal R-3 space group. The structure is zero-dimensional and consists of three MgO6 clusters and three TeCl6 clusters. In each MgO6 cluster, Mg is bonded in a distorted octahedral geometry to six equivalent O atoms. All Mg–O bond lengths are 2.18 Å. O is bonded in a 1-coordinate geometry to one Mg and two equivalent O atoms. Both O–O bond lengths are 1.52 Å. In each TeCl6 cluster, Te is bonded in an octahedral geometry to six equivalent Cl atoms. All Te–Cl bond lengths are 2.57 Å. Cl is bonded in a single-bond geometry to one Te atom.

36 MATERIALS SCIENCE↗
DOE OSTI2022

ThAu 2 – , ThAu 2 O – , and ThAuOH – anions: Photoelectron spectroscopic and theoretical characterization

The thorium–gold negative ions ThAu 2 – , ThAu 2 O – , and ThAuOH – have been observed and experimentally characterized by anion photoelectron spectroscopy. These experiments are accompanied by extensive ab initio electronic structure calculations using a relativistic composite methodology based primarily on coupled cluster singles and doubles with perturbative triples calculations. The theoretical electron affinities (EAs) at 0 K agree with the experimental adiabatic EAs to within 0.02 eV for all species. Two separate isomers were located in the calculations for ThAuOH – , and detachment from both of these appears to be present in the photoelectron spectrum. Excited electronic states of the neutral molecules are reported at the equation of motion-coupled cluster singles and doubles level of theory. Atomization energies and heats of formation are also calculated for each neutral species and have expected uncertainties of 3 and 4 kcal/mol, respectively. The σ bonds between Th and Au are determined by natural bond orbital analysis to consist of predominately sd hybrids on Th bonding with the Au 6s orbital. In order to investigate the correspondence between the bonding in Th–Au and Th–F molecules, a limited number of calculations were also carried out on most of the F-analogs of this study. These results demonstrate that Au does behave like F in these cases, although the Th–F σ bonds are much more ionic compared to Th–Au. This results in an EA for ThF 2 that is 10 kcal/mol smaller than that of ThAu 2 . The EA values for the Th(IV) species, i.e., ThX 2 O and ThXOH, only differed, however, by 3–4 kcal/mol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Materials Data on CuBi2Se2O by Materials Project

CuSe2Bi2O is alpha Niobium phosphide-like structured and crystallizes in the tetragonal P4/mmm space group. The structure is zero-dimensional and consists of one Bi2O cluster and one CuSe2 cluster. In the Bi2O cluster, Bi+2.50+ is bonded in a single-bond geometry to one O2- atom. The Bi–O bond length is 2.08 Å. O2- is bonded in a linear geometry to two equivalent Bi+2.50+ atoms. In the CuSe2 cluster, Cu1+ is bonded in a linear geometry to two equivalent Se2- atoms. Both Cu–Se bond lengths are 2.27 Å. Se2- is bonded in a distorted single-bond geometry to one Cu1+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on C3N2 by Materials Project

C3N2 is alpha Po structured and crystallizes in the cubic Pm-3m space group. The structure is zero-dimensional and consists of one C3N2 cluster. C2+ is bonded in a bent 120 degrees geometry to two equivalent N3- atoms. Both C–N bond lengths are 1.44 Å. N3- is bonded in a trigonal planar geometry to three equivalent C2+ atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on CuBi2Te2O by Materials Project

CuTe2Bi2O is alpha Niobium phosphide-like structured and crystallizes in the tetragonal P4/mmm space group. The structure is zero-dimensional and consists of one Bi2O cluster and one CuTe2 cluster. In the Bi2O cluster, Bi+2.50+ is bonded in a single-bond geometry to one O2- atom. The Bi–O bond length is 2.09 Å. O2- is bonded in a linear geometry to two equivalent Bi+2.50+ atoms. In the CuTe2 cluster, Cu1+ is bonded in a linear geometry to two equivalent Te2- atoms. Both Cu–Te bond lengths are 2.47 Å. Te2- is bonded in a distorted single-bond geometry to one Cu1+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on CaC4 by Materials Project

CaC4 is Silicon tetrafluoride-like structured and crystallizes in the cubic Pn-3m space group. The structure is zero-dimensional and consists of two CaC4 clusters. Ca2+ is bonded in a tetrahedral geometry to four equivalent C+0.50- atoms. All Ca–C bond lengths are 2.47 Å. C+0.50- is bonded in a single-bond geometry to one Ca2+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on CuClF10 by Materials Project

CuF4ClF6 crystallizes in the monoclinic P2_1/c space group. The structure is zero-dimensional and consists of two ClF6 clusters and two CuF4 clusters. In each ClF6 cluster, Cl is bonded in an octahedral geometry to six F atoms. There is four shorter (1.67 Å) and two longer (1.69 Å) Cl–F bond length. There are two inequivalent F sites. In the first F site, F is bonded in a single-bond geometry to one Cl atom. In the second F site, F is bonded in a single-bond geometry to one Cl atom. In each CuF4 cluster, Cu is bonded in a square co-planar geometry to four equivalent F atoms. All Cu–F bond lengths are 1.75 Å. F is bonded in a single-bond geometry to one Cu atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on AsS2NF6 by Materials Project

NS2AsF6 crystallizes in the monoclinic C2/m space group. The structure is zero-dimensional and consists of two AsF6 clusters and two NS2 clusters. In each AsF6 cluster, As5+ is bonded in an octahedral geometry to six F1- atoms. There is two shorter (1.77 Å) and four longer (1.78 Å) As–F bond length. There are two inequivalent F1- sites. In the first F1- site, F1- is bonded in a single-bond geometry to one As5+ atom. In the second F1- site, F1- is bonded in a single-bond geometry to one As5+ atom. In each NS2 cluster, N5+ is bonded in a linear geometry to two equivalent S2- atoms. Both N–S bond lengths are 1.49 Å. S2- is bonded in a distorted single-bond geometry to one N5+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on CoF4 by Materials Project

CoF4 is alpha Po structured and crystallizes in the triclinic P1 space group. The structure is zero-dimensional and consists of two CoF4 clusters. Co4+ is bonded in a square co-planar geometry to four equivalent F1- atoms. All Co–F bond lengths are 1.72 Å. F1- is bonded in a single-bond geometry to one Co4+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on FeN3Cl5 by Materials Project

FeNCl4N2Cl crystallizes in the orthorhombic Pnma space group. The structure is zero-dimensional and consists of four FeNCl4 clusters and four N2Cl clusters. In each FeNCl4 cluster, Fe2+ is bonded in a 5-coordinate geometry to one N1+ and four Cl1- atoms. The Fe–N bond length is 1.52 Å. There are a spread of Fe–Cl bond distances ranging from 2.17–2.22 Å. N1+ is bonded in a single-bond geometry to one Fe2+ atom. There are three inequivalent Cl1- sites. In the first Cl1- site, Cl1- is bonded in a single-bond geometry to one Fe2+ atom. In the second Cl1- site, Cl1- is bonded in a single-bond geometry to one Fe2+ atom. In the third Cl1- site, Cl1- is bonded in a single-bond geometry to one Fe2+ atom. In each N2Cl cluster, N1+ is bonded in a single-bond geometry to one Cl1- atom. The N–Cl bond length is 1.51 Å. Cl1- is bonded in a distorted bent 150 degrees geometry to two equivalent N1+ atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Definitive Assessment of the Accuracy, Variationality, and Convergence of Relativistic Coupled Cluster and Density Matrix Renormalization Group in 100-Orbital Space

Accuracy, variationality, and convergence underpin the reliability of modern electronic structure methods, yet definitive benchmarks in the relativistic regime remain elusive due to the absence of numerically exact full configuration interaction (CI) references. Recent algorithmic advances in the CI framework, enabled by the small-tensor-product (STP) decomposition approach, have dramatically extended the tractable size of the configuration space, making numerically exact CI calculations feasible in large active spaces previously beyond reach. In this paper, we employ the recently developed STP-CI framework to perform large-scale numerically exact CI calculations and directly benchmark relativistic coupled cluster and density matrix renormalization group methods. Definitive benchmarking of approximate relativistic electronic structure methods is ensured through the application of the gap theorem, which provides rigorous error bounds on the CI reference and establishes a controlled standard for assessing accuracy, variationality, and convergence.

Chemical calculations↗