scholarly journals Structural Analysis of a Nitrogenase Iron Protein from Methanosarcina acetivorans: Implications for CO2 Capture by a Surface-Exposed [Fe4S4] Cluster

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Lee A. Rettberg ◽  
Wonchull Kang ◽  
Martin T. Stiebritz ◽  
Caleb J. Hiller ◽  
Chi Chung Lee ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Methanosarcina Acetivorans ◽  
Ambient Conditions ◽  
Content Type ◽  
Fe Protein ◽  
Nitrogenase Iron Protein

ABSTRACT Nitrogenase iron (Fe) proteins reduce CO2 to CO and/or hydrocarbons under ambient conditions. Here, we report a 2.4-Å crystal structure of the Fe protein from Methanosarcina acetivorans (MaNifH), which is generated in the presence of a reductant, dithionite, and an alternative CO2 source, bicarbonate. Structural analysis of this methanogen Fe protein species suggests that CO2 is possibly captured in an unactivated, linear conformation near the [Fe4S4] cluster of MaNifH by a conserved arginine (Arg) pair in a concerted and, possibly, asymmetric manner. Density functional theory calculations and mutational analyses provide further support for the capture of CO2 on MaNifH while suggesting a possible role of Arg in the initial coordination of CO2 via hydrogen bonding and electrostatic interactions. These results provide a useful framework for further mechanistic investigations of CO2 activation by a surface-exposed [Fe4S4] cluster, which may facilitate future development of FeS catalysts for ambient conversion of CO2 into valuable chemical commodities. IMPORTANCE This work reports the crystal structure of a previously uncharacterized Fe protein from a methanogenic organism, which provides important insights into the structural properties of the less-characterized, yet highly interesting archaeal nitrogenase enzymes. Moreover, the structure-derived implications for CO2 capture by a surface-exposed [Fe4S4] cluster point to the possibility of developing novel strategies for CO2 sequestration while providing the initial insights into the unique mechanism of FeS-based CO2 activation.

Structural analysis of metastable pharmaceutical loratadine form II, by 3D electron diffraction and DFT+D energy minimisation

CrystEngComm ◽  
2020 ◽  
Vol 22 (43) ◽  
pp. 7490-7499
Author(s):  
Grahame R. Woollam ◽  
Partha P. Das ◽  
Enrico Mugnaioli ◽  
Iryna Andrusenko ◽  
Athanassios S. Galanis ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Structural Analysis ◽  
Electron Diffraction ◽  
Density Functional ◽  
Ambient Conditions ◽  
Functional Theory ◽  
Energy Minimisation ◽  
3D Electron

Coupling 3D electron diffraction and density functional theory provided the metastable pharmaceutical crystal structure within nanometre range, under ambient conditions.

scholarly journals Role of Chemistry and Crystal Structure on the Electronic Defect States in Cs-Based Halide Perovskites

Materials ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 1032
Author(s):  
Anirban Naskar ◽  
Rabi Khanal ◽  
Samrat Choudhury
Keyword(s):  
Crystal Structure ◽  
Density Functional ◽  
Covalent Bond ◽  
Density Functional Theory Calculations ◽  
Antisite Defect ◽  
Defect States ◽  
Functional Theory ◽  
Electronic Defect ◽  
Constituent Elements

The electronic structure of a series perovskites ABX3 (A = Cs; B = Ca, Sr, and Ba; X = F, Cl, Br, and I) in the presence and absence of antisite defect XB were systematically investigated based on density-functional-theory calculations. Both cubic and orthorhombic perovskites were considered. It was observed that for certain perovskite compositions and crystal structure, presence of antisite point defect leads to the formation of electronic defect state(s) within the band gap. We showed that both the type of electronic defect states and their individual energy level location within the bandgap can be predicted based on easily available intrinsic properties of the constituent elements, such as the bond-dissociation energy of the B–X and X–X bond, the X–X covalent bond length, and the atomic size of halide (X) as well as structural characteristic such as B–X–B bond angle. Overall, this work provides a science-based generic principle to design the electronic states within the band structure in Cs-based perovskites in presence of point defects such as antisite defect.

The crystal structure of Na(NH4)Mo3O10·H2O

2017 ◽  
Vol 32 (2) ◽  
pp. 140-147 ◽  
Author(s):  
Joel W. Reid ◽  
James A. Kaduk ◽  
Jeremy A. Olson
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Rietveld Refinement ◽  
Software Package ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Parallel Tempering ◽  
Powder Diffraction Data ◽  
Functional Theory ◽  
Synchrotron Powder Diffraction

The crystal structure of Na(NH4)Mo3O10·H2O has been solved by parallel tempering using the FOX software package with synchrotron powder diffraction data obtained from beamline 08B1-1 at the Canadian Light Source. Rietveld refinement, performed with the software package GSAS, yielded orthorhombic lattice parameters of a = 13.549 82(10), b = 7.618 50(6), and c = 9.302 74(7) Å (Z = 4, space group Pnma). The structure is composed of molybdate chains running parallel to the b-axis. The Rietveld refinement results were compared with density functional theory calculations performed with CRYSTAL14, and show excellent agreement with the calculated structure.

scholarly journals Ab initio study of elastic anisotropies and thermal conductivities of rhenium diborides in different crystal structures

RSC Advances ◽  
2020 ◽  
Vol 10 (61) ◽  
pp. 37142-37152
Author(s):  
Yi X. Wang ◽  
Ying Y. Liu ◽  
Zheng X. Yan ◽  
W. Liu ◽  
Jian B. Gu
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Crystal Structures ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Ab Initio Study ◽  
Ambient Conditions ◽  
Functional Theory ◽  
Thermal Conductivities

The phase stabilities, elastic anisotropies, and thermal conductivities of ReB2 diborides under ambient conditions have been investigated by using density functional theory calculations.

scholarly journals Synthesis, Characterization, and Crystal Structure Determination of a New Lithium Zinc Iodate Polymorph LiZn(IO3)3

Crystals ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 464 ◽  
Author(s):  
Hebboul ◽  
Galez ◽  
Benbertal ◽  
Beauquis ◽  
Mugnier ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Density Functional ◽  
Second Harmonic ◽  
Infrared Absorption Spectrum ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Synthesis and characterization of anhydrous LiZn(IO3)3 powders prepared from an aqueous solution are reported. Morphological and compositional analyses were carried out by using scanning electron microscopy and energy-dispersive X-ray measurements. The synthesized powders exhibited a needle-like morphology after annealing at 400 °C. A crystal structure for the synthesized compound was proposed from powder X-ray diffraction and density-functional theory calculations. Rietveld refinements led to a monoclinic structure, which can be described with space group P21, number 4, and unit-cell parameters a = 21.874(9) Å, b = 5.171(2) Å, c = 5.433(2) Å, and  = 120.93(4)°. Density-functional theory calculations supported the same crystal structure. Infrared spectra were also collected, and the vibrations associated with the different modes were discussed. The non-centrosymmetric space group determined for this new polymorph of LiZn(IO3)3, the characteristics of its infrared absorption spectrum, and the observed second-harmonic generation suggest it is a promising infrared non-linear optical material.

Direct observation of incommensurate structure in Mo3Si

2016 ◽  
Vol 72 (6) ◽  
pp. 660-666 ◽  
Author(s):  
Ahmet Gulec ◽  
Xiaoxiang Yu ◽  
Matthew Taylor ◽  
John H. Perepezko ◽  
Laurence Marks
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Atom Probe Tomography ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Atom Probe ◽  
Atomic Resolution ◽  
Contrast Imaging ◽  
Functional Theory ◽  
Incommensurate Structure

Z-contrast imaging, electron diffraction, atom-probe tomography (APT) and density functional theory calculations were used to study the crystal structure of the Mo3Si phase which was previously reported to have an A15 crystal structure. The results showed that Mo3Si has an incommensurate crystal structure with a non-cubic unit cell. The small off-stoichiometry in composition of the sample which was revealed by APT and atomic resolutionZ-contrast imaging suggested that site substitution caused the development of split atomic positions, disorder and vacancies.

Metal carbonyl complexes of potentially ambidentate 2,1,3-benzothiadiazole and 2,1,3-benzoselenadiazole acceptors

2017 ◽  
Vol 72 (11) ◽  
pp. 839-846
Author(s):  
Sebastian Plebst ◽  
Martina Bubrin ◽  
David Schweinfurth ◽  
Stanislav Záliš ◽  
Wolfgang Kaim
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Electron Transfer ◽  
Density Functional ◽  
Metal Carbonyl ◽  
Density Functional Theory Calculations ◽  
Carbonyl Complexes ◽  
Functional Theory ◽  
Metal Carbonyl Complexes ◽  
Reduced Forms

AbstractThe compounds [W(CO)5(btd)], [W(CO)5(bsd] and [Re(CO)3(bpy)(bsd)](BF4), btd=2,1,3-benzothiadiazole and bsd=2,1,3-benzoselenadiazole were isolated and characterized experimentally (crystal structure, spectroscopy, spectroelectrochemistry) and by density functional theory calculations. The results confirm single N-coordination in all cases, binding to Se was calculated to be less favorable. Studies of one-electron reduced forms indicate that the N-coordination is maintained during electron transfer.

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