Ammonium perchlorate detection in natural environments using specific lux biosensors

Balabanov, V. P.; Khrulnova, S. A.; Kotova, V. Yu.; Zavilgelsky, G. B.

doi:10.1134/s1990793117040133

Cited by 19 publications

(29 citation statements)

References 6 publications

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“…To check for the effects of basis set convergence, we performed some calculations at the quadruple-ζ level with augcc-pVQZ-DK basis sets on all atoms. [93] We found that the calculated spin-state energetics are all very close to those obtained at the triple-ζ level.…”

Section: Single-point Calculationssupporting

confidence: 69%

“…Coupled-cluster single-point calculations. Scalarrelativistic CCSD(T) calculations were, except where stated, performed with triple-ζ cc-pwCVTZ basis sets recontracted for calculations with the DKH2 Hamiltonian; cc-pwCVTZ-DK on the transition metal atoms [93] and cc-pVTZ-DK on the hydrogen, oxygen and carbon atoms. [94,95] The 1s2s2p electrons of the 3d elements and the 1s electrons on oxygen and carbon are kept frozen and uncorrelated.…”

Section: Single-point Calculationsmentioning

confidence: 99%

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Performance of density functional theory for describing hetero‐metallic active‐site motifs for methane‐to‐methanol conversion in metal‐exchanged zeolites

et al. 2018

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Methane‐to‐methanol conversion (MMC) can be facilitated with high methanol selectivities by copper‐exchanged zeolites. There are however two open questions regarding the use of these zeolites to facilitate the MMC process. The first concerns the possibility of operating the three cycles in the stepwise MMC process by these zeolites in an isothermal fashion. The second concerns the possibility of improving the methanol yields by systematic substitution of some copper centers in these active sites with other earth‐abundant transition metals. Quantum‐mechanical computations can be used to compare methane activation by copper oxide species and analogous mixed‐metal systems. To carry out such screening, it is important that we use theoretical methods that are accurate and computationally affordable for describing the properties of the hetero‐metallic catalytic species. We have examined the performance of 47 exchange‐correlation density functionals for predicting the relative spin‐state energies and chemical reactivities of six hetero‐metallic [M‐O‐Cu]2+ and [M‐O2‐Cu]2+, (where MCo, Fe, and Ni), species by comparison with coupled cluster theory including iterative single, double excitations as well as perturbative treatment of triple excitations, CCSD(T). We also performed multireference calculations on some of these systems. We considered two types of reactions (hydrogen addition and oxygen addition) that are relevant to MMC. We recommend the use of τ‐HCTH and OLYP to determine the spin‐state energy splittings in the hetero‐metallic motifs. ωB97, ωB97X, ωB97X‐D3, and MN15 performed best for predicting the energies of the hydrogen and oxygen addition reactions. In contrast, local, and semilocal functionals do poorly for chemical reactivity. Using [Fe‐O‐Cu]2+ as a test, we see that the nonlocal functionals perform well for the methane CH activation barrier. In contrast, the semilocal functionals perform rather poorly. © 2018 Wiley Periodicals, Inc.

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Section: Single-point Calculationssupporting

confidence: 69%

Section: Single-point Calculationsmentioning

confidence: 99%

Performance of density functional theory for describing hetero‐metallic active‐site motifs for methane‐to‐methanol conversion in metal‐exchanged zeolites

et al. 2018

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“…[33,34] The Tier-1 basis set together with the light grid options has been chosen. Since the numerical accuracy of the NOA basis sets is not yet broadly known, in the next section we provide evidence that the quality of this basis set is of (or higher than) double-f plus polarization with results comparable to those obtained with Dunning [43,44] GTO aug-cc-pVDZ basis set optimized for providing accurate results in calculation explicitly including electron correlation. Integration in the reciprocal space was carried out using a 17 3 17 3 17 Monkhorst-Pack grid of special kpoints.…”

Section: Models and Methodsmentioning

confidence: 73%

Electronic structure of stoichiometric and reduced ZnO from periodic relativistic all electron hybrid density functional calculations using numeric atom‐centered orbitals

Viñes

2017

J Comput Chem

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The atomic and electronic structure of stoichiometric and reduced ZnO wurtzite has been studied using a periodic relativistic all electron hybrid density functional (PBE0) approach and numeric atom-centered orbital basis set with quality equivalent to aug-cc-pVDZ. To assess the importance of relativistic effects calculations were carried out without and with explicit inclusion of relativistic effects through the zero order regular approximation. The calculated band gap is ~0.2 eV smaller than experiment, close to previous PBE0 results including relativistic calculation through the pseudopotential and ~0.25 eV smaller than equivalent non-relativistic all electron PBE0 calculations indicating possible sources of error in non-relativistic all electron density functional calculations for systems containing elements with relatively high atomic number. The oxygen vacancy formation energy converges rather fast with the supercell size, the predicted value agrees with previously hybrid density functional calculations and analysis of the electronic structure evidences the presence of localized electrons at the vacancy site with a concomitant well localized peak in the density of states ~0.5 eV above the top of the valence band and a significant relaxation of the Zn atoms near to the oxygen vacancy. Finally, present work shows that accurate results can be obtained in systems involving large supercells containing up to ~450 atoms using a numeric atomic centered orbital basis set within a full all electron description including scalar relativistic effects at an affordable cost.

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“…[37][38][39] Electronic energies and molecular orbitals were further refined by the all-electron basis cc-pVTZ for Co and cc-pVDZ for all other atoms. [40,41] For the single point calculations, the group $dft and the keyword nrad = 125 were included. The keyword nrad is related to the grid selection in DFT calculations; nrad governs the number of radial grid points in Euler-Maclaurin quadrature whose default value is 96.…”

Section: Theoretical Calculationsmentioning

confidence: 99%

Approach to the Mechanism of Hydrogen Evolution Electrocatalyzed by a Model Co Clathrochelate: A Theoretical Study by Density Functional Theory

Antuch

Millet

2018

ChemPhysChem

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The hydrogen evolution reaction (HER) has attracted much attention within the scientific community because of increasing demands of modern society for clean and renewable energy sources. Molecular complexes of 3d-transition metals, such as cobalt, hold potential to replace platinum for the HER in acidic media. Among these, cage complexes such as tris-glyoximate metal clathrochelates, have demonstrated promising catalytic properties towards the HER. However, it is not clear whether the catalytic activity of this molecule stems from metal-centered activation of H , due to a low oxidation state of the metal stabilized by the surrounding organic cage, or if it is the organic cage playing a further cooperative role in bringing protons together. Herein, we report on a density functional theory study of two possible mechanisms for the HER catalyzed by a model Co clathrochelate. To assess the putative ligand involvement in the mechanism, several combinations of single and double protonation sites were investigated. The structural and energetic analysis of relevant intermediates suggests that the electrocatalytic mechanism is not based on the cooperation between the ligand and the metal. Instead, it is mainly due to the activation of H by the Co metallocenter. Our calculations further suggest that the last step in the mechanism is a proton coupled electron transfer step.

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Ammonium perchlorate detection in natural environments using specific lux biosensors

Cited by 19 publications

References 6 publications

Performance of density functional theory for describing hetero‐metallic active‐site motifs for methane‐to‐methanol conversion in metal‐exchanged zeolites

Performance of density functional theory for describing hetero‐metallic active‐site motifs for methane‐to‐methanol conversion in metal‐exchanged zeolites

Electronic structure of stoichiometric and reduced ZnO from periodic relativistic all electron hybrid density functional calculations using numeric atom‐centered orbitals

Approach to the Mechanism of Hydrogen Evolution Electrocatalyzed by a Model Co Clathrochelate: A Theoretical Study by Density Functional Theory

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