Observation of a promethium complex in solution.

Lanthanide rare-earth metals are ubiquitous in modern technologies, but we know little about chemistry of the 61st element, promethium (Pm), a lanthanide that is highly radioactive and inaccessible. Despite its importance, Pm has been conspicuously absent from the experimental studies of lanthanides, impeding our full comprehension of the so-called lanthanide contraction phenomenon: a fundamental aspect of the periodic table that is quoted in general chemistry textbooks. Here we demonstrate a stable chelation of the Pm radionuclide (half-life of 2.

Corrigendum: Coupled cluster theory on modern heterogeneous supercomputers.

[This corrects the article DOI: 10.3389/fchem.2023.

Coupled cluster theory on modern heterogeneous supercomputers.

This study examines the computational challenges in elucidating intricate chemical systems, particularly through methodologies. This work highlights the Divide-Expand-Consolidate (DEC) approach for coupled cluster (CC) theory-a linear-scaling, massively parallel framework-as a viable solution. Detailed scrutiny of the DEC framework reveals its extensive applicability for large chemical systems, yet it also acknowledges inherent limitations.

Massively parallel GPU enabled third-order cluster perturbation excitation energies for cost-effective large scale excitation energy calculations.

We present here a massively parallel implementation of the recently developed CPS(D-3) excitation energy model that is based on cluster perturbation theory. The new algorithm extends the one developed in Baudin et al. [J.

[FeS] cubane in sulfite reductases: new insights into bonding properties and reactivity.

The dissimilatory sulfite reductase enzyme has very characteristic active site where the substrate binds to an iron site, ligated by a siroheme macrocycle and a thiol directly connected to a [FeS] cluster. This arrangement gives the enzyme remarkable efficiency in reducing sulfite and nitrite all the way to hydrogen sulfide and ammonia. For the first time we present a theoretical study where substrate binding modalities and activation are elucidated using active site models containing proton supply side chains and the [FeS] cluster.

Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor.

Inhibition of the SARS-CoV-2 main protease (M) is a major focus of drug discovery efforts against COVID-19. Here we report a hit expansion of non-covalent inhibitors of M. Starting from a recently discovered scaffold (The COVID Moonshot Consortium.

Multilayer Divide-Expand-Consolidate Coupled-Cluster Method: Demonstrative Calculations of the Adsorption Energy of Carbon Dioxide in the Mg-MOF-74 Metal-Organic Framework.

The implementation and evaluation of a multilayer extension of the divide-expand-consolidate (DEC) scheme within the LSDalton program is presented. The DEC scheme is a linear-scaling, fragmentation-based local coupled-cluster (CC) method that provides a means of overcoming the scaling wall associated with canonical CC electronic structure calculations on large molecular systems. Taking advantage of the local nature of correlation effects, the correlation energy for the full molecule is calculated from a set of independent fragments using localized molecular orbitals.

Cluster perturbation theory. III. Perturbation series for coupled cluster singles and doubles excitation energies.

The cluster perturbation series, CPS(D), for coupled cluster singles and doubles excitation energies is considered. It is demonstrated that the second-order model CPS(D-2) is identical to the configuration interaction singles with perturbative doubles, CIS(D) model. The third-order model, CPS(D-3), provides excitation energies of coupled cluster singles and doubles (CCSD) quality in the sense that the difference between CPS(D-3) and CCSD excitation energies is of the same size or smaller than the effect of adding triples corrections to CCSD excitation energies.

Activation of olefins via asymmetric Brønsted acid catalysis.

The activation of olefins for asymmetric chemical synthesis traditionally relies on transition metal catalysts. In contrast, biological enzymes with Brønsted acidic sites of appropriate strength can protonate olefins and thereby generate carbocations that ultimately react to form natural products. Although chemists have recently designed chiral Brønsted acid catalysts to activate imines and carbonyl compounds, mimicking these enzymes to protonate simple olefins that then engage in asymmetric catalytic reactions has remained a substantial synthetic challenge.

Indefinitely stable iron(IV) cage complexes formed in water by air oxidation.

In nature, iron, the fourth most abundant element of the Earth's crust, occurs in its stable forms either as the native metal or in its compounds in the +2 or +3 (low-valent) oxidation states. High-valent iron (+4, +5, +6) compounds are not formed spontaneously at ambient conditions, and the ones obtained synthetically appear to be unstable in polar organic solvents, especially aqueous solutions, and this is what limits their studies and use. Here we describe unprecedented iron(IV) hexahydrazide clathrochelate complexes that are assembled in alkaline aqueous media from iron(III) salts, oxalodihydrazide and formaldehyde in the course of a metal-templated reaction accompanied by air oxidation.

The GPU-enabled divide-expand-consolidate RI-MP2 method (DEC-RI-MP2).

We report porting of the Divide-Expand-Consolidate Resolution of the Identity second-order Møller-Plesset perturbation (DEC-RI-MP2) method to the graphic processing units (GPUs) using OpenACC compiler directives. It is shown that the OpenACC compiler directives implementation efficiently accelerates the rate-determining step of the DEC-RI-MP2 method with minor implementation effort. Moreover, the GPU acceleration results in a better load balance and thus in an overall scaling improvement of the DEC algorithm.

The molecular gradient using the divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation theory: The DEC-RI-MP2 gradient.

We report an implementation of the molecular gradient using the divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation theory (DEC-RI-MP2). The new DEC-RI-MP2 gradient method combines the precision control as well as the linear-scaling and massively parallel features of the DEC scheme with efficient evaluations of the gradient contributions using the RI approximation. We further demonstrate that the DEC-RI-MP2 gradient method is capable of calculating molecular gradients for very large molecular systems.

Six-electron reduction of nitrite to ammonia by cytochrome c nitrite reductase: insights from density functional theory studies.

In this Forum Article, an extensive discussion of the mechanism of six-electron, seven-proton nitrite reduction by the cytochrome c nitrite reductase enzyme is presented. On the basis of previous studies, the entire mechanism is summarized and a unified picture of the most plausible sequence of elementary steps is presented. According to this scheme, the mechanism can be divided into five functional stages.

Heme-bound nitroxyl, hydroxylamine, and ammonia ligands as intermediates in the reaction cycle of cytochrome c nitrite reductase: a theoretical study.

In this article, we consider, in detail, the second half-cycle of the six-electron nitrite reduction mechanism catalyzed by cytochrome c nitrite reductase. In total, three electrons and four protons must be provided to reach the final product, ammonia, starting from the HNO intermediate. According to our results, the first event in this half-cycle is the reduction of the HNO intermediate, which is accomplished by two PCET reactions.

Electronic structure of the unique [4Fe-3S] cluster in O2-tolerant hydrogenases characterized by 57Fe Mossbauer and EPR spectroscopy.

Iron-sulfur clusters are ubiquitous electron transfer cofactors in hydrogenases. Their types and redox properties are important for H(2) catalysis, but, recently, their role in a protection mechanism against oxidative inactivation has also been recognized for a [4Fe-3S] cluster in O(2)-tolerant group 1 [NiFe] hydrogenases. This cluster, which is uniquely coordinated by six cysteines, is situated in the proximity of the catalytic [NiFe] site and exhibits unusual redox versatility.

Reductive activation of the heme iron-nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study.

Cytochrome c nitrite reductase catalyzes the six-electron, seven-proton reduction of nitrite to ammonia without release of any detectable reaction intermediate. This implies a unique flexibility of the active site combined with a finely tuned proton and electron delivery system. In the present work, we employed density functional theory to study the recharging of the active site with protons and electrons through the series of reaction intermediates based on nitrogen monoxide [Fe(II)-NO(+), Fe(II)-NO·, Fe(II)-NO(-), and Fe(II)-HNO].

Dynamic hydrogen-bonding network in the distal pocket of the nitrosyl complex of Pseudomonas aeruginosa cd1 nitrite reductase.

cd(1) nitrite reductase (NIR) is a key enzyme in the denitrification process that reduces nitrite to nitric oxide (NO). It contains a specialized d(1)-heme cofactor, found only in this class of enzymes, where the substrate, nitrite, binds and is converted to NO. For a long time, it was believed that NO must be released from the ferric d(1)-heme to avoid enzyme inhibition by the formation of ferrous-nitroso complex, which was considered as a dead-end product.

Substrate binding and activation in the active site of cytochrome c nitrite reductase: a density functional study.

Cytochrome c nitrite reductase is a homodimeric enzyme, containing five covalently attached c-type hemes per subunit. Four of the heme irons are bishistidine-ligated, whereas the fifth, the active site of the protein, has an unusual lysine coordination and calcium site nearby. A fascinating feature of this enzyme is that the full six-electron reduction of the nitrite is achieved without release of any detectable reaction intermediate.