Search results for "Chemical Bonding"
showing 8 items of 8 documents
A Simple Complex on the Verge of Breakdown: Isolation of the Elusive Cyanoformate Ion
2014
Cyanide Hitches a Ride Cyanide is a by-product of the biosynthesis of ethylene in plants and it has been somewhat puzzling how the ion is safely removed before it can shut down enzymatic pathways by coordination to catalytic iron centers. A proposed mechanism has implicated the cyanoformate ion—essentially, a weak adduct of cyanide and carbon dioxide—as the initial product, although its lifetime was uncertain. Murphy et al. (p. 75 ; see the Perspective by Alabugin and Mohamed ) crystallized this previously elusive adduct and found that its solution-phase stability varies inversely with the dielectric properties of the medium. The results bolster a picture in which the adduct shuttles the cy…
Mechanistic insights into the phosphoryl transfer reaction in cyclin-dependent kinase 2: a QM/MM study
2019
AbstractCyclin-dependent kinase 2 (CDK2) is an important member of the CDK family exerting its most important function in the regulation of the cell cycle. It catalyzes the transfer of the gamma phosphate group from an ATP (adenosine triphosphate) molecule to a Serine/Threonine residue of a peptide substrate. Due to the importance of this enzyme, and protein kinases in general, a detailed understanding of the reaction mechanism is desired. Thus, in this work the phosphoryl transfer reaction catalyzed by CDK2 was revisited and studied by means of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. Our results show that the base-assisted mechanism is preferred over the substrat…
In silico discovery of substituted pyrido[2,3-d]pyrimidines and pentamidine-like compounds with biological activity in myotonic dystrophy models
2016
Myotonic dystrophy type 1 (DM1) is a rare multisystemic disorder associated with an expansion of CUG repeats in mutant DMPK (dystrophia myotonica protein kinase) transcripts; the main effect of these expansions is the induction of pre-mRNA splicing defects by sequestering muscleblind-like family proteins (e.g. MBNL1). Disruption of the CUG repeats and the MBNL1 protein complex has been established as the best therapeutic approach for DM1, hence two main strategies have been proposed: targeted degradation of mutant DMPK transcripts and the development of CUG-binding molecules that prevent MBNL1 sequestration. Herein, suitable CUG-binding small molecules were selected using in silico approach…
Optimizing density-functional simulations for two-dimensional metals
2022
Unlike covalent two-dimensional (2D) materials like graphene, 2D metals have non-layered structures due to their non-directional, metallic bonding. While experiments on 2D metals are still scarce and challenging, density-functional theory (DFT) provides an ideal approach to predict their basic properties and assist in their design. However, DFT methods have been rarely benchmarked against metallic bonding at low dimensions. Therefore, to identify optimal DFT attributes for a desired accuracy, we systematically benchmark exchange-correlation functionals from LDA to hybrids and basis sets from plane waves to local basis with different pseudopotentials. With 1D chain, 2D honeycomb, 2D square, …
In silico identification and experimental validation of hits active against KPC-2 β-lactamase
2018
Bacterial resistance has become a worldwide concern, particularly after the emergence of resistant strains overproducing carbapenemases. Among these, the KPC-2 carbapenemase represents a significant clinical challenge, being characterized by a broad substrate spectrum that includes aminothiazoleoxime and cephalosporins such as cefotaxime. Moreover, strains harboring KPC-type β-lactamases are often reported as resistant to available β-lactamase inhibitors (clavulanic acid, tazobactam and sulbactam). Therefore, the identification of novel non β-lactam KPC-2 inhibitors is strongly necessary to maintain treatment options. This study explored novel, non-covalent inhibitors active against KPC-2, …
Insights into the inhibited form of the redox-sensitive SufE-like sulfur acceptor CsdE
2017
17 p.-8 fig.
Uranocenium: Synthesis, Structure, and Chemical Bonding
2019
Abstraction of iodide from [(η5 -C5 i Pr5 )2 UI] (1) produced the cationic uranium(III) metallocene [(η5 -C5 i Pr5 )2 U]+ (2) as a salt of [B(C6 F5 )4 ]- . The structure of 2 consists of unsymmetrically bonded cyclopentadienyl ligands and a bending angle of 167.82° at uranium. Analysis of the bonding in 2 showed that the uranium 5f orbitals are strongly split and mixed with the ligand orbitals, thus leading to non-negligible covalent contributions to the bonding. Investigation of the dynamic magnetic properties of 2 revealed that the 5f covalency leads to partially quenched anisotropy and fast magnetic relaxation in zero applied magnetic field. Application of a magnetic field leads to domin…
Isolation of a perfectly linear uranium(II) metallocene
2020
Reduction of the uranium(III) metallocene [(eta(5)-(C5Pr5)-Pr-i)(2)UI] (1) with potassium graphite produces the "second-generation" uranocene [(eta(5)-(C5Pr5)-Pr-i)(2)U] (2), which contains uranium in the formal divalent oxidation state. The geometry of 2 is that of a perfectly linear bis(cyclopentadienyl) sandwich complex, with the ground-state valence electron configuration of uranium(II) revealed by electronic spectroscopy and density functional theory to be 5f(3) 6d(1). Appreciable covalent contributions to the metal-ligand bonds were determined from a computational study of 2, including participation from the uranium 5f and 6d orbitals. Whereas three unpaired electrons in 2 occupy orbi…