A mixed-valence diruthenium(<scp>ii</scp>,<scp>iii</scp>) complex endowed with high stability: from experimental evidence to theoretical interpretation

Barresi, Elisabetta; Tolbatov, Iogann; Pratesi, Alessandro; Notarstefano, Valentina; Baglini, Emma; Daniele, Simona; Taliani, Sabrina; Re, Nazzareno; Giorgini, Elisabetta; Martini, Claudia; Settimo, Federico Da; Marzo, Tiziano; Mendola, Diego La

doi:10.1039/d0dt02527e

Cited by 28 publications

(22 citation statements)

References 57 publications

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“…All DFT calculations were performed with the Gaussian 09 A.02 [25] quantum chemistry package. The DFT functionals are known to give a good description of geometries and reaction profiles for transition metal-containing compounds [26][27][28][29][30]. Optimizations, frequency calculations, electronic and solvation energy evaluations were carried out in solvated phase (C-PCM) [31,32] and by using the range-corrected density functional wB97X [33] which is known to give a good description of geometries and reaction profiles for transition metal-containing compounds [34][35][36].…”

Section: Dft Calculationsmentioning

confidence: 99%

Molecular dynamics simulation of the Pb(II) coordination in biological media via cationic dummy atom models

Tolbatov

Marrone

2021

Theor Chem Acc

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The coordination of Pb(II) in aqueous solutions containing thiols is a pivotal topic to the understanding of the pollutant potential of this cation. Based on its hard/soft borderline nature, Pb(II) forms stable hydrated ions as well as stable complexes with the thiol groups of proteins. In this paper, the modeling of Pb(II) coordination via classical molecular dynamics simulations was investigated to assess the possible use of non-bonded potentials for the description of the metal–ligand interaction. In particular, this study aimed at testing the capability of cationic dummy atom schemes—in which part of the mass and charge of the Pb(II) is fractioned in three or four sites anchored to the metal center—in reproducing the correct coordination geometry and, also, in describing the hard/soft borderline character of this cation. Preliminary DFT calculations were used to design two topological schemes, PB3 and PB4, that were subsequently implemented in the Amber force field and employed in molecular dynamics simulation of either pure water or thiol/thiolate-containing aqueous solutions. The PB3 scheme was then tested to model the binding of Pb(II) to the lead-sensing protein pbrR. The potential use of CDA topological schemes in the modeling of Pb(II) coordination was here critically discussed.

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Section: Dft Calculationsmentioning

confidence: 99%

Molecular dynamics simulation of the Pb(II) coordination in biological media via cationic dummy atom models

Tolbatov

Marrone

2021

Theor Chem Acc

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“…Frequency calculations were performed to verify the correct nature of the stationary points as well as to estimate zero-point energy (ZPE) and thermal corrections to thermodynamic properties. Indeed, Density-functional Theory DFT gives a good description of geometries and reaction profiles for transition-metal-containing compounds [ 50 , 51 ], including Au- and Ru-based metallodrugs [ 16 , 52 ]. The density functional ωB97X is known to yield accurate geometrical structures and was reported to have reached a high accuracy in the calculation of electronic energies [ 53 , 54 ].…”

Section: Methodsmentioning

confidence: 99%

In Vitro Anti-SARS-CoV-2 Activity of Selected Metal Compounds and Potential Molecular Basis for Their Actions Based on Computational Study

et al. 2021

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Metal-based drugs represent a rich source of chemical substances of potential interest for the treatment of COVID-19. To this end, we have developed a small but representative panel of nine metal compounds, including both synthesized and commercially available complexes, suitable for medical application and tested them in vitro against the SARS-CoV-2 virus. The screening revealed that three compounds from the panel, i.e., the organogold(III) compound Aubipyc, the ruthenium(III) complex KP1019, and antimony trichloride (SbCl3), are endowed with notable antiviral properties and an acceptable cytotoxicity profile. These initial findings prompted us to perform a computational study to unveil the likely molecular basis of their antiviral actions. Calculations evidenced that the metalation of nucleophile sites in SARS-CoV-2 proteins or nucleobase strands, induced by Aubipyc, SbCl3, and KP1019, is likely to occur. Remarkably, we found that only the deprotonated forms of Cys and Sec residues can react favorably with these metallodrugs. The mechanistic implications of these findings are discussed.

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“…Since mid-1960’s when Stephenson and Wilkinson [1] described the synthesis of the first mixed-valent [Ru 2 Cl(O 2 CR) 4 ] (R = alkyl) compound and Cotton and col [2] the first crystal structure, a big number of Ru 2 5+ paddlewheel diruthenium complexes with Ru-Ru bond order of 2.5 have been synthesized and characterized [3] , [4] , [5] , [6] , [7] , [8] . These compounds have attracted interest for their practical applications in catalysts [9] , [10] , [11] , [12] , [13] , [14] , [15] , [16] , biomedicine [17] , [18] , [19] , [20] , biotechnology [21] , [22] , [23] , [24] , [25] , [26] or by their potential in material science due to their unique magnetic [27] , [28] , [29] , [30] , [31] , [32] , [33] , [34] , [35] , [36] and redox properties [37] .…”

Section: Introductionmentioning

confidence: 99%

Ultrasound-assisted synthesis of water-soluble monosubstituted diruthenium compounds

Terán

Cortijo

Gutiérrez

et al. 2021

Ultrasonics Sonochemistry

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A mixed-valence diruthenium(ii,iii) complex endowed with high stability: from experimental evidence to theoretical interpretation

Cited by 28 publications

References 57 publications

Molecular dynamics simulation of the Pb(II) coordination in biological media via cationic dummy atom models

Molecular dynamics simulation of the Pb(II) coordination in biological media via cationic dummy atom models

In Vitro Anti-SARS-CoV-2 Activity of Selected Metal Compounds and Potential Molecular Basis for Their Actions Based on Computational Study

Ultrasound-assisted synthesis of water-soluble monosubstituted diruthenium compounds

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