RESUMO
We present a comprehensive theoretical examination of the structural properties of dianionic polysulfides [Sn]2- (n = 2-6), their conjugated monoacids [HSn]- (n = 2-6), and a selection of 1e--oxidized radical anions [Sn]â¢- (n = 2-4), in aqueous and dimethyl sulfoxide (DMSO) solutions. We investigated the structures and stabilities of various conformational isomers within these families of compounds by employing Quantum Mechanics-Molecular Mechanics (QM-MM) Molecular Dynamics (MD) simulations. The explicit inclusion of solvent molecules in the calculations revealed stable conformational structures that were previously unreported and might have appreciable concentrations in real systems. The interconversions between the isomeric structures proceed on the order of hundreds of picoseconds and are energetically similar to the isomerization processes in substituted cyclohexanes. We also conducted a detailed analysis of the stability of different isomers of the radical anion [S4]â¢- in solution. Our findings highlight the significant influence of the solvent on the isomerizations, a result that could be particularly relevant for enhancing the performance of metal-sulfur batteries.
RESUMO
The acid-base speciation of coordinated azanone (HNO) remains a highly relevant topic in bioinorganic chemistry. Ruthenium nitroxyl complexes with sufficient robustness towards ligand loss have gained significance as operating platforms to delve into such studies. In this work, we revisit an octahedral {RuNO}6 complex containing the cyclam-based pentadentate ligand Lpy = 1-(pyridine-2-ylmethyl)-1,4,8,11-tetraazacyclotetradecane and explore the thermodynamic and spectroscopic aspects of its reduced states in aqueous media. Upon in situ electro-generation of the bound HNO moiety, we have undertaken different strategies to determine both its acidity and electrochemical properties. This robust HNO complex does not undergo deprotonation in a wide pH range. We have found pKa ([Ru(Lpy)(HNO)]2+) = 13.0 ± 0.1 and . There are indications that pKa (HNO) values in several ruthenium-based species correlate with the redox potential associated with the {RuNO}6,7 and {RuNO}7,8 couples. The present pKa extends the range of acidity of bound HNO to more than five pH units, confirming a remarkable sensitivity to the nature of the coordination sphere. This result lays new foundations to continue rational ligand design that may contribute to a better understanding of the different biological roles of both HNO and NO- by investigating key chemical aspects of model complexes.
RESUMO
The redox chemistry of H2S with NO and other oxidants containing the NO group is discussed on a mechanistic basis because of the expanding interest in their biological relevance, with an eye open to the chemical differences of H2S and thiols RSH. We focus on the properties of two "crosstalk" intermediates, SNO- (thionitrite) and SSNO- (perthionitrite, nitrosodisulfide) based in the largely controversial status on their identity and chemistry in aqueous/nonaqueous media, en route to the final products N2O, NO2-, NH2OH/NH3, and S8. Thionitrous acid, generated either in the direct reaction of NO + H2S or through the transnitrosation of RSNO's (nitrosothiols) with H2S at pH 7.4, is best described as a mixture of rapidly interconverting isomers, {(H)SNO}. It is reactive in different competitive modes, with a half-life of a few seconds at pH 7.4 for homolytic cleavage of the N-S bond, and could be deprotonated at pH values of up to ca. 10, giving SNO-, a less reactive species than {(H)SNO}. The latter mixture can also react with HS-, giving HNO and HS2- (hydrogen disulfide), a S0(sulfane)-transfer reagent toward {(H)SNO}, leading to SSNO-, a moderately stable species that slowly decomposes in aqueous sulfide-containing solutions in the minute-hour time scale, depending on [O2]. The previous characterization of HSNO/SNO- and SSNO- is critically discussed based on the available chemical and spectroscopic evidence (mass spectrometry, UV-vis, 15N NMR, Fourier transform infrared), together with computational studies including quantum mechanics/molecular mechanics molecular dynamics simulations that provide a structural and UV-vis description of the solvatochromic properties of cis-SSNO- acting as an electron donor in water, alcohols, and aprotic acceptor solvents. In this way, SSNO- is confirmed as the elusive "yellow intermediate" (I412) emerging in the aqueous crosstalk reactions, in contrast with its assignment to polysulfides, HSn-. The analysis extends to the coordination abilities of {(H)SNO}, SNO-, and SSNO- into heme and nonheme iron centers, providing a basis for best unraveling their putative specific signaling roles.
RESUMO
In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.
RESUMO
A chemometric procedure to deal with spectroscopically monitored processes involving photochemical steps is fully described. The methodology makes it possible to work with reactions that involve several components with unknown (and eventually overlapping) spectra and provides a tool for the simultaneous determination of both the quantum yields of the reaction and the spectra of all the species present in a multi-step photochemical process. As a benchmark, we apply these ideas to extract the quantum yields of photodetachment of coordinated ligands employing data recorded over the course of the decomposition of [Ru(tpm)(bpy)(CH3CN)]2+ and cis-[Ru(bpy)2(CH3CN)2]2+ under stationary photolysis conditions. The approach is fast and robust and it is easily implemented in scientific programming languages.
RESUMO
trans-[(NC)Ru(py)(4)(mu-CN)Ru(py)(4)(NO)](3+) (py = pyridine) is a stable species in aqueous solution. It displays an intense absorption in the visible region of the spectrum (lambda(max) = 518 nm; epsilon(max) = 6100 M(-1) cm(-1)), which turns this compound into a promising agent for the photodelivery of NO. The quantum yield for the photodelivery process resulting from irradiation with 455 nm visible light was found experimentally to be (0.06 +/- 0.01) x 10(-3) mol einstein(-1), almost 3 orders of magnitude smaller than that in the closely related cis-[RuL(NH(3))(4)(mu-pz)Ru(bpy)(2)(NO)](5+) species (L = NH(3) or pyridine, pz = pyrazine, bpy = 2,2'-bipyridine; phi(NO) = 0.02-0.04 mol einstein(-1) depending on L) and also much smaller than the one in the mononuclear compound trans-[ClRu(py)(4)(NO)](2+) (phi(NO) = (1.63 +/- 0.04) x 10(-3) mol einstein(-1)). DFT computations provide an electronic structure picture of the photoactive excited states that helps to understand this apparently abnormal behavior.