Larger Coulombic repulsion between divalent cations compared to the monovalent counterparts dictates the cation–cation distance in the central ion channel of quadruplexes. In this work, density ...functional theory and a continuum solvation model were employed to study bond energies of alkaline earth cations in adjacent cavities of the central ion channel. Four crystallized tetramolecular quadruplexes with various geometric constraints and structural motifs available in the Protein Data Bank were examined in order to understand how the cation binding affinities could be increased in aqueous solution. A cytosine quartet sandwiched between guanine quartets has a larger bond energy of the second alkaline earth cation in comparison with guanine and uracil quartets. Four highly conserved hydrogen-bonded water molecules in the center of the cytosine quartet are responsible for a higher electrostatic interaction with the cations in comparison with guanines’ carbonyl groups. The reported findings are valuable for the design of synthetic quadruplexes templated with divalent cations for optoelectronic applications.
The possibility to target noncanonical guanine structures with specific ligands for therapeutic purposes inspired numerous theoretical and experimental investigations of a guanine quartet and its ...stacked composites. In this work, we employed the interacting quantum atoms methodology to study interactions among different fragments in complexes composed of a guanine quartet and alkali (Li+, Na+, K+) or alkaline earth (Be2+, Mg2+, Ca2+) cations in vacuo: metal–quartet interaction, influence of the cation on guanine–guanine interaction, as well as hydrogen bond cooperativity in the guanine quartet and its complexes with metal ions. Interestingly, although the presence of a cation intensifies interaction among guanine molecules, it lowers their binding energy because of notable quartet’s distortion which is responsible for guanines’ substantial deformation energy. This phenomenon is particularly pronounced with Be2+ which, out of the six analyzed cations, enhances hydrogen bond cooperativity to the greatest extent.
Despite many studies, the mechanisms of nonradiative relaxation of uracil in the gas phase and in aqueous solution are still not fully resolved. Here we combine theoretical UV absorption spectroscopy ...with nonadiabatic dynamics simulations to identify the photophysical mechanisms that can give rise to experimentally observed decay time constants. We first compute and theoretically assign the electronic spectra of uracil using the second-order algebraic-diagrammatic-construction (ADC(2)) method. The obtained electronic states, their energy differences and state-specific solvation effects are the prerequisites for understanding the photodynamics. We then use nonadiabatic trajectory-surface-hopping dynamics simulations to investigate the photoinduced dynamics of uracil and uracil-water clusters. In contrast to previous studies, we found that a single mechanism - the ethylenic twist around the Cdouble bond, length as m-dashC bond - is responsible for the ultrafast component of the nonradiative decay, both in the gas phase and in solution. Very good agreement with the experimentally determined ultrashort decay time constants is obtained.
In this work, six groups of non-toxic compounds were tested as inhibitors for mild steel in 1 M HCl solution: glycine (Gly), glutamic acid (Glu), cysteine (Cys), a mixture of three amino acids ...glycine, glutamic acid, and cysteine (Gly + Glu + Cys); a mixture of dipeptide composed of glycine and glutamic acid with amino acid cysteine (Gly-Glu + Cys); and a tripeptide composed of glycine, cysteine and glutamic acid which is called glutathione (Glt). The inhibition performances of inhibitor systems for steel corrosion were investigated by electrochemical tests (polarization measurements and electrochemical impedance spectroscopy) and surface analyses (atomic force microscopy-AFM, optical microscope, and photoelectron spectroscopy-XPS). Experimental results showed that all six groups of inhibitors affect the reduction of steel corrosion rate, with Glt having the highest efficiency during 4-h immersion (97.3%). Atomic force microscopy and optical microscope showed that the inhibitors are able to protect the metal surface and reduce the extent of corrosion. The existence of the Glt inhibitory film on the steel surface was confirmed by the XPS method. DFT calculations provided useful insights into adsorption of the corrosion inhibitors.
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•The cations bound at adjacent cavities of the quadruplex stabilize CT states.•Increasing the number of the layers and cations in the quadruplex tends to redshift CT ...states.•Stabilization of cations’ d orbitals assists in redshifting of nucleobase-metal CT states.
Quadruplexes formed by nucleic acids and their derivates tend to chelate different monovalent and bivalent cations, which simultaneously affect their excited electronic states properties. Cation binding to every and every other cavity of the central ion channel could be exploited for tuning exited-state charge transfer properties. In this work we utilize set of descriptors constructed on the basis of the one-electron transition density matrix obtained using linear-response TDDFT to study excited states properties of four crystallized tetramolecular quadruplexes that chelate alkaline earth cations (Ca2+, Sr2+ and Ba2+). Here, we show that alkaline earth cations situated at adjacent vacancies promote existence of the nucleobase-metal charge separation (CS) states, contrary to the structures with cations that occupy every second available vacancy. We argued that stabilization of these CS states is due to the strong electric field that stabilizes d orbitals of the cations which accept an excited-electron. Moreover, CS content is increased and redshifted below the first bright transition when number of the chelated cations is increased. Hydration effects stabilized CS states and increased their relative content. We also identified electron detachment states in the broad energy range for the Ca2+ containing system. These findings are valuable for understanding and development of the novel nanostructures based on the quadruplex scaffold with adjustable optical properties.
The world has faced a coronavirus outbreak, which, in addition to lung complications, has caused other serious problems, including cardiovascular. There is still no explanation for the mechanisms of ...coronavirus that trigger dysfunction of the cardiac autonomic nervous system (ANS). We believe that the complex mechanisms that change the status of ANS could only be solved by advanced multidimensional analysis of many variables, obtained both from the original cardiovascular signals and from laboratory analysis and detailed patient history. The aim of this paper is to analyze different measures of entropy as potential dimensions of the multidimensional space of cardiovascular data. The measures were applied to heart rate and systolic blood pressure signals collected from 116 patients with COVID-19 and 77 healthy controls. Methods that indicate a statistically significant difference between patients with different levels of infection and healthy controls will be used for further multivariate research. As a result, it was shown that a statistically significant difference between healthy controls and patients with COVID-19 was shown by sample entropy applied to integrated transformed probability signals, common symbolic dynamics entropy, and copula parameters. Statistical significance between serious and mild patients with COVID-19 can only be achieved by cross-entropies of heart rate signals and systolic pressure. This result contributes to the hypothesis that the severity of COVID-19 disease is associated with ANS disorder and encourages further research.
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•RE-thioglycolate complexes were tested as eco-friendly corrosion inhibitors.•RE-thiog proved to be effective mixed-type bifunctional inhibitors of AA2024.•MD simulation indicates ...formation of different inhibitory species in the electrolyte.•RE-thiog strengthen the passive film on AA2024 with over 90% efficiency.•RE-thiog promote the formation of heterogeneous inhibitory film on AA2024 surface.
The hybrid inorganic–organic compounds, RE-thioglycolates (RE = Ce, Nd, Sm), were analyzed as effective green corrosion inhibitors of AA2024 alloy in 0.1 M NaCl solution. Utilizing Electrochemical Impedance Spectroscopy the protective inhibitory film on the alloy’s surface was affirmed, alongside the persistence of a natural oxide layer over time. These complexes demonstrated notable corrosion inhibition efficiency over immersion from 1 h to 3 days, with Sm-thiog retaining the high inhibition efficiency of over 95 % during 72 h. All RE-thioglycolates are mixed-type inhibitors, imparting resistance against both general and pitting corrosion.
The presence of a protective inhibitory film on the AA2024 surface in NaCl solution has been substantiated through various analytical techniques including FTIR, SEM/EDS and XPS. A detailed examination of the differential inhibition exhibited by these bifunctional complexes is elucidated through theoretical calculations. The smallest difference of HOMO and LUMO orbitals for Sm-thiog of 3.21 eV indicates that this inhibitor attains the strongest donor–acceptor interactions with the metal surface. Predictions generated by Density Functional Theory/Molecular Dynamics simulations suggest the potential formation of diverse inhibitory species within the electrolyte. The corrosion inhibition mechanism proposed for RE-thioglycolates is grounded in electrochemical and theoretical insights, and subsequently validated through surface analysis methods.
Guanine self-assemblies are promising supramolecular platforms for optoelectronic applications. The study (Hua et al., J. Phys. Chem. C 2012, 116, 14,682–14,689) reported that alkaline cations cannot ...modulate the electronic absorption spectrum of G-quadruplexes, although a cation effect is observable during electronic relaxation due to different mobility of Na+ and K+ cations. In this work, we theoretically examined whether divalent Mg2+ and Ca2+ cations and hydration might shift excited charge-transfer states of a cation-templated stacked G-quartet to the absorption red tail. Our results showed that earth alkaline cations blue-shifted nπ* states and stabilized charge-transfer ππ* states relative to those of complexes with alkaline cations, although the number of charge-separation states was not significantly modified. Earth alkaline cations were not able to considerably increase the amount of charge-transfer states below the Lb excitonic states. Hydration shifted charge-transfer states of the Na+-coordinated G-octet to the absorption red tail, although this part of the spectrum was still dominated by monomer-like excitations. We found G-octet electron detachment states at low excitation energies in aqueous solution. These states were distributed over a broad range of excitation energies and could be responsible for oxidative damage observed upon UV irradiation of biological G-quadruplexes.
Nucleobases spontaneously aggregate in water by forming stacked dimers and multimers. It is assumed that the main contributions to the aggregation stem from hydrophobic and base–base dispersion ...interactions. By studying the uracil monomer and dimer in bulk water with the first principle molecular dynamics, we discuss dimer structure and provide evidence that stacking increases the uracil–water hydrogen bonding strength and alters the hydration structure of uracil. These changes have a significant influence on the intensity and shift of the carbonyl stretching band as revealed by simulated infrared absorption spectra of the monomer and dimer and available experimental spectra. The contributions of dipole–dipole, dispersion, and water mediated forces to the stacking are discussed. The reported findings are valuable for understanding the microscopic mechanism of heteroaromatic association in water which is relevant to a large range of chemical and biological systems.
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•Selectivity of two crown ethers towards Na+ and K+ is theoretically analyzed.•Solvent is responsible for crowns’ preference towards specific ions in solutions.•Na+-crown interaction ...is predominantly electrostatic.•Classical and non-classical contributions are comparable in K+-crown interaction.
Deviation of sodium and potassium concentrations from their optimal values in living organisms is associated with severe health conditions, thus their precise determination in blood samples requires design of sensitive sensors. Additionally, excess of the two alkali cations should be removed from drinking water. Crown ethers are well-known metal ion traps, as careful choice of crown’s size and its substituents might tune it towards favoring a specific ion. It has been proved experimentally that dibrominated bithiophene crown ethers with five and six oxygen atoms selectively capture the Na+ and the K+ ion, respectively (Giovannitti et al., Adv. Funct. Mater. 26, 2016, 514) in acetonitrile solution. In the present contribution, we analyzed the nature of ion–crown, ion–solvent, and crown–solvent interactions, and demonstrated that the solvent molecules are responsible for the decorated crown’s preference for a particular alkali cation. While past research focused on the ring size and the ion radius compatibillity, which is important for a formation of a stable ion–crown complex, our findings highlight the decisive role of solvent molecules in the selectivity of crown ethers toward particular cations.
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