Systematic studies on the binding of metal ions in aggregates of humic acid: Aggregation kinetics, spectroscopic analyses and MD simulations.

The binding of metal ions with humic acid (HA) plays an important role in the aggregation of HA and the migration of metal ions in the environments. The effects of common cations (Na+, Mg2+, Ca2+ and Al3+) and heavy metal ions (Ag+, Cd2+, Cu2+, Cr3+ and Eu3+) on the aggregation of HA were investigated systematically by aggregation kinetics, spectroscopic techniques and molecular dynamic (MD) simulations. The critical coagulation concentration (CCC) of mono-, di- and trivalent cations could be predicted by the Schulze-Hardy rule. The aggregation of HA in the presence of Na+ and Ag+ was mainly due to the reduction of repulsive force and the hydrogen bonds between HA molecules. While the complexation of di- and trivalent cations with carboxylic/phenolic groups, or the cation-π interactions enhanced the intra- or inter-molecular bridges in HA and then contributed greatly to the aggregation of HA. Heavy metal ions could easily pass through the electric double-layer of HA compared with common cations. MD simulations further signified the strong aggregation ability of HA molecules in solutions containing high valence metal ions. These findings are important for understanding not only how the influence of metal ions on the aggregation of HA, but also the conditions which ions more efficient for aggregation.

Computational Study on the Excited-State Decay of 5-Methylcytosine and 5-Hydroxymethylcytosine: The Common Form of DNA Methylation and Its Oxidation Product.

5-Methylcytosine (5mC) is the predominant epigenetic modification of DNA. 5mC and its sequential oxidation product, 5-hydroxymethylcytosine (5hmC), are crucial epigenetic markers which have a profound impact on gene stability, expression, and regulation. In the present work, ab initio electronic structure computations were performed to investigate the excited-state decay pathways for 5mC and 5hmC in both the neutral and protonated forms. Based on the theoretical quantities, four nonradiative decay pathways via conical intersections (CIs) were identified: ring distortion, ring opening, N-H dissociation, and intersystem crossing (ISC) pathways. Additional calculated potential energy surfaces revealed that ring distortion and ISC pathways were the most effective routes for 5mC and 5hmC, respectively. The influence of environmental factors, such as the solution and an acidic environment, was also explored in this study. Our study demonstrated that excited-state decay pathways via CIs are indispensable for the photostability of DNA epigenetic modifications and may be involved in ingenome stability and mammalian development.

Excited-State Decay Pathways of Flavin Molecules in Five Redox Forms: The Role of Conical Intersections.

Flavin molecules play an important role in light-driven biological activities. They have drawn significant interest for decades because of their rich photochemistry. In addition to the well-explored FADH- (anionic hydroquinone), which is supposed to be the only catalytic active state to repair DNA lesions, other four flavin molecules (i.e., FAD, FAD·-, FADH·, and FADH2) in three redox forms combined the redox cycle of flavins. Although extensive studies have been carried out for steady-state spectroscopic properties of five redox flavins in various proteins and solutions, the photochemistry and photophysical properties of those different redox states significantly complicate the corresponding theoretical studies. In present work, we employed the ab initio wave function based CASSCF method to systematically investigate the excited state decay pathways of flavins in five redox forms through two approaches. First, the comparison of the absorption and emission spectra from both theoretical calculation and experiment allows a detailed mapping of the transition properties of different redox states in flavins. Second, we identified four kinds of conical intersections (CIs) for five different redox states as the possible deactivation mechanisms responsible for internal conversion or intersystem crossing from the initially populated excited state. The theoretical calculations provide atomic details for the photochemical and photophysical properties of flavins on photoinduced processes. Our findings highlight the indispensable effects of CIs in the excited state decay of flavin molecules and thereby provide basic theoretical information for light-driven biological activities.

A novel magnetite nanorod-decorated Si-Schiff base complex for efficient immobilization of U(vi) and Pb(ii) from water solutions.

A novel silicon Schiff base complex (Si-SBC) and magnetite nanorod-decorated Si-SBC (M/SiO2-Si-SBC) were synthesized and well characterized in detail. The synthesized materials were applied for the removal of U(vi) and Pb(ii) from water solutions under various experimental conditions. The monolayer maximum adsorption capacities of M/SiO2-Si-SBC (6.45 × 10-4 mol g-1 for Pb(ii) and 4.82 × 10-4 mol g-1 for U(vi)) obtained from the Langmuir model at 25 °C and pH = 5.00 ± 0.05 were higher than those of Si-SBC (5.18 × 10-4 mol g-1 for Pb(ii) and 3.70 × 10-4 mol g-1 for U(vi)). Moreover, DFT calculations showed that the high adsorption energies (Ead) of 7.61 kcal mol-1 for Pb2+-(Si-SBC) and 2.72 kcal mol-1 for UO22+-(Si-SBC) are mainly attributed to stronger electrostatic interactions. The results revealed that the Si-SBC and M/SiO2-Si-SBC could be used as efficient adsorbents for the effective elimination of U(vi) and Pb(ii) from contaminated wastewater. High sorption capacity and reusability indicated the practical applications of the synthesized materials in environmental pollution cleanup.

Theoretical Studies on the Photophysics and Photochemistry of 5-Formylcytosine and 5-Carboxylcytosine: The Oxidative Products of Epigenetic Modification of Cytosine in DNA.

Cytosine methylation and demethylation play crucial roles in understanding the genomic DNA expression regulation. The epigenetic modification of cytosine and its continuous oxidative products are called the "new four bases of DNA" including 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). However, compared to the abundant studies on the classical DNA bases, the photophysical and photochemical properties of those new bases have not yet aroused people's excessive attention. In this contribution, a systematic study on the nonradiative decay and photochemical pathways via excited states or conical intersections upon photoexcitation has been explored through high-level computational approaches such as the complete active space self-consistent field method, complete active space with second-order perturbation theory, and density functional theory. Pathways like the ring-distortion deactivation, hydrogen dissociation, hydrogen transfer, and also Norrish type I and II photochemical reactions have been investigated, and it was proposed that intersystem crossing from the S1 state to the T1 state is the most effective route for 5fC. For 5caC, ring-pucking and intramolecular isomerism are effective deactivation ways at both neutral and protonated forms. In the meantime, the influences of two important environmental factors, the solution and acidic environment (i.e., the protonated state), were also considered in this study. From the theoretical perspective, the initial properties of the photostability and photochemical reactivity for 5fC and 5caC have become a crucial aspect to facilitate a further comprehension of their potential role in gene regulation and transcription.