Multiple spectroscopic insights into the interaction mechanisms between proteins and humic acid.

Proteins are important constituents of dissolved organic matter (DOM) in aqueous environments, and their interaction with humic acid (HA), another key component of DOM, substantially affects the environmental behaviors of DOM. In this work, the interaction mechanisms between tryptophan-containing proteins and HA were systematically investigated using multiple molecular spectroscopic approaches. The fluorescence quenching tests indicate that bovine serum albumin (BSA) was more readily quenched by HA and the coexisting phenolic, carboxyl, and quinone groups in HA contributed to this process significantly. By comparison, the fluorescence of L-tryptophan (L-Trp) was more stable under the same conditions. Furthermore, with multiple groups in HA, static quenching with the binding constants and the number of sites were calculated in the protein-HA and L-Trp-HA mixtures. In addition, the differential fluorescence spectra, UV‒Vis spectra, and two-dimensional correlation spectroscopy results confirmed that L-tryptophan amino acid could indeed form a complex with HA, while did not lead to fluorescence quenching. Finally, the molecular docking and density functional theory (DFT) simulations highlighted the contribution of multiple residues surrounding the HA groups to their interactions. The direct interaction between the tryptophan residue and HA might not be the prerequisite for the fluorescence response. Therefore, our work provides further insights into protein-HA interactions and implies other reasonable elucidations for further explanation.

One-step fluorometric determination of multiple-component dissolved organic matter in aquatic environments.

Dissolved organic matter (DOM) is ubiquitous in aqueous environments and is composed of different components that play different but important roles in the migration and the fate of pollutants, emergence of the disinfect byproduct, thus requiring quantitative characterization. However, until now, simultaneous quantification of the main contents in DOM, i.e., saccharides, proteins, and humic substances, has been difficult, impeding us from understanding and predicting the environmental behaviors of typical pollutants. In this work, a fluorescence approach based on the excitation emission matrix (EEM), combined with a new algorithm, denoted matrix reconstruction coupled with prior linear decomposition (MR-PLD), was developed to quantify multiple DOM simultaneously. First, a set of simulated water samples consisting of glucose, tryptones, and humic acid (HA) were analyzed using MR-PLD to validate the feasibility of the method. The DOM components could be reliably determined with a higher accuracy than parallel factor analysis (PARAFAC) and Parallel Factor Framework-Linear Regression (PFFLR), also with a more convenient procedure than conventional PLD. Second, both actual simulated and experimental methods were performed to test the anti-interference performance of MR-PLD, indicating that the quantification of DOM would not be significantly impacted by other fluorophores. Finally, several actual water samples from natural waters and wastewater treatment plants were also analyzed to confirm the robustness of this method in actual aqueous environments. This study provides a new approach to characterize DOM with EEM, contributing to its convenient concentration monitoring and the further exploration of the environmental impacts.

Predicting the Mechanisms for H2O2 Activation and Phenol Oxidation Catalyzed by Modified Graphene-Based Systems Using Density Functional Theory.

The heterogeneous Fenton-like reaction on metal-free graphene-based catalysts attracts great attention. However, a systematic and comprehensive understanding of the mechanisms for H2O2 activation and pollutant oxidation is still lacking. In this study, the heterogeneous Fenton-like mechanisms on doped and oxygen-containing graphene are investigated using density functional theory. The H2O2 tends to form a surface oxygen and a water molecule on the doped graphene. For the oxygen-containing graphene-based systems, relative to the groups in the basal plane, the separated groups on the edge including hydroxyl, carbonyl, and carboxyl readily activate H2O2 to hydroxyls. However, when the groups are close to each other, more additional side reactions might occur upon H2O2 adsorption, which may inhibit catalyst retrieval. Phenol is selected as a model pollutant to study its oxidation reaction with the adsorbed oxygen formed from the dissociated H2O2. The thermodynamics of the reactions depends significantly on the co-adsorption strengths over different catalysts. Our work provides key fundamental insights into the catalytic performance of various modified graphene-based systems, which could guide the future design and applications of heterogeneous Fenton reactions.

Evaluation of optical band gaps and dopant state energies in transition metal oxides using oxidation-state constrained density functional theory.

We report the use of oxidation-state constrained density functional theory (OS-CDFT) to calculate the optical band gaps of transition metal oxides and dopant state energies of different doped anatase. OS-CDFT was used to control electron transfer from the valence band maximum of the transition metal system to the conduction band minimum or to the dopant state in order to calculate the band gap or the dopant state energies respectively. The calculation of the dopant state energies also allows identification of the transition responsible for the reduced band gap of the doped system in ambiguous cases. We applied this approach to the band gap calculation in TiO2anatase and rutile, vanadium pentoxide (V2O5), chromium(III) oxide (Cr2O3), manganese(IV) oxide (MnO2), ferric oxide (Fe2O3), ferrous oxide (FeO) and cobalt(II) oxide (CoO). The dopant state energies calculations were carried out in the V-, Cr-, Mn-, and Fe-doped anatase.

First-Principles Understanding of the Staging Properties of the Graphite Intercalation Compounds towards Dual-Ion Battery Applications.

Graphite-based dual-ion batteries are a promising alternative to the lithium-ion batteries for energy storage because of its potentially lower cost, higher voltage, and better safety. Among the most important materials in the dual-ion battery are the graphite and graphite intercalation compounds (GICs), whose properties determine the performance of electrodes. The GICs are formed at both anode and the cathode sides during the charging process in which the graphene sheets and the intercalants are arranged in an ordered way called the staging of GICs. Staging is one of the important structural features of GICs related to the volume expansion of the electrodes, the charging rate, and the capacity of the battery. However, the details of the staging mechanism, such as the structural properties, the electronic structure, and the voltage dependence on the stages are still poorly understood. In this regard, we perform density functional theory studies to explore these issues in GICs. Using staging models, we examine the stability of GICs at different stages of intercalation with a range of species (i.e., Li, Na, K, PF6, BF4, TFSI, AlCl4, and ClO4). We then study the contribution of intercalants to the electronic band structures in GICs. In addition, the voltage profiles of the dual-ion batteries with different intercalation species, intercalation stages, and battery capacities are also analyzed. The present work is important for the better understanding of graphite-based dual-ion batteries and helpful in development of novel energy storage systems.

Hydro-Assisted Self-Regenerating Brominated N-Alkylated Thiophene Diketopyrrolopyrrole Dye Nanofibers-A Sustainable Synthesis Route for Renewable Air Filter Materials.

With rising global concerns over the alarming levels of particulate pollution, a sustainable air quality management is the need of the hour. Air filtration research has gained momentum in recent years. However, the research perspective is still blinkered toward formulating new fiber systems for the energy-intensive electrospinning process to fabricate high quality factor air filters. A holistic approach on sustainable air filtration models is still lacking. The air filter model presented in this work uses a simple process involving water-induced self-organization and self-regeneration of nanofibers, and an easy recycling route after the filter life that not only facilitates reuse of the microfibrous scaffold holding the nanofibers but also allows renewal of nanofibers. Three generations of air filters are fabricated and tested, all having high particulate matter (PM)-adsorbing tendency, high filtration efficiency (>95%), and high Young's modulus (≈5 GPa). The renewable air filters offer a sustainable alternative to the present cost-intensive electrospun air filters.

Thermodynamic Properties of Hydrogen-Producing Cobaloxime Catalysts: A Density Functional Theory Analysis.

Density functional theory calculations were carried out to study the electrochemical properties including reduction potentials, pK a values, and thermodynamic hydricities of three prototypical cobaloxime complexes, Co(dmgBF2)2 (dmgBF2 = difluoroboryl-dimethylglyoxime), Co(dmgH)2 (dmgH = dimethylglyoxime), and Co(dmgH)2(py)(Cl) (py = pyridine) in the acetonitrile (AN)-water solvent mixture. The electrochemical properties of Co(dmgBF2)2 in pure AN and pure water were also considered for comparison to reveal the key roles of the solvent on the catalytic reaction. In agreement with previous studies, hydrogen production pathways starting from reduction of the resting state of CoII and involving formation of the CoIIIH and CoIIH intermediates are the favorable ones for both bimetallic and monometallic pathways. However, we found that in pure AN, both the CoIIIH and CoIIH intermediates can react with a proton to produce H2. In the presence of water in the solvent, the reduction of CoIIIH to CoIIH is necessary for the reaction with a proton to occur to form H2. This suggests that it is possible to design catalytic systems by suitably tuning the composition of the AN-water mixture. We also identified the key role of axial coordination of the solvent molecules in affecting the catalytic reaction, which allows further catalyst design strategy. The highest hydride donor ability of Co(dmgH)2(py)(Cl) indicates that this complex displays the best catalytic hydrogen-producing performance among the three cobaloximes studied in this work.

Oxidation-State Constrained Density Functional Theory for the Study of Electron-Transfer Reactions.

We propose a new constrained density functional theory (CDFT) approach which directly controls the oxidation state of the target atoms. In this new approach called oxidation-state constrained density functional theory (OS-CDFT), the eigenvalues of the occupation matrix obtained from projecting the Kohn-Sham wave functions onto the valence orbitals are constrained to obtain the desired oxidation states. This approach is particularly useful to study electron transfer problems in transition metal-containing systems due to the multivalent nature of the transition metal ions. The calculation of the forces on the ions and of the coupling constant was implemented under the OS-CDFT scheme to allow efficient and accurate study of electron transfer reactions. We demonstrated the application of this method in the study of different electron transfer reactions including the aqueous ferrous-ferric self-exchange reaction, polaron hopping in the TiO2 anatase and bismuth vanadate, and photoexcited electron transfer in the sapphire.

Density Functional Theory and Car-Parrinello Molecular Dynamics Study of the Hydrogen-Producing Mechanism of the Co(dmgBF2)2 and Co(dmgH)2 Cobaloxime Complexes in Acetonitrile-Water Solvent.

The catalytic hydrogen-producing processes of two prototypical cobaloxime catalysts, Co(dmgBF2)2 (dmgBF2 = difluoroboryl-dimethylglyoxime) and Co(dmgH)2 (dmgH = dimethylglyoxime), were studied by density functional theory (DFT) and Car-Parrinello molecular dynamics (CPMD) simulations in the explicit acetonitrile-water solvent. Our study demonstrates the key role of water molecules as shuttles to deliver protons to the cobalt active centers of these catalysts. However, the transfer of protons to the cobalt centers also competes with the diffusion of the proton away from the complex via the hydrogen bond network of water. Protons were found to react with the oxygen of the side group of Co(dmgH)2, while a similar reaction was not observed for Co(dmgBF2)2. This explains the experimentally observed relative instability of Co(dmgH)2 in the acidic medium. The rate-limiting step of the hydrogen-producing process was found to be the first proton transfer to the cobalt center for both cobaloxime complexes. Structural and electron population analysis was carried out to provide insight into the origin of the difference of the proton transfer free-energy barriers of these two cobalt complexes. Our study has contributed to the key microscopic understanding of the hydrogen-producing process by this class of catalysts.

Oxygen tolerance of an in silico-designed bioinspired hydrogen-evolving catalyst in water.

Certain bacterial enzymes, the diiron hydrogenases, have turnover numbers for hydrogen production from water as large as 10(4)/s. Their much smaller common active site, composed of earth-abundant materials, has a structure that is an attractive starting point for the design of a practical catalyst for electrocatalytic or solar photocatalytic hydrogen production from water. In earlier work, our group has reported the computational design of [FeFe](P)/FeS(2), a hydrogenase-inspired catalyst/electrode complex, which is efficient and stable throughout the production cycle. However, the diiron hydrogenases are highly sensitive to ambient oxygen by a mechanism not yet understood in detail. An issue critical for practical use of [FeFe](P)/FeS(2) is whether this catalyst/electrode complex is tolerant to the ambient oxygen. We report demonstration by ab initio simulations that the complex is indeed tolerant to dissolved oxygen over timescales long enough for practical application, reducing it efficiently. This promising hydrogen-producing catalyst, composed of earth-abundant materials and with a diffusion-limited rate in acidified water, is efficient as well as oxygen tolerant.

Interaction of Oxygen and Water with the (100) Surface of Pyrite: Mechanism of Sulfur Oxidation.

We present a density-functional study of the adsorption and reactions of oxygen and water with the (100) surface of pyrite. We find that dissociative adsorption is energetically favorable for oxygen, forming ferryl-oxo, Fe(4+)═O(2-), species. These transform easily to ferric-hydroxy, Fe(3+)-OH(-), in the presence of coadsorbed water, and the latter fully covers the surface under room conditions. A mechanism for surface oxidation is identified, which involves successive reactions with molecular oxygen and water, and leads to the complete oxidation of a surface sulfur to SO4(2-). The crucial recurring process is the surface O(2-) and OH(-) species acting as proton acceptors for incoming water molecules. Using a recently proposed method, we examine the oxidation state changes of the surface ions and the electron flow during the adsorption and oxidation processes. The oxidation mechanism is consistent with isotopic labeling experiments, suggesting that the oxygens in SO4(2-) from gas-phase oxidation are derived from water.

Simple, unambiguous theoretical approach to oxidation state determination via first-principles calculations.

We introduce a novel theoretical approach for determining oxidation states (OS) from quantum-mechanical calculations. For a transition-metal ion, for example, the metal-ligand orbital mixing contribution to the charge allocated to the ion is separated from that due to the actual occupation of the d-orbitals from which OS can then be inferred. We report the application of this approach to different transition-metal systems: molecular complexes, ruthenium-dye molecules, ruthenium complexes with noninnocent ligands, and bulk semiconductors. The computations were carried out using density-functional theory with a Hubbard U correction. The oxidation states were determined without ambiguity.

Oxidation state changes and electron flow in enzymatic catalysis and electrocatalysis through Wannier-function analysis.

In catalysis by metalloenzymes and in electrocatalysis by clusters related in structure and composition to the active components of such enzymes transition-metal atoms can play a central role in the catalyzed redox reactions. Changes to their oxidation states (OSs) are critical for understanding the reactions. The OS is a local property and we introduce a new, generally useful local method for determining OSs, their changes, and the associated bonding changes and electron flow. The method is based on computing optimally localized orbitals (OLOs). With this method, we analyze two cases, superoxide reductase (SOR) and a proposed hydrogen-producing model electrocatalyst [FeS(2)]/[FeFe](P), a modification of the active site of the diiron hydrogenase enzymes. Both utilize an under-coordinated Fe site where a one-electron reduction (for SOR) or a two-electron reduction (for [FeFe](P)) of the substrate occurs. We obtain the oxidation states of the Fe atoms and of their critical ligands, the changes of the bonds to those ligands, and the electron flow during the catalytic cycle, thereby demonstrating that OLOs constitute a powerful interpretive tool for unraveling reaction mechanisms by first-principles computations.

Quantum Mechanical and Quantum Mechanical/Molecular Mechanical Studies of the Iron-Dioxygen Intermediates and Proton Transfer in Superoxide Reductase.

Classical and quantum-chemical computations are employed to probe the reaction intermediates and proton-transfer processes in superoxide reductase (SOR) from Desulfoarculus baarsii. Ab initio studies of the SOR active site, as well as classical and QM/MM MD simulations on the overall enzymatic reaction, are performed. We explore the use of a Hubbard U correction to standard density functional theory (DFT) in order to obtain a better description of the strongly correlated d electrons in the transition-metal center. The results obtained from the standard and Hubbard-U-corrected DFT approaches are compared with those obtained using different hybrid-DFT functionals. We show that the Hubbard U correction gives a significant improvement in the description of the structural, energetic, and electronic properties of SOR. We establish that adopting the Hubbard U correction in the QM/MM approach leads to increased accuracy with essentially no additional computational cost. Our results suggest that Lys(48) is one of the likely sources of the first proton donation to the superoxide, either directly or through an interstitial water molecule. Our QM/MM calculations highlight the important role of the interactions and hydrogen-bond network created by the imidazole rings of the His ligands and the internal water molecules. Whereas the hydrogen-bonding pattern due to internal waters can facilitate the protonation event, the interactions with the His ligands and the hydrogen bonds with water can stabilize the dioxygen ligand in a side-on conformation, which, in turn, prevents the immediate proton transfer from Lys(48), as indicated by recent experimental studies.

Evaluation of Electronic Coupling in Transition-Metal Systems Using DFT: Application to the Hexa-Aquo Ferric-Ferrous Redox Couple.

We present a density-functional theory (DFT) approach, with fractionally occupied orbitals, for studying the prototypical ferric-ferrous electron-transfer (ET) process in liquid water. We use a recently developed ab initio method to calculate the transfer integral (also named electronic-coupling or ET matrix element) between the solvated ions. The computed transfer integral is combined with previous ab initio values of the reorganization energy, within the framework of Marcus' theory, to estimate the rate of the electron self-exchange reaction. The self-interaction correction incorporated (through an appropriate treatment of the electronic correlation effects) into a Hubbard U extension to the DFT scheme leads to a theoretical value of the ET rate relatively close to an experimental estimate from kinetic measurements. The use of fractional occupation numbers (FON) turned out to be crucial for achieving convergence in most self-consistent calculations because of the open-shell d-multiplet electronic structure of each iron ion and the near degeneracy of the redox groups involved. We provide a theoretical justification for the FON approach, which allows a description of the chemical potential and orbital relaxation, and possible extension to other transition-metal redox systems. Accordingly, the methodology developed in this paper, which rests on a suitable combination of Hubbard U correction and a FON approach to DFT, seems to offer a fruitful approach for the quantitative description of ET reactions in biochemical systems.