The stability of [Zn(NH(3))(4)](2+) in water: A quantum mechanical/molecular mechanical molecular dynamics study

A High-Energy and Long-Life Aqueous Zn/Birnessite Battery via Reversible Water and Zn2+ Coinsertion

Aqueous rechargeable Zn/birnessite batteries have recently attracted extensive attention for energy storage system because of their low cost and high safety. However, the reaction mechanism of the birnessite cathode in aqueous electrolytes and the cathode structure degradation mechanics still remain elusive and controversial. In this work, it is found that solvation water molecules coordinated to Zn²⁺ are coinserted into birnessite lattice structure contributing to Zn²⁺ diffusion. However, the birnessite will suffer from hydroxylation and Mn dissolution with too much solvated water coinsertion. Through engineering Zn²⁺ primary solvation sheath with strong-field ligand in aqueous electrolyte, highly reversible [Zn(H₂ O)₂ ]²⁺ complex intercalation/extraction into/from birnessite cathode is obtained. Cathode-electrolyte interface suppressing the Mn dissolution also forms. The Zn metal anode also shows high reversibility without formation of "death-zinc" and detrimental dendrite. A full cell coupled with birnessite cathode and Zn metal anode delivers a discharge capacity of 270 mAh g^-1 , a high energy density of 280 Wh kg^-1 (based on total mass of cathode and anode active materials), and capacity retention of 90% over 5000 cycles.

Fe-Doped ZnO/Reduced Graphene Oxide Nanocomposite with Synergic Enhanced Gas Sensing Performance for the Effective Detection of Formaldehyde

Here, we report the synthesis of Fe-doped ZnO/reduced graphene oxide (rGO) nanocomposites for gas sensing applications via a one-pot hydrothermal process. A wide range of characterization techniques were used to confirm the successful fabrication of the nanocomposite material and to determine the surface area, the structural and morphological properties, the chemical composition, and the purity of the samples, such as Brunauer-Emmett-Teller, X-ray diffraction, Fourier transform infrared, Raman spectroscopy, scanning electron microscopy, transmission electron microscopy, UV-vis spectroscopy, and X-ray photoelectron spectroscopy techniques. The gas sensing performance to formaldehyde was studied thoroughly in a temperature-controlled test chamber. Compared to that of the bare ZnO and ZnO/rGO nanocomposites, the as-prepared 5 atom % Fe-doped ZnO/rGO nanocomposites presented significantly enhanced gas sensing performance to formaldehyde at relatively low temperatures. Whereas most formaldehyde sensors operate at 150 °C and can detect as low as 100 ppm concentrations, the presented sensor can detect 5 ppm formaldehyde at 120 °C. Its fast response-recovery time, high stability, and high selectivity make it an ideal sensor; however, it can exhibit degenerative gas sensing performance at elevated relative humidity. The enhanced gas sensing mechanism was explained as the synergic effect of rGO and Fe doping. The results demonstrate that Fe doping and decorating the nanocomposite with rGO are promising approaches for achieving a superior gas sensing performance for the development of ZnO gas sensors for the detection of formaldehyde.

Solid-State Rechargeable Zinc-Air Battery with Long Shelf Life Based on Nanoengineered Polymer Electrolyte

Zinc-air batteries (ZABs) are vulnerable to the ambient environment (e.g., humidity and CO₂ ), and have serious selfdischarge issues, resulting in a short shelf life. To overcome these challenges, a near-neutral quaternary ammonium (QA) functionalized polyvinyl alcohol electrolyte membrane (different from conventional alkali-type membranes) has been developed. QA functionalization leads to the formation of interconnected nanochannels by creating hydrophilic/-phobic separations at the nanoscale. These nanochannels selectively transport OH^- ions with a reduced migration barrier, while inhibiting [Zn(NH₃ )₆ ]²⁺ crossover. Owing to the superior water retention ability and enhanced chemical stability of the membrane, the solid-state zinc-air battery (SZAB) displays outstanding flexibility, a promising cycle lifetime, and a large volumetric energy density. More importantly, the self-discharge rate of SZAB is depressed to less than 7 % per month, and the fully dehydrated SZAB could recover its rechargeability upon replenishment of the solution of NH₄ Cl.

Temperature effect on the structure and conformational fluctuations in two zinc knuckles from the mouse mammary tumor virus

Zinc fingers are small protein domains in which zinc plays a structural role, contributing to the stability of the zinc-peptide complex. Zinc fingers are structurally diverse and are present in proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and translation, metabolism and signaling, cell proliferation, and apoptosis. Zinc fingers typically function as interaction modules and bind to a wide variety of compounds, such as nucleic acids, proteins, and small molecules. In this study, we investigated the structural properties, in solution, of the proximal and distal zinc knuckles of the nucleocapsid (NC) protein from the mouse mammary tumor virus (MMTV) (MMTV NC). For this purpose, we performed a series of molecular dynamics simulations in aqueous solution at 300 K, 333 K, and 348 K. The temperature effect was evaluated in terms of root mean square deviation of the backbone atoms and root mean square fluctuation of the coordinating residue atoms. The stability of the zinc coordination sphere was analyzed based upon the time profile of the interatomic distances between the zinc ions and the chelator atoms. The results indicate that the hydrophobic character of the proximal zinc finger is dominant at 333 K. The low mobility of the coordinating residues suggests that the strong electrostatic effect exerted by the zinc ion on its coordinating residues is not influenced by the increase in temperature. The evolution of the structural parameters of the coordination sphere of the distal zinc finger at 300 K gives us a reasonable picture of the unfolding pathway, as proposed by Bombarda and coworkers (Bombarda et al., 2005), which can predict the binding order of the four conserved ligand-binding residues. Our results support the conclusion that the structural features can vary significantly between the two zinc knuckles of MMTV NC.

Rational Development of Neutral Aqueous Electrolytes for Zinc-Air Batteries

Neutral aqueous electrolytes have been shown to extend both the calendar life and cycling stability of secondary zinc-air batteries (ZABs). Despite this promise, there are currently no modeling studies investigating the performance of neutral ZABs. Traditional continuum models are numerically insufficient to simulate the dynamic behavior of these complex systems because of the rapid, orders-of-magnitude concentration shifts that occur. In this work, we present a novel framework for modeling the cell-level performance of pH-buffered aqueous electrolytes. We apply our model to conduct the first continuum-scale simulation of secondary ZABs using aqueous ZnCl₂ -NH₄ Cl as electrolyte. We first use our model to interpret the results of two recent experimental studies of neutral ZABs, showing that the stability of the pH value is a significant factor in cell performance. We then optimize the composition of the electrolyte and the design of the cell considering factors including pH stability, final discharge product, and overall energy density. Our simulations predict that the effectiveness of the pH buffer is limited by slow mass transport and that chlorine-containing solids may precipitate in addition to ZnO.

Zinc- and copper-porphyrins in aqueous solution - two similar complexes with strongly contrasting hydration

We present detailed analysis of the hydration behavior of zinc and copper bound porphyrins treated via ab initio quantum mechanical charge field molecular dynamics which agrees well with available experimental data. The computed metal-water coordination in the case of zinc bound porphyrin demonstrates a strong association of water with zinc compared to the copper-water interaction which correlates well with the calculated free energy of binding. The H-bond dynamics in these hydrated systems yield weaker H-bond interactions as compared to that observed in the case of metal-free porphyrin; nevertheless, the effect of metal association with porphyrin resulted in shifts in the vibrational frequencies. These characteristic data suggest a contrasting behavior between these metalloporphyrins in solution which could also serve to correlate with the properties of biological systems.

The influence of metal-ion binding on the structure and surface composition of Sonic Hedgehog: a combined classical and hybrid QM/MM MD study

The interaction of metal ions with Shh binding-sites and their structural impact are assessed via classical and quantum mechanical simulations.

A Comparative Study of [CaEDTA](2-) and [MgEDTA](2-): Structural and Dynamical Insights from Quantum Mechanical Charge Field Molecular Dynamics

Structure and dynamics of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution have been investigated via quantum mechanical/molecular mechanical (QM/MM) simulations. While for the first a 6-fold octahedral complex has been observed, the presence of an additional coordinating water ligand has been observed in the latter case. Because of rapidly exchanging water molecules, this 7-fold coordination complex was found to form pentagonal bipyramidal as well as capped trigonal prismatic configurations along the simulation interchanging on the picosecond time scale. Also in the case of [MgEDTA](2-) a trigonal prismatic configuration has been observed for a very short time period of approximately 1 ps. This work reports for the first time the presence of trigonal prismatic structures observed in the coordination sphere of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution. In addition to the detailed characterization of structure and dynamics of the systems, the prediction of the associated infrared spectra indicates that the ion-water vibrational mode found at approximately 250 cm(-1) provides a distinctive measure to experimentally detect the presence of the coordinating water molecule via low-frequency IR setups.

QM/MM investigations of organic chemistry oriented questions

About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.

Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential

As the second most abundant cation in human body, zinc is vital for the structures and functions of many proteins. Zinc-containing matrix metalloproteinases (MMPs) have been widely investigated as potential drug targets in a range of diseases ranging from cardiovascular disorders to cancers. However, it remains a challenge in theoretical studies to treat zinc in proteins with classical mechanics. In this study, we examined Zn(2+) coordination with organic compounds and protein side chains using a polarizable atomic multipole based electrostatic model. We find that polarization effect plays a determining role in Zn(2+) coordination geometry in both matrix metalloproteinase (MMP) complexes and in zinc-finger proteins. In addition, the relative binding free energies of selected inhibitors binding with MMP13 have been estimated and compared with experimental results. While not directly interacting with the small molecule inhibitors, the permanent and polarizing field of Zn(2+) exerts a strong influence on the relative affinities of the ligands. The simulation results also reveal the polarization effect on binding is ligand dependent and thus difficult to be incorporated into fixed-charge models implicitly.