Search

Rechargeable Mg batteries are a promising energy storage technology to overcome the limitations inherent to Li ion batteries. A critical challenge in advancing Mg batteries is the lack of suitable cathode materials. In this work, we report a cathode design that incorporates S functionality into two‐dimensional metal‐organic‐frameworks (2D‐MOFs). This new cathode material enables good Mg2+ storage capacity and outstanding cyclability. It was found that upon the initial Mg2+ insertion and disinsertion, there is an apparent structural transformation that crumbles the layered 2D framework, leading to amorphization. The resulting material serves as the active material to host Mg2+ through reduction and/or oxidation of S and, to a limited extent, O. The reversible nature of S and O redox chemistry was confirmed by spectroscopic characterizations and validated by density functional calculations. Importantly, during the Mg2+ insertion and disinsertion process, the 2D nature of the framework was maintained, which plays a key role in enabling the high reversibility of the MOF cathode. [ABSTRACT FROM AUTHOR]

RNA is highly sensitive to the ionic environment and typically requires Mg(2+) to form compact structures. There is a need for models capable of describing the ion atmosphere surrounding RNA with quantitative accuracy. We present a model of RNA electrostatics and apply it within coarse-grained molecular dynamics simulation. The model treats Mg(2+) ions explicitly to account for ion-ion correlations neglected by mean-field theories. Since mean-field theories capture KCl well, it is treated implicitly by a generalized Manning counterion condensation model. The model extends Manning condensation to deal with arbitrary RNA conformations, nonlimiting KCl concentrations, and the ion inaccessible volume of RNA. The model is tested against experimental measurements of the excess Mg(2+) associated with the RNA, Γ(2+), because Γ(2+) is directly related to the Mg(2+)-RNA interaction free energy. The excellent agreement with experiment demonstrates that the model captures the ionic dependence of the RNA free energy landscape.

The stability of RNA tertiary structures depends heavily on Mg(2+). The Mg(2+)-RNA interaction free energy that stabilizes an RNA structure can be computed experimentally through fluorescence-based assays that measure Γ2+, the number of excess Mg(2+) associated with an RNA molecule. Previous explicit-solvent simulations predict that the majority of excess Mg(2+) ions interact closely and strongly with the RNA, unlike monovalent ions such as K(+), suggesting that an explicit treatment of Mg(2+) is important for capturing RNA dynamics. Here we present a reduced model that accurately reproduces the thermodynamics of Mg(2+)-RNA interactions. This model is able to characterize long-timescale RNA dynamics coupled to Mg(2+) through the explicit representation of Mg(2+) ions. KCl is described by Debye-Hückel screening and a Manning condensation parameter, which represents condensed K(+) and models its competition with condensed Mg(2+). The model contains one fitted parameter, the number of condensed K(+) ions in the absence of Mg(2+). Values of Γ2+ computed from molecular dynamics simulations using the model show excellent agreement with both experimental data on the adenine riboswitch and previous explicit-solvent simulations of the SAM-I riboswitch. This agreement confirms the thermodynamic accuracy of the model via the direct relation of Γ2+ to the Mg(2+)-RNA interaction free energy, and provides further support for the predictions from explicit-solvent calculations. This reduced model will be useful for future studies of the interplay between Mg(2+) and RNA dynamics.

Experiments demonstrate that Mg(2+) is crucial for structure and function of RNA systems, yet the detailed molecular mechanism of Mg(2+) action on RNA is not well understood. We investigate the interplay between RNA and Mg(2+) at atomic resolution through ten 2-μs explicit solvent molecular dynamics simulations of the SAM-I riboswitch with varying ion concentrations. The structure, including three stemloops, is very stable on this time scale. Simulations reveal that outer-sphere coordinated Mg(2+) ions fluctuate on the same time scale as the RNA, and that their dynamics couple. Locally, Mg(2+) association affects RNA conformation through tertiary bridging interactions; globally, increasing Mg(2+) concentration slows RNA fluctuations. Outer-sphere Mg(2+) ions responsible for these effects account for 80% of Mg(2+) in our simulations. These ions are transiently bound to the RNA, maintaining interactions, but shuttled from site to site. Outer-sphere Mg(2+) are separated from the RNA by a single hydration shell, occupying a thin layer 3-5 Å from the RNA. Distribution functions reveal that outer-sphere Mg(2+) are positioned by electronegative atoms, hydration layers, and a preference for the major groove. Diffusion analysis suggests transient outer-sphere Mg(2+) dynamics are glassy. Since outer-sphere Mg(2+) ions account for most of the Mg(2+) in our simulations, these ions may change the paradigm of Mg(2+)-RNA interactions. Rather than a few inner-sphere ions anchoring the RNA structure surrounded by a continuum of diffuse ions, we observe a layer of outer-sphere coordinated Mg(2+) that is transiently bound but strongly coupled to the RNA.

This review examines the free-solution electrophoretic mobility of oligomeric DNA in polyacrylamide gels. Research demonstrates that the mobility is governed by counterion condensation theory applicable to the migration of very short DNA fragments. The behavior of the phosphate-labeled DNA fragments and end-labeled DNA fragments in polyacrylamide gels is also discussed.

Applying simulations with structure‐based Go¯−like models has proven to be an effective strategy for investigating the factors that control biomolecular dynamics. The common element of these models is that some (or all) of the intra/inter‐molecular interactions are explicitly defined to stabilize an experimentally determined structure. To facilitate the development and application of this broad class of models, we previously released the SMOG 2 software package. This suite allows one to easily customize and distribute structure‐based (i.e., SMOG) models for any type of polymer‐ligand system. The force fields generated by SMOG 2 may then be used to perform simulations in highly optimized MD packages, such as Gromacs, NAMD, LAMMPS, and OpenMM. Here, we describe extensions to the software and demonstrate the capabilities of the most recent version (SMOG v2.4.2). Changes include new tools that aid user‐defined customization of force fields, as well as an interface with the OpenMM simulation libraries (OpenSMOG v1.1.0). The OpenSMOG module allows for arbitrary user‐defined contact potentials and non‐bonded potentials to be employed in SMOG models, without source‐code modifications. To illustrate the utility of these advances, we present applications to systems with millions of atoms, long polymers and explicit ions, as well as models that include non‐structure‐based (e.g., AMBER‐based) energetic terms. Examples include large‐scale rearrangements of the SARS‐CoV‐2 Spike protein, the HIV‐1 capsid with explicit ions, and crystallographic lattices of ribosomes and proteins. In summary, SMOG 2 and OpenSMOG provide robust support for researchers who seek to develop and apply structure‐based models to large and/or intricate biomolecular systems. [ABSTRACT FROM AUTHOR]

Research was conducted to examine the inhibition of bubble coalescence in aqueous electrolyte solutions. All the electrolytes examined were observed to have a measurable effect on coalescence even at concentrations in the range of 0.001 M. Results indicate that the inhibition of coalescence at low concentrations is dominated by a completely different mechanism than in the range of concentrations studied by Craig, Ninham and Pashley.

We investigate the nature of cooperative relaxation at the crossover temperature. The relaxation time for a cooperative rearranging region at the crossover temperature is related to the ratio of the entropy and the heat capacity of the supercooled liquid, and the ratio of the glass transition to the crossover temperatures. The lifetime of “elementary” excitations in supercooled liquid is determined by a variational technique. By imposing self-consistency between lifetime of elementary excitations and hopping relaxation time on the potential energy surface, the relaxation time at the crossover temperature is estimated. The predictions are in excellent agreement with available experimental data. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The ion atmosphere of three-armed symmetric Y-shaped and asymmetric y-shaped A-RNA junctions in aqueous solution containing multivalent ions is described within the framework of a polyelectrolyte model. The fraction of screening counterions per polyion charge that shield the residual unneutralized charges from interacting with one another and the condensed counterions per polyion as a function of sodium and magnesium ion concentrations are determined.