More Like this

1. Theory and simulations for RNA folding in mixtures of monovalent and divalent cations

   https://doi.org/10.1073/pnas.1911632116  

   Nguyen, Hung T.; Hori, Naoto; Thirumalai, D. (October 2019, Proceedings of the National Academy of Sciences)

   RNA molecules cannot fold in the absence of counterions. Experiments are typically performed in the presence of monovalent and divalent cations. How to treat the impact of a solution containing a mixture of both ion types on RNA folding has remained a challenging problem for decades. By exploiting the large concentration difference between divalent and monovalent ions used in experiments, we develop a theory based on the reference interaction site model (RISM), which allows us to treat divalent cations explicitly while keeping the implicit screening effect due to monovalent ions. Our theory captures both the inner shell and outer shell coordination of divalent cations to phosphate groups, which we demonstrate is crucial for an accurate calculation of RNA folding thermodynamics. The RISM theory for ion–phosphate interactions when combined with simulations based on a transferable coarse-grained model allows us to predict accurately the folding of several RNA molecules in a mixture containing monovalent and divalent ions. The calculated folding free energies and ion-preferential coefficients for RNA molecules (pseudoknots, a fragment of the rRNA, and the aptamer domain of the adenine riboswitch) are in excellent agreement with experiments over a wide range of monovalent and divalent ion concentrations. Because the theory is general, it can be readily used to investigate ion and sequence effects on DNA properties. 

   more » « less
2. Partition energy in polyamide membranes and its link to ion-ion selectivity

   https://doi.org/10.1016/j.memlet.2025.100099  

   Birnhack, Liat; Porat, Oren Ben; Fridman, Ori; Tong, Tiezheng; Epsztein, Razi (June 2025, Journal of Membrane Science Letters)

   Understanding the mechanisms of molecular transport in polyamide membranes is imperative to improve their solute-specific selectivity. We explored the partitioning behaviors of water and salts in polyamide membranes to elucidate the role of ion-membrane interactions in the transport. Quartz crystal microbalance (QCM) was employed to quantify the mass uptake at different temperatures and determine partition energies (Ek) for water and salts under two different pH values. Zeta potential and permeability tests were conducted to support the ionmembrane affinity trends observed with QCM and link these trends to ion-ion selectivity. Our results demonstrate a high affinity of water to the polyamide membrane (Ek < 0), with a significant swelling effect attributed to dipole interactions and hydrogen bonding. Ion partitioning revealed distinct differences between monovalent and divalent cations, as well as between kosmotropic and chaotropic anions. Specifically, divalent cations (Ca2+ and Mg2+) exhibited considerably lower partition energies (-0.99 and 0.29 kcal mol-1, respectively) and more efficient charge neutralization, indicating stronger interactions with the membrane compared to monovalent cations (~2.2 kcal mol-1). The partition energies of the chaotropic iodide and kosmotropic sulphate anions were substantially different (-5.5 and 4.0 kcal mol-1, respectively), likely due to the different tendency of these anions to shed their hydration shell and stick to the polymer. Last, our permeability tests indicate the potential existence of an intrinsic tradeoff between ion partitioning and intrapore diffusion, presumably due to the opposite effects that ion-membrane interactions have on these transport steps. Overall, our work underscores the role of ionspecific interactions in membrane transport and selectivity. 

   more » « less
3. Computational predictions of metal–macrocycle stability constants require accurate treatments of local solvent and pH effects

   https://doi.org/10.1039/D1CP00611H  

   Gentry, Brian M.; Choi, Tae Hoon; Belfield, William S.; Keith, John A. (April 2021, Physical Chemistry Chemical Physics)

   Rational design of molecular chelating agents requires a detailed understanding of physicochemical ligand–metal interactions in solvent phase. Computational quantum chemistry methods should be able to provide this, but computational reports have shown poor accuracy when determining absolute binding constants for many chelating molecules. To understand why, we compare and benchmark static- and dynamics-based computational procedures for a range of monovalent and divalent cations binding to a conventional cryptand molecule: 2.2.2-cryptand ([2.2.2]). The benchmarking comparison shows that dynamics simulations using standard OPLS-AA classical potentials can reasonably predict binding constants for monovalent cations, but these procedures fail for divalent cations. We also consider computationally efficient static procedure using Kohn–Sham density functional theory (DFT) and cluster-continuum modeling that accounts for local microsolvation and pH effects. This approach accurately predicts binding energies for monovalent and divalent cations with an average error of 3.2 kcal mol −1 compared to experiment. This static procedure thus should be useful for future molecular screening efforts, and high absolute errors in the literature may be due to inadequate modeling of local solvent and pH effects. 

   more » « less
4. Progress in Electronic, Energy, Biomedical and Environmental Applications of Boron Nitride and MoS2 Nanostructures

   https://doi.org/10.3390/mi15030349  

   Uddin, Join; Dubey, Raksha; Balasubramaniam, Vinaayak Sivam; Kabel, Jeff; Khare, Vedika; Salimi, Zohreh; Sharma, Sambhawana; Zhang, Dongyan; Yap, Yoke Khin (March 2024, Micromachines)

   In this review, we examine recent progress using boron nitride (BN) and molybdenum disulfide (MoS2) nanostructures for electronic, energy, biomedical, and environmental applications. The scope of coverage includes zero-, one-, and two-dimensional nanostructures such as BN nanosheets, BN nanotubes, BN quantum dots, MoS2 nanosheets, and MoS2 quantum dots. These materials have sizable bandgaps, differentiating them from other metallic nanostructures or small-bandgap materials. We observed two interesting trends: (1) an increase in applications that use heterogeneous materials by combining BN and MoS2 nanostructures with other nanomaterials, and (2) strong research interest in environmental applications. Last, we encourage researchers to study how to remove nanomaterials from air, soil, and water contaminated with nanomaterials. As nanotechnology proceeds into various applications, environmental contamination is inevitable and must be addressed. Otherwise, nanomaterials will go into our food chain much like microplastics. 

   more » « less
5. Reversed Cation Selectivity of G ₈ ‐Octamer and G ₁₆ ‐Hexadecamer towards Monovalent and Divalent Cations

   https://doi.org/10.1002/asia.202000016  

   He, Ying; Zhang, Yanbin; Wojtas, Lukasz; Akhmedov, Novruz_G; Pan, Qinhe; Guo, Hao; Shi, Xiaodong (March 2020, Chemistry – An Asian Journal)

   Abstract A reverse‐binding‐selectivity between monovalent and divalent cations was observed for two different self‐assembly G₁₆‐hexadecamer and G₈‐octamer systems. The dissociation constant between G₄‐quadruplex and monomer was calculated via VT‐¹H NMR experiments. Quantitative energy profiles revealed entropy as the key factor for the weaker binding toward Ba²⁺compared with K⁺in the G₈‐octamer system despite stronger ion‐dipole interactions. This study is the first direct comparison of the G₄‐quartet binding affinity between mono and divalent cations and will benefit future applications of G‐quadruplex‐related research. Further competition experiments between the G₈‐octamer and 18‐crown‐6 with K⁺demonstrated the potential of this G₈system as a new potassium receptor. 

   more » « less