Computational Investigation of Structure-Function Relationship in Fluorine-Functionalized MOFs for PFOA Capture from Water

A strategy that can be used to develop metal-organic frameworks (MOFs) to capture per- and poly-fluoroalkyl substances (PFAS) from water is functionalizing them with fluorine moieties. We investigated different fluorine-functionalization strategies and their performance in removing PFAS from water using molecular simulations. Perfluorooctanoic acid (PFOA), one of the most widely encountered PFAS in water sources, was used as the probe molecule. Our simulations show that fluorine functionalization by incorporating fluorinated anions as bridging ligands in MOFs creates additional binding sites for PFOA; however, the same sites also attract water molecules, which casts doubt on their potential use. In contrast, trifluoromethyl or fluorine substitution of the MOF ligands results in higher hydrophobicity. However, the pores fluorinated with this method should have the optimum size to accommodate PFOA. Likewise, post-synthetic fluorine functionalization of MOFs through grafting of perfluorinated alkanes showed increased PFOA affinity. Fluorine-functionalized MOFs with high hydrophobicity and optimized pore sizes can effectively capture PFOA from water at very low concentrations of PFOA

Rapid and Efficient Removal of Perfluorooctanoic Acid from Water with Fluorine-Rich Calixarene-Based Porous Polymers

On account of its nonbiodegradable nature and persistence in the environment, perfluorooctanoic acid (PFOA) accumulates in water resources and poses serious environmental issues in many parts of the world. Here, we present the development of two fluorine-rich calix[4]arene-based porous polymers, FCX4-P and FCX4-BP, and demonstrate their utility for the efficient removal of PFOA from water. These materials featured Brunauer–Emmett–Teller (BET) surface areas of up to 450 m^{2} g^{-1}, which is slightly lower than their nonfluorinated counterparts (up to 596 m^{2} g^{-1}). FCX4-P removes PFOA at environmentally relevant concentrations with a high rate constant of 3.80 g mg^{-1} h^{-1} and reached an exceptional maximum PFOA uptake capacity of 188.7 mg g^{-1}. In addition, it could be regenerated by simple methanol wash and reused without a significant decrease in performance

Noncovalent Interactions of Hydrated DNA and RNA Mapped by 2D-IR Spectroscopy

Biomolecules couple to their aqueous environment through a variety of noncovalent interactions. Local structures at the surface of DNA and RNA are frequently determined by hydrogen bonds with water molecules, complemented by non-specific electrostatic and many-body interactions. Structural fluctuations of the water shell result in fluctuating Coulomb forces on polar and/or ionic groups of the biomolecular structure and in a breaking and reformation of hydrogen bonds. Two-dimensional infrared (2D-IR) spectroscopy of vibrational modes of DNA and RNA gives insight into local hydration geometries, elementary molecular dynamics, and the mechanisms behind them. In this chapter, recent results from 2D-IR spectroscopy of native and artificial DNA and RNA are presented, together with theoretical calculations of molecular couplings and molecular dynamics simulations. Backbone vibrations of DNA and RNA are established as sensitive noninvasive probes of the complex behavior of hydrated helices. The results reveal the femtosecond fluctuation dynamics of the water shell, the short-range character of Coulomb interactions, and the strength and fluctuation amplitudes of interfacial electric fields.Comment: To appear as Chapter 8 of Springer Series in Optical Sciences: Coherent Multidimensional Spectroscopy -- Editors: Cho, Minhaeng (Ed.), 201

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called ANMPathway, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints. The two-state potential has a cusp hypersurface in the configuration space where the energies from both the ENMs are equal. We first search for the minimum energy structure on the cusp hypersurface and then treat it as the transition state. The continuous pathway is subsequently constructed by following the steepest descent energy minimization trajectories starting from the transition state on each side of the cusp hypersurface. Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach. Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied. An open-access web server has been created to deliver ANMPathway results. © 2014 Das et al

Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions

Abstract An explosion of new data from high-resolution cryo-electron microscopy (cryo-EM) studies has produced a large number of data sets for many species of ribosomes in various functional states over the past few years. While many methods exist to produce structural models for lower resolution cryo-EM reconstructions, high-resolution reconstructions are often modeled using crystallographic techniques and extensive manual intervention. Here, we present an automated fitting technique for high-resolution cryo-EM data sets that produces all-atom models highly consistent with the EM density. Using a molecular dynamics approach, atomic positions are optimized with a potential that includes the cross-correlation coefficient between the structural model and the cryo-EM electron density, as well as a biasing potential preserving the stereochemistry and secondary structure of the biomolecule. Specifically, we use a hybrid structure-based/ab initio molecular dynamics potential to extend molecular dynamics fitting. In addition, we find that simulated annealing integration, as opposed to straightforward molecular dynamics integration, significantly improves performance. We obtain atomistic models of the human ribosome consistent with high-resolution cryo-EM reconstructions of the human ribosome. Automated methods such as these have the potential to produce atomistic models for a large number of ribosome complexes simultaneously that can be subsequently refined manually

Calix[4]arene-Based Porous Organic Nanosheets

Copyright © 2018 American Chemical Society. Calixarenes are a common motif in supramolecular chemistry but have rarely been incorporated in structurally well-defined covalent 2D materials. Such a task is challenging, especially without a template, because of the nonplanar configuration and conformational flexibility of the calixarene ring. Here, we report the first-of-a-kind solvothermal synthesis of a calix[4]arene-based 2D polymer (CX4-NS) that is porous, covalent, and isolated as few-layer thick (3.52 nm) nanosheets. Experimental and theoretical characterization of the nanosheets is presented. Atomic force microscopy and transmission electron microscopy results are consistent with the calculated lowest energy state of the polymer. In the lowest energy state, parallel layers are tightly packed, and the calixarenes adopt the 1,2-alternate conformation, which gives rise to a two-dimensional pattern and a rhombic unit cell. We tested the material's ability to adsorb I2 vapor and observed a maximum capacity of 114 wt %. Molecular simulations extended to model I2 capture showed excellent agreement with experiments. Furthermore, the material was easily regenerated by mild ethanol washings and could be reused with minimal loss of efficiency