Nanofiltration across Defect-Sealed Nanoporous Monolayer Graphene

Nano Letters
Monolayer nanoporous graphene represents an ideal membrane for molecular separations, but its practical realization is impeded by leakage through defects in the ultrathin graphene. Here, we report a multiscale leakage–sealing process that exploits the nonpolar nature and impermeability of pristine graphene to selectively block defects, resulting in a centimeter-scale membrane that can separate two fluid reservoirs by an atomically thin layer of graphene. After introducing subnanometer pores in graphene, the membrane exhibited rejection of multivalent ions and small molecules and water flux consistent with prior molecular dynamics simulations. The results indicate the feasibility of constructing defect-tolerant monolayer graphene membranes for nanofiltration, desalination, and other separation processes.Read more

Accurate and efficient linear scaling DFT calculations with universal applicability

Physical Chemistry Chemical Physics
Density functional theory calculations are computationally extremely expensive for systems containing many atoms due to their intrinsic cubic scaling. This fact has led to the development of so-called linear scaling algorithms during the last few decades. In this way it becomes possible to perform ab initio calculations for several tens of thousands of atoms within reasonable walltimes. However, even though the use of linear scaling algorithms is physically well justified, their implementation often introduces some small errors. Consequently most implementations offering such a linear complexity either yield only a limited accuracy or, if one wants to go beyond this restriction, require a tedious fine tuning of many parameters. In our linear scaling approach within the BigDFT package, we were able to overcome this restriction. Using an ansatz based on localized support functions expressed in an underlying Daubechies wavelet basis – which offers ideal properties for accurate...  Read more

Quantum chemical insights into the dependence of porphyrin basicity on the meso-aryl substituents: thermodynamics, buckling, reaction sites and molecular flexibility

Physical Chemistry Chemical Physics
The chemical and sensing properties of porphyrins are frequently tuned via the introduction of peripheral substituents. In the context of the exceptionally fast second protonation step in the case of 5,10,15,20-tetraphenylporphyrin (TPP), as compared to porphin and 5,10,15,20-tetramesitylporphyrin (TMesP), we investigated the macrocycle-substituent interactions of these three porphyrin derivatives in detail. Using quantum chemical thermodynamics calculations, the analysis of geometric structures, torsional profiles, electrostatic potential distributions, and particularly the analysis of molecular flexibilities via ab initio molecular dynamics simulations, we obtained a comprehensive picture of the reactivities of the studied porphyrins and how these are influenced by the meso-substituents. As compared to porphin and TMesP the second protonation of TPP is energetically more favorable and is particularly energetically comparable to its first protonation,...  Read more

Theoretical Computer‐Aided Mutagenic Study on the Triple Green Fluorescent Protein Mutant S65T/H148D/Y145F

Green fluorescent protein (GFP) mutant S65T/H148D has been proposed to host a photocycle that involves an excited-state proton transfer between the chromophore (Cro) and the Asp148 residue and takes place in less than 50 fs without a measurable kinetic isotope effect. It has been suggested that the interaction between the unsuspected Tyr145 residue and the chromophore is needed for the ultrafast sub-50 fs rise in fluorescence. To verify this, we have performed a computer-aided mutagenic study to introduce the additional mutation Y145F, which eliminates this interaction. By means of QM/MM molecular dynamics simulations and time-dependent density functional theory studies, we have assessed the importance of the Cro–Tyr145 interaction and the solvation of Asp148 and shown that in the triple mutant S65T/H148D/Y145F a significant loss in the ultrafast rise of the Stokes-shifted fluorescence should be expected.Read more

Accurate Modeling of Ionic Surfactants at High Concentration

The Journal of Physical Chemistry B
Molecular dynamics (MD) simulation is a useful tool for simulating formulations of surfactant mixtures from first-principles, which can be used to predict surfactant morphology and other industrially relevant thermodynamic properties. However, the surfactant structure is sensitive to the parameters used in MD simulations, and in the absence of extensive validation against experimental data, it is often not obvious a priori which range of parameter sets to choose. In this work, we compare the performance of ion parameters implemented in nonpolarizable classical MD simulations, and its effect on simulations of an idealized solution of sodium dodecyl sulfate (SDS). We find that previous artifacts reported in simulations of larger SDS constructs are a direct consequence of using parameters that poorly model ionic interactions at high concentration. Using osmotic pressure and/or other thermodynamic properties measured at finite concentration, such as Kirkwood–Buff integrals, is...  Read more

β-Cyclodextrin at the Water/1-Bromobutane Interface: Molecular Insight into Reverse Phase Transfer Catalysis

Molecular insight into the role of β-cyclodextrin (βCD) as a phase transfer catalyst at the liquid/liquid interface is obtained by molecular dynamics simulations of the structure and dynamics of βCD adsorbed at the interface between water and 1-bromobutane. In particular, we consider the structure and dynamics of the water and bromobutane molecules inside the βCD cavity and compare them with the behavior when βCD is dissolved in bulk water. βCD is preferentially oriented at the interface, with the cavity opening along the interface normal. While in bulk water the cavity includes 6–8 water molecules that are relatively mobile with short residence time, at the interface the cavity is mostly dehydrated and includes a single bromobutane molecule. This inclusion complex is stable in bulk water. The implication of this behavior for reverse phase transfer catalysis is discussed.Read more

Gluing Potential Energy Surfaces with Rare Event Simulations

Journal of Chemical Theory and Computation
We develop a new method combining replica exchange transition interface sampling with two distinct potential energy surfaces. The method can be used to combine different levels of theory in a simulation of a molecular process (e.g., a chemical reaction), and it can serve as a dynamical version of QM-MM, connecting classical dynamics with Ab Initio dynamics in the time domain. This new method, which we coin QuanTIS, could be applied to use accurate but expensive density functional theory based molecular dynamics for the breaking and making of chemical bonds, while the diffusion of reactants in the solvent are treated with classical force fields. We exemplify the method by applying it to two simple model systems (an ion dissociation reaction and a classical hydrogen model), and we discuss a possible extension of the method in which classical force field parameters for chemical reactions can be optimized on the fly.Read more

Reaction mechanism from quantum molecular dynamics for the initial thermal decomposition of 2,4,6-triamino-1,3,5-triazine-1,3,5-trioxide (MTO) and 2,4,6-trinitro-1,3,5-triazine-1,3,5-trioxide (MTO3N), promising green energetic materials

Journal of Materials Chemistry A
Klapötke and co-workers recently designed two new materials, 2,4,6-triamino-1,3,5-triazine-1,3,5-trioxide (MTO) and 2,4,6-trinitro-1,3,5-triazine-1,3,5-trioxide (MTO3N), envisioned as candidates for green high-energy materials. However, all attempts at synthesis have failed. In order to validate the expected properties for these systems and to determine why these materials are too unstable to synthesize, we used the PBE flavor of Density Functional Theory (DFT) to predict the crystal structures for MTO and MTO3N and then we carried out DFT molecular dynamics simulations (DFT-MD) to determine the initial reaction mechanisms for decomposition. Klapötke estimated that MTO would have a density of ρ = 1.859 g cm−3 with an estimated detonation velocity (Dv) of 8.979 km s−1, making it comparable to RDX...  Read more

Comparative study on confinement effects of graphene and graphene oxide on structure and dynamics of water

RSC Advances
In this work, we compared the structural and dynamical properties of water confined between two graphene oxide (GO) sheets with water confined between two graphene sheets through molecular dynamics simulations. Our results showed how the structure and dynamics of the water near the GO surfaces changes under confinement conditions. Different orientations of the water molecules to the GO sheets confirm the heterogeneous nature of the confined water. The density distribution of water near the GO sheets is different from the graphene surfaces due to the presence of hydrophilic functional groups of the GO sheets. Also, the hydrogen bonds between the water molecules are disturbed due to the presence of these groups on the GO surfaces. The results showed that as water molecules in areas which are close to the GO surfaces are isolated, and due to hydrogen bond formation between water molecules and the substituents of the GO, the water molecules have fewer hydrogen bonds with other water...  Read more

Exotic carbon nanostructures obtained through controllable defect engineering

RSC Advances
We numerically demonstrate the spontaneous formation of various 3D carbon nanostructures, like multi-tube carbon nanotubes, nanopyramids, nanocubes, artificially rippled graphene, and other exotic nanomaterials, starting from graphene nanoribbons and inducing controllably engineered defects consisting of carbon adatoms or inverse Stone–Wales defects. The evolution of the initial defected planar structures towards the final 3D nanoarchitectures is obtained through molecular dynamics simulations, using different force fields to ensure the reproducibility of the derived results. The presented carbon nanostructures of different shapes, sizes, and morphologies, can be used in applications ranging from storage of hydrogen or other molecules, enhanced chemical reactions or catalysis in confined compartments, to drug delivery nanodevices and biosensors.Read more

Structural Features of a 3′ Splice Site in Influenza A

Influenza A is an RNA virus with a genome of eight negative sense segments. Segment 7 mRNA contains a 3′ splice site for alternative splicing to encode the essential M2 protein. On the basis of sequence alignment and chemical mapping experiments, the secondary structure surrounding the 3′ splice site has an internal loop, adenine bulge, and hairpin loop when it is in the hairpin conformation that exposes the 3′ splice site. We report structural features of a three-dimensional model of the hairpin derived from nuclear magnetic resonance spectra and simulated annealing with restrained molecular dynamics. Additional insight was provided by modeling based on 1H chemical shifts. The internal loop containing the 3′ splice site has a dynamic guanosine and a stable imino (cis Watson–Crick/Watson–Crick) GA pair. The adenine bulge also appears to be dynamic with the A either stacked in the stem or forming a base triple with a Watson–Crick GC pair. The hairpin...  Read more

Sulfation and Cation Effects on the Conformational Properties of the Glycan Backbone of Chondroitin Sulfate Disaccharides

The Journal of Physical Chemistry B
Chondroitin sulfate (CS) is one of several glycosaminoglycans that are major components of proteoglycans. A linear polymer consisting of repeats of the disaccharide −4GlcAβ1–3GalNAcβ1–, CS undergoes differential sulfation resulting in five unique sulfation patterns. Because of the dimer repeat, the CS glycosidic “backbone” has two distinct sets of conformational degrees of freedom defined by pairs of dihedral angles: (ϕ1, ψ1) about the β1–3 glycosidic linkage and (ϕ2, ψ2) about the β1–4 glycosidic linkage. Differential sulfation and the possibility of cation binding, combined with the conformational flexibility and biological diversity of CS, complicate experimental efforts to understand CS three-dimensional structures at atomic resolution. Therefore, all-atom explicit-solvent molecular dynamics simulations with Adaptive Biasing Force sampling of the CS backbone were applied to obtain high-resolution, high-precision...  Read more

The Acetylation Landscape of the H4 Histone Tail: Disentangling the Interplay between the Specific and Cumulative Effects

Journal of the American Chemical Society
Histone tails, the intrinsically disordered terminal regions of histone proteins, are key modulators of the structure and dynamics of chromatin and, consequently, are central to many DNA template-directed processes including replication, repair, and transcription. Acetylation of histone tails is a major post-translational modification (PTM) involved in regulating chromatin, yet it remains unclear how acetylation modifies the disordered state of histone tails and affects their function. We investigated the consequences of increasing acetylation on the isolated H4 histone tail by characterizing the conformational ensembles of unacetylated, mono-, di-, tri-, and tetra-acetylated H4 histone tails using Replica Exchange Molecular Dynamics (REMD) simulations. We found that progressive acetylation has a cumulative effect on the H4 tail, decreasing conformational heterogeneity, increasing helical propensity, and increasing hydrogen bond occupancies. The monoacetylation of lysine 16, however,...  Read more

Mechanism of Membrane Poration by Shock Wave Induced Nanobubble Collapse: A Molecular Dynamics Study

The Journal of Physical Chemistry B
We performed coarse-grained molecular dynamics simulations in order to understand the mechanism of membrane poration by shock wave induced nanobubble collapse. Pressure profiles obtained from the simulations show that the shock wave initially hits the membrane and is followed by a nanojet produced by the nanobubble collapse. While in the absence of the nanobubble, the shock wave with an impulse of up to 18 mPa s does not create a pore in the membrane, in the presence of a nanobubble even a smaller impulse leads to the poration of the membrane. Two-dimensional pressure maps depicting the pressure distributed over the lateral area of the membrane reveal the differences between these two cases. In the absence of a nanobubble, shock pressure is evenly distributed along the lateral area of the membrane, while in the presence of a nanobubble an unequal distribution of pressure on the membrane is created, leading to the membrane poration. The size of the pore formed depends on both shock...  Read more

Enhanced Ligand Sampling for Relative Protein–Ligand Binding Free Energy Calculations

The Journal of Physical Chemistry B
Free energy calculations are used to study how strongly potential drug molecules interact with their target receptors. The accuracy of these calculations depends on the accuracy of the molecular dynamics (MD) force field as well as proper sampling of the major conformations of each molecule. However, proper sampling of ligand conformations can be difficult when there are large barriers separating the major ligand conformations. An example of this is for ligands with an asymmetrically substituted phenyl ring, where the presence of protein loops hinders the proper sampling of the different ring conformations. These ring conformations become more difficult to sample when the size of the functional groups attached to the ring increases. The Adaptive Integration Method (AIM) has been developed, which adaptively changes the alchemical coupling parameter λ during the MD simulation so that conformations sampled at one λ can aid sampling at the other λ values. The Accelerated Adaptive...  Read more

Conformational Stability and Thermal Pathways of Relaxation in Triclosan (Antibacterial/Excipient/Contaminant) in Solid-State: Combined Spectroscopic (1H NMR) and Computational (Periodic DFT) Study

The Journal of Physical Chemistry A
The mechanism of molecular dynamics in the antibacterial/antifungal agent, triclosan (5-chloro-2-(2′,4′-dichlorophenoxy)-phenol), in solid state was studied by 1H NMR spectroscopy and periodic density functional theory (DFT) calculations. Temperature dependencies of the proton spin–lattice relaxation time (T1) in the ranges 86–293 and 90–250 K (at 15 and 24.667 MHz, respectively) and the second moment (M2) of the 1H NMR resonant line in the range 103–300 K were measured. Two minima in the temperature dependence of T1 revealed a classical Arrhenius governed activation processes. The low temperature shallow minimum T1(T) of 71 s at 115 K, 15 MHz, which shifts with frequency, was assigned to classical hindered jumps of hydroxyl group around OC axis and with respect to a 5-chloro-2-phenol ring. The activation energy of this motion estimated on the basis of the fit of the theoretical model to the...  Read more

Molecular Models of Cesium and Rubidium Adsorption on Weathered Micaceous Minerals

The Journal of Physical Chemistry A
Understanding the adsorption mechanisms of metal cations onto soils and sediments is of critical importance in the protection of the environment, especially for the case of radioactive materials including the fission product 137Cs. Mechanism-based adsorption models for the long-term interaction of chemical and radionuclide species with clay minerals are needed to improve the accuracy of groundwater reaction and flow models, as well as related simulations for performance assessment of waste sites and repositories. Toward this goal, molecular simulation using geometry optimization and molecular dynamics methods have been used to investigate the adsorption behavior of Cs+ and Rb+ cations at frayed edge wedges (a proxy for frayed edge sites, FES) and in the interlayer region formed as a result of the transformation of muscovite to Al-hydroxy interlayered vermiculite (HIV) during weathering and pedogenesis. Frayed edge wedges, formed both on individual...  Read more

Speciation, Conductivities, Diffusivities, and Electrochemical Reduction as a Function of Water Content in Mixtures of Hydrated Chromium Chloride/Choline Chloride

The Journal of Physical Chemistry B
We report experiments and simulations to understand the factors that control chromium (Cr3+) electrodeposition from ionic liquid solutions. Speciation, conductivities and diffusivities in mixtures of trivalent chromium chloride, water and choline chloride (CrCl3/xH2O/yChCl) were computed from molecular dynamics simulations and compared to measured ultraviolet–visible spectra, conductivities from electrical impedance spectroscopy, and cyclic voltammograms. Computed changes in Cr3+ first solvation shell and conductivity with solution composition qualitatively agree with experimental observations. The Cr3+ first solvation shell contains predominantly H2O and Cl and the proportion of the two ligands changes with the relative bulk concentrations of each. Conductivities and diffusivities are observed to be functions of these composition variables. Variations in observed reduction current are...  Read more

NMR crystallography of monovalent cations in inorganic matrixes: Li+ siting and the local structure of Li+ sites in ferrierites

Chemical Communications
7Li–7Li correlation MAS NMR spectroscopy, interpreted using periodic DFT including molecular dynamics conformational sampling of Li+ sites, is employed to obtain the siting of Li+ at exchangeable positions of ferrierites and the local structure of these Li+ sites. The former is controlled by the Al siting in the zeolite framework.Read more

Coordination properties of a metal chelator clioquinol to Zn2+ studied by static DFT and ab initio molecular dynamics

Physical Chemistry Chemical Physics
Several lines of evidence supporting the role of metal ions in amyloid aggregation, one of the hallmarks of Alzheimer's disease (AD), have turned metal ion chelation into a promising therapeutic treatment. The design of efficient chelating ligands requires proper knowledge of the electronic and molecular structure of the complexes formed, including their hydration properties. Among various potential chelators, clioquinol (5-chloro-7-iodo-8-hydroxyquinoline, CQH) has been evaluated with relative success in in vitro experiments and even in phase 2 clinical trials. Clioquinol interacts with Zn(II) to lead to a binary metal/ligand 1 : 2 stoichiometric complex in which the phenolic group of CQH is deprotonated, resulting in Zn(CQ)2 neutral complexes, to which additional water molecules...  Read more