Molecular dynamics simulations of the effect of starch on transport of water and ions through graphene nanopores.

CONTEXT: We use molecular dynamics simulations to unravel the molecular level mechanisms underlying the structure and dynamics of water and ions flowing through nanoporous starch-graphene membranes. Our findings indicate that there is a significant tendency for the formation of short-range order in close proximity to the graphene membrane surface. This leads to a greater concentration of water and ions, suggesting strong interactions between the membrane and the saltwater solution. Furthermore, we found that the starch-graphene membrane was most efficient in sieving out ions when the starch loading is 15 wt.%, and the pore diameter is 14 Å. At these conditions, the starch-graphene membrane showed a high water transport rate and maintained a high level of ion rejection. METHODS: We investigated the effect of loading of starch and the pore diameter on the pressure-induced transport, structure, and dynamics of Na+, Cl-, and water using the GROMACS 2021.4 package. We further analyze the density profiles of water and ions in the context of ion-polymer and water-polymer interactions and provide mechanistic insights into the piston-induced flow of saltwater through the starch-graphene membranes using Visual Molecular Dynamics (VMD) software.

Ion transport mechanisms in pectin-containing EC-LiTFSI electrolytes.

Using all-atom molecular dynamics simulations, we report the structure and ion transport characteristics of a new class of solid polymer electrolytes that contain the biodegradable and mechanically stable biopolymer pectin. We used highly conducting ethylene carbonate (EC) as a solvent for simulating lithium-trifluoromethanesulfonimide (LiTFSI) salt containing different weight percentages of pectin. Our simulations reveal that the pectin chains reduce the coordination number of lithium ions around their counterions (and vice versa) because of stronger lithium-pectin interactions compared to lithium-TFSI interactions. Furthermore, the pectin is found to promote smaller ionic aggregates over larger ones, in contrast to the results typically reported for liquid and polymer electrolytes. We observed that the loading of pectin in EC-LiTFSI electrolytes increases their viscosity (η) and relaxation timescales (τc), indicating higher mechanical stability, and, consequently, a decrease of the mean squared displacement, diffusion coefficient (D), and Nernst-Einstein conductivity (σNE). Interestingly, while the lithium diffusivities are related to the ion-pair relaxation timescales as D+ ∼ τc-3.1, the TFSI- diffusivities exhibit excellent correlations with ion-pair relaxation timescales as D- ∼ τc-0.95. On the other hand, the NE conductivities are dictated by distinct transport mechanisms and scales with ion-pair relaxation timescales as σNE ∼ τc-1.85.

Insights into the structure and Ion transport of pectin-[BMIM][PF6] electrolytes.

We investigate the effect of pectin on the structure and ion transport properties of the room-temperature ionic liquid electrolyte 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) using molecular dynamics simulations. We find that pectin induces intriguing structural changes in the electrolyte that disrupt large ionic aggregates and promote the formation of smaller ionic clusters, which is a promising finding for ionic conductivity. Due to pectin in [BMIM][PF6] electrolytes, the diffusion coefficient of cations and anions is observed to decrease by a factor of four for a loading of 25 wt. % of pectin in [BMIM][PF6] electrolyte. A strong correlation between the ionic diffusivities (D) and ion-pair relaxation timescales (τc) is observed such that D ∼ τc-0.75 for cations and D ∼ τc-0.82 for anions. The relaxation timescale exponents indicate that the ion transport mechanisms in pectin-[BMIM][PF6] electrolytes are slightly distinct from those found in neat [BMIM][PF6] electrolytes (D∼τc-1). Since pectin marginally affects ionic diffusivities at the gain of smaller ionic aggregates and viscosity, our results suggest that pectin-ionic liquid electrolytes offer improved properties for battery applications, including ionic conductivity, mechanical stability, and biodegradability.

Effect of succinonitrile on ion transport in PEO-based lithium-ion battery electrolytes.

We report the ion transport mechanisms in succinonitrile (SN) loaded solid polymer electrolytes containing polyethylene oxide (PEO) and dissolved lithium bis(trifluoromethane)sulphonamide (LiTFSI) salt using molecular dynamics simulations. We investigated the effect of temperature and loading of SN on ion transport and relaxation phenomenon in PEO-LiTFSI electrolytes. It is observed that SN increases the ionic diffusivities in PEO-based solid polymer electrolytes and makes them suitable for battery applications. Interestingly, the diffusion coefficient of TFSI ions is an order of magnitude higher than the diffusion coefficient of lithium ions across the range of temperatures and loadings investigated. By analyzing different relaxation timescales and examining the underlying transport mechanisms in SN-loaded systems, we find that the diffusivity of TFSI ions correlates excellently with the Li-TFSI ion-pair relaxation timescales. In contrast, our simulations predict distinct transport mechanisms for Li-ions in SN-loaded PEO-LiTFSI electrolytes. Explicitly, the diffusivity of lithium ions cannot be uniquely determined by the ion-pair relaxation timescales but additionally depends on the polymer segmental dynamics. On the other hand, the SN loading induced diffusion coefficient at a given temperature does not correlate with either the ion-pair relaxation timescales or the polymer segmental relaxation timescales.

Insights on choline chloride-based deep eutectic solvent (reline) + primary alcohol mixtures: a molecular dynamics simulation study.

Deep eutectic solvents (DESs) emerged as green solvents for new generation technologies owing to their high chemical and thermal stability. Addition of restricted amount of organic solvents into the DESs plays a significant role in the improvement of thermodynamic and the transport properties to work as a potential solvent in process industries. In this paper, molecular dynamics (MD) simulations were performed to understand the thermophysical and transport properties of choline chloride-based DES (reline) and primary alcohol (methanol and ethanol) mixture in relation to microscopic structure. Density, radial distribution function, coordination number, average number of H-bond, diffusion coefficient and spatial distribution function was calculated in order to understand the structure and involvement of H-bond network at an atomic level. H-bond and spatial distribution function analyses revealed that the chloride ion prefers to be spatially distributed around hydroxyl group of alcohol and found to be more pronounced upon increase in alcohol concentration. As a consequence, it was observed that the H-bonds between Cl- and urea decreases overall with the loading of alcohol and effect is more pronounced beyond a concentration of 0.4. Self-diffusion values for choline, Cl- and urea were found to be increased significantly upon increase in concentration of alcohol from 0.6 to 0.8. Overall, our simulation points to the interplay and interactions between the chloride ions and the solvents in determining the structural and transport properties of choline chloride-based DES.

Existence of ß-diketone form of curcuminoids revealed by NMR spectroscopy.

Curcumin (CUR), demethoxycurcumin (DMC) and bisdemethoxycurcumin (BDMC) - the class of natural compound derived from turmeric can exist as keto-enol and ß-diketone tautomer form. The structure and dynamics of particular relevance CUR is reported in prior studies, whereas DMC and BDMC, by far, have not been scrutinized. In the present studies, we have investigated the detailed molecular structure of CUR, DMC and BDMC by employing NMR spectroscopy as a key tool. The bridging carbon as methylene in ß-diketone form and methine in keto-enol form shows significant difference in NMR spectrum. The results justified that Curcuminoids (CC) has nearly 3% of ß-diketone tautomer in DMSO solvent at 298 K. Further, results revealed that ß-diketone form was favoured in alkaline pH condition whereas acidic and neutral pH conditions favour keto-enol tautomer. However, at higher temperature equilibrium shift towards ß-diketone tautomer. Moreover, this is the first report by NMR for observing the presence of ß-diketone tautomer.

Computational and spectroscopic studies of biologically active coumarin-based fluorophores.

We used density functional theory (DFT) calculations to examine the various molecular properties of two coumarin derivatives, namely 4-(5-amino-[1,3,4]thiadiazol-2-ylsulfanylmethyl)-7-methyl-chromen-2-one and 4-(5-amino-[1,3,4]thiadiazol-2-ylsulfanylmethyl)-7-methoxy-chromen-2-one at different levels of theory and basis sets. The calculated highest occupied molecular orbital and lowest unoccupied molecular orbital energies revealed that the investigated molecules were chemically active with a tendency for molecular interactions. The theoretical vibrational frequencies of these molecules were found to be consistent with the experimentally obtained frequencies. Moreover, solvatochromic measurements indicated no significant change in absorption spectral peak by varying the polarity of solvent. Under the same conditions we found that there was a red shift of 39 nm in the fluorescence spectral peak with increase in solvent polarity. The solvatochromic data were used to estimate excited dipole moments and the change in dipole moment was interpreted based on resonance structure of molecules.

What do we know about DNA mechanics so far?

The DNA molecule, apart from carrying the genetic information, plays a crucial role in a variety of biological processes and finds applications in drug design, nanotechnology and nanoelectronics. The molecule undergoes significant structural transitions under the influence of forces due to physiological and non-physiological environments. Here, we summarize the insights gained from simulations and single-molecule experiments on the structural transitions and mechanics of DNA under force, as well as its elastic properties, in various environmental conditions, and discuss appealing future directions.

R-VAPOL-phosphoric acid based 1H and 13C-NMR for sensing of chiral amines and acids.

Enantiomers have significant importance in pharmaceuticals, biology and modern chemistry and therefore distinguishing and quantifying the enantiomeric forms is of utmost importance. Herein, we propose diphenyl-3,3'-biphenanthryl-4,4'-diyl phosphate (R-VAPOL-PA) as a promising chiral solvating agent to discriminate amines and acids of poly-functional groups such as chiral amines, amino alcohols and hydroxy acids. The methodological approach involves using the nature of hydrogen bonds and ion pairs as a mode of weak interactions to form diastereomers where the probe is associated with enantiomers. The resulting diastereomer difference in the NMR spectrum enables the chiral discrimination with a complete baseline peak separation and an accurate enantiomeric excess (ee) analysis. We also carried out density functional theory (DFT) calculations to understand the complex formation to explain enantiodiscrimination by analysing the formation and stability of different chiral complexes. The binding energy differences between enantiomeric forms revealed by DFT calculations are qualitatively in agreement with the diastereomer difference in the NMR spectrum and unequivocally establishes the suggested experimental protocol of R-VAPOL-PA-based enantiomeric discrimination.

Rotational Diffusion of Proteins in Nanochannels.

The rotational diffusion coefficient is an essential parameter in determining the mechanistic features of biomolecules in both crowded and confined environments. Understanding the influence of nanoconfinement on rotational diffusion is vital in conceptualizing dynamics of biomolecules (such as proteins) in nanopores. The control of the translational movement of biomolecules is practiced widely in nanopore experiments. However, the restrictions on the translational movement may affect other dynamic properties such as rotational diffusion. In this paper, we use a coarse-grained molecular dynamics approach to study the rotational dynamics of a sample protein under the influence of cylindrical nanopore confinement. Our simulation reveals a 2-fold reduction in magnitude from the bulk rotational diffusion coefficient value as the confinement radius reaches double the size of protein's hydrodynamic radius. However, the changes in the rotational diffusion coefficient are relatively small compared to the changes in the translational diffusion coefficient. Interestingly, the rotational anisotropy also varies considerably when pore radii approach protein dimensions. Our simulations point out that the confinement effects cause the breakdown of small angular displacement theory when the pore radius is close to the protein hydrodynamic radius.

Mechanistic insight into the improved Li ion conductivity of solid polymer electrolytes.

Polymer based solid electrolytes (SEs) are envisaged as futuristic components of safer solid state energy devices. But the semi-crystalline nature and slow dynamics of the host polymer matrix are found to hamper the ion transport through the solid polymer network and hence solid state devices are still far beyond the scope of practical application. In this study, we unravel the synergistic roles of Li salt (LiClO4) and two different polymers - polyethylene oxide (PEO) and polydimethyl siloxane (PDMS), in the Li ion transport through their solid blend based electrolyte. A detailed study using dielectric spectroscopy and thermo-mechanical analysis is conducted to understand the tunability of the PEO chain dynamics with LiClO4 and the mechanism of hopping of Li ions by forming ion pairs with oxygen dipoles on the PEO backbone is established. Despite the lack of PDMS's capability to solvate ions and promote ion transport directly, its proper mixing within the PEO host matrix is demonstrated to enhance ion transport due to the influence of PDMS on the segmental dynamics of PEO. A detailed molecular dynamics study supported by experimental validation suggests that even inert polymers can affect the dynamics of the active host matrix and increase ion transport, leading to next generation high ionic conductivity solid matrices, and opens new avenues in designing polymer based transparent electrolytes.

Phonons and thermal conducting properties of borocarbonitride (BCN) nanosheets.

Hexagonal borocarbonitrides (BCN) are a class of 2D materials, which display excellent catalytic activity for water splitting. Here, we report the analysis of thermal stability, phonons and thermal conductivity of BCN monolayers over a wide range of temperatures using classical molecular dynamics simulations. Our results show that in contrast to the case of graphene and boron nitride monolayers, the out-of-plane phonons in BCN monolayers induce an asymmetry in the phonon density of states at all temperatures. Despite possessing lower thermal conducting properties compared to graphene and BN monolayers, the BCN nanosheets do not lose thermal conductivity as much as graphene and BN in the studied temperature range of 200-1000 K, and thus, BCN nanosheets are suitable for thermal interface device applications over a wide range of temperatures. Besides their promising role in water splitting, the above-mentioned results highlight the possibility of expanding the use of BCN 2D materials in thermal management applications and thermoelectrics.

Translational mobilities of proteins in nanochannels: A coarse-grained molecular dynamics study.

We investigated the translation of a protein through model nanopores using coarse-grained (CG) nonequilibrium molecular dynamics (NEMD) simulations and compared the mobilities with those obtained from previous coarse-grained equilibrium molecular dynamics model. We considered the effects of nanopore confinement and external force on the translation of streptavidin through nanopores of dimensions representative of experiments. As the nanopore radius approaches the protein hydrodynamic radius, r_{h}/r_{p}→1 (where r_{h} is the hydrodynamic radius of protein and r_{p} is the pore radius), the translation times are observed to increase by two orders of magnitude. The translation times are found to be in good agreement with the one-dimensional biased diffusion model. The results presented in this paper provide useful insights on nanopore designs intended to control the motion of biomolecules.

Mechanically Strong Polymer Sheets from Aligned Ultrahigh-Molecular-Weight Polyethylene Nanocomposites.

Ultrahigh-molecular-weight polyethylene (UHMWPE) is of great interest as a next-generation body armor material because of its superior mechanical properties. However, such unique properties depend critically on its microscopic structure characteristics, including the degree of crystallinity, chain alignment, and morphology. Here, we present a highly aligned UHMWPE and its composite sheets containing uniformly dispersed boron nitride (BN) nanosheets. The dispersion of BN nanosheets into the UHMWPE matrix increases its mechanical properties over a broad temperature range. Experiments and simulation confirm that the alignment of chain segments in the composite matrix increases with temperature, leading to an improvement in mechanical properties at high temperature. Together with the large thermal conductivity of UHMWPE and BN, our findings serve to expand the application spectrum of highly aligned polymer nanocomposite materials for ballistic panels and body armor over a broad range of temperatures.

Intramolecular Hydrogen Bonding Appetency for Conformational Penchants in Oxalohydrazide Fluoro Derivatives: NMR, MD, QTAIM, and NCI Studies.

The conformational stability of synthesized diphenyloxalohydrazide and dibenzoyloxalohydrazide fluoro derivatives has been investigated by extensive NMR studies that are ascertained by various levels of theoretical calculations. Two-dimensional 1H-19F HOESY NMR experiments revealed the close spatial proximity between two NMR-active nuclei, confirming the hydrogen bond (HB)-mediated interaction between them, further aiding in establishing the probable stable conformations of these molecules. The relaxed potential energy scan disclosed the energy-minimized most stable structure among the several possible multiple conformations, which is in concurrence with NMR interpretations. Atomistic molecular dynamics simulations have been employed to unequivocally establish the conformational stability and the nature of HB formation at varied temperatures. With the possibility of occurrence of a number of probable conformations, the percentage of occurrences of different types of HBs in them was determined by MD simulations. Their population analysis was carried out using a Boltzmann distribution, in addition to deriving their Gibbs free energies. The molecular interactions governing the stable conformations have not only been ascertained by experimental NMR interpretations but also corroborated by other theoretical computations, viz., quantum theory of atoms in molecules (QTAIM) and noncovalent interaction (NCI).

Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA.

We report a structural polymorphism of the S-DNA when a canonical B-DNA is stretched under different pulling protocols and provide a fundamental molecular understanding of the DNA stretching mechanism. Extensive all atom molecular dynamics simulations reveal a clear formation of S-DNA when the B-DNA is stretched along the 3' directions of the opposite strands (OS3) and is characterized by the changes in the number of H-bonds, entropy, and free energy. Stretching along the 5' directions of the opposite strands (OS5) leads to force induced melting form of the DNA. Interestingly, stretching along the opposite ends of the same strand leads to a coexistence of both the S- and melted M-DNA structures. We also do the structural characterization of the S-DNA by calculating various helical parameters. We find that the S-DNA has a twist of ∼10° which corresponds to a helical repeat length of ∼36 base pairs in close agreement with the previous experimental results. Moreover, we find that the free energy barrier between the canonical and overstretched states of DNA is higher for the same termini pulling protocol in comparison to all other protocols considered in this work. Overall, our observations not only reconcile with the available experimental results qualitatively but also enhance the understanding of different overstretched DNA structures.

Influence of molecular weight on ion-transport properties of polymeric ionic liquids.

We report the results of atomistic molecular dynamics simulations on polymerized 1-butyl-3-vinylimidazolium-hexafluorophosphate ionic liquids, studying the influence of the polymer molecular weight on the ion mobilities and the mechanisms underlying ion transport, including ion-association dynamics, ion hopping, and ion-polymer coordinations. With an increase in polymer molecular weight, the diffusivity of the hexafluorophosphate (PF6-) counterion decreases and plateaus above seven repeat units. The diffusivity is seen to correlate well with the ion-association structural relaxation time for pure ionic liquids, but becomes more correlated with ion-association lifetimes for larger molecular weight polymers. By analyzing the diffusivity of ions based on coordination structure, we unearth a transport mechanism in which the PF6- moves by "climbing the ladder" while associated with four polymeric cations from two different polymers.

Ion transport mechanisms in lamellar phases of salt-doped PS-PEO block copolymer electrolytes.

We use a multiscale simulation strategy to elucidate, at an atomistic level, the mechanisms underlying ion transport in the lamellar phase of polystyrene-polyethylene oxide (PS-PEO) block copolymer (BCP) electrolytes doped with LiPF6 salts. Explicitly, we compare the results obtained for ion transport in the microphase separated block copolymer melts to those for salt-doped PEO homopolymer melts. In addition, we also present results for dynamics of the ions individually in the PEO and PS domains of the BCP melt, and locally as a function of the distance from the lamellar interfaces. When compared to the PEO homopolymer melt, ions were found to exhibit slower dynamics in both the block copolymer (overall) and in the PEO phase of the BCP melt. Such results are shown to arise from the effects of slower polymer segmental dynamics in the BCP melt and the coordination characteristics of the ions. Polymer backbone-ion residence times analyzed as a function of distance from the interface indicate that ions have a larger residence time near the interface compared to that near the bulk of lamella, and demonstrates the influence of the glassy PS blocks and microphase segregation on the ion transport properties. Ion transport mechanisms in BCP melts reveal that there exist five distinct mechanisms for ion transport along the backbone of the chain and exhibit qualitative differences from the behavior in homopolymer melts. We also present results as a function of salt concentration which show that the mean-squared displacements of the ions decrease with increasing salt concentration, and that the ion residence times near the polymer backbone increase with increasing salt concentration.

Mechanisms Underlying Ion Transport in Polymerized Ionic Liquids.

We report the results of atomistic molecular dynamics simulations informed by quantum-mechanically parametrized force fields, which identify the mechanisms underlying ion motion and diffusivities in poly(1-butyl-3-vinylimidazolium-hexafluorophosphate) polymerized ionic liquid (polyIL) electrolytes. Our results demonstrate that anion transport in polyILs occurs through a mechanism involving intra- and intermolecular ion hopping through formation and breaking of ion-associations involving four polymerized cationic monomers bonded to two different polymer chains. The resulting ion mobilities are directly correlated to the average lifetimes of the ion-associations. Such a trend is demonstrated to contrast with the behavior in pure ILs, wherein structural relaxations and the associated times are dominant mechanism. Our results establish the basis for experimental findings that reported ion transport in polyILs to be decoupled from polymer segmental relaxations.

Structure and mechanisms underlying ion transport in ternary polymer electrolytes containing ionic liquids.

We use all atom molecular dynamics simulations to investigate the influence of 1-butyl-3-methylimidazolium hexafluorophosphate (BMIMPF6) ionic liquid on the structure and transport properties of poly(ethylene oxide) (PEO) polymer electrolytes doped with LiPF6 salt. We observe enhanced diffusivities of the Li+, PF6-, and BMIM+ ions with increasing loading of the ionic liquid. Interplay between the different ion-ion and ion-polymer interactions is seen to lead to a destabilization of the Li-PF6 coordination and increase in the strength of association between the Li+ cations and the polymer backbone. As a consequence, the polymer segmental relaxation times are shown to be only moderately affected by the addition of ionic liquids. The ionic-liquid induced changes in the mobilities of Li+ ions are seen to be correlated to polymer segmental relaxation times. However, the mobilities of BMIM+ ions are seen to be more strongly correlated to the BMIM-PF6 ion-pair relaxation times.