Drug repurposing for SARS-CoV-2: a high-throughput molecular docking, molecular dynamics, machine learning, and DFT study.

A micro-molecule of dimension 125 nm has caused around 479 million human infections (80 M for the USA) and 6.1 million human deaths (977,000 for the USA) worldwide and slashed the global economy by US$ 8.5 Trillion over two years period. The only other events in recent history that caused comparative human life loss through direct usage (either by human or nature, respectively) of structure-property relations of 'nano-structures' (either human-made or nature, respectively) were nuclear bomb attacks during World War II and 1918 Flu Pandemic. This molecule is called SARS-CoV-2, which causes a disease known as COVID-19. The high liability cost of the pandemic had incentivized various private, government, and academic entities to work towards finding a cure for this and emerging diseases. As an outcome, multiple vaccine candidates are discovered to avoid the infection in the first place. But so far, there has been no success in finding fully effective therapeutic candidates. In this paper, we attempted to provide multiple therapy candidates based upon a sophisticated multi-scale in-silico framework, which increases the probability of the candidates surviving an in-vivo trial. We have selected a group of ligands from the ZINC database based upon previously partially successful candidates, i.e., Hydroxychloroquine, Lopinavir, Remdesivir, Ritonavir. We have used the following robust framework to screen the ligands; Step-I: high throughput molecular docking, Step-II: molecular dynamics analysis, Step-III: density functional theory analysis. In total, we have analyzed 242,000(ligands)*9(proteins) = 2.178 million unique protein binding site/ligand combinations. The proteins were selected based on recent experimental studies evaluating potential inhibitor binding sites. Step-I had filtered that number down to 10 ligands/protein based on molecular docking binding energy, further screening down to 2 ligands/protein based on drug-likeness analysis. Additionally, these two ligands per protein were analyzed in Step-II with a molecular dynamic modeling-based RMSD filter of less than 1Å. It finally suggested three ligands (ZINC001176619532, ZINC000517580540, ZINC000952855827) attacking different binding sites of the same protein(7BV2), which were further analyzed in Step-III to find the rationale behind comparatively higher ligand efficacy. Supplementary Information: The online version contains supplementary material available at 10.1007/s10853-022-07195-8.

Variation in the interface strength of silicon with surface engineered Ti3C2 MXenes.

Current advancements in battery technologies require electrodes to combine high-performance active materials such as Silicon (Si) with two-dimensional materials such as transition metal carbides (MXenes) for prolonged cycle stability and enhanced electrochemical performance. More so, it is the interface between these materials, which is the nexus for their applicatory success. Herein, the interface strength variations between amorphous Si and Ti3C2Tx MXenes are determined as the MXene surface functional groups (Tx) are changed using first principles calculations. Si is interfaced with three Ti3C2 MXene substrates having surface -OH, -OH and -O mixed, and -F functional groups. Density functional theory (DFT) results reveal that completely hydroxylated Ti3C2 has the highest interface strength of 0.6 J m-2 with amorphous Si. This interface strength value drops as the proportion of surface -O and -F groups increases. Additional analysis of electron redistribution and charge separation across the interface is provided for a complete understanding of underlying physico-chemical factors affecting the surface chemistry and resultant interface strength values. The presented comprehensive analysis of the interface aims to develop sophisticated MXene based electrodes by their targeted surface engineering.

Understanding the Strength of the Selenium-Graphene Interfaces for Energy Storage Systems.

We present comprehensive first-principles density functional theory (DFT) analyses of the interfacial strength and bonding mechanisms between crystalline and amorphous selenium (Se) with graphene (Gr), a promising duo for energy storage applications. Comparative interface analyses are presented on amorphous silicon (Si) with graphene and crystalline Se with a conventional aluminum (Al) current collector. The interface strengths of monoclinic Se (0.43 J m-2) and amorphous Si with graphene (0.41 J m-2) are similar in magnitude. While both materials (c-Se, a-Si) are bonded loosely by van der Waals (vdW) forces over graphene, interfacial electron exchange is higher for a-Si/graphene. This is further elaborated by comparing the potential energy step and charge transfer (Δq) across the graphene interfaces. The interface strength of c-Se on a 3D Al current collector is higher (0.99 J m-2), suggesting a stronger adhesion. Amorphous Se with graphene has comparable interface strength (0.34 J m-2), but electron exchange in this system is slightly distinct from monoclinic Se. The electronic characteristics and bonding mechanisms are different for monoclinic and amorphous Se with graphene as they activate graphene via surface charge doping divergently. The implications of these interfacial physicochemical attributes on electrode performance have been discussed. Our findings highlight the complex electrochemical phenomena in Se interfaced with graphene, which may profoundly differ from their "free" counterparts.

Computational study of the water-driven graphene wrinkle life-cycle towards applications in flexible electronics.

The ubiquitous presence of wrinkles in two-dimensional materials alters their properties significantly. It is observed that during the growth process of graphene, water molecules, sourced from ambient humidity or transferred method used, can get diffused in between graphene and the substrate. The water diffusion causes/assists wrinkle formation in graphene, which influences its properties. The diffused water eventually dries, altering the geometrical parameters and properties of wrinkled graphene nanoribbons. Our study reveals that the initially distributed wrinkles tend to coalesce to form a localized wrinkle whose configuration depends on the initial wrinkle geometry and the quantity of the diffused water. The movement of the localized wrinkle is categorized into three modes-bending, buckling, and sliding. The sliding mode is characterized in terms of velocity as a function of diffused water quantity. Direct bandgap increases linearly with the initial angle except the highest angle considered (21°), which can be attributed to the electron tunneling effect observed in the orbital analysis. The system becomes stable with an increase in the initial angle of wrinkle as observed from the potential energy plots extracted from MD trajectories and confirmed with the DOS plot. The maximum stress generated is less than the plastic limit of the graphene.

Controlled edge dependent stacking of WS2-WS2 Homo- and WS2-WSe2 Hetero-structures: A Computational Study.

Transition Metal Dichalcogenides (TMDs) are one of the most studied two-dimensional materials in the last 5-10 years due to their extremely interesting layer dependent properties. Despite the presence of vast research work on TMDs, the complex relation between the electro-chemical and physical properties make them the subject of further research. Our main objective is to provide a better insight into the electronic structure of TMDs. This will help us better understand the stability of the bilayer post growth homo/hetero products based on the various edge-termination, and different stacking of the two layers. In this regard, two Tungsten (W) based non-periodic chalcogenide flakes (sulfides and selenides) were considered. An in-depth analysis of their different edge termination and stacking arrangement was performed via Density Functional Theory method using VASP software. Our finding indicates the preference of chalcogenide (c-) terminated structures over the metal (m-) terminated structures for both homo and heterobilayers, and thus strongly suggests the nonexistence of the m-terminated TMDs bilayer products.

Effect of cobalt content on the electrochemical properties and structural stability of NCA type cathode materials.

At present, the most common type of cathode materials, NCA (Li1-xNi0.80Co0.15Al0.05O2, x = 0 to 1), have a very high concentration of cobalt. Since cobalt is toxic and expensive, the existing design of cathode materials is neither cost-effective nor environmentally benign. We have performed density functional theory (DFT) calculations to investigate electrochemical, electronic, and structural properties of four types of NCA cathode materials with the simultaneous decrease in Co content along with the increase in Ni content. Our results show that even if the cobalt concentration is significantly decreased from 16.70% (NCA_I) to 4.20% (NCA_IV), variation in intercalation potential and specific capacity is not significant. For example, in the case of 50% Li concentration, the voltage drop is only ∼17% while the change in specific capacity is negligible. Moreover, we have also explored the influence of sodium doping in the intercalation site on the electrochemical, electronic, and structural properties. By considering two extreme cases of NCAs (i.e., with highest and lowest Co content: NCA_I and NCA_IV, respectively), we have demonstrated the importance of Na doping from the structural and electronic point of view. Our results provide insight into the design of environmentally benign, low-cost cathode materials with reduced cobalt concentration.

Utilizing van der Waals Slippery Interfaces to Enhance the Electrochemical Stability of Silicon Film Anodes in Lithium-Ion Batteries.

High specific capacity anode materials such as silicon (Si) are increasingly being explored for next-generation, high performance lithium (Li)-ion batteries. In this context, Si films are advantageous compared to Si nanoparticle based anodes since in films the free volume between nanoparticles is eliminated, resulting in very high volumetric energy density. However, Si undergoes volume expansion (contraction) under lithiation (delithiation) of up to 300%. This large volume expansion leads to stress build-up at the interface between the Si film and the current collector, leading to delamination of Si from the surface of the current collector. To prevent this, adhesion promotors (such as chromium interlayers) are often used to strengthen the interface between the Si and the current collector. Here, we show that such approaches are in fact counter-productive and that far better electrochemical stability can be obtained by engineering a van der Waals "slippery" interface between the Si film and the current collector. This can be accomplished by simply coating the current collector surface with graphene sheets. For such an interface, the Si film slips with respect to the current collector under lithiation/delithiation, while retaining electrical contact with the current collector. Molecular dynamics simulations indicate (i) less stress build-up and (ii) less stress "cycling" on a van der Waals slippery substrate as opposed to a fixed interface. Electrochemical testing confirms more stable performance and much higher Coulombic efficiency for Si films deposited on graphene-coated nickel (i.e., slippery interface) as compared to conventional nickel current collectors.

Surface hydrogenation regulated wrinkling and torque capability of hydrogenated graphene annulus under circular shearing.

Wrinkles as intrinsic topological feature have been expected to affect the electrical and mechanical properties of atomically thin graphene. Molecular dynamics simulations are adopted to investigate the wrinkling characteristics in hydrogenated graphene annulus under circular shearing at the inner edge. The amplitude of wrinkles induced by in-plane rotation around the inner edge is sensitive to hydrogenation, and increases quadratically with hydrogen coverage. The effect of hydrogenation on mechanical properties is investigated by calculating the torque capability of annular graphene with varying hydrogen coverage and inner radius. Hydrogenation-enhanced wrinkles cause the aggregation of carbon atoms towards the inner edge and contribute to the critical torque strength of annulus. Based on detailed stress distribution contours, a shear-to-tension conversion mechanism is proposed for the contribution of wrinkles on torque capacity. As a result, the graphane annulus anomalously has similar torque capacity to pristine graphene annulus. The competition between hydrogenation caused bond strength deterioration and wrinkling induced local stress state conversion leads to a U-shaped evolution of torque strength relative to the increase of hydrogen coverage from 0 to 100%. Such hydrogenation tailored topological and mechanical characteristics provides an innovative mean to develop novel graphene-based devices.

Defect-induced plating of lithium metal within porous graphene networks.

Lithium metal is known to possess a very high theoretical capacity of 3,842 mAh g(-1) in lithium batteries. However, the use of metallic lithium leads to extensive dendritic growth that poses serious safety hazards. Hence, lithium metal has long been replaced by layered lithium metal oxide and phospho-olivine cathodes that offer safer performance over extended cycling, although significantly compromising on the achievable capacities. Here we report the defect-induced plating of metallic lithium within the interior of a porous graphene network. The network acts as a caged entrapment for lithium metal that prevents dendritic growth, facilitating extended cycling of the electrode. The plating of lithium metal within the interior of the porous graphene structure results in very high specific capacities in excess of 850 mAh g(-1). Extended testing for over 1,000 charge/discharge cycles indicates excellent reversibility and coulombic efficiencies above 99%.

Defective graphene as a high-capacity anode material for Na- and Ca-ion batteries.

Because of their abundance, sodium and calcium can be attractive in ion batteries for large-scale grid storage. However, many of the anode materials being pursued have limitations including volume expansion, lack of passivating films, and slow kinetics. Here, we investigate the adsorption of Na and Ca on graphene with divacancy and Stone-Wales defects in graphene. Our results show that although adsorption of Na and Ca is not possible on pristine graphene, enhanced adsorption is observed on defective graphene because of increased charge transfer between the adatoms and defects. We find that the capacity of graphene increases with the density of the defects. For the maximum possible divacancy defect densities, capacities of 1450 and 2900 mAh/g for Na- and Ca-ion batteries, respectively, can be achieved. For Stone-Wales defects, we find maximum capacities of 1071 and 2142 mAh/g for Na and Ca, respectively. Our results provide guidelines to create better high-capacity anode materials for Na- and Ca-ion batteries.

Graphene-based environmental barriers.

Many environmental technologies rely on containment by engineered barriers that inhibit the release or transport of toxicants. Graphene is a new, atomically thin, two-dimensional sheet material, whose aspect ratio, chemical resistance, flexibility, and impermeability make it a promising candidate for inclusion in a next generation of engineered barriers. Here we show that ultrathin graphene oxide (GO) films can serve as effective barriers for both liquid and vapor permeants. First, GO deposition on porous substrates is shown to block convective flow at much lower mass loadings than other carbon nanomaterials, and can achieve hydraulic conductivities of 5 × 10(-12) cm/s or lower. Second we show that ultrathin GO films of only 20-nm thickness coated on polyethylene films reduce their vapor permeability by 90% using elemental mercury as a model vapor toxicant. The barrier performance of GO in this thin-film configuration is much better than the Nielsen model limit, which describes ideal behavior of flake-like fillers uniformly imbedded in a polymer. The Hg barrier performance of GO films is found to be sensitive to residual water in the films, which is consistent with molecular dynamics (MD) simulations that show lateral diffusion of Hg atoms in graphene interlayer spaces that have been expanded by hydration.

Aerosol synthesis of cargo-filled graphene nanosacks.

Water microdroplets containing graphene oxide and a second solute are shown to spontaneously segregate into sack-cargo nanostructures upon drying. Analytical modeling and molecular dynamics suggest the sacks form when slow-diffusing graphene oxide preferentially accumulates and adsorbs at the receding air-water interface, followed by capillary collapse. Cargo-filled graphene nanosacks can be nanomanufactured by a simple, continuous, scalable process and are promising for many applications where nanoscale materials should be isolated from the environment or biological tissue.

Plastic deformation drives wrinkling, saddling, and wedging of annular bilayer nanostructures.

We describe the spontaneous wrinkling, saddling, and wedging of metallic, annular bilayer nanostructures driven by grain coalescence in one of the layers. Experiments revealed these different outcomes based on the dimensions of the annuli, and we find that the essential features are captured using finite element simulations of the plastic deformation in the metal bilayers. Our results show that the dimensions and nanomechanics associated with the plastic deformation of planar nanostructures can be important in forming complex three-dimensional nanostructures.