Exploring the methods on improving CH4 delivery performance to surpass the Advanced Research Project Ageney-Energy target

CH_4 storage associated with adsorbed natural gas(ANG) technology is an issue attracting great concern.Following the Advanced Research Project Agency-Energy(ARPA-E) targeted deliverable capacity of 315 cm~3·cm~(-3)(STP), hundreds of thousands of materials have been experimentally or theoretically evaluated,while the best results still show a 35% gap from the target. Moreover, recent theoretical research reveals that the target is beyond the possibility that real materials can be designed. To get rid of the awkward situation, we make attempts on investigating the CH_4 delivery performance under other operation conditions. Methods of raising the discharge temperature(to infinite high) or elevating the storage pressure(to 25 MPa) have been proved to show limited effectiveness. In this work, it is found that the ARPA-E target can be achieved by using a decreasing storage temperature strategy. By taking 280 Co RE(computation-ready, experimental) COFs(covalent organic frameworks) as ANG materials, when reduce the storage temperature to 190.6 K, the highest deliverable capacity can reach 392 cm~3·cm~(-3)(STP), and16.1% Co RE COFs can surpass the target. The target is also achievable when storage at 220 K. Structure performance relationships study shows strong correlation between deliverable capacity and void fraction. Hence, 120 hypothetical COFs are generated to ascertain the optimum void fraction. In addition,the performance of 2 D-COFs can be greatly enhanced by increasing the interlayer spacings, e.g. CH_4 deliverable capacity(storage at 190.6 K) of ATFG-COF can be improved from 239 to 411 cm~3·cm~(-3)(STP) when interlayer spacing is enlarged to 1.65 nm.     

AKT Inhibitors: The Road Ahead to Computational Modeling-Guided Discovery

AKT, is a serine/threonine protein kinase comprising three isoforms—namely: AKT1, AKT2 and AKT3, whose inhibitors have been recognized as promising therapeutic targets for various human disorders, especially cancer. In this work, we report a systematic evaluation of multi-target Quantitative Structure-Activity Relationship (mt-QSAR) models to probe AKT’ inhibitory activity, based on different feature selection algorithms and machine learning tools. The best predictive linear and non-linear mt-QSAR models were found by the genetic algorithm-based linear discriminant analysis (GA-LDA) and gradient boosting (Xgboost) techniques, respectively, using a dataset containing 5523 inhibitors of the AKT isoforms assayed under various experimental conditions. The linear model highlighted the key structural attributes responsible for higher inhibitory activity whereas the non-linear model displayed an overall accuracy higher than 90%. Both these predictive models, generated through internal and external validation methods, were then used for screening the Asinex kinase inhibitor library to identify the most potential virtual hits as pan-AKT inhibitors. The virtual hits identified were then filtered by stepwise analyses based on reverse pharmacophore-mapping based prediction. Finally, results of molecular dynamics simulations were used to estimate the theoretical binding affinity of the selected virtual hits towards the three isoforms of enzyme AKT. Our computational findings thus provide important guidelines to facilitate the discovery of novel AKT inhibitors.     

Structural Investigation and Molecular Modeling Studies of Strobilurin-Based Fungicides Active against the Rice Blast Pathogen Pyricularia oryzae

The increasing emergence of fungicide-resistant pathogens requires urgent solutions for crop disease management. Here, we describe a structural investigation of new fungicides obtained by combining strobilurin and succinate dehydrogenase inhibitor pharmacophores. We identified compounds endowed with very good activity against wild-type Pyricularia oryzae, combined in some cases with promising activity against strobilurin-resistant strains. The first three-dimensional model of P. oryzae cytochrome bc1 complex containing azoxystrobin as a ligand was developed. The model was validated with a set of commercially available strobilurins, and it well explains both the resistance mechanism to strobilurins mediated by the mutation G143A and the activity of metyltetraprole against strobilurin-resistant strains. The obtained results shed light on the key recognition determinants of strobilurin-like derivatives in the cytochrome bc1 active site and will guide the further rational design of new fungicides able to overcome resistance caused by G143A mutation in the rice blast pathogen.     

Virtual Screening of FDA-Approved Drugs against Triose Phosphate Isomerase from Entamoeba histolytica and Giardia lamblia Identifies Inhibitors of Their Trophozoite Growth Phase

Infectious diseases caused by intestinal protozoan, such as Entamoeba histolytica (E. histolytica) and Giardia lamblia (G. lamblia) are a worldwide public health issue. They affect more than 70 million people every year. They colonize intestines causing primarily diarrhea; nevertheless, these infections can lead to more serious complications. The treatment of choice, metronidazole, is in doubt due to adverse effects and resistance. Therefore, there is a need for new compounds against these parasites. In this work, a structure-based virtual screening of FDA-approved drugs was performed to identify compounds with antiprotozoal activity. The glycolytic enzyme triosephosphate isomerase, present in both E. histolytica and G. lamblia, was used as the drug target. The compounds with the best average docking score on both structures were selected for the in vitro evaluation. Three compounds, chlorhexidine, tolcapone, and imatinib, were capable of inhibit growth on G. lamblia trophozoites (0.05–4.935 μg/mL), while folic acid showed activity against E. histolytica (0.186 μg/mL) and G. lamblia (5.342 μg/mL).     

分子动力学在材料科学中的应用

分子动力学方法是进行物质原子或分子层次计算机模拟时所采用的一种基本方法。通过分子动力学模拟，可以给出原子尺度上材料及其演化过程细节的可能性，具有无先例的准确性，使材料设计和性能预测成为可能。本文分析了分子动力学模拟的基本原理和算法；综述了分子动力学在材料科学中的应用，介绍了最近发展的第一原理分子动力学模拟，指出材料科学中第一原理分子动力学模拟的应用还有待进一步发展。     

8-羟基喹啉-N-氧化物和5,7-二硝基-8-羟基喹啉-N-氧化物与Au(Ⅲ)、Pd(Ⅱ)的配合物之合成

合成4种标题配合物,用元素分析、红外和紫外光谱、摩尔电导、核磁共振氢谱、荧光光谱及X射线粉末衍射物相分析研究了它们的组成和性质及其结构。按结构将配合物分为两类,一是含氢键的离子缔合物;一是含金属—氧键的螯环型配合物。     

A modified embedded-atom method interatomic potential for the Fe–H system

A modified embedded-atom method (MEAM) interatomic potential for the Fe–H binary system has been developed using previously developed MEAM potentials of Fe and H. The potential parameters were determined by fitting to experimental data on the dilute heat of solution of hydrogen in body-centered cubic (bcc) and face-centered cubic (fcc) Fe, the vacancy–hydrogen binding energy in bcc Fe, and to a first-principles calculation for the lattice parameter and bulk modulus of a hypothetical NaCl-type FeH. The potential accurately reproduces the known physical properties of hydrogen as an interstitial solute element in bcc and fcc Fe. The applicability of the potential to atomistic approaches for investigating interactions between hydrogen atoms and other defects such as vacancies, dislocations and grain boundaries, and also for investigating the effects of hydrogen on various deformation and mechanical behaviors of iron is demonstrated.     

MD simulations of the collision between a copper ion and a polyethylene surface: an application to the plasma-insulating material interaction

To allow a better understanding of the physical phenomena occurred between a plasma and an insulating material, we have developed a specific MD code to study this type of interaction. We report results of MD simulations of the interaction of an incoming copper ion with a polyethylene crystal surface. Three initial incoming velocities and four impact angle values are used to check the influence of both the incident energy and impact direction to the resulting surface damage. When the incoming ion velocity is sufficiently high, MD results show that the impact can cause bond breaking leading to uncoordinated carbon atoms and free hydrogen atoms. The values of local temperatures associated with the structural changes show a possible ablation of the polyethylene surface.     

STUDY ON PERMEATION OF ACETONE/NITROGEN MIXED GAS THROUGH AL2O3 MICROPOROUS MEMBRANES: MOLECULAR DYNAMICS

In this work, by applying Materials Studio 2.2 software package, molecular dynamics (MD) was performed to investigate the dynamic processes of 1:4 acetone/nitrogen mixed gas permeating through different Al₂O₃ microporous membranes. Three systems were modeled by considering different box lengths, microporous sizes, and textures of Al₂O₃ membranes to compare different permeation behaviors. In each system, initial mixed gas contained 20 acetone molecules and 80 nitrogen molecules, and its density was set to 0.1 g/cm³. Analysis on the concentration profiles of nitrogen molecules (N2) and acetone molecules (Ace) in each system at different sampling times was implemented to discuss the permeation behaviors of smaller N2 and larger Ace. The results showed that adsorption and diffusion occurred synchronously but adsorption was dominant for acetone molecules and that the adsorption on the floor surface of the feed gas region more easily reached equilibrium (local equilibrium) than the diffusion and the adsorption on the ceiling of the initially vacuum region. Furthermore, for nitrogen, adsorption followed diffusion. Higher temperature is in favor of the enrichment of acetone on the floor surface of the feed gas region but against the adsorption of nitrogen. The adsorptive layer was found to be a double-layer with COMPASS force field and to be a monolayer with PCFF force field.     

Analysis of the oscillatory behavior of double-walled carbon nanotube-based oscillators

Molecular dynamics simulations of oscillatory behaviors of double-walled carbon nanotube-based oscillators are performed. The second-generation empirical bond-order potential is used for the atomic interactions within a wall, and a registry-dependent and four different registry-independent van der Waals potentials are used for the atomic interactions between walls. It is found that the frequencies of the nanotube oscillators are sensitive to the choice of the van der Waals potentials. An almost non-decay oscillation is observed for the registry-dependent potential when there is no rocking motion. However, an apparent decay oscillation is observed when rocking motion occurs. A decay oscillation is observed for all registry-independent potentials even without rocking motion. Mechanisms leading to unstable oscillatory behavior are analyzed.