Molecular Systems Design & Engineering最新文献

With increasing concerns over antimicrobial resistance worldwide, antimicrobial peptides (AMPs) can be a potential alternative to conventional antibiotics. Generating new AMPs is challenging as there can be enormous combinations of amino acid residues leading to a vast number of possibilities. To alleviate this hurdle, a computer-aided AMP design framework is proposed in this study. Statistical analysis was performed to identify various physicochemical properties that characterize AMPs and their respective median values were used as design targets. A genetic algorithm (GA)-based optimization approach was formulated to design AMPs with maximum antimicrobial activity for any given peptide length. The peptide sequences generated in each generation of GA were first screened using a support vector machine-based antimicrobial activity classifier. A fitness function that measures the proximity of physicochemical property values to their respective design targets was then evaluated for all sequences classified as AMPs. Based on fitness scores, a new population of peptide sequences was generated by GA. The sequence with the maximum value of fitness function was finally reported as the optimal AMP. The performance of this framework was accessed using several case studies. Results obtained from this framework corroborated well with the findings reported in the literature. Thus, the proposed optimization-based design framework can be used to generate new AMP sequences. We have also developed an easy-to-use executable version of the proposed framework that can be accessed freely.

In this work, we have investigated the sensing ability of four organic semiconductors namely, H₂TPPCOOH and ZnTPPCOOH porphyrins, H₂Pc and FePc phthalocyanines for the detection of 16 different volatile organic compounds (VOCs) through first-principles density functional theory (DFT) calculations. We have calculated various electronic properties of VOCs and organic molecules such as HOMO–LUMO, dipole moment, and global reactivity descriptors. The reactivity of VOCs mainly depends on the LUMO and the orbital energy gap. Similarly, the prime descriptors that are needed for understanding the organic molecules are softness, electrophilicity, and HOMO values. Most of the VOCs are physisorbed on the organic molecules. Few VOCs like ammonia (−1.42 eV) and acetonitrile (−1.21 eV) are chemisorbed on FePc with strong adsorption energies. H₂Pc has better adsorption to diethylene glycol (−0.24 eV). H₂TPPCOOH and ZnTPPCOOH show good binding affinity towards ammonia (−0.42 and −0.50 eV). Furthermore, the chemiresistive sensing properties of the sensors have revealed that H₂Pc is sensitive and selective towards diethylene glycol, a potential pollutant that causes renal failure. FePc is sensitive towards all 16 VOCs and hence, it can be used as a universal sensor. Also, it can be used as a single-time sensor due to its strong chemisorption towards VOCs. H₂TPPCOOH is highly sensitive to triethylamine and ZnTPPCOOH has high sensitivity to ammonia. Both triethylamine and ammonia cause severe respiratory diseases. Being a powerful tool, the DFT investigations have yielded results that are well-matched with the previously reported experimental works. In summary, we believe that our computational investigations will be useful to build sensor devices composed of highly sensitive and selective porphyrins and phthalocyanines for sensing VOCs from various sources in and around us.

Rubber materials possess remarkable properties, rendering them indispensable in numerous sectors including national defense, military industry, healthcare and automotive tire manufacturing. Consequently, they hold significant importance as engineering materials. This study employs all-atom molecular dynamics simulation to comprehensively investigate the static and dynamic characteristics of pure rubber systems, rubber/SiO₂ nanocomposite systems and crosslinked rubber systems, focusing on natural rubber (NR), butadiene rubber (BR) and styrene–butadiene rubber (SBR) under varying pressure and temperature conditions. Our findings reveal a strongly positive correlation between the glass transition temperature (T_g) and pressure. It was observed that with every 100 atm increase in pressure, T_g experienced a rise of approximately 2–3 K. Moreover, the thermal expansion coefficient (TEC) of rubber systems in the glassy state is lower than that in the rubbery state and experiences reduction as pressure intensifies or with the introduction of SiO₂ nanoparticles and crosslinking. Additionally, the study investigates the P–V–T relationship and bulk modulus of diverse rubber systems, establishing that elevated pressure or reduced temperature leads to an enhancement in the isothermal bulk modulus. Further, as temperature escalates or pressure diminishes, the mean square displacement (MSD) of all the rubber systems displays an upward trend, indicative of augmented molecular chain mobility. However, the incorporation of SiO₂ nanoparticles or the implementation of crosslinking serves to impede the mobility of rubber chains. Evaluations of the mechanical properties of the rubber systems indicate that elevated temperature results in a reduction in the tensile strength. Notably, a comparison of the mechanical properties across different rubber systems demonstrates that NR exhibits the highest tensile strength, while BR exhibits the lowest. In conclusion, this work systematically explores the intricate interplay between the structure, dynamics and mechanics of distinct rubber materials induced by pressure and temperature, providing valuable theoretical guidance for the design and fabrication of rubber materials under extreme conditions.

Stimulus-switchable Pickering emulsions have been widely researched in recent years, and the use of CO₂ as an interesting stimulus has been of special interest. However, CO₂-switchable MOF-based Pickering emulsions have rarely been reported, although they are important in applications in interfacial catalysis, the synthesis of nanoparticles, and crude oil transport. In this study, a new class of amidine-modified ZIF-90 was developed through a post-synthesis functionalization, and then employed to build CO₂-switchable Pickering emulsions. The results showed that the amidine-modified ZIF-90 was capable of emulsifying cyclohexane–water mixtures to fabricate stable emulsions at no less than 0.35 wt% content. Once CO₂ was added at a normal pressure and temperature, the Pickering emulsion was found to undergo a switch from the emulsifying to the demulsifying state. Through combining various spectroscopic methods, it was revealed that the mechanism for this phase switching originated from the reaction of amidine and CO₂ on the ZIF-90, as well as the production of hydrophilic salts. When CO₂ was driven out, the Pickering emulsion was reconstructed via a reverse reaction. By applying the emulsion as a micro-reactor, an efficient and controllable Knoevenagel condensation reaction was obtained, wherein amidine-modified ZIF-90 was employed as the catalyst and controller for the reaction.

Amorphous polymers are considered promising materials for separation applications due to their excellent transport properties and low fabrication costs. The separation performance of a polymer membrane is characterized by its permeability and selectivity. Both permeability and selectivity are controlled by the diffusion of penetrants through the matrix, which is strongly influenced by the distribution and morphology of the free volume elements (FVEs). FVEs are void spaces in the polymer matrix that result from the inefficient packing of bulky and rigid groups on the polymer backbone. Thus, FVEs dictate the efficiency of membrane polymers, and it is imperative to understand how processing conditions such as high pressures and temperatures influence their structure. In this work, we apply uniaxial tensile deformation on three polymers, polystyrene (PS), polymethylpentene (PMP), and HAB-6FDA thermally rearranged polymer (TRP), at varying temperatures and strain rates. We characterize the stress strain behavior, tensile modulus, and free volume element evolution at these conditions. We find that PMP and PS with low and moderate glass transition temperature, respectively, exhibit the most change in mechanical properties as a function of strain rate and temperature. The properties of TRP, however, do not vary as much, which we attribute to the rigidity of the chains. We also find that FVEs shift to broader distributions with deformation, and the extent of this change is in line with the overall change of mechanical properties of the material.

A chitosan/ZIF-8 hydrogel (CGsZx) was fabricated by in situ nucleation and growth of ZIF-8 crystals with a tunable morphology in chitosan hydrogel (CG) networks, and used as an ideal adsorbent for CO₂. The CG has heterogeneous nucleation sites and was then soaked sequentially in a methanolic solution of Zn(NO₃)₂·6H₂O and then a methanolic solution of 2-methylimidazole (2MeIM), and then combined with Zn²⁺ by forming a Zn–N coordination bond, and then the ZIF-8 crystals were formed on the CG. The growth and distribution of the ZIF-8 crystals in the CG network were achieved by regulating the molar ratio of Zn²⁺ to the glucosamine of the CS. In particular, the ZIF-8 crystals with spherical, cubic, tetrahedral, and cuboid shapes on the CGsZx were tuned by adjusting the molar ratio of Zn²⁺ to the glucosamine of CS. In addition, the ZIF-8 crystal with a petaloid morphology on the CG was obtained by using sodium tripolyphosphate (STPP) as a crosslinker. The synergistic effect of heterogeneous nucleation and coordination modulation were the main factors for the change of morphology and size of ZIF-8. The CGsZx exhibited a 441.7% adsorption capacity for CO₂ which was higher than that of CG, and 65.3% higher than that of ZIF-8. After recycling five times, the adsorption capacity of the composite for C₂ remained at 89.6%. The kinetics simulation indicates that the adsorption behaviour of CGsZx for CO₂ was physical adsorption.

The main challenges to Li–S battery use include poor conductivity, the shuttling effect, and slow LiPS transition. In this work, a 3D framework of N-doped graphene interconnected with defect-rich TiO₂ nanotubes acts as a sulfur host. A narrow TiO₂ nanotube reduces lithium-ion diffusion length and facilitates fast charge transport. The unique 3D porous nanostructure holds a wide range of sulfur species and provides optimal pathways for electrolyte penetration. It also counters volume expansion during cycling and serves as a platform for the successful absorption of LiPSs. The TiO₂ nanowire with oxygen vacancy/N-doped graphene aerogel/sulfur (S-OVTNW/NGA) electrode has a small aspect ratio and is attached to graphene layers, which anchors LiPSs through a strong chemical interaction. Oxygen deficiency boosts electrical conductivity, reduces LiPS flow into the electrolyte, improves catalytic performance, and speeds up LiPS transformation. This design provides excellent electrochemical performance. The cathode has a notable primary specific capacity of 1370.2 mAh g⁻¹ at J = 0.2 C, with a sulfur ratio of 80%. Following 100 cycles, the observed capacity of the specimen remains at 879.2 mAh g⁻¹, signifying a retention rate of 66.5%. Its capacity of 635.5 mAh g⁻¹ under 4 C shows its excellent rate performance. The findings may accelerate the development of electrode materials for lithium–sulfur (Li–S) batteries that are more efficient and cost-effective.

The in situ experimental characterization of highly reactive cyclo[18]carbon using STM-AFM at 5 K has opened a new avenue in the field of carbon chemistry. Owing to its instability, C₁₈ is recognized as a precursor for the synthesis of novel carbon-based structures. Inspired by the polyynic structure of C₁₈, herein, bridged bicyclic molecular cages are rationally designed. Based on state-of-the-art electronic structure methods, the structure, stability, and electronic and photophysical properties of the cages are predicted. The results reveal that the polyynic cages are stable structures that enable host–guest interactions. Further, the open-caged architecture is flexible enough to facilitate reversible switching between endohedral and exohedral configurations. These systems can be regarded as optical switches for promising applications in next-generation functional optical devices that can be operated in the visible range. The report elucidates that the sizeable cage acts as a scavenger and shows a propensity to encapsulate Li and Na with an exclusive endohedral stability. The report reveals that the complexes of the cage with alkali metal atoms exist as charge-separated states (CSSs) in their low-lying energy states. Moreover, the work sheds light on the lower electronic energy levels of alkali metal complexes in a CSS compared with non-CSS based on the contribution of interaction energy components. It is worth mentioning that the properties of complexes can be remarkably modulated by varying the nature and size of the guest/cage, thus opening the opportunity for further modification. It is certain that the work will lay a theoretical foundation and receive widespread attention in both theoretical as well as experimental research.

N-Methyl-6-hydroxyquinolinium-based IL dyes are a promising class of dyes with a wide range of potential applications. In this work, the photophysical and photo acidic properties of N-methyl-6-oxyquinolonium-based ionic liquid dyes [6MQc][Y1–6] (Y1–6 = CH₃CO₂⁻, CF₃CO₂⁻, NTf₂⁻, CF₃SO₃⁻, BF₄⁻, and PF₆⁻) were investigated in three solvent media at the TD-PBE0-D3/6-311++G(d,p) level of theory. The impact of solvent and anion on the absorption and emission spectra and the excited-state properties of these dyes were explored. The optimized structures revealed an increase in the O–H⋯X (X = O or F) and a decrease in the C–H⋯X hydrogen bond distances formed between the [6MQc]⁺ cation and anions due to S₀ to S₁ photoexcitation. The pairing of the [6MQc]⁺ cation with [CH₃COO]⁻ and [CF₃COO]⁻ anions leads to the formation of strong Brønsted acids, which exhibit the largest absorption wavelength and Stokes shift in the fluorescence emission (116–145 nm and 168–204 nm) and solvatochromic effect. The studied IL dyes have fluorescence emissions in the range of 430 to 565 nm. Our study contributes to the understanding of the unique properties of IL dyes and provides insights into the design and optimization of N-methyl-6-hydroxyquinolinium-based ionic liquid dyes for a range of applications.

A novel light-responsive poly(arylene ether) copolymer with both azobenzene and perfluorinated biphenylene units as well as meta-linked fragments in the main polymer chain is synthesized. The copolymer is synthesized using aromatic nucleophilic substitution reaction from decafluorobiphenyl and two dihydroxyl-substituted monomers, fluorinated bis-azobenzene-based phenol derivative, and resorcinol. The chemical structure of the copolymer is characterized using ¹H, ¹⁹F NMR, FTIR, Raman and UV/vis spectroscopy techniques. The polymer shows remarkable solubility in organic solvents resulting in the formation of robust, self-supporting films. It displays impressive mechanical characteristics as well as remarkable resistance to thermo-oxidative degradation. Under UV light irradiation, photoisomerization occurs both in solution and in the solid copolymer film. The solid polymer films exhibit intense and stable birefringence changes upon the irradiation, enabling the fabrication of diffraction gratings. The study indicates that this synthetic approach is a simple and effective method for designing light-responsive materials.