Molecular Systems Design & Engineering最新文献

Rational designs of pharmaceutical compounds targeting specific RNAs require a comprehensive understanding of molecular recognition mechanisms. Knowledge of binding affinity and specificity can be gained via computational modeling and simulation techniques. In this work, an integrated computational strategy combining QM calculation, molecular docking, conventional and adaptive steered MD simulations, and the var-MM/GBSA approach was proposed to probe the binding behaviors of daunomycin (DAU) and phenylalanine transfer RNA (tRNA^Phe) at a micro-scale level. Gathering experimental information enables us to eliminate improper predictions for the binding of DAU and tRNA^Phe, and the calculations of PMF and ΔG_binding lead to the identification of the binding structure of the complex. Further, structural and energetic analysis of the DAU:tRNA^Phe complex revealed that daunomycinone of DAU contributes the intermolecular VDW energies to nucleotides G₁₅, C₄₈ and U₅₉ on tRNA^Phe, responsible for the binding specificity; meanwhile daunosamine contributes the intermolecular ELE + EGB energies to U₅₀, responsible for the binding affinity.

This work aimed to combine different experiments and multi-scale theoretical approaches to understand the adsorption process of methylene blue in three-dimensional graphene-based materials. For this, experiments were carried out on the adsorption of methylene blue dye onto three-dimensional graphene containing different amounts of reducing agent and, consequently, different pore sizes and degrees of oxidation. Kinetic studies and equilibrium isotherms were obtained, and kinetic and isothermal models were applied. Furthermore, we employ density functional theory (DFT) simulations to cover quantum details to unveil how methylene blue will interact with GO flakes. In addition, large-scale coarse-grained simulations based on the Martini force field were used to analyze the system at the micrometer scale. Our experimental results showed that the more oxidized the material, the greater the dye removal efficiency, with adsorptive capacities up to 1034.70 mg g^?1. Theoretical studies showed how the dye interacts with the graphene surface and the oxygenated groups and how the grouping of dye molecules is relevant for adsorption, mainly as a function of pore sizes. Also, according to theoretical studies, binding energies, binding distances, and charge transfer between oxidized graphene and MB dye are compatible with physical adsorption, dependent on functional groups on the graphene surface. Thus, the combination of different theoretical approaches allowed an unprecedented understanding of the adsorption process of methylene blue dye in graphene materials with different characteristics obtained during their synthesis.

Functional thin films and interphases are omnipresent in modern technology and often determine the performance and life-time of devices. However, existing coating strategies are incompatible with emerging mesoscaled 3D architected and porous materials, and fail to uniformly apply functional thin films on their large and complex interior 3D surface. In this report, we introduce an approach for obtaining conformal polymeric thin films using custom-designed dual-functional monomers possessing both self-limiting electrodeposition capability and the functionality of interest in separate molecular motifs. We exemplify this approach with the monomer triethylene glycol-diphenol and demonstrate the full coating of a 3D mesoscaled battery electrode with an ultrathin lithium-ion permeable film. Our comprehensive study of the processing–structure–property relationships enables the tailorable control over the conformal thickness (7–80 nm), molecular permeability, and electronic properties. The modularity and tunability of this approach make it a promising candidate for functional polymer film deposition on arbitrary 3D structures.

Molecular dynamics (MD) and quantum mechanics (QM) calculations can be used to characterize novel materials and phenomena that experimental methods cannot capture. While QM provides accurate results, it has high computational costs and is applicable only to small system sizes. On the other hand, MD can work with larger systems and has better computational efficiency but is incapable of studying novel materials/phenomena due to its dependency on experimental data in the literature. Therefore, complex systems such as solid–electrolyte interface (SEI) layer formation cannot be comprehensively investigated by (I) experimental methods due to small time scales, (II) MD simulations because of the absence of experimental data, and (III) QM calculations due to the relatively large system. Herein, we report a suite of new nano-scale algorithms to facilitate studying complex material interphases and molecular systems with the accuracy and precision of QM calculations and at a speed and system size permissible using MD simulations. Our formulation addresses the most challenging aspect of performing an MD simulation, i.e., finding accurate potential (force field) parameters that are often derived from experimental methods. The computational framework presented in this work consists of seven main functions/algorithms that collectively help us account for the effects of nonbonded, bonded, angle, dihedral, and improper interactions in a system/molecule. It is now possible to use these simulations to design and study wholly new and novel materials and investigate phenomena at an atomic/molecular scale under different conditions without the need for prior experimental investigations. We have successfully validated our algorithms with respect to the experimental data of established materials such as H₂O (a polar molecule), LiPF₆ (an ionic compound), C₂H₅OH (ethanol), C₈H₁₈ (a long chain molecule), and ethylene carbonate (EC) (a complex molecular system). The obtained results have an accuracy of over 90%.

A hydrolytically stable luminous metal–organic framework (MOF) sensor was strategically designed for precise dual phase recognition of biologically relevant yet toxic nitric oxide (NO). Judicious utilization of the enabling post-synthetic modification (PSM) technology in chemically robust MOF-808 yielded amine decorated and highly luminescent PABA@MOF-808. The thus-prepared functionalized sensory probe was employed for sensitive detection of NO in both aqueous and gaseous phases in a selective manner. An exclusive fluorogenic “turn-off” response was observed for NO over other relevant reactive nitrogen and oxygen species (RNS and ROS) with high quenching efficiency via deamination reaction as the modus operandi. The potency of PABA@MOF-808 toward accurate detection of NO was further punctuated by a high K_sv value (6.10 × 10³ M^?1) and an exceptional limit of detection (LOD) value of 0.715 μM (21.45 ppb). Additionally, the underlying sensing mechanism was disseminated with the help of experimental data as well as theoretical insights. Pertaining to processability toward practical implementation, a flexible self-standing mixed-matrix membrane (MMM) of PABA@MOF-808 was further devised for efficient sensing of NO in both water medium and vapor phase.

The detailed excited state intramolecular proton transfer (ESIPT) mechanism of coumarin–benzothiazole fluorescent dyes (BT–Cou–R_1–8; R_1–8 = –H, –NH₂, –OH, –OCH₃, –CH₃, –CF₃, –CN, –NO₂) with potential application in drug delivery systems was investigated at the TD-PBE0/6-311++G(d,p) level of theory in the gas phase and three solvent media. The potential energy curves in the ground (S₀) and first excited states (S₁) were constructed to demonstrate the enol → keto ESIPT mechanism. The results revealed that the ESIPT in BT–Cou–R_1–5 is an energy barrier-less process while there is an energy barrier for BT–Cou–R_6–8 having electron-withdrawing substituents. It was found that BT–Cou–R_1–5 exhibited a single keto fluorescence emission while BT–Cou–R_6–8 showed double enol and keto fluorescence emissions with the dominance of keto emission. Both the enol and keto emission wavelengths of BT–Cou–R₈ (R = NO₂) are larger than those of BT–Cou–R_6–7, and in the solvent media, they are close to the near-infrared region with a red shift value of 236–259 nm for the keto form and 326–339 nm for the enol one. However, the intensity of enol emission in BT–Cou–R₈ is lower than the keto one and the S₁(E) state can be considered as a dark state. Because S₁(K) emission possesses an extremely large Stokes shift, thereby this molecule can be an attractive material for chemosensors, fluorescent probes, laser dyes, and optoelectronic devices. The natural bond orbital (NBO) and atoms-in-molecules (AIM) population analyses were carried out to calculate the atomic charges and electron density properties as well as to characterize the nature of the hydrogen bonding interaction along the proton transfer.

Adsorption heat pumps (AHPs) powered by low-grade waste heat or renewable energy can reduce electricity consumption and carbon emission. The exploration of the high-performing adsorbents of AHPs is the key to improving their coefficient of performance (COP) by tuning their adsorption capacity and step location. The structure–property relationship of adsorbents can provide useful guidance for developing and designing potential adsorbents for AHPs. However, given the complexity of the chemical composition and structural diversity of adsorbents, it is extremely challenging to extract the structure–property relationship from high-throughput computational screening based on molecular simulations of existing adsorbents. In this study, ideal nanoporous crystal structures comprising Lennard-Jones (LJ) spheres were generated to simplify this process. The effects of pore size and LJ interaction parameters (σ and ε) on the adsorption performance of the structures, including the saturation uptake (W_s), step location of adsorption isotherms (α) and the uptake change at step location (W_α), were investigated by grand canonical Monte Carlo (GCMC) simulations. It was demonstrated that large σ, ε and cell length or pore size are favorable for W_s and W_α. 0 < α < 0.4 is favorable for W_s and W_α for small-pore structures, and 0.6 < α < 1 is preferential for large-pore structures, which can be attributed to the strong interaction strength of small-pore structures and the relatively weak interaction in large-pore structures. Given the various optimal pore sizes of W_s and W_α, developing an effective strategy to simultaneously improve W_s and W_α by tuning the structural properties of adsorbents is key in the future.

Polymer-metal organic frameworks (polyMOFs) offer a pathway toward processable polymer–MOF hybrid materials; however, because polymeric ligands are incorporated throughout the MOF lattice, polyMOFs have an inherent shortcoming of reduced pore accessability and surface area compared to traditional MOFs. Herein, a strategy for altering the degree of polymer incorporation in polyMOFs by mixing a multivalent polymer ligand containing MOF-forming linkers with “free” linkers is investigated as a means to tune the properties of polyMOFs, resulting in polyMOFs with superior N₂ and CO₂ uptake. The mixed ligand approach is further extended to distinct MOF-forming polymer ligands to create multivariate (MTV)-polyMOFs, which provides a method for incorporating low-dispersity polymer ligands with complex architectures into polyMOF lattices without the addition of small molecule components.

Molds are microorganisms capable of both contaminating different food matrices, leading to their organoleptic deterioration, and causing risks to humans due to the development of mycotoxins. To control this type of contamination process, silver nanoparticles are an effective alternative, particularly if they are applied through hosting in carriers that allow their gradual dosage. In this work, a green functionalization strategy of the metal–organic framework UiO-66 with dispersed cationic silver species was analyzed and optimized, obtaining a nanomaterial with a remarkable performance in fungal control. First, the MOF was obtained under an eco-sustainable protocol and, afterwards, the incorporation of silver with sodium citrate as additive was analyzed. The physicochemical properties of the obtained Ag/UiO-66 solids were analyzed through several characterization techniques such as XRD, FTIR, UV-DRS, TGA-SDTA, SEM-EDS, TEM and XPS. Then, the materials were evaluated in the growth control of the mold P. roqueforti isolated from contaminated food of industrial origin which was taken as a model microorganism. It is shown that Ag/UiO-66 has a strong antifungal action, reducing the growth of the colonies of P. roqueforti by a magnitude of 5?log after 72 h, and positioning it as a promising nanomaterial towards the control of fungal contamination.

π-Conjugated dendrimers, with unique optical properties, have the potential to be used as light-harvesting antenna in organic solar cells and photodetectors. Here, the broadband absorption and light-energy transfer in a phenyl-core thiophene dendrimer, Ph-(7T)₃, have been investigated using quantum calculations and absorption, photoluminescence, and excitation spectroscopy. The broadband absorption of the highly branched Ph-(7T)₃ macromolecule could be attributed to multiple π-conjugations in Ph-(7T)₃ (due to phenylthiophene and thiophene oligomers with different numbers of thiophene units). The divergency of the wavelengths between photoluminescence and excitation light indicated that the multiple π-conjugating system exhibited various modes of excited-state relaxation, which could explain the light-energy transfer from the core to the thiophene dendrons. The fluorescent quantum yield and lifetime of this molecular system are also presented.