Molecular Mechanism and Molecular Design of Lubricating Oil Antioxidants

To overcome the limitations of traditional experimental“trial and error”methods in lubricant additive design,a new molecular design method based on molecular structure parameters is established here.The molecular mechanism of the antioxidant reaction of hindered phenol,diphenylamine,and alkyl sulfide are studied via molecular simulations.Calculation results show that the strong electron-donating ability and high hydrogen-donating activity of the antioxidant molecule and the low hydrogen-abstracting activity of free radicals formed after dehydrogenation are the internal molecular causes of the shielding of phenol and diphenylamine from scavenging peroxy free radicals,and the strong electron-donating ability is the internal molecular cause of the high activity of thioether in decomposing alkyl hydrogen peroxide.Based on this antioxidant molecular mechanism,a molecular design rule of antioxidant is proposed,namely“high EHOMO,large Q(S),low bond dissociation energy BDE(O—H)and BDE(N—H)”.Two new antioxidants,PAS-I and PAS-II,are designed and prepared by chemical bonding of hindered phenol,diphenylamine,and sulfur atoms.Experimental results show that these antioxidants both have excellent antioxidant effects in lubricating oil,and that PAS-II is the superior antioxidant,consistent with theoretical predictions.

Molecular Design and Electronic Structure Investigation of Novel Nitrogen Heteroatom 2-β-Naphthylbenzoxazoles

For the aim of finding new available functional materials, a series of nitrogen heteroatom 2 β naphthylbenzoxazole molecules were designed based on the experiment and theoretical studies of 2 β naphthylbenzoxazole molecule. Geometry optimization of the 2 β naphthylbenzoxazole was carried out by using Hyperchem Molecular Mechanics plus MM+. The planar molecular structure was obtained. The quantum chemistry calculating method PPP SCF CI, which is specially available to treat electron spectrum, was applied to investigate each novel designed molecules. Their electronic structures were analyzed in detail, it shows that total π electron energy decreased linearly with the number of replaced nitrogen. Single nitrogen atom located in benzoxazole ring or naphthalene ring results in contrary changes of level difference of FMO; multiple nitrogen atoms located in different molecular positions will lead to polarization of extremum in the level difference of FMO; and 5 nitrogen heteroatoms reach the culmination. Considering other electronic structure information, some favorable designed molecules were identified.

Binding Mechanism and Molecular Design of Benzimidazole/Benzothiazole Derivatives as Potent Abl T3151 Mutant Inhibitors

Despite the efficacy of imatinib therapy in chronic myelogenous leukemia, the development of drug-resistant Abl mutants, especially the most difficult overcoming T3151 mutant, makes the search for new Abl T3151 inhibitors a very interesting challenge in medicinal chem- istry. In this work, a multistep computational framework combining the three dimensional quantitative structure-activity relationship （3D-QSAR）, molecular docking, molecular dy- namics （MD） simulation and binding free energy calculation, was performed to explore the structural requirements for the Abl T315I activities of benzimidazole/benzothiazole derivatives and the binding mechanism between the inhibitors and Abl T315I. The established 3D-QSAR models exhibited satisfactory internal and external predictability. Docking study elucidated the comformations of compounds and the key amino acid residues at the binding pocket, which were confirmed by MD simulation. The binding free energies correlated well with the experimental activities. The MM-GBSA energy decomposition revealed that the van der Waals interaction was the major driving force for the interaction between the ligands and Abl T3151. The hydrogen bond interactions between the inhibitors and Met318 also played an important role in stablizing the binding of compounds to Abl T315I. Finally, four new compounds with rather high Abl T3151 activities were designed and presented to experimenters for reference.

Molecular design, synthesis strategies and recent advances of hydrogels for wound dressing applications

With the changes in the modern disease spectrum,pressure ulcers,diabetic feet,and vascular-derived diseases caused refractory wounds is increasing rapidly.The development of wound dressings has partly improved the effect of wound management.However,traditional wound dressings can only cover the wound and block bacteria,but are generally powerless to recurrent wound infection and tissue healing.There is an urgent need to develop a new type of wound dressing with comprehensive performance to achieve multiple effects such as protecting the wound site from the external environment,absorbing wound exudate,anti-inflammatory,antibacterial,and accelerating wound healing process.Hydrogel wound dressings have the aforementioned characteristics,and can keep the wound in a moist environment because of the high water content,which is an ideal choice for wound treatment.This review introduces the wound healing process and the development and performance advantages of hydrogel wound dressings.The choice of different preparation materials gives the particularities of different hydrogel wound dressings.It also systematically explains the main physical and chemical crosslinking methods for hydrogel synthesis.Besides,in-depth discussion of four typical hydrogel wound dressings including double network hydrogels,nanocomposite hydrogels,drug-loaded hydrogels and smart hydrogels fully demonstrates the feasibility of developing hydrogels as wound dressing products and their future development trends.

Molecular design,synthesis and biological activities of amidines as new ketol-acid reductoisomerase inhibitors

Diamidine （A） was identified in our in vitro bio-assay as a possible inhibitor of ketol-acid reductoisomerase （KARI） from the ACD database search based on the known three-dimensional crystal structure of KARI. An investigation on interaction of A on KARI active sites, led to the design and synthesis of 15 novel monoamidines. Some of those showed better biological activity than A on rice KARI （in vitro） and in greenhouse herbicidal tests （in vivo）. The structure-biological activity relationship was investigated, which provides valuable information to further study of potential KARI inhibitors.

Molecular Design of Conjugated Small Molecule Nanoparticles for Synergistically Enhanced PTT/PDT

Simultaneous photothermal therapy(PTT)and photodynamic therapy(PDT)is beneficial for enhanced cancer therapy due to the synergistic effect.Conventional materials developed for synergistic PTT/PDT are generally multicomponent agents that need complicated preparation procedures and be activated by multiple laser sources.The emerging monocomponent diketopyrrolopyrrole(DPP)-based conjugated small molecular agents enable dual PTT/PDT under a single laser irradiation,but suffer from low singlet oxygen quantum yield,which severely restricts the therapeutic efficacy.Herein,we report acceptor-oriented molecular design of a donor-acceptor-donor(D-A-D)conjugated small molecule(IID-ThTPA)-based phototheranostic agent,with isoindigo(IID)as selective acceptor and triphenylamine(TPA)as donor.The strong D-A strength and narrow singlet-triplet energy gap endow IID-ThTPA nanoparticles(IID-ThTPA NPs)high mass extinction coefficient(18.2 L g^-1 cm^-1),competitive photothermal conversion efficiency(35.4%),and a dramatically enhanced singlet oxygen quantum yield(84.0%)comparing with previously reported monocomponent PTT/PDT agents.Such a high PTT/PDT performance of IID-ThTPA NPs achieved superior tumor cooperative eradicating capability in vitro and in vivo.

INTERFACIAL MOLECULAR DESIGN OF A RIGID- PARTICLE TOUGHENED POLYAMIDE 6 COMPOSITE

The effects of interfacial modifier on the mechanical properties of kaolin-filled polyamide 6 (PA6) have been studied. The interracial interaction between polyamide 6 and kaolin has been character ized by means of infrared spectroscopy (IR) and scanning electron microscopy (SEM). The results show that the role of the interracial modifier lies in forming an elastic interlayer with good adhesion between kaolin and PA 6. A composite with high impact strength, high tensile strength and high elastic modulus can be obtained by inserting the elastic interfacial modifier into the rigid-particle-filled polymer system.

Molecular design towards two-dimensional electron acceptors for efficient non-fullerene solar cells

Non-fullerene polymer solar cells(NF-PSCs) have gained wide attention recently. Molecular design of non-fullerene electron acceptors effectively promotes the photovoltaic performance of NF-PSCs. However,molecular electron acceptors with 2-dimensional(2 D) configuration and conjugation are seldom reported.Herein, we designed and synthesized a series of novel 2 D electron acceptors for efficient NF-PSCs. With rational optimization on the conjugated moieties in both vertical and horizontal direction, these 2 D electron acceptors showed appealing properties, such as good planarity, full-spectrum absorption, high absorption extinction coefficient, and proper blend morphology with donor polymer. A high PCE of 9.76%was achieved for photovoltaic devices with PBDB-T as the donor and these 2 D electron acceptors. It was also found the charge transfer between the conjugated moieties in two directions of these 2 D molecules contributes to the utilization of absorbed photos, resulting in an exceptional EQE of 87% at 730 nm. This work presents rational design guidelines of 2 D electron acceptors, which showed great promise to achieve high-performance non-fullerene polymer solar cells.

A Property Based Approach for Simultaneous Process and Molecular Design

In this work, property clustering techniques and group contribution methods are combined to enable simultaneous consideration of process performance requirements and molecular property constraints. Using this methodology, the process design problem is solved to identify the property targets corresponding to the desired process performance. A significant advantage of the developed methodology is that for problems that can be satisfactorily described by only three properties, the process and molecular design problems can be simultaneously solved visually on a ternary diagram, irrespective of how many molecular fragments are included in the search space. On the ternary cluster diagram, the target properties are represented as individual points if given as discrete values or as a region if given as intervals. The structure and identity of candidate components is then identified by combining or ＂mixing＂ molecular fragments until the resulting properties match the targets.

Molecular Design and Electronic Structure of Polynuclear Rare Earth Complexes and Clusters

Studies on the electronic structure,molecular design,syntheses of some novel series of tetranuclear rare earth complexes in our laboratory have been reviewed.Spin-unrestricted localized INDO method was used to calculate the electronic structure and the chemical bonding in the typical rare earth cluster Sc[Sc_6Cl_(12)Co]was discussed.

Receptor-based Molecular Designs of DABO Derivatives as HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors

A series of 46 dihydro-alkoxy-benzyl-oxopyrimidines （DABOs）, a class of highly potent non-nucleoside reverse transcriptase inhibitors （NNRTIs）, was studied by molecular docking followed by comparative molecular field analysis （CoMFA） and comparative molecular similarity index analysis （CoMSIA）. The results showed that the H-bonding interactions between the C=O and NH of the pyrimidine ring and Lys101, hydrophobic interactions between R, R1, X sites of ligands and neighboring amino acid residuals, and the electrostatic interactions between ligands and His235 and Lys101 residues were the dominant factors affecting the binding affinities. Based on an optimal docking conformation, 3D-QSAR models of 46 DABO derivatives were developed. The r^2 and cross-validated r^2 （q^2） of an optimal CoMSIA model were 0.862 and 0.532, respectively. Based on the QSAR studies, 9 new compounds were designed by the method of LeapFrog. The binding energies and docking scores （GScore） of 9 new compounds were better than that of a template molecule with the highest observed activity. The results showed that the molecular designs of DABOs should be focused on the hydrophobic interactions with the bottom of the binding pocket as well as van der Waals interactions with the entrance of binding pocket.

Quantum chemical aided molecular design of ionic liquids as green electrolytes for electrodeposition of active metals

Quantum chemical calculation was used to estimate the reduction potentials of 25 organic cations and the oxidation potentials of 11 anions.This information was used to select promising cations and anions for the preparation of ionic liquids as green electrolytes for electrodeposition of active metals.The reasonable linear correlations between the lowest unoccupied molecular orbital(LUMO)energies and the reduction potentials of cations,and the linear relationships between the oxidation potentials and the highest occupied molecular orbital(HOMO)energies of anions were obtained.The orders of electrochemical stability for cations and anions being obtained agree well with the experimental measurements.The suitable ionic liquids with sufficiently wide electrochemical windows for electrodeposition of active metals are suggested to be[Emim]NTf2,[Bmim]NTf2,[Bmim]BF4, [Bmim]PF6,[Bmim]CTf3,[Emim]BF4,[Emim]PF6,[Emim]CTf3..

Computer-aided molecular design and optimization of potent inhibitors disrupting APC-Asef interaction

Colorectal cancer(CRC)is the second leading cause of cancer mortality worldwide.At initial diagnosis,approximately 20%of patients are diagnosed with metastatic CRC(mCRC).Although the APC-Asef interaction is a well-established target for mCRC therapy,the discovery and development of effective and safe drugs for mCRC patients remains an urgent and challenging endeavor.In this study,we identified a novel structural scaffold based on MAI inhibitors,the first-in-class APC-Asef inhibitors we reported previously.ONIOM model-driven optimizations of the N-terminal cap and experimental evaluations of inhibitory activity were performed,and 24-fold greater potency was obtained with the best inhibitor compared to the parental compound.In addition,the cocrystal structure validated that the two-layerπ-πstacking interactions were essential for inhibitor stabilization in the bound state.Furthermore,in vitro and in vivo studies have demonstrated that novel inhibitors suppressed lung metastasis in CRC by disrupting the APC-Asef interaction.These results provide an intrinsic structural basis to further explore drug-like molecules for APC-Asef-mediated CRC therapy.

Molecular design for enhanced spin transport in molecular semiconductors

Molecular semiconductors(MSCs),characterized by a longer spin lifetime than most of other materials due to their weak spin relaxation mechanisms,especially at room temperature,together with their abundant chemical tailorability and flexibility,are regarded as promising candidates for spintronic applications.Molecular spintronics,as an emerging subject that utilizes the unique properties of MSCs to study spin-dependent phenomena and properties,has attracted wide attention.In molecular spintronic devices,MSCs play the role as medium for information transport,process,and storage,in which the efficient spin inject–transport process is the prerequisite.Herein,we focus mainly on summarizing and discussing the recent advances in theoretical principles towards spin transport of MSCs in terms of the injection of spin-polarized carriers through the ferromagnetic metal/MSC interface and the subsequent transport within the MSC layer.Based on the theoretical progress,we cautiously present targeted design strategies of MSCs that contribute to the optimization of spin-transport efficiency and give favorable approaches to exploring accessional possibilities of spintronic materials.Finally,challenges and prospects regarding current spin transport are also presented,aiming to promote the development and application of the rosy and energetic field of molecular spintronics.

Design method of extractant for liquid-liquid extraction based on elements and chemical bonds

In the petrochemical industry process, the relative volatility between the components to be separated is close to one or the azeotrope that systems are difficult to separate. Liquid-liquid extraction is a common and effective separation method, and selecting an extraction agent is the key to extraction technology research. In this paper, a design method of extractants based on elements and chemical bonds was proposed. A knowledge-based molecular design method was adopted to pre-select elements and chemical bond groups. The molecules were automatically synthesized according to specific combination rules to avoid the problem of “combination explosion” of molecules. The target properties of the extractant were set, and the extractant meeting the requirements was selected by predicting the correlation physical properties of the generated molecules. Based on the separation performance of the extractant in liquid-liquid extraction and the relative importance of each index, the fuzzy comprehensive evaluation membership function was established, the analytic hierarchy process determined the mass ratio of each index, and the consistency test results were passed. The results of case study based on quantum chemical analysis demonstrated that effective determination of extractants for the analysis of benzene-cyclohexane systems. The results unanimously prove that the method has important theoretical significance and application value.

Machine-Learning-Assisted Design of Deep Eutectic Solvents Based on Uncovered Hydrogen Bond Patterns

Non-ionic deep eutectic solvents(DESs)are non-ionic designer solvents with various applications in catalysis,extraction,carbon capture,and pharmaceuticals.However,discovering new DES candidates is challenging due to a lack of efficient tools that accurately predict DES formation.The search for DES relies heavily on intuition or trial-and-error processes,leading to low success rates or missed opportunities.Recognizing that hydrogen bonds(HBs)play a central role in DES formation,we aim to identify HB features that distinguish DES from non-DES systems and use them to develop machine learning(ML)models to discover new DES systems.We first analyze the HB properties of 38 known DES and 111 known non-DES systems using their molecular dynamics(MD)simulation trajectories.The analysis reveals that DES systems have two unique features compared to non-DES systems:The DESs have①more imbalance between the numbers of the two intra-component HBs and②more and stronger inter-component HBs.Based on these results,we develop 30 ML models using ten algorithms and three types of HB-based descriptors.The model performance is first benchmarked using the average and minimal receiver operating characteristic(ROC)-area under the curve(AUC)values.We also analyze the importance of individual features in the models,and the results are consistent with the simulation-based statistical analysis.Finally,we validate the models using the experimental data of 34 systems.The extra trees forest model outperforms the other models in the validation,with an ROC-AUC of 0.88.Our work illustrates the importance of HBs in DES formation and shows the potential of ML in discovering new DESs.

Molecular engineering binuclear copper catalysts for selective CO_(2) reduction to C_(2) products

Molecular copper catalysts serve as exemplary models for correlating the structure-reaction-mechanism relationship in the electrochemical CO_(2) reduction(eCO_(2)R),owing to their adaptable environments surrounding the copper metal centres.This investigation,employing density functional theory calculations,focuses on a novel family of binuclear Cu molecular catalysts.The modulation of their coordination configuration through the introduction of organic groups aims to assess their efficacy in converting CO_(2) to C_(2)products.Our findings highlight the crucial role of chemical valence state in shaping the characteristics of binuclear Cu catalysts,consequently influencing the eCO_(2)R behaviour,Notably,the Cu(Ⅱ)Cu(Ⅱ)macrocycle catalyst exhibits enhanced suppression of the hydrogen evolution reaction(HER),facilitating proton trans fer and the eCO_(2)R process.Fu rthermore,we explo re the impact of diverse electro n-withdrawing and electron-donating groups coordinated to the macrocycle(R=-F,-H,and-OCH_3)on the electron distribution in the molecular catalysts.Strategic placement of-OCH_3 groups in the macrocycles leads to a favourable oxidation state of the Cu centres and subsequent C-C coupling to form C_(2) products.This research provides fundamental insights into the design and optimization of binuclear Cu molecular catalysts for the electrochemical conversion of CO_(2) to value-added C_(2) products.

Toward Rational and Modular Molecular Design in Soft Matter Engineering

This essay discusses some preliminary thoughts on the development of a rational and modular approach for molecular design in soft matter engineering and proposes ideas of structural and functional synthons for advanced functional materials. It echoes the Materials Genome Initiative by practicing a tentative retro-functional analysis （RFA） scheme. The importance of hierarchical structures in transferring and amplifying molecular functions into macroscopic properties is recognized and emphasized. According to the role of molecular segments in final materials, there are two types of building blocks： structural synthon and functional synthon. Guided by a specific structure for a desired function, these synthons can be modularly combined in various ways to construct molecular scaffolds. Detailed molecular structures are then deduced, designed and synthesized precisely and modularly. While the assembled structure and property may deviate from the original design, the study may allow further refinement of the molecular design toward the target function, The strategy has been used in the development of soft fullerene materials and other giant molecules. There are a few aspects that are not yet well addressed： （1） function and structure are not fully decoupled and （2） the assembled hierarchical structures are sensitive to secondary interactions and molecular geometries across different length scales. Nevertheless, the RFA approach provides a starting point and an alternative thinking pathway by provoking creativity with considerations from both chemistry and physics. This is particularly useful for engineering soft matters with supramolecular lattice formation, as in giant molecules, where the synthons are relatively independent of each other.

CoMFA Model of Anti-tumor Activity for Fluoroquinolon-3-yl s-Triazole Sulfide-ketone Derivatives and Implications for Molecular Design

Comparative molecular field analysis(CoMFA)techniques were used to perform three-dimensional quantitative structure-activity relationship(3D-QSAR)studies on the anti-tumor activity(pIH and pIC)of 28 fluoroquinolon-3-yl s-triazole sulfide-ketone derivatives(FQTSDs)against two cancer cell lines,including human hepatoma Hep-3B cells and human pancreatic cancer Capan-1 cells.23 compounds were randomly selected as the training set to establish the prediction models,which were verified by the test set of 6 compounds containing template molecule.The obtained cross-validation(Rcv2)and non-cross-validation correlation coefficients(R2)of the CoMFA models were 0.477 and 0.850 for pIH,and 0.421 and 0.836 for pIC,respectively.The contributions of steric and electrostatic fields to pIH were determined to be 48.1%and 51.9%,and those to pIC were 49.4%and 50.6%,respectively.The CoMFA models were then used to predict the activities of the compounds in the training and testing sets,and the models had a strong stability and good predictability.Based on the 3D contour maps,four novel FQTSDs with a higher anti-tumor activity were designed.However,the effectiveness of these novel FQTSDs is still needed to be verified by experimental results.

QSAR Study and Molecular Design of Isoquinolone Derivative JNK1 Inhibitors

JNK1 is a drug target for the treatment of type 2 diabetes,and it plays a key mediator role in metabolic disorders.In this paper,holographic quantitative structure-activity relationship(HQSAR)technology and Topomer comparative molecular field analysis(Topomer CoMFA)technology are used to analyze the quantitative structure-activity relationship(QSAR)of 39 isoquinolone derivatives.The cross validation correlation coefficient(q^(2))is 0.696(Topomer CoMFA)and 0.826(HQSAR),and the non-cross validation correlation coefficient(r^(2))is 0.935(Topomer CoMFA)and 0.987(HQSAR).The results showed that the models have good stability and predictive ability.The Topomer search module was applied to define high contribution fragments in the ZINC database,designing 20 new isoquinolone compounds with theoretically high inhibitory activity.The molecular docking was carried out to explore the interaction between the ligand and target JNK1 protein.This study can provide a theoretical basis for the design of new JNK1 inhibitors.