H-bond Formation Research Articles

Generation of 3-aminopropanamide and its cluster formation with nucleation precursors- a theoretical exploration

Aminoamides are formed in the atmospheric environments by the auto-oxidation of the parent diamines. In this work, the oxidation chemistry of diamine (1,3-Diaminopropane, Dap) to the amino amide (3- aminopropanamide, 3-APA) and its new particle formation potential with small atmospheric molecules such as NH3 (A), H2O (W) and H2SO4 (SA) are theoretically investigated using the M062X/6–311++G** theory. The bimolecular rate coefficient of the ·OH initiated H-atom abstraction is computed to be 1.01 × 10−11 cm3 molecule−1 s−1. Further reaction of the peroxy radical intermediate indicates that the pathway involving γ H- shift of the initially formed radical intermediates to be more favourable on kinetic grounds with the effective bimolecular rate coefficient of 3.87 × 10−14 cm3 molecule−1s−1. The thermodynamic barrier associated with the H-shifts involved in this pathway is in the range of 13–20 kcal/mol. The cluster formation of APA with SA is more favourable than the clusters with W and A, wherein the free energy of formation of (APA)(SA) and (APA)(SA)2 are −11.3 and −22.6 kcal/mol, respectively. However, the feasibility of cluster formation with W and A increases with the altitude and becomes spontaneous in the case of water at an altitude of 12 km. The present work indicates that aminoamides like 3-APA can participate in the initial stages of new particle formation events by forming clusters with SA molecules. The scattering parameters and topological analysis of different (Amide)(SA) clusters indicate more scattering properties for the (APA)(SA) cluster, which has an adverse effect on the atmosphere. Furthermore, topological analysis indicates that H-bond formation is more prominent in the (APA)(SA) cluster.

Tannic acid self-aggregation and adsorption onto a polyethersulfone membrane: An all-atom molecular dynamics study

Atomic scale modeling is crucial for characterizing the interactions responsible for fouling, which is a major limitation in the use of membrane filtration technologies for the recovery of polyphenols. In this work, a methodology to model a porous ultrafiltration polyethersulfone (PES) membrane is presented. Subsequently, various systems containing tannic acid (TA) molecules at different concentrations (9 or 30 g/L) were studied, with two additional systems incorporating a PES membrane, through 100 ns all-atom molecular dynamics simulations. The results show that up to 90% of the TAs are self-aggregated, associated with the formation of intermolecular H-bond and π-stacking interactions. Furthermore, adsorption of 48–67% of the TAs onto PES was observed. TA-PES H-bond and π-stacking interactions are also formed. The number of adsorbed TAs molecules over time and the evolution of the mean size of TA aggregates exhibits similar temporal trends, suggesting a parallel progression in both phenomena. Moreover, the same atoms were involved in both aggregation and adsorption, leading to the conclusion that the two phenomena compete. These results shed light on the fouling mechanism, which appears to occur through the formation of a cake layer combined with adsorptive fouling, and could support the design of new antifouling agents adapted for polyphenol filtration.

MD-DFT Calculations on Dissociative Absorption Configurations of FOX-7 on (001)- and (101)-Oriented Crystalline Parylene Protective Membranes.

Crystalline poly-para-xylylene (parylene) has the potential for use as a protective membrane to delay the nucleation of explosives by separating the explosives and their decomposition products to decrease the explosive sensitivity. Here, molecular dynamics (MD) and density functional theory (DFT) techniques were used to calculate the dissociative adsorption configurations of 1,1-diamino-2,2-dinitroethylene (FOX-7) on (001)- and (101)-oriented crystalline parylene membranes. Based on the results of the calculations, this work demonstrates that the -NO2-π electrostatic interactions are the dominant passivation mechanism of FOX-7 on these oriented surfaces. FOX-7 can dissociatively adsorb on oriented parylene membranes due to the interactions between the LUMO of the toluene (or methyl) groups on parylene and the HOMO of the -NO2 (or -NH2) groups on FOX-7. The formation of a new intermolecular H-bond with the ONO group leads to FOX-7 decomposition via intramolecular C-NO2 bond fission and nitro-to-nitrite rearrangement. The most likely adsorption configurations are described in terms of the decomposition products, surface active groups of parylene, binding behaviors, and N charge transfer. Importantly, the (001)-oriented parylene AF8 membrane is promising for use as a protective membrane to passivate the high-energy -NO2 bonds during the dissociative adsorption of FOX-7. This study offers a new perspective on the development of protective membranes for explosives.

A computational study of H-bonded networks in cyclic water clusters, (H2O)n (n = 3-12).

We have performed a detailed MM and DFT investigation of neutral water clusters (H2O)n (n = 3-12). Our results show the trend of interaction energies in these clusters as a function of the size of the cluster. They show that the H-bond strength increases with cluster size and that the model of water is better described if two different partial charges are used on the hydrogen, depending on whether hydrogen is H-bonded or not. The average binding enthalpy change due to the formation of H-bonds between water molecules is found to be - 25.9kJmol-1 at B3LYP/aug-cc-pVDZ level of theory. We observe the formation of cyclic H-bonded networks through the analysis of frontier orbitals and IR vibrational frequencies spectra. For the water cluster with n = 11, we observe an unusual reduction of the bandgap indicative of a cyclic H-bonded network. Calculations were performed with the MMFF94 force field and the B3LYP method using various large basis sets. Molecular orbital diagrams and population analysis were done using standard tools in Gaussian.

Enhanced Electrochemical Hydrogenation of Benzaldehyde to Benzyl Alcohol on Pd@Ni-MOF by Modifying the Adsorption Configuration.

Electrocatalytic hydrogenation (ECH) approaches under ambient temperature and pressure offer significant potential advantages over thermal hydrogenation processes but require highly active and efficient hydrogenation electrocatalysts. The performance of such hydrogenation electrocatalysts strongly depends not only on the active phase but also on the architecture and surface chemistry of the support material. Herein, Pd nanoparticles supported on a nickel metal-organic framework (MOF), Ni-MOF-74, are prepared, and their activity toward the ECH of benzaldehyde (BZH) in a 3 M acetate (pH 5.2) aqueous electrolyte is explored. An outstanding ECH rate up to 283 μmol cm-2 h-1 with a Faradaic efficiency (FE) of 76% is reached. Besides, higher FEs of up to 96% are achieved using a step-function voltage. Materials Studio and density functional theory calculations show these outstanding performances to be associated with the Ni-MOF support that promotes H-bond formation, facilitates water desorption, and induces favorable tilted BZH adsorption on the surface of the Pd nanoparticles. In this configuration, BZH is bonded to the Pd surface by the carbonyl group rather than through the aromatic ring, thus reducing the energy barriers of the elemental reaction steps and increasing the overall reaction efficiency.

Negative cooperativity in the formation of H-bond networks involving primary anilines.

Networks of H-bonds can show non-additive behaviour, where the strength of one interaction perturbs another. The magnitude of such cooperative effects can be quantified by measuring the effect of the presence of an intramolecular H-bond at one site on a molecule on the association constant for formation of an intermolecular H-bond at another site. This approach has been used to quantify the cooperativity associated with the interaction of a primary amine with two H-bond acceptors. A series of compounds that have an intramolecular H-bond between an aniline NH2 group and a pyridine nitrogen were prepared, using polarising substituents on the pyridine ring to vary the strength of the intramolecular H-bond. The presence of the intramolecular interaction was confirmed by X-ray crystallography in the solid state and NMR spectroscopy in n-octane solution. UV-vis absorption titrations were used to measure the association constants for formation of an intermolecular H-bond with tri-n-butyl phosphine oxide in n-octane. Electron-donating substituents on the pyridine ring, which increase the strength of the intramolecular H-bond, were found to decrease the strength of the intermolecular H-bond between the aniline and the phosphine oxide. The results were used to determine the H-bond donor parameters for the anilines, α, and there is a linear relationship between the values of α and the H-bond acceptor parameter of the pyridine group involved in the intramolecular H-bond, β. The slope of this relationship was used to determine the cooperativity parameter (κ = -0.10), which quantifies the negative allosteric cooperativity between the two H-bonding interactions. Calculated molecular electrostatic potential surfaces of the anilines quantitatively reproduce the experimental result, which suggests that effects are electrostatic in origin, either due to polarisation of the NH bonds or due to secondary electrostatic interactions between the two H-bond acceptors.

AVPI analogs and conjugates: Molecular docking studies and in vitro biological evaluation

In recent years, small peptide and non-peptide AVPI-/Smac-mimetics have been developed as IAP antagonists and are in clinical trials to overcome resistance to apoptosis in various cancer types. In this study, we present molecular modeling studies and in vitro biological evaluation of a set of AVPI-mimetics, including parent AVPI, tetrapeptide AVPI-mimetics and AVPI-conjugates.Combined molecular modeling studies and HYDE analyses provided valuable information regarding the protein–ligand interactions within the binding site of cIAP1-BIR3 and XIAP-BIR3 domains, showing that the binding part of both domains (cIAP1- and XIAP-BIR3) are formed from 22 amino acid residues, and their active part of 11 AAs. Moreover, 5 amino acids are defined common for both targets, namely Lys299, Gly306, Leu307, Trp310, and Trp323. Based on the observed docking models, six amino acid residues for cIAP1-BIR3 and five amino acids for XIAP-BIR3 are recognized actively involved in the formation of H-bonds with the respective ligand. The amino acid sequence 308 (Arg308 in cIAP1-BIR3, Thr308 in XIAP-BIR3), simultaneously forming two H-hydrogen bonds, seems to plays a key role in improvement of binding affinity.Apart from docking results the synthesized set of AVPI-mimetics was tested in vitro using cell biology (MTT assay) and parallel artificial membrane permeability assay (PAMPA). The results showed that the double modification of AVPI via substitution of Pro3 with Hyp3, as well as elongation of AVPI’s C-terminus by its conjugation with RGD-analogs, significantly increase the antiproliferative effects of AVPI-conjugates on all tested cancer cell lines (MDA-MB-231, MCF-7, HepG2 and HT-29 cells) compared to the parent AVPI peptide. SARs analysis defined this modification beneficial for the overall biological activity of the AVPI-mimetics and pointed out AVHypI-AgbGD as the most active conjugate with an IC50 of 348 µM for MDA-MB-231, 457 µM for MCF-7, 399 µM for HepG2, and 578 µM for HT-29 cells. Though the calculated IC50 values were still high, we consider AVHypI-AgbGD peptide as a good basis for further modifications. In addition, PAMPA results showed that substitution of Pro with Hyp improved the BBB permeability of AVHypI peptide compared to its parent molecule.

Salicylhydroxamic acid containing structural adhesive.

The feasibility of utilizing salicylhydroxamic acid (SHAM) as a new adhesive molecule for designing structural adhesives is investigated in this study. SHAM-containing polymers were prepared with a hydroxyethyl methacrylate (HEMA) or methoxyethyl acrylate (MEA) backbone and mixed with polyvinylidene fluoride (PVDF). PVDF was included to increase the cohesive property of the adhesive through hydrogen bond (H-bond) formation with the adhesive polymers. SHAM-containing adhesive demonstrated lap shear adhesion strength (S adh) greater than 0.9 MPa to glass, metal, and polymeric surfaces. Adhesive formulations with elevated SHAM-content also demonstrated increased adhesive properties with S adh values reaching as high as 4.8 MPa. Due to the physically crosslinked nature of these adhesives, formulations with extensive H-bonding resulted in strong adhesion and stability. HEMA consists of a terminal hydroxyl group with both H-bond donor and acceptor, which enabled HEMA-containing adhesives to demonstrate strong adhesion even without PVDF. On the other hand, MEA contains a methoxy group that lacks H-bond donors for forming H-bonding and MEA-containing adhesives required PVDF to provide H-bond acceptors to increase its cohesive property. An aging study was performed on the bonded joints. While the adhesive joints did not demonstrate any reduction in S adh values over 25 days when incubated in a dry condition, S adh values decreased by 80% over 48 h when incubated in water. This is potentially due to the hydrophilic and physically crosslinked nature of the adhesive. Nevertheless, the SHAM-containing adhesive outperformed a catechol-containing adhesive and epoxy glue and is a promising new adhesive molecule for designing structural adhesives.

Chitosan dual gel-like functionalized with flavonoid extract and cinnamaldehyde oil using dual cross-linking agents: Characterization, antioxidant, and antimicrobial effects

This study evaluated antioxidant and antimicrobial properties of chitosan gel (Cs-gel) functionalized with cinnamaldehyde oil (CN) and orange peel-derived flavonoid extract (Fs) using the ionic-gelation method. Results showed that the encapsulation efficiencies of CCF-9 and CCN were 83.14 ± 3.34 and 80.56 ± 1.17%, respectively. The interaction of CN or Fs on Cs-gel indicates the presence of H-bonding formation, as observed by UV–vis spectroscopy, Fourier transform infrared spectrophotometry (FTIR), and Raman-spectroscopy showed a good corroboration with Surflex-dock findings. Scanning electron microscopy also showed the integration that occurred between Cs and both ligands, which was further supported with X-ray diffraction and X-Ray photoelectron spectroscopy spectra. The textural properties of CCF-5 gel showed high hardness, chewiness, and gumminess values, indicating that the integration of Fs and CN altered the microstructure of Cs-gel. Chotison-functionalized based gels exhibited higher antioxidant abilities against DPPH and ABTS free radicals than Cs-gel. The CCF-9 gel showed a good inhibition value of 29.91 ± 1.22 and 93.61 ± 2.12% against Penicillium expansum and Alternaria westerdijkiae, respectively. Additionally, CCF-9 inhibition zones against Staphylococcus aureus, Escherichia coli, and Bacillus cerues were 28.65 ± 0.05, 27.69 ± 0.04, and 26.16 ± 0.02 mm, respectively. These findings demonstrated the potential antioxidant and antimicrobial effects of functionalized chitosan gel indicating its potential as a bioactive additive for food preservation.

STUDYING THE MODIFICATION OF NANOSTRUCTURED POLYURETHANE ELASTOMER/POLYVINYL CHLORIDE BLEND BY LOW-MOLECULAR PLASTICIZERS

The effect of chemical structure of low molecular weight plasticizers (LMWP) on intermolecular interactions and mechanical properties of nanostructured polyurethane elastomer (PU)/polyvinyl chloride (PVC) was investigated. Polymer composite films were prepared by solution casting technique using dimethylformamide (DMF) or by rolling the melt. FTIR data showed a maximum level of intermolecular hydrogen bond degradation for PU or the polymer blend modified with trichloroethyl phosphate (TCEP) due to the formation of H-bonds between NH of rigid urethane/urea fragments of PU elastomer and chlorine of TCEP. The low compatibility of di-(2-ethylhexyl)-о-phthalate (DOP), compared with di-n-butyl-о-phthalate (DBP), and PU elastomer provided a minor effect of plasticizer on intramolecular and interfaсial interactions in PU or polymer blend. The resulting composites are characterized by increased tensile strength in the whole composition range. The results of DSC analysis of melt-rolled blends of PU/PVC modified by DOP had one wide glass relaxation transition range and their thermal and mechanical properties could be controlled by changing the ratio of initial components. The aforementioned results provide new possibilities of manufacturing the novel nanostructured thermoplastic elastomers with improved mechanical properties.

In the presence of the other: How glyphosate and peptide molecules alter the dynamics of sorption on goethite

The interactions with soil mineral surfaces are among the factors that determine the mobility and bioavailability of organic contaminants and of nutrients present in dissolved organic matter (DOM) in soil and aquatic environments. While most studies focus on high molar mass organic matter fractions (e.g., humic and fulvic acids), very few studies investigate the impact of DOM constituents in competitive sorption. Here we assess the sorption behavior of a heavily used herbicide (i.e., glyphosate) and a component of DOM (i.e., a peptide) at the water/goethite interface, inclusive of potential glyphosate-peptide interactions. We used in-situ ATR-FTIR (attenuated total reflectance Fourier-transform infrared) spectroscopy to study sorption kinetics and mechanisms of interaction as well as conformational changes to the secondary structure of the peptide. NMR (nuclear magnetic resonance) spectroscopy was used to assess the level of interaction between glyphosate and the peptide and changes to the peptide' secondary structure in solution. For the first time, we illustrate competition for sorption sites results in co-sorption of glyphosate and peptide molecules that affects the extent, kinetics, and mechanism of interaction of each with the surface. In the presence of the peptide, the formation of outer-sphere glyphosate-goethite complexes is favored albeit inner-sphere glyphosate-goethite bonds (i.e., POFe) are still formed. The presence of glyphosate induces secondary structural shifts of the sorbed peptide that maximizes the formation of H-bonds with the goethite surface. However, glyphosate and the peptide do not seem to interact with one another in solution nor at the goethite surface upon sorption. The results of this work highlight potential consequences of competition for sorption sites, for example the transport of organic contaminants and nutrient-rich (i.e., nitrogen) DOM components in relevant environmental systems. Predicting the rate and extent with which organic pollutants are removed from solution by a given solid is also one of the most critical factors for the design of effective sorption systems in engineering applications.

The Construction of Binary Phase Electrolyte Interface for Highly Stable Zinc Anodes.

Metal zinc is a promising anode candidate of aqueous zinc-ion batteries due to high theoretical capacity, low cost, and high safety. However, it often suffers from hydrogen evolution reaction (HER), dendrite growth, and formation of by-products. Herein, a triethyl phosphate (TEP)/H2 O binary phase electrolyte (BPE) interface is developed by introducing TEP-based electrolyte-wetted hydrophobic polypropylene (PP) separator onto the Zn anode surface. The equilibrium of the BPE interface depends on the comparable surface tensions of H2 O-based and TEP-based electrolytes on hydrophobic PP separator surfaces. The BPE interface induces Zn2+ solvation structure conversion from [Zn(H2 O)x ]2+ to [Zn(TEP)n (H2 O)y ]2+ , where most solvated H2 O molecules are removed. In [Zn(TEP)n (H2 O)y ]2+ , the residual H2 O molecules can be further constrained by the formation of H bonds between TEP and H2 O molecules. Consequently, the ionization of solvated H2 O molecules is effectively suppressed, and HER and by-products are effectively restricted on Zn anode surfaces in BPE. As a result, Zn anodes exhibit a high Coulombic efficiency of 99.12% and superior cycling performance of 6000h, which is much higher than the case in single-phase aqueous electrolytes. To illustrate the feasibility of BPE in full cells, the Zn/Alx V2 O5 batteries are assembled based on the BPE and exhibited enhanced cycling performance.

Interplay of two low-barrier hydrogen bonds in long-distance proton-coupled electron transfer for water oxidation.

D1-Tyr161 (TyrZ) forms a low-barrier H-bond with D1-His190 and functions as a redox-active group in photosystem II. When oxidized to the radical form (TyrZ-O•), it accepts an electron from the oxygen-evolving Mn4CaO5 cluster, facilitating an increase in the oxidation state (Sn; n = 0-3). In this study, we investigated the mechanism of how TyrZ-O• drives proton-coupled electron transfer during the S2 to S3 transition using a quantum mechanical/molecular mechanical approach. In response to TyrZ-O• formation and subsequent loss of the low-barrier H-bond, the ligand water molecule at the Ca2+ site (W4) reorients away from TyrZ and donates an H-bond to D1-Glu189 at Mn4 of Mn4CaO5 together with an adjacent water molecule. The H-bond donation to the Mn4CaO5 cluster triggers the release of the proton from the lowest pKa site (W1 at Mn4) along the W1…D1-Asp61 low-barrier H-bond, leading to protonation of D1-Asp61. The interplay of the two low-barrier H-bonds, involving the Ca2+ interface and forming the extended Grotthuss-like network [TyrZ…D1-His190]-[Mn4CaO5]-[W1…D1-Asp61], rather than the direct electrostatic interaction, is likely a basis of the apparent long-distance interaction (11.4 Å) between TyrZ-O• formation and D1-Asp61 protonation.

Removal of Malachite Green by Poly(acrylamide-co-acrylic acid) Hydrogels: Analysis of Coulombic and Hydrogen Bond Donor-Acceptor Interactions.

Water pollution caused by dyes poses a significant threat to life on earth. Poly(acrylamide-co-acrylic acid) hydrogels are widely used to treat wastewater from various pollutants. This study aims to examine the removal of malachite green (MG), a harmful and persistent dye that could cause extensive environmental damage, from an aqueous solution by adjusting the initial concentration of acrylamide (AM) and the degree of copolymer crosslinking. The copolymer hydrogels efficiently eliminate MG in a brief timeframe. The most successful hydrogel accomplished a removal rate exceeding 96%. The copolymer of 4 wt % 1,6-hexanediol diacrylate and a concentration of 100 mg/mL AM was effective. The degree of swelling was affected by crosslinking density as expected, with low crosslinking ratios resulting in significant swelling and high ratios resulting in less swelling. To evaluate the results, a docking approach was used which presented three crosslinked models: low, medium, and high. The copolymer-dye hydrogel system displayed robust hydrogen bonding interactions, as confirmed by the high quantities of both donors and acceptors. It was determined that MG contains six rotatable bonds, enabling it to adapt and interact with the copolymer chains. The dye and copolymer enhance H-bond formation by providing two hydrogen bond donors and 16 hydrogen bond acceptors, respectively. Through capitalizing on cationic and anionic effects, the ionic MG/copolymer hydrogel system improves retention efficiency by enhancing attraction between opposing charges. It is interesting to note that the synthesized copolymer is able to remove 96.4% of MG from aqueous media within one hour of contact time.

Modelling of novel bornoel analogs as Influenza A Virus inhibitors through genetic function approximation, comparative molecular fields, molecular docking, and ADMET/Pharmacokinetic studies

Influenza A Virus (IAV) is a human respiratory pathogen prone to mutations and genome re-assortment leading to global pandemics. In this study, we applied the molecular modelling strategies such as, two-dimensional (2D), three-dimensional (3D)-quantitative structure–activity relationship (QSAR), and molecular docking simulation on a novel series of borneol compounds as influenza inhibitors. The best developed 2D-QSAR models, MLR (Q2 ​= ​0.8735, R2(train) ​= ​0.9096) and ANN [3-2-1] (Q2 ​= ​0.8987, R2(train) ​= ​0.9171) revealed good and acceptable statistical validation metrics for the inhibitory activity predictions. The 3D-QSAR models were generated using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA), which showed CoMFA_S ​+ ​E (Q2 ​= ​0.559, R2(train) ​= ​0.939) and CoMSIA_S ​+ ​E (Q2 ​= ​0.577, R2(train) ​= ​0.941) as the best-observed models in accordance with the model acceptability standards. In addition, the contour maps generated from the CoMFA and CoMSIA models illustrates the steric and electrostatic molecular field relationships with the inhibitory effects of the studied molecules. Moreover, the binding modes of the active ligands were studied through molecular docking simulation with the Human Hemagglutinin (HA) receptor of influenza A virus (A/Puerto Rico/8/34(H1N1)). The studied compounds revealed the formation of H-bonds, CH-bonds, and hydrophobic interactions with the active amino acid residues such as Asn 543, Asn 614, Asn 617, Leu 618, Ser 540, Lys 539, and Lys 621 in the HA binding cavity. The prediction of drug-likeness and ADMET properties of the compounds revealed their good bioavailability and pharmacokinetic profiling. This study may provide a valuable in-silico guideline for discovering novel potent influenza inhibitors.

Promotional mechanism of nitrogen-doping in activated carbon for formaldehyde removal: Enhanced attractive noncovalent interactions coupled with Cannizzaro-type disproportionation reaction

Inserting nitrogen (N) heteroatoms into the carbonaceous adsorbents has been confirmed to be one of efficient strategies for enhancing HCHO removal. However, the essential promotion mechanisms of specific N-containing groups (such as pyridinic-N, pyrrolic-N, and quaternary-N) remain blurred. Herein, a series of N-doped activated carbons were prepared by annealing the melamine impregnated activated carbons at 600–900 °C and used for HCHO elimination. It manifested that the HCHO elimination performance of samples was remarkably improved after N-doping and their HCHO adsorption capacities were in the order of ACN-600 (16.37 mg/g) > ACN-750 (9.87 mg/g) > ACN-900 (7.28 mg/g) > AC (5.09 mg/g). DFT calculation results revealed that there existed stronger attractive noncovalent interactions between pyrrolic-N doped carbon and HCHO due to the formation of stronger H-bonds. Therefore, the HCHO physisorption energy on pyrrolic-N doped carbon was the highest (−32.83 kJ/mol). Compared with the single physisorption mechanism of previous studies, the in-situ DRIFTS results manifested that the pyridinic-N atom (as a typical strong Lewis base) could trigger the Cannizzaro-type disproportionation reaction, which would transform toxic HCHO into relatively less toxic methanol and formic acid. Benefiting from the dual enhanced mechanisms of attractive noncovalent interactions and Cannizzaro-type disproportionation reaction, the ACN-600 manifested excellent HCHO removal performance. This study not only intrinsically discloses the promotion mechanism of specific N-containing groups on HCHO removal at molecular level but also provides guidelines for rational design and development of carbonaceous materials for effective HCHO elimination.

Understanding silica aerogel-carbon nanotube composite structures by molecular simulation

Silica aerogel-carbon nanotube composites are remarkable materials but with engineering principles poorly understood, particularly with regards to the structure of the silica aerogel at the interface with the carbon nanotubes (CNTs), and the physical phenomena behind it. This work provides valuable insights on this topic through classical molecular dynamics simulations. The effects on aggregation and adsorption on nanotubes caused by different types of silica primary particles, oxidation degree of the CNTs and solvent composition were explored. Silica monomers interact appreciably only with oxidized nanotubes via H-bonds with O-containing groups, whereas condensed primary particles adsorb almost completely to the surface due to siloxane-aromatic C van der Waals interactions. The adsorbed layer is highly structured owing to the preferential orientation of siloxane bonds tangentially to the CNT surface and formation of intralayer H-bonds.

Manipulating Cis-Trans Copolymer Chain Conformation to Simultaneously Improve Permittivity and DC Breakdown Strength in Polythiourea.

Polythioureas (PTUs) show great potentials for applications in the new generation of film capacitors due to their excellent dielectric properties. Herein, the cis-trans copolymer chain of PTU is successfully tailored by employing cis and trans cyclohexyl spacers. The relationship between the copolymer chain conformation, microstructure, and dielectric properties is carefully explored by a series of analysis. Compared with cis conformation, the trans with less steric hindrance can promote the formation of H-bonds. The enhanced H-bonding interactions not only reduce the molecular inter-chain spacing, but also drive the self-assembly of molecular chains to form cylindrical and droplet nano-morphologies. The phase separation between cis and trans PTUs is confirmed by combining the experimental results of TEM and DSC, and the CT64-PTU with the most two-phase interface thus obtains the highest permittivity of 5.5 (@10Hz). The reduced molecular inter-chain spacing is accompanied by a decreased hopping distance of charges, which improves breakdown strength by 17% from 498 MV/m to 580 MV/m. Therefore, the cis-trans copolymer chain conformation in PTU provides a simultaneous high permittivity and breakdown strength. This research offers a strategy to further design high-performance dielectrics via regulation of copolymer chain conformation.

Effect of various aryl substitutions on the interfacial interaction energy of graphene/conductive polymer nanocomposites

Studying intermolecular interactions in polymer nanocomposites is highly effective in achieving high-efficiency nanocomposites. To investigate the polymer nanocomposites including conductive polymers, namely poly (3-phenylhydrazone thiophene) (PPHT), poly (3-(4-n-octyl)-phenylthiophene) (POPT), and functionalized graphene nanosheet (FGN), reactive molecular dynamics (RMD) simulation were employed. The FGN structures were a result of the arylation of graphene nanosheets containing different substitutions including sulfide, amine, di-amine, and thiol functional groups. According to interaction energies at polymers / arylated graphene nanosheet, the most interaction energies resulted in nanocomposites of PPHT/graphene-thiophenyl amine (G-PATP) and POPT/graphene-p-Phenylenediamine (G-PPD). Due to the polarity of PPHT, the formation of hydrogen bonding (H-bonding) was expected at specific sites, which were confirmed based on H-bonding interaction criteria. In reality, the criteria required for detecting H-bonding through RDF and the relevant angle measurement have been established. On the other hand, due to the acidic-sensitive hydrazone bond in PPHT, it was expected that the increasing trend in interaction energy of nanocomposites of PPHT could be solely justified based on the acidity of the functional groups employed. However, based on the obtained results, other factors such as the topological polar surface area (TPSA) and the formation of unconventional H-bonding, in addition to the acidity of functional groups, have been considered as influential factors in the changing of interaction energy. Also, the dynamic behavior of polymers was examined by plotting the radius of the gyration (Rg) parameter via time and functional groups. Finally, the temperature effect on interaction energy was determined, too.

“From shadows to shores”-quantitative analysis of CuO nanoparticle-induced apoptosis and DNA damage in fish erythrocytes: A multimodal approach combining experimental, image-based quantification, docking and molecular dynamics

The usage of copper (II) oxide nanoparticles (CuO NPs) has significantly expanded across industries and biomedical fields. However, the potential toxic effects on non-target organisms and humans lack comprehensive understanding due to limited research on molecular mechanisms. With this study, by combining the 96 h in vivo exposure of crucian carp fish, Carassius carassius, to sub-lethal CuO NPs doses (0.5 and 1 mg/dL) with image-based quantification, and docking and molecular dynamics approaches, we aimed to understand the mechanism of CuO NPs-induced cyto-genotoxicity in the fish erythrocytes. The results revealed that both doses of copper NPs used were toxic to erythrocytes causing oxidative stress response and serious red blood cell morphological abnormalities, and genotoxicity. Docking and 10-ns molecular dynamics confirmed favorable interactions (ΔG = −2.07 kcal mol−1) and structural stability of Band3-CuO NP complex, mainly through formation of H-bonds, implying the potential of CuO NPs to induce mitotic nuclear abnormalities in C. carassius erythrocytes via Band3 inhibition. Moreover, conventional and multiple ligand simultaneous docking with DNA revealed that single, double and triple CuO NPs bind preferentially to AT-rich regions consistently in the minor grooves of DNA. Of note, the DNA-binding strength subtantially increased (ΔG = −2.13 kcal mol−1, ΔG = −4.08 kcal mol−1, and ΔG = −6.03 kcal mol−1, respectively) with an increasing number of docked CuO NPs, suggesting that direct structural perturbation on DNA could also count for the molecular basis of in-vivo induced DNA damage in C. carassius erythrocytes. This study introduces the novel term “erythrotope” to describe comprehensive red blood cell morphological abnormalities. It proves to be a reliable and cost-effective biomarker for evaluating allostatic erythrocyte load in response to metallic nanoparticle exposure, serving as a distinctive fingerprint to assess fish erythrocyte health and physiological fitness.