pH-Dependent adsorption of aromatic compounds on graphene oxide: An experimental, molecular dynamics simulation and density functional theory investigation

Iron single atoms anchored on ultrathin carbon nitride photocatalyst for visible light-driven water decontamination

Graphitic carbon nitride has gained considerable attention as a visible-light photocatalyst. However, its photocatalytic efficiency is restricted by its limited capacity for absorbing visible light and swift recombination of charge carriers. To overcome this bottleneck, we fabricated an atomic Fe-dispersed ultrathin carbon nitride (Fe-UTCN) photocatalyst via one-step thermal polymerization. Fe-UTCN showed high efficiency in the photodegradation of acetaminophen (APAP), achieving > 90 % elimination within 60-min visible light irradiation. The anchoring of Fe atoms improved the photocatalytic activity of UTCN by narrowing the bandgap from 2.50 eV to 2.33 eV and suppressing radiative recombination. Calculations by density functional theory revealed that the Fe-N4 sites (adsorption energy of - 3.10 eV) were preferred over the UTCN sites (adsorption energy of - 0.18 eV) for the adsorption of oxygen and the subsequent formation of O2•-, the dominant reactive species in the degradation of APAP. Notably, the Fe-UTCN catalyst exhibited good stability after five successive runs and was applicable to complex water matrices. Therefore, Fe-UTCN, a noble-metal-free photocatalyst, is a promising candidate for visible light-driven water decontamination.

Influence of Hydrothermal Modification on Adsorptive Performance of Clay Minerals for Malachite Green

Artificially modified adsorbing materials mainly aim to remedy the disadvantages of natural materials as much as possible. Using clay materials such as rectorite, sodium bentonite and metakaolinite (solid waste material) as base materials, hydrothermally modified and unmodified materials were compared. CM-HT and CM (adsorbing materials) were prepared and used to adsorb and purify wastewater containing malachite green (MG) dye, and the two materials were characterized through methods such as BET, FT-IR, SEM and XRD. Results: (1) The optimal conditions for hydrothermal modification of CM-HT were a temperature of 150 °C, a time of 2 h, and a liquid/solid ratio 1:20. (2) Hydrothermal modification greatly increased the adsorptive effect. The measured maximum adsorption capacity of CM-HT for MG reached 290.45 mg/g (56.92% higher than that of CM). The theoretical maximum capacity was 625.15 mg/g (186.15% higher than that of CM). (3) Because Al-OH and Si-O-Al groups were reserved in unmodified clay mineral adsorbing materials with good adsorbing activity, after hydrothermal modification, the crystal structure of the clay became loosened along the direction of the c axis, and the interlayer space increased to partially exchange interlayer metal cations connected to the bottom oxygen, giving CM-HT higher electronegativity and creating more crystal defects and chemically active adsorbing sites for high-performance adsorption. (4) Chemical adsorption was the primary way by which CM-HT adsorbed cationic dye, while physical adsorption caused by developed pore canal was secondary. The adsorption reaction occurred spontaneously.

Identifying the Stripping of Oxide Debris from Graphene Oxide: Evidence from Experimental Analysis and Molecular Simulation

In this study, characteristics of oxidation debris (OD) and its stripping mechanism from graphene oxide (GO) were explored. The results demonstrated that OD contains three components, namely, protein-, fulvic acid-, and humic acid-like substances; among these, protein-like substances with lower molecular weight and higher hydrophilicity were most liable to be stripped from GO and were the primary components stripped from GO at pH < 10, whereas humic acid- and fulvic acid-like substances were stripped from GO at pH > 10. During the stripping of OD, hydrogen bonds from carboxyl and carbonyl were the first to break, followed by hydrogen bonds from epoxy. Subsequently, π-π interactions were broken, and hydrogen bond interactions induced by hydroxyl groups were the hardest to break. After the stripping of OD, the recombination of OD on GO was observed, and regions containing relatively fewer oxygen-containing functional groups were favorable binding sites for the readsorbed OD. The stripping and recombination of OD on GO resulted in an uneven GO surface, which should be considered during the development of GO-based environmental materials and the evaluation of their environmental behavior.

Integration of covalent organic frameworks and molecularly imprinted polymers for selective extraction of flavonoid naringenin from grapefruit (Citrus × paradisi Macf.) peels

Grapefruit (Citrus × paradisi Macf.) peel, a by-product of the citrus-processing industry, possesses an important economic value due to the richness of bioactive compounds. In this study, boron-linked covalent organic frameworks integrated with molecularly imprinted polymers (CMIPs) were developed via a facile one-pot bulk polymerization approach for the selective extraction of naringenin from grapefruit peel extract. The obtained CMIPs possessed a three-dimensional network structure with uniform pore size distribution, large surface areas (476 m2/g), and high crystallinity. Benefiting from the hybrid functional monomer APTES-MAA, the acylamino group can coordinate with the boronate ligands of the boroxine-based framework to form B-N bands, facilitating the integration of imprinted cavities with the aromatic skeleton. The composite materials exhibited a high adsorption capacity of 153.65 mg/g, and a short adsorption equilibrium time of 30 min for naringenin, together with favorable selectivity towards other flavonoid analogues. Additionally, the CMIPs captured the template molecules through π-π* interaction and hydrogen bonding, as verified by FT-IR and XPS. Furthermore, they had good performance when employed to enrich naringenin in grapefruit peels extract compared with the common adsorbent materials including AB-8, D101, cationic exchange resin, and active carbon. This research highlights the potential of CMIPs composite materials as a promising alternative adsorbent for naringenin extraction from grapefruit peel.

Selective stepwise adsorption for enhanced removal of multi-component dissolved organic chemicals from petrochemical wastewater

The coexistence of multi-component dissolved organic chemicals causes tremendous challenge in purifying petrochemical wastewater, and stepwise selective adsorption holds the most promise for enhanced treatments. This study is designed to enhance the removal of multiple dissolved organic chemicals by stepwise adsorption. Special attention is given to the selective removal mechanisms for the major pollutant N,N-dimethylformamide (DMF), the sensitive pollutant fluorescent dissolved organic matter (FDOM) and other components. The results indicated that the combination of coal activated carbon and aluminum silica gel produced a synergistic effect and broke the limitation of removing only certain pollutants. Combined removal rates of 80.5 % for the dissolved organic carbon and 86.7 % for the biotoxicity in petrochemical wastewater were obtained with the enhanced two-step adsorption. The adsorption performance of both adsorbents remained stable even after five cycles. The selective adsorption mechanism revealed that hydrophobic organics such as DMF was adsorbed by the macropores of coal activated carbon, while the FDOM was eliminated by π-π stacking, electrostatic interaction and hydrophobic interaction. The hydrophilic organics were removed by the mesopores of aluminum silica gel, the silica hydroxyl groups and hydrophilic interaction. This study provides a comprehensive understanding of the selective adsorption mechanism and enhanced stepwise removal of multiple pollutants in petrochemical wastewater, which will guide the deep treatment of complex wastewater.

Investigating the ibrutinib resistance mechanism of L528W mutation on Bruton's tyrosine kinase via molecular dynamics simulations

Drug resistance to Bruton's Tyrosine Kinase (BTK) inhibitors presents a challenge in treating B-cell malignancies, and the mechanism behind drug resistance remains unclear. In this study, we focused on the BTK L528W mutation and investigated the underlying mechanisms of resistance to ibrutinib (including prototype and its active metabolite from, PCI-45227) using a combination of bioinformatics analysis, and molecular dynamics (MD) simulations. Protein stability of wild type (WT) BTK and L528W mutant was predicted using DUET, PoPMuSiC, and I-Mutant2.0. We performed MD simulations of six systems, apo-WT, metabolite-WT, prototype-WT and their mutants, to analyze the significant conformational and BTK-inhibitor binding affinity changes induced by the L528W mutation. Results show that the L528W mutation reduces the conformational stability of BTK compared to the WT. Principal component analysis (PCA) based free energy landscape (FEL) analysis shows that the L528W mutant ensemble tends to form more conformation clusters and exhibit higher levels of local minima than the WT counterpart. The interaction analysis reveal that the L528W mutation disrupts the strong hydrogen bond between Cys481 and inhibitors and reduces the number of hydrogen bonds between inhibitors and BTK in the L528W mutant complex structures compared to the WT. Porcupine plot analysis in association with cross-correlation analysis show the high-intensity flexible motion exhibited by the P-loop region. MM/GBSA calculations show that the L528W mutation in metabolite-BTK and prototype-BTK complexes increases binding free energy compared to the WT, with a reduction in binding affinity confirmed by per-residue energy decomposition. Specifically, the binding free energy increases from -57.86 kcal/mol to -48.26 kcal/mol for the metabolite-BTK complex and from -62.04 kcal/mol to -50.55 kcal/mol for the prototype-BTK complex. Overall, our study finds that the L528W mutation reduces BTK stability, decreases binding affinity, and leads to drug resistance and potential disease recurrence.

Shape-Anisotropic Assembly of Protein Nanocages with Identical Building Blocks by Designed Intermolecular π-π Interactions

Protein lattices that shift the structure and shape anisotropy in response to environmental cues are closely coupled to potential functionality. However, to design and construct shape-anisotropic protein arrays from the same building blocks in response to different external stimuli remains challenging. Here, by a combination of the multiple, symmetric interaction sites on the outer surface of protein nanocages and the tunable features of phenylalanine-phenylalanine interactions, a protein engineering approach is reported to construct a variety of superstructures with shape anisotropy, including 3D cubic, 2D hexagonal layered, and 1D rod-like crystalline protein nanocage arrays by using one single protein building block. Notably, the assembly of these crystalline protein arrays is reversible, which can be tuned by external stimuli (pH and ionic strength). The anisotropic morphologies of the fabricated macroscopic crystals can be correlated with the Å-to-nm scale protein arrangement details by crystallographic elucidation. These results enhance the understanding of the freedom offered by an object's symmetry and inter-object π-π stacking interactions for protein building blocks to assemble into direction- and shape-anisotropic biomaterials.

Adsorption Affinities of Small Volatile Organic Molecules on Graphene Surfaces for Novel Nanofiller Design: A DFT Study

The adsorption of organic molecules on graphene surfaces is a crucial process in many different research areas. Nano-sized carbon allotropes, such as graphene and carbon nanotubes, have shown promise as fillers due to their exceptional properties, including their large surface area, thermal and electrical conductivity, and potential for weight reduction. Surface modification methods, such as the "pyrrole methodology", have been explored to tailor the properties of carbon allotropes. In this theoretical work, an ab initio study based on Density Functional Theory is performed to investigate the adsorption process of small volatile organic molecules (such as pyrrole derivatives) on graphene surface. The effects of substituents, and different molecular species are examined to determine the influence of the aromatic ring or the substituent of pyrrole's aromatic ring on the adsorption energy. The number of atoms and presence of π electrons significantly influence the corresponding adsorption energy. Interestingly, pyrroles and cyclopentadienes are 10 kJ mol-1 more stable than the corresponding unsaturated ones. Pyrrole oxidized derivatives display more favorable supramolecular interactions with graphene surface. Intermolecular interactions affect the first step of the adsorption process and are important to better understand possible surface modifications for carbon allotropes and to design novel nanofillers in polymer composites.

Efficient removal of per- and polyfluoroalkyl substances from biochar composites: Cyclic adsorption and spent regenerant degradation

In order to solve the problem of efficient desorption of per- and polyfluoroalkyl substances (PFAS) and regeneration of adsorbents, a novel biochar composite was prepared based on the quaternary ammonium groups and hydrophobicity of sulfobetaine polymer, which can be used for the efficient removal of various PFASs and has great regeneration ability. Through adsorption, regeneration and degradation experiment, the comprehensive effect of the novel biochar composite on the whole process of removal of PFAS was systematically investigated. The results showed that the maximum adsorption capacity of PFOS, PFOA, PFBS, and PFBA reached 634 mg/g, 536 mg/g, 301 mg/g and 264 mg/g, respectively. The adsorption process involved hydrophobicity, electrostatic, pore diffusion and complexation. The NaI + NaOH solution was used at 50 °C to achieve efficient regeneration of the adsorbent, which can be recycled more than 4 times. When the vacuum-ultraviolet (VUV)/sulfite reduction system was used for deep degradation of the regenerated solution, the effect of hydrated electrons on PFAS was enhanced due to the inclusion of NaI and NaOH in the regeneration reagent, resulting in an increase in the degradation efficiency (89.1%-99.9%) and defluorination efficiency (63.3%-84.1%). Based on the performance of BC-P(SB-co-AM) and the treatment efficiency of PFAS, the design idea of the whole process treatment technology of PFAS proposed in this work is expected to hold great promise in environmental applications. This work provides a novel idea and system for the efficient adsorption removal and desorption of PFAS, and subsequent deep degradation.

Interaction between graphene oxide and acetaminophen in water under simulated sunlight: Implications for environmental photochemistry of PPCPs

In recent years, graphene oxide (GO) as a new carbon material has been widely investigated as adsorbent and catalyst. However, effects of GO on the micro-pollutants such as pharmaceuticals and personal care products (PPCPs) under sunlight remains unclear. In this study, the degradation of PPCPs in a simulated sunlight-GO photocatalytic system was systematically investigated. Specifically, GO rapidly degrade 95% of acetaminophen (APAP) within 10 min under simulated sunlight irradiation (λ ≥ 350 nm). The influencing factors such as APAP concentration, pH, GO dosage, water matrixes (Cl^-, NO₃^-, HCO₃^-, SO₄^2-, Ca²⁺, Fe³⁺and fulvic acid) were investigated. At a GO dosage of 100 mg L^-1 and an initial pH of 7, the APAP (5 μM) photodegradation kinetic constant k_obs was calculated to be 0.4547 min^-1. In practical applications, the GO photocatalysis system still degrade over 90% APAP within 60 min in real surface water. The electron spin resonance and radical scavenging experiments revealed that the dominated active species for degrading APAP was photogenerated holes (h⁺), while other mechanisms (¹O₂ and O₂^•-/HO₂^•) played a minor role. Furthermore, the photochemical transformation of some other typical PPCPs were comparatively studied to reveal the relationship between degradation kinetics and molecular structure. Based on descriptive variables including molar refractive index parameter, octanol-water partition coefficient, dissociation constant and dipole moment, a quantitative structural-activity relationship (QSAR) model for predicting pseudo-first-order rate constants was established with a high significance (R² = 0.996, p < 0.05). This study helps to understand the interaction between GO and PPCPs and its effects on the photochemical transformation of PPCPs in water.

The fate of aggregated graphene oxide upon the increasing of pH: An experimental and molecular dynamic study

Given the possible ecological dangers of graphene oxide (GO), a thorough understanding of its aggregation behavior is essential. During industrial applications, GOs may be used as multi-layered, and there is some possibility that GOs are released into the water environment in the aggregated state. Thus, elucidating the fate of aggregated GO is valuable for evaluating their environmental fate. In this work, the effect of pH on the fate of aggregated graphene oxide (GO) was explored using experimental measurements and molecular dynamic simulations and promoted aggregation of GO upon the increase of pH was observed. Additional investigations show that the presence of oxidation debris (ODs) on GO served as the primary driver of the unanticipated trend in aggregation behavior. GO consists of lightly oxidized functionalized graphene sheets and highly oxidized ODs. Upon the increase of pH and the deprotonation of functional groups, ODs are stripped from GO due to electrostatic repulsions and steric hindrance of water molecules. The stripping of ODs decreased the zeta potential and increased the hydrophobicity of GO, thus accelerating the aggregation. Additionally, the stripped ODs may recombine to GO edges and bridged GOs, which also contribute to further aggregation. Functional group deprotonation, ODs stripping, OD bridging, double layer compression, and charge neutralization all worked together to promote aggregation, resulting in the formation of FG-water-OD aggregates. Overall, the presence of ODs complicates the structures and properties of GO and should be considered during the development of GO-related nanomaterials and the evaluation of their environmental impact.

The Role of Oxidation Pattern and Water Content in the Spatial Arrangement and Dynamics of Oxidized Graphene-Based Aqueous Dispersions

In this work, we employ fully atomistic molecular dynamics simulations to elucidate the effects of the oxidation pattern and of the water content on the organization of graphene sheets in aqueous dispersions and on the dynamic properties of the different moieties at neutral pH conditions. Analysis of the results reveals the role of the oxidation motif (peripherally or fully oxidized flakes) in the tendency of the flakes to self-assemble and in the control of key structural characteristics, such as the interlayer distance between the sheets and the average size and the distribution of the formed aggregates. In certain cases, the results are compared to a pertinent experimental system, validating further the relevant computational models. Examination of the diffusional motion of the oxidized flakes shows that different degrees of spatial restriction are imposed upon the decrease in the water content and elucidates the conditions under which a motional arrest of the flakes takes place. At constant water content, the structural differences between the formed aggregates appear to additionally impart distinct diffusional characteristics of a water molecule. A detailed examination of the counterion dynamics describes their interaction with the oxidized flakes and their dependence on the water content and on the oxidation pattern, offering new insight into the expected electrical properties of the dispersions. The detailed information provided by this work will be particularly useful in applications such as molecular sieving, nanofiltration, and in cases where conductive membranes based on oxidized forms of graphene are used.

Effect of the R126C mutation on the structure and function of the glucose transporter GLUT1: A molecular dynamics simulation study

Glucose transporter 1 (GLUT1) is responsible for basal glucose uptake and is expressed in most tissues under normal conditions. GLUT1 mutations can cause early-onset absence epilepsy and myoclonus dystonia syndrome (MDS), with MDS potentially lethal. In this study, the effect of the R126C mutation, which is associated with MDS, on structural stability and substrate transport of GLUT1 was investigated. Various bioinformatics tools were used to predict the stability of GLUT1, revealing that the R126C mutation reduces the structural stability of GLUT1. Molecular dynamics (MD) simulations were used to further characterize the effect of the R126C mutation on GLUT1 structural stability. Based on the MD simulations, specific conformational changes and dominant motions of the GLUT1 mutant were characterized by Principal component analysis (PCA). The mutation disrupts hydrogen bonds between substrate-binding residues and glucose, thus likely reducing substrate affinity. The R126C mutation reduces the conformational stability of the protein, and fewer intramolecular hydrogen bonds were present in the mutated GLUT1 when compared with that of wild-type GLUT1. The mutation increased the free energy of glucose transport through GLUT1 significantly, especially at the mutation site, indicating that passage of glucose through the channel is hindered, and this mutant may even release cytoplasmic glucose. This study provides a detailed atomic-level explanation for the reduced structural stability and substrate transport capacity of a GLUT1 mutant. The results aid our understanding of the structure of GLUT1 and provide a framework for developing drugs to treat GLUT1-related diseases, such as MDS.

Theoretical Study on the Aggregation and Adsorption Behaviors of Anticancer Drug Molecules on Graphene/Graphene Oxide Surface

Graphene and its derivatives are frequently used in cancer therapy, and there has been widespread interest in improving the therapeutic efficiency of targeted drugs. In this paper, the geometrical structure and electronic effects of anastrozole(Anas), camptothecin(CPT), gefitinib (Gefi), and resveratrol (Res) on graphene and graphene oxide(GO) were investigated by density functional theory (DFT) calculations and molecular dynamics (MD) simulation. Meanwhile, we explored and compared the adsorption process between graphene/GO and four drug molecules, as well as the adsorption sites between carriers and payloads. In addition, we calculated the interaction forces between four drug molecules and graphene. We believe that this work will contribute to deepening the understanding of the loading behaviors of anticancer drugs onto nanomaterials and their interaction.

Ring defects-rich and pyridinic N-doped graphene aerogel as floating adsorbent for efficient removal of tetracycline: Evidence from NEXAFS measurements and theoretical calculations

The rational design of carbon-based adsorbents with a high uptake efficiency for polar organic molecules is a key challenge in water purification research. Herein, we report a graphene aerogel that is doped with pyridinic-N and has abundant ring defects (denoted by DNGA). The aerogel sample exhibits a high adsorption capacity of 607.1 mg/g toward tetracycline (TC), a fast adsorption process (20 min), and good reusability (with a declining efficiency < 10.0% after five cycles), while being easy to recycle. C/N K-edge X-ray absorption near-edge structure (XANES) measurements demonstrate that the efficient adsorption capacity of the DNGA sample is related to the presence of ring defects and the pyridinic-N species. Density functional theory (DFT) calculations demonstrate that ring defects of type 5-8-5 and the pyridinic-N species at the edge location are primarily responsible for TC removal. In this study, we resolve a controversial issue regarding the origin of the adsorption performance origin of N-doped carbon-based adsorbents. The findings of this study can guide the development of novel and improved N-doped carbon-based adsorbents for the removal of target contaminants.

A New Strategy for Highly Efficient Separation between Monovalent Cations by Applying Opposite-Oriented Pressure and Electric Fields

Biological ion channels exhibit excellent ion selectivity, but it has been challenging to design their artificial counterparts, especially for highly efficient separation of similar ions. Here, a new strategy to achieve high selectivity between alkali metal ions with artificial nanostructures is reported. Molecular dynamics (MD) simulations and experiments are combined to study the transportation of monovalent cations through graphene oxide (GO) nanoslits by applying pressure or/and electric fields. It is found that the ionic transport selectivity under the pressure driving reverses compared with that under the electric field driving. Moreover, MD simulations show that different monovalent cations can be separated with unprecedentedly high selectivity by applying opposite-oriented pressure and electric fields. This highly efficient separation originates from two distinctive ionic transporting modes, that is, hydration shells drive ions under pressure, but drag ions under the electric field. Hence, ions with different hydration strengths can be efficiently separated by tuning the net mobility induced by the two types of driving forces when the selected ions are kept moving while the other ones are immobilized. And nanoconfinement is confirmed to enhance the separation efficacy. This discovery paves a new avenue for separating similar ions without elaborately designing biomimetic nanostructures.

Adsorption of a wide variety of antibiotics on graphene-based nanomaterials: A modelling study

The knowledge on the sorption behaviour of antibiotics on nanomaterials is limited, especially regarding the reaction mechanism on the surface of carbon nanomaterials, which may determine both the adsorptive capacity and regeneration efficiency of graphene adsorbers. In this work, we used molecular modelling to generate the most comprehensive (to date) adsorption dataset for pristine and functionalised graphene interacting with 8 β-lactams, 3 macrolide, 12 quinolone, 4 tetracycline, 15 sulphonamide, trimethoprim, 2 lincosamide, 2 phenicole and 4 nitroimidazole antibiotics, and their transformation products in water and n-octanol. Results show that various non-covalent interactions that operate simultaneously, including van der Waals dispersion forces, π-interactions, hydrophobic interaction and hydrogen bonding, facilitate adsorption. The molecular properties of antibiotics and graphene/graphene oxide, as well as the composition of the background solution regulate the magnitude of these interactions. Our findings demonstrate that the most efficient method for the removal of antibiotics from aquatic environments is the use of graphene at environmental pH. The subsequent regeneration of the sorbent is best achieved through washing with slightly basic (pH 8-10) non-polar solvents. The obtained theoretical insights expand and complement experimental observations and provide important information that can contribute to further exploration into the adsorbent properties of graphene-based materials, and towards the development of predictive adsorption models.

Behavior of two classes of organic contaminants in the presence of graphene oxide: Ecotoxicity, physicochemical characterization and theoretical calculations

Graphene oxide (GO) production has increased considerably and therefore its presence in the environment is inevitable. When in aquatic environment GO can interact with co-existing compounds, modifying their toxicities for several organisms. However, the toxic effects of co-exposure of GO and organic compounds are rarely reported in the literature. Herein, we studied the behavior of four organic aquatic contaminants found in surface water such as 2-phenylbenzotriazoles (non-Cl PBTA-9 and PBTA-9) and phenoxyphenyl pesticides, pyriproxyfen (PYR) and lambdacyhalothrin (LCT), in the presence of GO. GO reduced 90% and 83% of the toxicity of non-Cl PBTA-9 and PBTA for Daphnia. When PBTAs were adsorbed onto GO surface their interactions caused GO agglomeration (up to 20 mm) and consequent precipitation, making PBTAs less bioavailable. PYR and LCT's toxicities increased up to 83% for PYR and 47% for LCT in the presence of GO, because their adsorption on GO lead to the stabilization of the suspensions (up to 0.5 μm). Those particles were then easily ingested and retained in the digestive tract of the daphnids, triggering the Trojan horse effect. Based on theoretical calculations we observed that PBTA compounds are planar, electron-poorer and more reactive than the studied pesticides, suggesting a better stability of the GO/PBTA complexes. PYR and LCT are nonplanar, electron-richer and less reactive towards GO than PBTAs, forming less stable GO complexes that could facilitate the desorption of pesticides, increasing toxic effects. Our results suggest that the properties of the organic toxicants can influence the stability of graphene oxide suspensions, playing a fundamental role in the modulation of their toxicity. Further research is needed for a deep understanding of the behavior of nanomaterials in the presence of contaminants and their effect in the toxicity of aquatic organisms.

Constant pH Coarse-Grained Molecular Dynamics with Stochastic Charge Neutralization

pH dependence abounds in biochemical systems; however, many simulation methods used to investigate these systems do not consider this property. Using a modified version of the hybrid non-equilibrium molecular dynamics (MD)/Monte Carlo algorithm, we include a stochastic charge neutralization method, which is particularly suited to the MARTINI force field and enables artifact-free Ewald summation methods in electrostatic calculations. We demonstrate the efficacy of this method by reproducing pH-dependent self-assembly and self-organization behavior previously reported in experimental literature. In addition, we have carried out experimental oleic acid titrations where we report the results in a more relevant way for the comparison with computational methods than has previously been done.

Structure analysis and non-invasive detection of cadmium-phytochelatin2 complexes in plant by deep learning Raman spectrum

Plants synthesize phytochelatins to chelate in vivo toxic heavy metal ions and produce nontoxic complexes for tolerating the stress. Detection of the complexes would simplify the identification of high phytoremediation cultivars, as well as assessment of plant food for safe consumption. Thus, a confocal Raman spectroscopy combined with density functional theory and deep learning was used for characterizing phytochelatin2 (PC₂), and Cd-PC₂ mixtures. Results showed the PC₂ chelate Cd²⁺ in a 2:1 ratio to produce Cd(PC₂)₂; Cd-S bonds of the Cd(PC₂)₂ have signature Raman vibrations at 305 and 610 cm^-1 which are the most distinctive spectral signatures for varieties of Cd-PCs complexes. The PC₂ was used as a natural probe to stabilize the chemical status of Cd, and to enrich and magnify Raman signature of the trace Cd for deep learning models which enabled condition of the Cd(PC₂)₂ in pak choi leaf to be visualized, quantified, and classified by directly using raw spectra of the leaf. This study provides a general protocol by using Raman information for structure analysis and non-invasive detection of heavy metal-PCs complexes in plants and provides a novel idea for simplifying identification of high phytoremediation cultivars, as well as assessment of heavy metal related food safeties.

Analyzing cadmium-phytochelatin2 complexes in plant using terahertz and circular dichroism information

Phytochelatins are plants' small metal-binding peptides which chelate internal heavy metals to form nontoxic complexes. Detecting the complexes in plants would simplify identification of cultivars with both high tolerance and enrichment capabilities for heavy metals which represent phytoextraction performance. Thus, a terahertz spectroscopy combined with density functional theory, chemometrics and circular dichroism was used for characterization of phytochelatin2 (PC₂), Cd-PC₂ mixture standards, and pak choi (Brassica chinensis) leaves as a plant model. Results showed PC₂ chelates Cd²⁺ in a 2:1 ratio to form Cd(PC₂)₂ complex; Cd connected to thoils of PC₂ and changed β-turn and random coil of PC₂ peptide chain to β-Sheet which presented as terahertz vibrations of PC₂ around 1.03 and 1.71 THz being suppressed; the best models for detecting the complex in pak choi were obtained by partial least squares regression modeling combined with successive projections algorithm selection; the models used PC₂ as a natural probe for visualizing and quantifying chelated Cd in pak choi leaf and achieved a limit of detection up to 1.151 ppm. This study suggested that terahertz information of the heavy metal-PCs complexes is qualified for representing a simpler alternative to classical index for evaluating phytoextraction performance of plant; it provided a general protocol for structure analysis and detection of heavy metal-PCs complexes in plant by terahertz absorbance.

Synthesis, Characterization and Application of Polypyrrole Functionalized Nanocellulose for the Removal of Cr(VI) from Aqueous Solution

Heavy metals are toxic substances that pose a real danger to humans and organisms, even at low concentration. Therefore, there is an urgent need to remove heavy metals. Herein, the nanocellulose (NC) was synthesized by the hydrolysis of cellulose using sulfuric acid, and then functionalized using polypyrrole (ppy) through a polymerization reaction to produce polypyrrole/nanocellulose (ppy/NC) nanocomposite. The synthesized nanocomposite was characterized using familiar techniques including XRD, FT-IR, SEM, TEM, and TGA. The obtained results showed a well-constructed nanocomposite with excellent thermal stability in the nano-sized scale. The adsorption experiments showed that the ppy/NC nanocomposite was able to adsorb hexavalent chromium (Cr(VI)). The optimum pH for the removal of the heavy metal was pH 2. The interfering ions showed minor effect on the adsorption of Cr(VI) resulted from the competition between ions for the adsorption sites. The adsorption kinetics were studied using pseudo 1st order and pseudo 2nd order models indicating that the pseudo second order model showed the best fit to the experimental data, signifying that the adsorption process is controlled by the chemisorption mechanism. Additionally, the nanocomposite showed a maximum adsorption capacity of 560 mg/g according to Langmuir isotherm. The study of the removal mechanism showed that Cr(VI) ions were removed via the reduction of high toxic Cr(VI) to lower toxic Cr(III) and the electrostatic attraction between protonated ppy and Cr(VI). Interestingly, the ppy/NC nanocomposite was reused for Cr(VI) uptake up to six cycles showing excellent regeneration results. Subsequently, Cr(VI) ions can be effectively removed from aqueous solution using the synthesized nanocomposite as reusable and cost-effective adsorbent.

Modelling of the adsorption of pharmaceutically active compounds on carbon-based nanomaterials

Understanding and acquiring knowledge about the adsorption of pharmaceuticals on carbon-based nanomaterials (CNMs) is imperative to the chemical engineering applications of CNMs, as well as to risk assessment and pollution control of both CNMs and pharmaceuticals. A computational assessment of the mechanism and thermodynamics of the adsorption of 18 most common pharmaceuticals (acetaminophen, acetylsalicylic acid, atenolol, caffeine, carbamazepine, clofibric acid, diclofenac, fenofibric acid, fluoxetine, gemfibrozil, ibuprofen, ketoprofen, naproxen, phenazone, primidone, propranolol, salicylic acid, tramadol) on four different CNMs (pristine/functionalised graphene and carbon nanotube) in two different solvents (water and n-octanol) was provided. We show that the adsorption of pharmaceuticals on pristine CNMs is controlled by dispersion forces, π-interactions and hydrophobic interaction. On the other hand, adsorption on functionalised CNMs is controlled by hydrogen bonding and Coulombic interactions. Furthermore, we demonstrate how functionalization of CNM, CNM curvature and background solution properties modulate the intensity of non-covalent interactions and their contribution towards adsorption free energy. With this knowledge, we pinpoint functionalised graphene at environmental pH as the most effective setting for the removal of a given set of pharmaceuticals from water and wastewater. Finally, we show that CNMs may transport pharmaceuticals into living organisms and release them in nonpolar mediums such as cellular membranes and fat cells.

Interaction with teichoic acids contributes to highly effective antibacterial activity of graphene oxide on Gram-positive bacteria

Graphene oxide (GO) has high-efficient antibacterial activity to diverse pathogenic bacteria. However, the detailed antibacterial mechanism of GO is not fully clear. Herein the antibacterial properties of GO against model Gram-positive (Gram+) (Staphylococcus aureus and Staphylococcus epidermidis) and Gram-negative (Gram-) bacteria (Pseudomonas aeruginosa and Escherichia coli) were compared by plate count method. Results showed that 4 mg/L of GO induced the mortality of Gram+ and Gram- bacteria by > 99% and < 25%, respectively. GO had greater adsorption affinity to teichoic acids, the unique components existing in the cell wall of Gram+ bacteria, mainly via π-π interaction. The adsorption efficiency of teichoic acids was 27 times higher than that of peptidoglycan when they were simultaneously exposed to 100 mg/L GO. The superior adsorption of teichoic acids onto GO increased one order of magnitude of atlA expression, the autolysin related gene. As a result, these accelerated bacterial death by hydrolyzing peptidoglycan in cell walls. Exogenous addition of 50 mg/L teichoic acids could impair 4-5 fold of antibacterial activity of GO against S. aureus. These new findings illuminate the antibacterial mechanism of GO against Gram+ bacteria, which paves the way for the further application of graphene-based materials in water disinfection and pathogen control.

Theoretical study of small aromatic molecules adsorbed in pristine and functionalised graphene

Small aromatic molecules are precursors for several biological systems such as DNA, proteins, drugs, and are also present in several pollutants. The understanding of the interaction of these small aromatic molecules with pristine and functionalised graphene (fGr) can generate different applications. We performed ab initio simulations based on the density functional theory to evaluate the interaction between the aromatic compounds, benzene, benzoic acid, aniline and phenol, with pristine and fGr. The results show that the binding energy for all cases is less than 103.24 kJ/mol (1.07 eV) without substantial modification of the electronic properties, indicating that the interaction occurs through a physical adsorption regime. The results are promising because they suggest that pristine graphene and functionalised graphene are suitable for removing these pollutants, or for carrying molecules for biological applications influenced by π-π and H-bonds interaction.

Adsorption of sulfonamides on biochars derived from waste residues and its mechanism

Waste residues have been prepared as biochar (BC) adsorbents to remove sulfonamides (SAs) at low cost, but the mechanisms of the differences in the SA adsorption performance of different BCs are not clear. Thus, the adsorption characteristics of two SAs (sulfadiazine and sulfathiazole) on three BCs derived from waste residues (sewage sludge (SB), pig manure (PB), and rice straw (RB)) were investigated. The results showed that the adsorption mechanism was chemisorption and RB was the preferred BC under the different tested conditions (pH, Ca²⁺, and humic acid), followed by PB and SB. To interpret the phenomena, FTIR, XRD, and XPS analyses were performed and results indicated that SB had the lowest C content, and there was a very significant difference in the concentrations of the two O functional groups (C˭O and C‒O) for PB and RB (P < 0.01). Density functional theory calculations revealed that the mechanisms of SA adsorption onto BCs were mainly through π-π electron donor acceptor interactions and H bonds. There was no significant difference in the π interactions between the SAs-BC containing C‒O (BC(OH)) and the SAs-BC containing C˭O (BC(C˭O)), whereas the H bond strength of SAs-BC(OH) was much stronger than that of SAs-BC(C˭O).

New insight into the photo-transformation mechanisms of graphene oxide under UV-A, UV-B and UV-C lights

Photo-transformation dominates the fate of graphene oxide (GO) in the environment. However, the photo-transformation mechanisms of GO under different UV bands remain unclear. Our results showed that UV bands played a crucial role in sunlight-induced GO transformation. UVA and UVB induced significant photo-reduction of GO as indicated by decreasing surface O/C ratio, which could be explained by an O₂-independent electron-hole pair-mediated mechanism (Mechanism I), and an O₂-dependent reactive oxygen species (ROS)-mediated reduction mechanism (Mechanism II). Mechanism II accounted for 62.7 % and 33.3 % of total GO photo-transformation under UVA and UVB, respectively. Different from UVA and UVB, UVC led to GO reduction under anaerobic condition via Mechanism I and Mechanism III (direct decarboxylation). However, under aerobic condition, UVC caused significant oxidation of GO, which was the combined effect of Mechanisms I-III and the oxidation of graphitic structure on GO with the assistance of O₂ (Mechanism IV). Moreover, it was demonstrated that the environmental factors (e.g., dissolved organic matter, phosphate) significantly enhanced the photo-transformation of GO in natural water. The information in the present work is useful for better understanding the fate of GO in aquatic environments.

Computational insights into the sorption mechanism of environmental contaminants by carbon nanoparticles through molecular dynamics simulation and density functional theory

Carbon nanomaterials like carbon nanotube, graphene or graphene oxide could significantly enhance contaminant sorption in aqueous solutions, offering a promising opportunity in water and air purification for removal of environmental contaminants.