Quantum Chemical Molecular Dynamics Simulations Research Articles

Preparation of magnetic core-shell Fe3O4@MBT-LDH composite and its application as an effective inhibitor for carbon steel

The core-shell structural Fe3O4@MBT-LDH was synthesized via the ion exchange method, with MBT (2-mercaptobenzothiazole) inhibitor ions intercalated lamellar ZnAlCe-LDH attaching closely to the Fe3O4 microspheres surface. The morphology, composition, structure, and magnetic properties of the composite were measured by transmission electron microscope, X-ray diffraction, Fourier transform infrared spectra, and vibrating sample magnetometer. The release behavior of MBT ions and corrosion inhibition performance of the Fe3O4@MBT-LDH under “no MF” (without an external magnetic field) and “MF ON” modes (under an external magnetic field) were measured by UV–vis spectroscopy, electrochemical tests, scanning electron microscopy, and X-ray photoelectron spectrometer (XPS). Calcinating the composite after the release test and redispersing the sintered products in MBT ions-containing solution, the composite was reestablished. Results showed that the Fe3O4@MBT-LDH possessed moderate MBT loadings amount (12.0%) and presented strong superparamagnetic properties with saturation magnetization (Ms) of 27.6 emu⋅g−1. The release behavior of the MBT− from the composite was sustainable and could be further slowed down by using an external magnetic field with changing the release mechanism. The release curve reached equilibrium with a longer time of 48 h and a lower release amount of 57.0% under MF ON mode than that of no MF mode with a time of 7 h and a release amount of 74.7%. The Fe3O4@MBT-LDH owned a good and long-term protection performance for Q235 carbon steel with maximum corrosion inhibition efficiency (ηe) of up to 93.30%. As a promising controlled-release inhibitor, it could be recycled and regenerated by simple treatment, still having high ηe higher than 80% and excellent magnetic properties with Ms of 21.47 emu⋅g−1 after five cycles. The corrosion mechanism for carbon steel was further analyzed by quantum chemical calculations and molecular dynamics simulation.

A study of pomegranate peel extract effect on corrosion inhibition performance on aluminum in HNO3 solution

Green corrosion inhibitors have an important role in reducing the corrosion rate of metals and the effects of toxic chemicals in the environment. In this study, the inhibition effect of pomegranate peel extract (PPE) with concentration of 0.5, 1, 1.5, 2, 2.5 and 3 g/L on the aluminum 1050 alloy corrosion behavior in the nitric acid solution investigates using the weight loss, electrochemical techniques, scanning electron microscope (SEM), atomic force microscope (AFM), contact angle images, gas chromatography-mass spectrometer (GC-MS) analysis, fourier transform Infrared spectroscopy (FTIR) and ultraviolet radiation (UV-IR). And, the (UV-IR), (GC-MS), and FTIR results confirm the presence of many organic compounds (Containing the N, S, and O atoms), which are responsible for inhibitor performance and absorption phenomena. Meanwhile, the electrochemical impedance results (EIS) indicate that the double layer capacity decreases and the corrosion resistance (Corrosion current density (icorr) from 0.128 to 0.009 mA/cm2) increases with the increase of the inhibitor concentration (The inhibition efficiency increased with increasing the inhibitor concentration from % 54.29 to the % 92.58 at (1–3 g/L). In addition, the corrosion current density decreases with the increase of the inhibitor concentration using the potentiodynamic polarization (PDP) test. However, the corrosion rate enhances with increasing the temperature. From the other hand, quantum chemical (QC) calculation and molecular dynamics (MD) simulation perform to investigate the theory of the adsorption mechanism. According to these studies, the adsorption of PPE on the aluminum 1050 alloy surface is agreement with the langmuir isotherm and as a result it is a mixed-type inhibitor. In final the SEM and AFM results show that the corrosion rate of the aluminum 1050 alloy surface is significantly reduced after the addition of the inhibitor to the corrosive environment. Furthermore, the contact angle image shows that the inhibited aluminum surface has a hydrophobic property in an aqueous solution. And, the QC calculation and MD simulation clarify well the thin layer formation due to the good adsorption of inhibitor (PPE) on the surface of aluminum 1050 alloy in the nitric acid solution, theoretically. It is concluded that PPE will inhibit the surface of aluminum against the corrosion agents in acidic environment and can use as a green inhibitor.

Multifacets of Fullerene-Metal Clusters: From Fundamental to Application.

ConspectusBuckminsterfullerene, C60, was discovered through a prominent mass peak containing 60 atoms produced from laser vaporization of graphite, driven by Kroto's interest in understanding the formation mechanisms of carbon-containing molecules in space. Inspired by the geodesic dome-shaped architecture designed by Richard Buckminster Fuller, after whom the particle was named, C60 was found to have a football-shaped structure comprising 20 hexagons and 12 pentagons. It sparked worldwide interest in understanding this new carbon allotrope, resulting in the awarding of the Noble Prize in Chemistry to Smalley, Kroto, and Curl in 1996.Intrinsically, C60 is an exceptional species because of its high stability and electron-accepting ability and its structural tunability by decorating or substituting either on its exterior surface or interior hollow cavity. For example, metal-decorated fullerene complexes have found important applications ranging from superconductivity, nanoscale electronic devices, and organic photovoltaic cells to catalysis and biomedicine. Compared to the large body of studies on atoms and molecules encapsulated by C60, studies on the exteriorly modified fullerenes, i.e., exohedral fullerenes, are scarcer. Surprisingly, to date, uncertainty exists about a fundamental question: what is the preferable exterior binding site of different kinds of single atoms on the C60 surface?In recent years, we have developed an experimental protocol to synthesize the desired fullerene-metal clusters and to record their infrared spectra via messenger-tagged infrared multiple photon dissociation spectroscopy. With complementary quantum chemical calculations and molecular dynamics simulations, we determined that the most probable binding site of a metal, specifically a vanadium cation, on C60 is above a pentagonal center in an η5 fashion. We explored the bonding nature between C60 and V+ and revealed that the high thermal stability of this cluster originates from large orbital and electrostatic interactions. Through comparing the measured infrared spectra of [C60-Metal]+ with the observational Spitzer data of several fullerene-rich planetary nebulae, we proposed that the complexes formed by fullerene and cosmically abundant metals, for example, iron, are promising carriers of astronomical unidentified spectroscopic features. This opens the door for a real consideration of Kroto's 30-year-old hypothesis that complexes involving cosmically abundant elements and C60 exhibit strong charge-transfer bands, similar to those of certain unidentified astrophysical spectroscopic features. We compiled a VibFullerene database and extracted a set of vibrational frequencies and intensities for fullerene derivatives to facilitate their potential detection by the James Webb Space Telescope. In addition, we showed that upon infrared irradiation C60V+ can efficiently catalyze water splitting to generate H2. This finding is attributed to the novel geometric-electronic effects of C60, acting as "hydrogen shuttle" and "electron sponge", which illustrates the important role of carbon-based supports in single-atom catalysts. Our work not only unveils the basic structures and bonding nature of fullerene-metal clusters but also elucidates their potential importance in astrophysics, astrochemistry, and catalysis, showing the multifaceted character of this class of clusters. More exciting and interesting aspects of the fullerene-metal clusters, such as ultrafast charge-transfer dynamics between fullerene and metal and their relevance to designing hybrid fullerene-metal junctions for electronic devices, are awaiting exploration.

Corrosion inhibition behavior of 2-(4-methoxyphenyl)-benzothiazole on mild steel corrosion through design of experiments approach, quantum chemical calculations and molecular dynamics simulation

Corrosion inhibition behavior of 2-(4-methoxyphenyl)-benzothiazole on mild steel corrosion through design of experiments approach, quantum chemical calculations and molecular dynamics simulation

Synergistic effect of KI on corrosion inhibition of carbon steel by Styphnolobium japonicum (L.) Schott in H2SO4 solution

This work explored the synergistic effect of Styphnolobium japonicum (L.) Schott extract (SE) and potassium iodide (KI) on the corrosion inhibition of carbon steel (CS) in 0.5 mol/L H2SO4 solution. Firstly, the functional groups in the SE were identified using FTIR. The results of UPLC–Q–TOF–MS analysis confirmed the major phytoconstituents presence in SE were Glutaric acid, 2,3-Dihydroxybenzoic acid, Oxoadipic acid, Isoleucine, 2-Oxovaleric acid, l-phenylalanine, Indoline, and Trigonelline. Further a comprehensive investigation of anticorrosive properties of SE in the absence and presence of KI was conducted employing various techniques, including electrochemical impedance spectroscopy (EIS), scanning electron microscopy (SEM), ultraviolet visible spectroscopy (UV‒vis), and X-ray photoelectron spectroscopy (XPS) and theoretical studies like quantum chemical calculations (QC) and molecular dynamics simulations (MS). The results demonstrated that the SE+KI blend outperforms SE or KI individually, achieving an appreciable corrosion inhibition of 94.6 % for CS in H2SO4 solution. SEM analysis confirmed that the CS surface was smoother when SE+KI was added in the aggressive solution. Theoretical calculations were carried out to determine the dipole moments, Mulliken charges, and Fukui parameters of the eight major molecules found in SE. The results showed that SE can inhibit corrosion.

Quantum chemical calculations and molecular dynamics simulations to investigate the mechanism of interaction of six dye levelers with copper surface

Six dye levelers are researched by quantum chemical calculations and molecular dynamics simulations. The electrostatic potential (ESP) and Hirshfeld charge of the levelers were calculated to compare the physical factors affecting their adsorption capacity (electrostatic effects) and to analyse the possible physical adsorption sites for each leveler. The average localised ionisation energy (ALIE) and the condensed Fukui function (CFF) of the levelers were calculated to compare the chemical factors (reactivity) affecting their adsorption capacity and to analyse the possible chemisorption sites for each leveler. On this basis, the adsorption capacity of the six levelers on the surface of Cu(111) at different temperatures was investigated through molecular dynamics simulations, and the adsorption characteristics of the six levelers were summarised.

Synthesis, Characterization, In Silico DFT, Molecular Docking, and Dynamics Simulation Studies of Phenylhydrazono Phenoxyquinolones for Their Hypoglycemic Efficacy.

A series of novel 24 phenylhydrazono phenoxyquinoline derivatives were synthesized with moderate to excellent yield and screened for their efficacy against the α-amylase enzyme through in silico studies. The structures were characterized using spectroscopic techniques such as 1HNMR, 13CNMR, and HREI-MS. Comprehensive computational studies including, drug-likeness and ADMET profiling, quantum chemical calculations, molecular docking, and molecular dynamics (MD) simulation studies, were performed. A density functional theory study of the synthesized compounds indicated a favorable reactivity profile. The synthesized novel analogues were docked against α-amylase (PDB 6OCN) enzymes to investigate the binding interactions. Based on the docking studies, one of the compounds was found to be the hit with the highest negative binding affinity for α-amylase. A MD simulation study indicated stable binding throughout the simulation.

Deciphering the Molecular Mechanisms of Reactive Metabolite Formation in the Mechanism-Based Inactivation of Cytochrome p450 1B1 by 8-Methoxypsoralen and Assessing the Driving Effect of phe268.

This study provides a comprehensive computational exploration of the inhibitory activity and metabolic pathways of 8-methoxypsoralen (8-MP), a furocoumarin derivative used for treating various skin disorders, on cytochrome P450 (P450). Employing quantum chemical DFT calculations, molecular docking, and molecular dynamics (MD) simulations analyses, the biotransformation mechanisms and the active site binding profile of 8-MP in CYP1B1 were investigated. Three plausible inactivation mechanisms were minutely scrutinized. Further analysis explored the formation of reactive metabolites in subsequent P450 metabolic processes, including covalent adduct formation through nucleophilic addition to the epoxide, 8-MP epoxide hydrolysis, and non-CYP-catalyzed epoxide ring opening. Special attention was paid to the catalytic effect of residue Phe268 on the mechanism-based inactivation (MBI) of P450 by 8-MP. Energetic profiles and facilitating conditions revealed a slight preference for the C4'=C5' epoxidation pathway, while recognizing a potential kinetic competition with the 8-OMe demethylation pathway due to comparable energy demands. The formation of covalent adducts via nucleophilic addition, particularly by phenylalanine, and the generation of potentially harmful reactive metabolites through autocatalyzed ring cleavage are likely to contribute significantly to P450 metabolism of 8-MP. Our findings highlight the key role of Phe268 in retaining 8-MP within the active site of CYP1B1, thereby facilitating initial oxygen addition transition states. This research offers crucial molecular-level insights that may guide the early stages of drug discovery and risk assessment related to the use of 8-MP.

Study on the corrosion inhibition properties of some quinoline derivatives as acidizing corrosion inhibitors for steel

In this paper, four quinoline quaternary ammonium salts were synthesized using quaternization reaction, which were benzyl quinolion (BQL), naphthylmethyl quinolinium chloride (NQL), benzyl-8-hydroxy quinolinium chloride (BHQ) and naphthylmethyl 8-hydroxy quinolinium chloride (NHQ). The corrosion inhibition properties of the quinoline derivatives as corrosion inhibitors on P110 steel in 20% HCl solution at 60°C at different concentrations were investigated by weight loss and electrochemical measurements. The results showed that as the concentration of corrosion inhibitor increases, the corrosion rate decreased and the inhibition efficiency improved. Among various corrosion inhibitors at the same concentration, their inhibition efficiencies can be ranked from lowest to highest as follows: QL(quinoline)<8-HQ(8-hydroxyquinoline)<BQL<BHQ<NQL<NHQ. The inhibitors synthesized from 1-chloromethyl naphthalene, NQL and NHQ, exhibited excellent inhibition property, in which the inhibition efficiencies reached to 99.8% and 99.9% even with concentration of 0.1%. It also demonstrated the adsorption of all inhibitors on the steel surface followed Langmuir adsorption isotherms, in which QL and 8-QH exhibited as physical adsorption, BQL and BHQ exhibited as mixed adsorption and NQL and NHQ exhibited as chemical adsorption. The inhibition mechanism of inhibitors was also investigated with scanning electron microscopy (SEM), quantum chemical analyses and molecular dynamics simulations, which proved BHQ and NHQ can facilitate an increase in electron cloud density on the benzene ring, thereby enhancing corrosion inhibition performance.

Dynamically or Kinetically Controlled? Computational Study of the Mechanisms of Electrophilic Aminoalkenylation of Heteroaromatics with Keteniminium Ions.

Quantum chemical calculations and molecular dynamics simulations were applied to study the electrophilic aminoalkenylation of heteroaromatics with keniminium ions. Post-transition state bifurcation (PTSB) was found in the electrophilic addition step for the aminoalkenylation of pyrroles and indoles, and the selectivity for these reactions was dynamically controlled. However, the aminoalkenylation of furan was kinetically controlled because no apparent PTSB was found in the electrophilic addition step. The substituents on the keteniminium ions can also affect the dynamic results for the aminoalkenylations to pyrroles: the C2-aminoalkenylated product is much more favored over the C3-aminoalkenylated product for keteniminium ions with electron-donating substituents, while the product ratio (C2 product/C3 product) decreased when stronger electron-withdrawing substituents were applied.

Study of essential oil extraction from Moroccan Rosmarinus officinalis L. by distillation based on quantum chemical calculation and molecular dynamics simulation

In this work, essential oils were extracted from rosemary leaves (Rosmarinus officinalis L.) from the eastern region of Morocco using hydrodistillation (Hd) and steam distillation (Sd). The yield, chemical composition, thermal stability, and antioxidant activity of the essential oils obtained by the two methods were compared. Determining the chemical composition of rosemary essential oil, with GC-MS, showed a significant qualitative and quantitative difference in certain components. The Sd method improved the extraction of sesquiterpene compounds with high molecular weight and low vapour pressure. The findings reveal that sesquiterpene and oxygenated monoterpenes in essential oils improved the antioxidant activity and thermal stability. Determining antioxidant activity using DPPH and the β-carotene bleaching assay showed that the Sd and Hd oils presented good radical scavenging activity (IC50 = 4960 μg/mL for Hd oil and 4570 μg/mL for Sd oil), capable of delaying β-carotene discolouration with 16.3 and 9.71% inhibition for Sd and Hd respectively. Thermal stability analysis of the oil products was performed using TGA/DTG analysis, and the results showed that the decomposition points of Hd oil and Sd oil were 362 and 368 K respectively. Furthermore, to identify intermolecular interactions and develop better knowledge of phenomena occurring during the extraction of the family of sesquiterpene compounds by water, quantum chemical calculation and molecular simulation by molecular dynamics (MD) were performed. The results suggested the relative stability of caryophyllene-water and the development of intermolecular bonding interactions of van der Walls and steric effect, improving extraction of the substance studied under steam distillation conditions.

Efficiency of alcohol and ester-imidazole in preventing mild steel corrosion: An integrated approach combining experimental and computational studies

In the present work, the two imidazopyridine derivatives namely ethyl 6,8-dibromoimidazo [1,2-a] pyridine-2-carboxylate (ES-IMD) and (5-methylimidazo [1,2-a] pyridine-2-yl) methanol (OL-IMD) were presented as powerful anti-polarizing agent for steel surface in aggressive system related to the obtained results in experimental and computational methods. 1H NMR and mass spectrometry (MS) were used to confirm the structures of resynthesized molecule. We assessed the effectiveness of OL-IMD and ES-IMD inhibitors in safeguarding mild steel from corrosion in a 1 M hydrochloric acid environment. We adopted an integrated experimental and computational approach to evaluate the inhibition efficiency and mechanism of OL-IMD and ES-IMD, utilizing gravimetric method, polarization curves and electrochemical impedance spectroscopy. Quantum chemical calculations and molecular dynamics simulations provided atomic-level insights into adsorption behaviour. Scanning electron microscopy characterized surface morphology. Findings revealed that OL-IMD and ES-IMD compounds performed as mixed-type inhibitors. At the greatest inhibitor concentration (10−3 M), the polarization curves gave inhibition efficiency values of 98.91% (ES-IMD) and 95.42% (OL-IMD). Thermodynamic activation parameters indicated a spontaneous adsorption process of OL-IMD and ES-IMD on the steel surface, which effectively increased the energy barrier for the corrosion process. The EIS parameters demonstrated that when inhibitor concentration raised, the double-layer capacitance (Cdl) dropped which suggested that the dielectric constant was decreasing. The results reveal a substantial correlation produced by the three analysed approaches EIS, PDP, and WL. Thermodynamic activation parameters indicated a spontaneous adsorption process of OL-IMD and ES-IMD on the steel surface, which effectively increased the energy barrier for the corrosion process. Furthermore, the calculated ΔGads values for the considered compounds were -47.39 (kJ/mol) and 49.26 (kJ/mol) for OL-IMD and ES-IMD respectively, proving the chemical nature of the adsorption. Furthermore, SEM surface studies displayed a homogeneous surface while the tested inhibitors were present, but a damaged surface in the blank solution. The theoretical models closely aligned with the experimental data, presented an excellent overview of the investigated inhibitors' reactivity against mild steel confirming the validity of the findings.

Inhibition Effect of Triphenylmethane Dyes for the Corrosion of Carbon Steel in CO2-Saturated NaCl Corrosion Medium.

Carbon dioxide corrosion presents a significant challenge in the oil and gas field. This study simulates the corrosive environment characteristics of oil and gas fields to investigate the corrosion inhibition properties of three triphenylmethane dyes. The inhibitive performance and mechanisms of these dyes were analyzed through weight loss and electrochemical testing, revealing that crystal violet (CV) exhibited a superior inhibition effectiveness over malachite green (MG) and Fuchsine basic (FB). At a concentration of 150 ppm in a CO2-saturated 5% NaCl solution at 25 °C, CV achieved an impressive maximum inhibition efficiency of 94.89%. With the increase in temperature, the corrosion rate slightly decreased, and the corrosion rate was 92.94% at 60 °C. The investigated CV acted as a mixed-type corrosion inhibitor and its protection obeyed the Langmuir adsorption isotherm. The corrosion morphology was characterized by scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and confocal laser scanning microscopy (CLMS). Quantum chemical calculations and molecular dynamics simulations were employed to validate the corrosion inhibition mechanisms, providing guidance for the further application of these dyes in corrosion control.

Elucidating the mechanisms of novel thiazole-based corrosion inhibitors in carbon steel/HCl interface: An integrated approach combining experimental and computational studies

Corrosion inhibitors serve as a paramount strategy in the domain of metal protection. This study investigates the efficacy of two thiazole derivatives, namely methyl (E)-5-(4-chlorophenyl)-2-((2-(1-hydroxynaphthalen-2-yl)vinyl)amino)thiazole-4-carboxylate (ThN), and methyl (E)-5-(4-chlorophenyl)-2-((2-hydroxystyryl)amino)thiazole-4-carboxylate (ThP) in mitigating corrosion of carbon steel in a 1 mol/L hydrochloric acid medium. Electrochemical Impedance Spectroscopy (EIS), Potentiodynamic Polarization (PDP), Scanning Electron Microscopy coupled with Energy-Dispersive X-ray Spectroscopy (SEM-EDX), and X-ray Diffraction analysis (XRD) were used to experimentally assess the corrosion inhibition performance of compounds under study. Experimental results revealed a concentration-dependent increase in the corrosion inhibition efficiencies of the thiazole derivatives, with ThP achieving 90 % and ThN attaining 93 %. The adsorption of both compounds adhered to the Langmuir adsorption model, indicating a physicochemical inhibition mechanism. PDP analyses revealed a mixed-type inhibitory behavior. Furthermore, SEM-EDX assessments validated the ability of the thiazole derivatives to enhance corrosion resistance. XRD studies revealed a marked decrease in corrosion-associated peaks upon the introduction of thiazole derivatives. The potential of zero charge (PZC) for the carbon steel was ascertained via EIS, clarifying the adsorption mechanism. Employing Conductor like Screening Model for Realistic Solvents (COSMO-RS), the solvation properties of the compounds were evaluated, while Quantum Chemical Calculations (QCCs) and Molecular Dynamics (MD) simulations contributed insights into reactivity descriptors and adsorption configurations on the Fe(110) surface. This study highlighted the impact of the aryl group on the adsorption and corrosion inhibition characteristics of investigated compounds, offering valuable guidance for future design and development.

The Nitro Group Reshapes the Effects of Pyrido[3,4-g]quinazoline Derivatives on DYRK/CLK Activity and RNA Splicing in Glioblastoma Cells.

Serine-threonine protein kinases of the DYRK and CLK families regulate a variety of vital cellular functions. In particular, these enzymes phosphorylate proteins involved in pre-mRNA splicing. Targeting splicing with pharmacological DYRK/CLK inhibitors emerged as a promising anticancer strategy. Investigation of the pyrido[3,4-g]quinazoline scaffold led to the discovery of DYRK/CLK binders with differential potency against individual enzyme isoforms. Exploring the structure-activity relationship within this chemotype, we demonstrated that two structurally close compounds, pyrido[3,4-g]quinazoline-2,10-diamine 1 and 10-nitro pyrido[3,4-g]quinazoline-2-amine 2, differentially inhibited DYRK1-4 and CLK1-3 protein kinases in vitro. Unlike compound 1, compound 2 efficiently inhibited DYRK3 and CLK4 isoenzymes at nanomolar concentrations. Quantum chemical calculations, docking and molecular dynamic simulations of complexes of 1 and 2 with DYRK3 and CLK4 identified a dramatic difference in electron donor-acceptor properties critical for preferential interaction of 2 with these targets. Subsequent transcriptome and proteome analyses of patient-derived glioblastoma (GBM) neurospheres treated with 2 revealed that this compound impaired CLK4 interactions with spliceosomal proteins, thereby altering RNA splicing. Importantly, 2 affected the genes that perform critical functions for cancer cells including DNA damage response, p53 signaling and transcription. Altogether, these results provide a mechanistic basis for the therapeutic efficacy of 2 previously demonstrated in in vivo GBM models.

Use of hybrid molecular simulation techniques for systematic analysis of polyphenols as promising therapeutic agent against SARS-CoV-2

In our current study, we systematically report the four phenol classes via three-layer in silico screening approaches consisting of quantum chemical methods, molecular docking and molecular dynamics simulations. We studied the interactions of main protease (Mpro) and Nsp9 proteins of SARS-CoV-2 with four classes of polyphenolic compounds, where both proteins are crucial for virus replication. The phenols are extensively reported for medicinal applications, as these are antioxidants, anti-parasitic, anti-viral, anti-diabetic and anti-inflammatory compounds. Initial molecular docking study shows that among forty phenolic compounds the L9, L17, L26 and, L32 reveal the best binding energies with Mpro protein. Their values of docking score in terms of binding energy with Mpro protein is ranging from -5.7 to -6.8 kcal.mol−1. While on the other hands, L8, L11, L22 and, L34 exhibit the best docking scores with Nsp9 protein, which are ranging from -5.8 to -6.8 kcal.mol−1. Additionally, the lead compounds (ligands) were studied by quantum chemical methods for their optimized or the lowest energy structures, electronic properties, frontier molecular orbitals (FMOs) as well as molecular electrostatic potentials (MEPs). The global chemical descriptors are also calculated to explain the global reactivity trend for the lead compounds. To mimic the aqueous like environment, we added ions according to the electrostatic potential of the macromolecule, water molecules are being added to create physiologically relevant environment for studying biological molecules. Proteins, nucleic acids, and other biomolecules are typically surrounded by water molecules in biological systems. The addition of water molecules in MD simulations may provide a more accurate representation of their natural environment. The molecular dynamics simulations are performed for the complexes of best-docked lead compounds and for both proteins (Mpro and, Nsp9) over multiple replicate trajectories of 320 ns. The flexibility and stability behavior of the lead compounds in terms of RMSD and RMSF plots are analyzed through MD simulations results. The binding free energy of the best-docked lead compounds with both proteins in terms of Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) analysis are calculated, which are found as -8.79 and -3.97 kcal.mol−1 for Mpro-L32 and Nsp9-L8 complexes, respectively. The pharmacokinetic analysis of the lead compounds are also performed to disclose their ADME (absorption, distribution, metabolism, and excretion) and toxic character using online server pkCSM. This allowed for a comprehensive understanding of how these compounds would behave in the organism, specifically focusing on their ADME properties. We believe that the current study can evoke the interest of scientific community by providing fundamental insights, which will ultimately lead in-vivo and in-vitro analysis to assess the studied phenolic therapeutic inhibitors against the SARS-CoV-2.

Dissociation of HNO3 in water revisited: experiment and theory.

Nitric acid dissociation in water is studied as a function of concentration, employing experimental techniques (1H NMR spectroscopy and calorimetry), quantum chemical methods (B3LYP and PBE functionals for molecular clusters) and molecular dynamics simulations (the PBE-D3 functional for solutions under periodic boundary conditions). The extent of dissociation, via proton transfer to a neighboring water molecule, as a function of concentration is studied computationally for molecular nitric acid clusters HNO3(H2O)x (x = 1-8), as well as periodic liquids (HNO3 mole fractions of 0.19 and 0.5, simulated at T = 300 K and 450 K). Despite the simple nature of these structural models, their computed and simulated average 1H chemical shifts compare well with the experimental measurements in this study. Finally, the measured and calculated chemical shifts have shown reasonable relationships with the enthalpy change upon mixing of this binary complex.

New insight into the role of the self-assembly of heteroatom compounds in heavy oil viscosity enhancement.

Unveiling the role of heteroatom compounds in heavy oil viscosity is pivotal for finding targeted viscosity reduction methods to improve oil recovery. This research investigates the impact of heteroatoms in asphaltene molecules by utilizing quantum chemical calculations and molecular dynamics simulations to analyze their electrostatic potential characteristics, pairwise interactions, and dynamic behavior within realistic reservoirs. Heteroatom compounds can influence the molecular-level properties of asphaltenes and thus impact the macroscopic behavior of heavy oils. Research results suggest that the presence of ketone and aromatic rings in asphaltene molecules leads to the unrestricted movement of pi electrons due to their collective electronegativity. Two distinct configurations of asphaltene dimers, face-to-face, and edge-to-face, were observed. Intermolecular interactions were predominantly governed by van der Waals forces, highlighting their significant role in stabilizing asphaltene aggregates. The distribution of asphaltene molecules in the oil phase can be summarized as the "rebar-cement" theory. In the heteroatom-free system, the face-to-face peaks in the radial distribution function exhibit significantly reduced magnitudes compared to those in the heteroatom-containing system. This emphasizes the pivotal function of heteroatoms in connecting molecular components to form a more compact asphaltene structure, which may result in a higher viscosity of heavy oil. These findings give insight into the significance of heteroatoms in bridging molecular components and shaping the intricate structure of asphaltene and advance our understanding of heavy oil viscosity properties.

The role of aldehydes on sulfur based-new particle formation: a theoretical study.

Aldehydes play a crucial role in the formation of atmospheric particles, attracting significant attention due to their environmental impact. However, the microscopic mechanisms underlying the formation of aldehyde-involved particles remain uncertain. In this study, through quantum chemical calculations and molecular dynamics (MD) simulations, we investigate the microscopic formation mechanisms of binary and ternary systems composed of three representative aldehydes, two sulfur-based acids, water, and two bases. Our research findings reveal that the most stable structures of acid-aldehyde clusters involve the connection of acids and aldehyde compounds through hydrogen bonds without involving proton transfer reactions, indicating relatively poor cluster stability. However, with the introduction of a third component, the stability of 18 clusters significantly increase. Among these, in ten systems, acids act as catalysts, facilitating reactions between aldehyde compounds and water or alkaline substances to generate glycols and amino alcohols. However, according to MD simulations conducted at 300 K, these acids readily dissociate from the resulting products. In the remaining eight systems, the most stable structural feature involves ion pairs formed by proton transfer reactions between acids and aldehyde compounds. These clusters exhibit remarkable thermodynamic stability. Furthermore, the acidity of the acid, the nature of nucleophilic agents, and the type of aldehyde all play significant roles in cluster stability and reactivity, and they have synergistic effects on the nucleation process. This study offers microscopic insights into the processes of new particle formation involving aldehydes, contributing to a deeper understanding of atmospheric chemistry at the molecular level.

Simultaneously promoting CO2 permeability and selectivity of polyethylene oxide membranes via introducing CO2-philic KAUST-7

To overcome the challenging trade-off between permeability and selectivity in polymer CO2 separation membranes, CO2-philic metal-organic framework (MOF) KAUST-7 was incorporated within polyethylene oxide (PEO)-type matrices to prepare mixed matrix membranes (MMMs). A cross-scale approach of quantum chemical calculations and molecular dynamics simulations was used to explore the behavior and mechanism of CO2 adsorption on KAUST-7. The strong affinity between KAUST-7 and CO2 enabled a dramatic increase in the CO2 solubility of MMMs. The 2 wt% KAUST-7 loaded MMM exhibited CO2 permeability and CO2/N2 selectivity of 608 Barrer and 75, respectively, representing 41.7% and 54% improvement compared to the neat membrane, exceeding the 2019 upper bound. Furthermore, long-term separation tests for 100 h demonstrated the stability of these membranes.