Molecular Dynamics Simulation Study Research Articles

Computational identification of potential bioactive compounds from Triphala against alcoholic liver injury by targeting alcohol dehydrogenase.

Alcoholic liver injury resulting from excessive alcohol consumption is a significant social concern. Alcohol dehydrogenase (ADH) plays a critical role in the conversion of alcohol to acetaldehyde, leading to tissue damage. The management of alcoholic liver injury encompasses nutritional support and, in severe cases liver transplantation, but potential adverse effects exist, and effective medications are currently unavailable. Natural products with their potential benefits and historical use in traditional medicine emerge as promising alternatives. Triphala, a traditional polyherbal formula demonstrates beneficial effects in addressing diverse health concerns, with a notable impact on treating alcoholic liver damage through enhanced liver metabolism. The present study aims to identify potential active phytocompounds in Triphala targeting ADH to prevent alcoholic liver injury. Screening 119 phytocompounds from the Triphala formulation revealed 62 of them showing binding affinity to the active site of the ADH1B protein. Promising lipid-like molecule from Terminalia bellirica, (4aS, 6aR, 6aR, 6bR, 7R, 8aR, 9R, 10R, 11R, 12aR, 14bS)-7, 10, 11-trihydroxy-9-(hydroxymethyl)-2, 2, 6a, 6b, 9, 12a-hexamethyl-1, 3, 4, 5, 6, 6a, 7, 8, 8a, 10, 11, 12, 13, 14b-tetradecahydropicene-4a-carboxylic acid showed high binding efficiency to a competitive ADH inhibitor, 4-Methylpyrazole. Pharmacokinetic analysis further confirmed the drug-likeness and non-hepatotoxicity of the top-ranked compound. Molecular dynamics simulation and MM-PBSA studies revealed the stability of the docked complexes with minimal fluctuation and consistency of the hydrogen bonds throughout the simulation. Together, computational investigations suggest that (4aS, 6aR, 6aR, 6bR, 7R, 8aR, 9R, 10R, 11R, 12aR, 14bS)-7, 10, 11-trihydroxy-9-(hydroxymethyl)-2, 2, 6a, 6b, 9, 12a-hexamethyl-1, 3, 4, 5, 6, 6a, 7, 8, 8a, 10, 11, 12, 13, 14b-tetradecahydropicene-4a-carboxylic acid from the Triphala formulation holds promise as an ADH inhibitor, suggesting an alternative therapy for alcoholic liver injury.

Design, Synthesis, Antifungal Activity, and Action Mechanism of Pyrazole-4-carboxamide Derivatives Containing Oxime Ether Active Fragment As Succinate Dehydrogenase Inhibitors.

The dearomatization at the hydrophobic tail of the boscalid was carried out to construct a series of novel pyrazole-4-carboxamide derivatives containing an oxime ether fragment. By using fungicide-likeness analyses and virtual screening, 24 target compounds with theoretical strong inhibitory effects against fungal succinate dehydrogenase (SDH) were designed and synthesized. Antifungal bioassays showed that the target compound E1 could selectively inhibit the in vitro growth of R. solani, with the EC50 value of 1.1 μg/mL that was superior to that of the agricultural fungicide boscalid (2.2 μg/mL). The observations by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) demonstrated that E1 could reduce mycelial density and significantly increase the mitochondrial number in mycelia cytoplasm, which was similar to the phenomenon treated with boscalid. Enzyme activity assay showed that the E1 had the significant inhibitory effect against the SDH from R. solani, with the IC50 value of 3.3 μM that was superior to that of boscalid (7.9 μM). The mode of action of the target compound E1 with SDH was further analyzed by molecular docking and molecular dynamics simulation studies. Among them, the number of hydrogen bonds was significantly more in the SDH-E1 complex than that in the SDH-boscalid complex. This research on the dearomatization strategy of the benzene ring for constructing pyrazole-4-carboxamides containing an oxime ether fragment provides a unique thought to design new antifungal drugs targeting SDH.

Unveiling the molecular basis of paracetamol-induced hepatotoxicity: Interaction of N-acetyl-p-benzoquinone imine with mitochondrial succinate dehydrogenase

Background and aimN-acetyl-p-benzoquinoneimine (NAPQI), a toxic byproduct of paracetamol (Acetaminophen, APAP), can accumulate and cause liver damage by depleting glutathione and forming protein adducts in the mitochondria. These adducts disrupt the respiratory chain, increasing superoxide production and reducing ATP. The goal of this study was to provide computational proof that succinate dehydrogenase (SDH), a subunit of complex II in the mitochondrial respiratory chain, is a favorable binding partner for NAPQI in this regard. MethodMolecular docking, molecular dynamics simulation, protein-protein interaction networks (PPI), and KEGG metabolic pathway analysis were employed to identify binding characteristics, interaction partners, and their associations with metabolic pathways. A lipid membrane was added to the experimental apparatus to mimic the natural cellular environment of SDH. This modification made it possible to develop a context for investigating the role and interactions of SDH within a cellular ecosystem that was more realistic and biologically relevant. ResultThe molecular binding affinity score for APAP and NAPQI with SDH was predicted −6.5 and −6.7 kcal/mol, respectively. Furthermore, RMSD, RMSF, and Rog from the molecular dynamics simulations study revealed that NAPQI has slightly higher stability and compactness compared to APAP at 100 ns timeframe with mitochondrial SDH. ConclusionThis study serves to predict the mechanistic process of paracetamol toxicity by using different computational approaches. In addition, this study will provide information about the drug target against APAP hepatotoxicity.

Computational design, docking, and molecular dynamics simulation study of RNA helicase inhibitors of dengue virus.

RNA viruses are complex pathogens in terms of their genetic makeup, mutation frequency, and transmission modes. They contain the RNA helicase enzyme, which plays a crucial role in the viral genome replication process. This work aims to develop and screen a potential molecule that could function as a dengue virus (DENV) RNA helicase inhibitor. The present study was performed by taking 26 potential derivatives of gedunin phytochemicals from the PubChem database as ligands. The binding study of the compounds were analyzed by in silico docking method considering DENV RNA helicase enzyme as the receptor. After a thorough analysis of the docking scores, toxicity, and physicochemical properties, compound tetrahydrogedunin was obtained as the best. Based on tetrahydrogedunin molecular structure, 100 drug-like molecules were designed using the Data Warrior tool. After the screening process for drug-likeness and ADMET properties, the derivative number 42 was considered as the promising. Further comparative docking of derivative 42 and a standard inhibitor molecule ST-610 with DENV RNA helicase enzyme showed binding affinity as -10.0 kcal/mol and -9.6 kcal/mol, respectively. The favorable interaction between DENV RNA helicase and derivative 42 was further validated by 50 nanoseconds molecular dynamics simulation and MM-GBSA analysis. Since the antiviral activity of derivative 42 has not been reported till date, the compound was predicted as a novel therapeutic molecule that can act against the dengue virus (DENV) RNA helicase enzyme.

Molecular dynamics simulation study of nitrogen vacancy color centers prepared by carbon ion implantation into diamond

Nitrogen vacancy (NV) color centers in diamond have useful applications in quantum sensing and fluorescent marking. They can be generated experimentally by ion implantation, femtosecond lasers, and chemical vapor deposition. However, there is a lack of studies of the yield of NV color centers at the atomic scale. In the molecular dynamics simulations described in this paper, NV color centers are prepared by ion implantation in diamond with pre-doped nitrogen and subsequent annealing. The differences between the yields of NV color centers produced by implantation of carbon (C) and nitrogen (N) ions, respectively, are investigated. It is found that C-ion implantation gives a greater yield of NV color centers and superior location accuracy. The effects of different pre-doping concentrations (400–1500 ppm) and implantation energies (1.0–3.0 keV) on the NV color center yield are analyzed, and it is shown that a pre-doping concentration of 1000 ppm with 2 keV C-ion implantation can produce a 13% yield of NV color centers after 1600 K annealing for 7.4 ns. Finally, a brief comparison of the NV color center identification methods is presented, and it is found that the error rate of an analysis utilizing the identify diamond structure + coordination analysis method is reduced by about 7% compared with conventional identification methods.

Molecular dynamics simulation study of post‐transition state bifurcation: A case study on the ambimodal transition state of dipolar/Diels–Alder cycloaddition

AbstractThe potential energy surfaces for the reactions of 1,3‐butadiene with 2‐hydroxythioacrolein and 2‐aminoacrolein exhibit ambimodal transition states leading to both dipolar (4 + 3) and Diels–Alder (4 + 2) cycloaddition products, thereby demonstrating a post transition state bifurcation feature. We have investigated the bifurcation dynamics of these reactions using three molecular dynamics (MD) methods: quasi‐classical trajectory, classical MD, and ring‐polymer MD simulations. The trajectory calculations were performed with the semiempirical GFN2‐xTB method with the element‐specific parameters optimized to reproduce the density‐functional theory calculations. The effect of water solvation was examined using an implicit solvation model, revealing significant differences in bifurcation dynamic between gas‐phase and solution‐phase reactions. Nuclear quantum effects were found to play a crucial role in the proton‐transfer process from the (4 + 3) intermediate to the (4 + 3) product in the case of the 2‐aminoacrolein reaction.

Improving the mechanical shock response of aluminum by graphene composition: molecular dynamic simulation study

Improving the mechanical shock response of aluminum by graphene composition: molecular dynamic simulation study

In silico Identification of HDAC Inhibitors for Multiple Myeloma: A Structure-based Virtual Screening, Drug Likeness, ADMET Profiling, Molecular Docking, and Molecular Dynamics Simulation Study

Background: Multiple myeloma (MM) is a hematological malignancy of plasma cells that produce a monoclonal immunoglobulin protein. Despite significant advances in the treatment of MM, currently available therapies are associated with toxicity and resistance. As a result, there is an increasing demand for novel, effective therapeutics. Inhibition of histone deacetylases (HDACs) is emerging as a potential method for treating cancer. HDAC6 is one of 18 different HDAC isoforms that regulate tubulin lysine 40 and function in the microtubule network. HDAC6 participates in tumorigenesis and metastasis through protein ubiquitination, tubulin, and Hsp90. Several studies have found that inhibiting HDAC6 causes AKT and ERK dephosphorylation, which leads to decreased cell proliferation and promotes cancer cell death via the PI3K/AKT and MAPK/ERK signaling pathways. Objective: The objective of this study is to target HDAC6 and identify potent inhibitors for the treatment of multiple myeloma by employing computer-aided drug design. Materials and Methods: A total of 199,611,439 molecules from five different chemical databases, such as CHEMBL25, ChemSpace, Mcule, MolPort, and ZINC, have been screened against HDAC6 by structure- based virtual screening, followed by filtering for various drug-likeness, ADME, toxicity, consensus molecular docking, and 100 ns MD simulation. Results: Our research work resulted in three molecules that have shown strong binding affinity (CHEMBL2425964 -9.99 kcal/mol, CHEMBL2425966 -9.89 kcal/mol, and CSC067477144 -9.86 kcal/mol) at the active site HDAC6, along with effective ADME properties, low toxicity, and high stability. Inhibiting HDAC6 with these identified molecules will induce AKT and ERK dephosphorylation linked to reduced cell proliferation and promote cancer cell death. Conclusion: CHEMBL2425964, CHEMBL2425966, and CSC067477144 could be effective against multiple myeloma.

The self-assembly of water reverse micelles with imidazolium ionic liquids in supercritical carbon dioxide: A molecular dynamics simulation study

Molecular dynamics (MD) simulations were employed to investigate the self-assembly of water reverse micelles (RMs) with imidazolium ionic liquids (ILs) stabilized by dodecyl polyoxyethylene (3) polyoxypropylene (6) ether (LS-36) in supercritical carbon dioxide (scCO2) at 308K and 20MPa. The study explored the impact of various factors, including the IL concentration, the alkyl chain length of the imidazolium cations (1-ethyl-3-methylimidazolium [EMIM]+, 1-octyl-3-methylimidazolium [OMIM]+), and the anion type (bis(trifluoromethylsulfonyl)imide [NTf2]-, tetrafluoroborate [BF4]-, acetate [ACE]-) on the solubilization of ILs by water reverse micelles. The findings revealed that water, ILs, and the surfactant formed spherical RMs in the fluid phase, with varying structures depending on the hydrophobicity of the IL. The presence of ILs was found to expedite the self-assembly process and increase the number of assembled surfactants. Higher IL concentrations resulted in greater water content in the polar core of the RMs and reduced water solubility in scCO2. The intermolecular interactions occurring between components of the systems as well as dynamical properties are discussed in terms of radial distribution functions, density distribution, hydrogen bond number and lifetime, number of contacts, and self-diffusion coefficients.

Salvimulticanol from Salvia multicaulis suppresses LPS-induced inflammation in RAW264.7 macrophages: in vitro and in silico studies.

Sustained inflammatory responses can badly affect several vital organs and lead to chronic inflammation-related disorders, such as atherosclerosis, pneumonia, rheumatoid arthritis, obesity, diabetes, Alzheimer's disease, and cancers. Salvia multicaulis is one of the widely distributed plants that contains several biologically active phytochemicals and diterpenoids with anti-inflammatory effects. Therefore, finding alternative and safer natural plant-extracted compounds with good curative anti-inflammatory efficiencies is an urgent need for the clinical treatment of inflammation-related diseases. In the current study, S. multicaulis Vahl was used to extract and isolate two compounds identified as salvimulticanol and candesalvone B methyl ester to examine their effects against inflammation in murine macrophage RAW264.7 cells that were induced by lipopolysaccharide (LPS). Accordingly, after culturing RAW264.7 cells and induction of inflammation by LPS (100ng/ml), cells were exposed to different concentrations (9, 18, 37.5, 75, and 150µM) of each compound. Then, Griess assay for detection of nitric oxide (NO) levels and western blotting for the determination of inducible nitric oxide synthase (iNOS) expression were performed. Molecular docking and molecular dynamics (MD) simulation studies were employed to investigate the anti-inflammatory mechanism. Our obtained results validated that the level of NO was significantly decreased in the macrophage cell suspensions as a response to salvimulticanol treatment in a dose-dependent manner (IC50: 25.1 ± 1.2µM) as compared to the methyl ester of candesalvone B which exerted a weaker inhibition (IC50: 69.2 ± 3.0µM). This decline in NO percentage was comparable with a down-regulation of iNOS expression by western blotting. Salvimulticanol strongly interacted with both the Toll-like receptor 4 (TLR4)/myeloid differentiation factor 2 (MD-2) complex and the inhibitor of nuclear factor kappa-B (NF-κB) kinase subunit beta (IKKβ) to disrupt their inflammatory activation due to the significant hydrogen bonds and effective interactions with amino acid residues present in the target proteins' active sites. S.multicaulis is a rich natural source of the aromatic abietane diterpenoid, salvimulticanol, which exerted a strong anti-inflammatory effect through targeting iNOS and diminishing NO production in LPS-induced RAW264.7 cells in a mechanism that is dependent on the inhibition of TLR4-MD-2 and IKKβ as activators of the classical NF-κB-mediated inflammatory pathway.

Structure and Non-reactive Dynamics of the Dimeric Catalytic Domain of Human Carbonic Anhydrase IX

Despite the availability of high resolution crystal structure of the catalytic domain of human carbonic anhydrase IX (HCA IX-c), its solution structure and functional dynamics are mostly unknown. In this article, we report classical molecular dynamics (MD) simulation studies on the structure and non-reactive dynamics of dimeric HCA IX-c (d-HCA IX-c, with chains A and B) in water and compare them to each chain simulated in water as a monomeric solute (mA/mB). While the average solution structures appear to be largely similar in all systems, d-HCA IX-c shows significant deviations from mA and mB in terms of non-reactive reorganization of the active site needed to initiate the rate determining proton transfer step between a zinc-bound water and one of the sidechain N-atoms of a distal histidine residue (His-64). First, 2−6 water molecules are found to form fluctuating hydrogen bonded networks that would serve as proton paths across the active site. A minimally frustrated core of each monomer in the dimeric protein is found to be associated with a significantly higher likelihood of forming complete proton transfer pathways mediated by 2 water molecules synchronously at the two active sites hosted by the monomeric chains. The relative stability and kinetics of transition between two major sidechain rotamers of His-64 are also found to be affected by dimerization. The sidechain rotation of His-64 is found to involve at least one transition as slow as 105 per second in chain A of d-HCA IX-c thereby rendering it slower than the actual rate determining proton transfer step and suggests important deviation from the widely accepted mechanism of catalysis by HCAs.

In silico energetic and molecular dynamic simulations studies demonstrate potential effect of the point mutations with implications for protein engineering in BDNF

Protein engineering by directed evolution is time-consuming. Hence, in silico techniques like FoldX-Yasara for ∆∆G calculation, and SNPeffect for predicting propensity for aggregation, amyloid formation, and chaperone binding are employed to design proteins. Here, we used in silico techniques to engineer BDNF-NTF3 interaction and validated it using mutations with known functional implications for NGF dimer. The structures of three mutants representing a positive, negative, or neutral ∆∆G involving two interface residues in BDNF and two mutations representing a neutral and positive ∆∆G in NGF, which is aligned with BDNF, were selected for molecular dynamics (MD) simulation. Our MD results conclude that the secondary structure of individual protomers of the positive and negative mutants displayed a similar or different conformation from the NTF3 monomer, respectively. The positive mutants showed fewer hydrophobic interactions and higher hydrogen bonds compared to the wild-type, negative, and neutral mutants with similar SASA, suggesting solvent-mediated disruption of hydrogen-bonded interactions. Similar results were obtained for mutations with known functional implications for NGF and BDNF. The results suggest that mutations with known effects in homologous proteins could help in validation, and in silico directed evolution experiments could be a viable alternative to the experimental technique used for protein engineering.

Synthesis of new peptide-based macrocycles: Evaluation of their in vitro anti-proliferative activity and molecular dynamic simulation studies

A simplified synthetic protocol was adopted for the preparation of the six novel cyclo-pentapeptide candidates of the structure cyclo-(m-phthaloyl)-bis-[L-Phe -Gly/Sar]-L-Lys–X, where X = COOMe (9a,b), COOH (10a,b) and NHNH2 (11a,b). The potential cytotoxicity (IC50, μg/mL) for cyclo-pentapeptides (9a,b), (10a,b), (11a,b) and doxorubicin® as reference drugs, is assayed against eight cell lines of human cancer namely; mamillary MCF-7 and T47D, hepatic HEPG2, colon HCT116,  cell line of cervix HELA, larynx HEP2, Prostate PC3, and gut Caco. Cyclo-[m-phthaloyl chloride-bis-(L-phalanine-sar)-L-Lys]-COOH 10b was proved as cytotoxically more potent than doxorubicin against most of the screened cell lines. It can be inferred that the proposed molecular structural characteristics associated with cytotoxicity in these m-phthaloyl-bridged cyclopeptides appear noteworthy and hold promise as potential candidates for further exploration as novel anticancer agents. Molecular dynamics simulation studies of 10b into the binding site of Human Epidermal Growth Factor Receptor tyrosine kinase exhibited the highest MM-GBSA value (-16.59 kcal/mol). KEY WORDS: Anticancer, Cytotoxicity, Cyclopeptides, Cyclopeptides, m-phthaloyl-bis-peptides Bull. Chem. Soc. Ethiop. 2024, 38(4), 1129-1144.                                                        DOI: https://dx.doi.org/10.4314/bcse.v38i4.25

Unveiling the Molecular Interactions Between Human Transferrin and Limonene: Natural Compounds in Alzheimer's Disease Therapeutics.

Neurodegeneration is a term describing an irreversible process of neuronal damage. In recent decades, research efforts have been directed towards deepening our knowledge of numerous neurodegenerative disorders, with a particular focus on conditions such as Alzheimer's disease (AD). Human transferrin (htf) is a key player in maintaining iron homeostasis within brain cells. Any disturbance in this equilibrium gives rise to the emergence of neurodegenerative diseases and associated pathologies, particularly AD. Limonene, a natural compound found in citrus fruits and various plants, has shown potential neuroprotective properties. In this study, our goal was to unravel the binding of limonene with htf, with the intention of comprehending the interaction mechanism of limonene with htf. Binding was scrutinized using fluorescence quenching and UV-Vis spectroscopic analyses. The binding mechanism of limonene was further investigated at the atomic level through molecular docking and extensive 200 ns molecular dynamic simulation (MD) studies. Molecular docking uncovered that limonene interacted extensively with the deep cavity located within the htf binding pocket. MD results indicated that binding of limonene to htf did not induce substantial structural alterations, ultimately forming stable complex. The findings from fluorescence binding indicated a pronounced interaction between limonene and htf, limonene binds to htf with a binding constant (K) of 0.1×105 M-1. UV spectroscopy also advocated stable htf-limonene complex formation. The study deciphered the binding mechanism of limonene with htf, providing a platform to use limonene in AD therapeutics in context of iron homeostasis.

Numerical validation of Yukawa fluid excitations within the quasilocalized charge approximation (QLCA) theory

Numerical validation of Yukawa fluid excitations within the quasilocalized charge approximation (<scp>QLCA</scp>) theory

Development of novel 9H-carbazole-4H-chromene hybrids as dual cholinesterase inhibitors for the treatment of Alzheimer's disease.

Alzheimer's disease (AD) is a neurodegenerative disease affecting mental ability and neurocognitive functions. Cholinesterase enzymes affect concentration of acetylcholine in the brain, leading to dementia. Thus, there is an urgent need to develop novel dual cholinesterase inhibitors as possible anti-AD drugs. Herein, we have designed and synthesized a novel series of 9H-carbazole-4H-chromenes 4(a-l) through a one-pot three-component reaction of salicylaldehydes (1), hydroxycarbazole (2) and N-methyl-1-(methylthio)-2-nitroethenamine (3) using triethylamine as a catalyst in ethanol. Synthetic transformation involves the formation of two C-C bonds and one C-O bond in a single step to obtain desired analogs. The rapid one-pot reaction does not require chromatographic purification, proceeds under mild conditions, and exhibits good tolerance toward various functional groups with high synthetic yields. Synthesized compounds were screened for cytotoxicity using MTT assay in BV-2 microglial cells. These compounds were then in-vitro screened against acetylcholinesterase (AChE) and butyrylcholinestrase (BuChE) enzymes. Most of these ligands have shown dual cholinesterase inhibitory activity compared to the standard drug. In-vitro results showed that the compounds 4a and 4d have promising anticholinesterase response against both cholinesterase enzymes (4a, AChE IC50: 5.76µM, BuChE IC50: 48.98µM; 4d, AChE IC50: 3.58µM, BuChE IC50: 42.73µM). In-vitro results were validated by molecular docking and dynamic simulation at 100ns. Molecular docking and molecular dynamics simulation study strongly supported structural features present in these analogs. Together, these analogs could be exploited to develop dual anti-cholinesterase candidates to treat AD in combination with other drugs.

Effects of Chemical Composition and Cross-Linking Degree on the Thermo-Mechanical Properties of Bio-Based Thermosetting Resins: A Molecular Dynamics Simulation Study.

Bio-based epoxy resins have received significant attention in terms of concerns regarding carbon emission. Epoxidized soybean oil (ESO) derived from sustainable feedstock has been widely used to blend with traditional diglycidyl ether of bisphenol-A (DGEBA) to replace some of the petroleum-based components. In this work, molecular dynamics (MD) simulations were applied to track the network formation and predict the performance of methyl hexahydrophthalic anhydride (MHHPA)-cured ESO/DGEBA blend systems. The effects of ESO content and cross-linking degree on the mass density, volumetric shrinkage, glass transition temperature (Tg), coefficient of thermal expansion (CTE), Young's modulus, yield strength, and Poisson's ratio of the epoxy resin were systematically investigated. The results show that systems with high ESO content achieve gelation at low cross-linking degree. The Tg value, Young's modulus, and yield strength increase with the increase in cross-linking degree, but the CTE at the glassy state and Poisson's ratio decrease. The comparison results between the simulated and experimental data demonstrated that the MD simulations can accurately predict the thermal and mechanical properties of ESO-based thermosets. This study gains insight into the variation in thermo-mechanical properties of anhydride-cured ESO/DGEBA-based epoxy resins during the cross-linking process and provides a rational strategy for optimizing bio-based epoxy resins.

Physical breakdown of CH4 hydrate under stress: a molecular dynamics simulation study

As a solid energy source, CH4 hydrate will inevitably break down physically as the result of geological movement or exploitation. Here, the molecular dynamics method was employed to simulate the uniaxial-deformation behavior of structure I (sI type) CH4 hydrate under stress. The stress increases regardless of whether the hydrate is stretched or squeezed, and other physical parameters also changed, such as hydrate cage numbers, order parameters, and the number of water molecules. A noticeable difference is observed between the two systems. Upon stretching, the stress immediately recovers to 0 GPa once the hydrate is completely stretched apart. During the squeeze process, the stress is ultimately not zero since solid and liquid are always in contact. When the hydrate is stretched apart, about 5% of water molecules change from solid to liquid, about 7.8% of CH4 molecules lose their shelter and become free due to the disintegration of water cages. While in the squeezing process, large cages (51262) are crushed more easily than small cages (512); in the end, about 93.5% of large cages and 73% of small cages are crushed, and approximately 87.5% CH4 is released from the cages. In mining CH4 hydrates, caution must be exercised, as if the hydrates break as a result of stress, a large release of CH4 may pose a security risk.

Molecular dynamics simulation study on the wetting characteristics of carbon dioxide droplets on smooth and rough surfaces

A thorough investigation of the wetting behavior of carbon dioxide (CO2) is crucial for enhancing carbon capture efficiency and improving carbon storage and sequestration processes. This work investigates the wetting characteristics of CO2 droplets on smooth and rough Cu-like surfaces using molecular dynamics simulations. The results indicate that an increase in surface energy causes a linear decrease in the contact angle of CO2 droplets on smooth surfaces. An increase in temperature enhances the wetting tendency of the smooth surface toward CO2 droplets. On CO2-phobic surfaces, CO2 droplets tend to detach from the surface, causing the contact angle to increase. On neutral surfaces, CO2 droplets generally maintain wettability, with contact angles remaining almost unchanged. On CO2-philic surfaces, CO2 droplets rapidly wet and spread to form liquid film layers, causing the contact angle to decrease rapidly. In addition, constructing rough surfaces is beneficial for enhancing the surface CO2-phobic property, but the wettability of CO2 droplets varies slightly on different rough surfaces (cylindrical pillars, square pillars, and grooves), the fluctuation of contact angles of CO2 droplets on the grooved surface is relatively small. For square pillared surfaces, in contrast to smooth surfaces, as the surface energy increases, the CO2-phobic property of CO2-phobic surfaces is enhanced, and neutral surfaces can be transformed into CO2-phobic surfaces, with the CO2-philic property of CO2-philic surfaces enhanced. For CO2-phobic square pillared surfaces (α = 0.08), the wetting morphology and wetting modes of CO2 droplets on the square pillared surface are jointly influenced by both the pillar height and the interpillar spacing. When the interpillar spacing is constant, there exists a critical pillar height that can induce the transition of the wetting mode of CO2 droplets from Wenzel to Cassie state.

Mechanism analysis of CO2 separation from pvdf-supported deep eutectic solvent:A molecular dynamics simulation study

Deep eutectic solvent (DES) represent a type of environmentally friendly solvent frequently employed in the carbon capture process of two dimensional (2D) materials. The utilization of DES for CO2 separation is frequently influenced by its hydrogen bond donor − acceptor (HBD-HBA) ratio and environmental conditions, as evidenced by molecular dynamics simulations. Ultimately, these effects will manifest as microscopic alterations in the membrane's structure. The results indicate that the optimal choline chloride and ethylene glycol (ChCl/EG) molar ratio for achieving the most effective separation remains consistent at 1:6, regardless of whether the environment is high-pressure or low-pressure. Additionally, maintaining a moderate humidity environment can enhance the separation selectivity and permeability at various loading ratios of DES. The gas–liquid accumulation phenomenon is commonly observed in the initial stages of separation processes, posing a challenge to enhancing permeability. This study elucidates the gas separation transport mechanism, offering a viable approach to regulate separation efficiency and advance the development of 2D materials.