Computational Study Research Articles

Experimental and computational study of Salvia officinalis leaf extract as an eco-friendly green corrosion inhibitor for zinc in 0.5 M sulfuric acid solution

Experimental and computational study of Salvia officinalis leaf extract as an eco-friendly green corrosion inhibitor for zinc in 0.5 M sulfuric acid solution

The Use of Organoclays as Excipient for Metformin Delivery: Experimental and Computational Study

This work combines experimental and computational modeling studies for the preparation of a composite of metformin and an organoclay, examining the advantages of a Tunisian clay used for drug delivery applications. The clay mineral studied is a montmorillonite-like smectite (Sm-Na), and the organoclay derivative (HDTMA-Sm) was used as a drug carrier for metformin hydrochloride (MET). In order to assess the MET loading into the clays, these materials were characterized by means of cation exchange capacity assessment, specific surface area measurement, and with the techniques of X-ray diffraction (XRD), differential scanning calorimetry, X-ray fluorescence spectroscopy, and Fourier-transformed infrared spectroscopy. Computational molecular modeling studies showed the surface adsorption process, identifying the clay–drug interactions through hydrogen bonds, and assessing electrostatic interactions for the hybrid MET/Sm-Na and hydrophobic interactions and cation exchange for the hybrid MET/HDTMA-Sm. The results show that the clays (Sm-Na and HDTMA-Sm) are capable of adsorbing MET, reaching a maximum load of 12.42 and 21.97 %, respectively. The adsorption isotherms were fitted by the Freundlich model, indicating heterogeneous adsorption of the studied adsorbate–adsorbent system, and they followed pseudo-second-order kinetics. The calculations of ΔGº indicate the spontaneous and reversible nature of the adsorption. The calculation of ΔH° indicates physical adsorption for the purified clay (Sm-Na) and chemical adsorption for the modified clay (HDTMA-Sm). The release of intercalated MET was studied in media simulating gastric and intestinal fluids, revealing that the purified clay (Sm-Na) and the modified organoclay (HDTMA-Sm) can be used as carriers in controlled drug delivery in future clinical applications. The molecular modeling studies confirmed the experimental phenomena, showing that the main adsorption mechanism is the cation exchange process between proton and MET cations into the interlayer space.

Mapping structure-property relationships in fullerene systems: a computational study from C20 to C60

Fullerenes, as characteristic carbon nanomaterials, offer significant potential for diverse applications due to their structural diversity and tunable properties. Numerous isomers can exist for a specific fullerene size, yet a comprehensive understanding of their fundamental properties remains elusive. In this study, we construct an up-to-date computational database for C20–C60 fullerenes, consisting of 5770 structures, and calculate 12 fundamental properties using DFT, including stability (binding energy), electronic properties (HOMO-LUMO gap), and solubility (partition coefficient logP). Our findings reveal that the HOMO-LUMO gap weakly correlates with both binding energy and logP, indicating that electronic properties can be tailored for specific uses without affecting stability or solubility. In addition, we introduce a set of topological features and geometric measures to investigate structure-property relationships. We apply atom, bond, and hexagon features to effectively predict the stability of C20–C60 fullerenes, surpassing the conventional qualitative isolated pentagon rule, and demonstrating their robust transferability to larger-size fullerenes beyond C60. Our work offers guidance for optimizing fullerenes as electron acceptors in organic solar cells and lays a foundational understanding of their functionalization and applications in energy conversion and nanomaterial sciences.

Structure–Function Relationship of a Novel MTX-like Peptide (MTX1) Isolated and Characterized from the Venom of the Scorpion Maurus palmatus

Maurotoxin (MTX) is a 34-residue peptide from Scorpio maurus venom. It is reticulated by four disulfide bridges with a unique arrangement compared to other scorpion toxins that target potassium (K+) channels. Structure–activity relationship studies have not been well performed for this toxin family. The screening of Scorpio maurus venom was performed by different steps of fractionation, followed by the ELISA test, using MTX antibodies, to isolate an MTX-like peptide. In vitro, in vivo and computational studies were performed to study the structure–activity relationship of the new isolated peptide. We isolated a new peptide designated MTX1, structurally related to MTX. It demonstrated toxicity on mice eight times more effectively than MTX. MTX1 blocks the Kv1.2 and Kv1.3 channels, expressed in Xenopus oocytes, with IC50 values of 0.26 and 180 nM, respectively. Moreover, MTX1 competitively interacts with both 125I-apamin (IC50 = 1.7 nM) and 125I-charybdotoxin (IC50 = 5 nM) for binding to rat brain synaptosomes. Despite its high sequence similarity (85%) to MTX, MTX1 exhibits a higher binding affinity towards the Kv1.2 and SKCa channels. Computational analysis highlights the significance of specific residues in the β-sheet region, particularly the R27, in enhancing the binding affinity of MTX1 towards the Kv1.2 and SKCa channels.

Cobalt(II) Complex Constructed from Pyrazinecarboxamide and Aromatic Carboxylic Acid: Synthesis, Single Crystal XRD Along with Computational Study

A cobalt (II) mononuclear complex was synthesized by two-nitrobenzoic acid and pyrazine-two- carboxamide ligands in the presence of sodium bicarbonate and aqueous solution of cobalt acetate tetrahydrate. The synthesized cobalt(II) complex was characterized by single crystal X-rays diffraction. The coordination geometry of the cobalt complex was octahedral with water molecules occupying the axial sites. A lot of intermolecular interactions were in response to stabilize the supramolecular assembly which were inspected by Hirshfeld surface analysis. Enrichment ratios were calculated to find the pair of atoms having the highest propensity to form crystal packing interactions. Void analysis was conducted to forecast how the crystal would respond to applied stress. Interaction energy calculations were carried out using the B3LYP/6-31G(d,p) electron density model to identify which energy types most significantly contributed to the supramolecular assembly. Moreover, the energy data obtained from DFT calculations showed an average level of stability of the molecule. The moderate HOMO-LUMO energy gap suggested reactivity, while a high electrophilicity index indicates a strong tendency for electron-accepting reactions.

Hemodynamics study of anterior cerebral artery with different sac centerline lengths for rupture risk assessment.

The present research extensively investigates the significance of the sac centerline length of the anterior cerebral artery (ACA) on aneurysm rupture risk. Hemodynamic factors influencing aneurysm rupture are assessed to identify critical regions prone to rupture. Wall shear stress is analyzed by modeling blood flow in three real saccular ACA cases with varying sac centerline lengths. A one-way fluid-solid interaction (FSI) model is employed to examine the interaction between blood flow and vessel deformation. The computational study reveals that wall shear stress on the ACA saccular aneurysm wall is significantly higher when the sac centerline length is shorter. Conversely, the mean oscillatory index changes with different sac centerline lengths, showing that an increase in sac centerline length leads to higher blood oscillation within the sac area in ACA cases.

Pyrazine-Based Aromatic Dyes as Novel Photosensitizers with Improved Conduction Band and Photovoltaic Features: DFT Insights for Efficient Dye-Sensitized Solar Cells

Dye-sensitized solar cells (DSSCs) have garnered significant attention due to their exceptional ability to convert solar energy into electricity at a relatively low cost. Novel organic photosensitizers (FZB1-FZB9) from the pyrazine-based aromatic dye (E)-3-(5-(2,3-bis(40-(diphenylamino)-[1,10-biphenyl]-4-yl)-7 (trifluoromethyl)quinoxalin-5-yl)thiophen-2-yl)-2-cyanoacrylic acid (TPPF) have been quantum chemically modeled for their application in dye-sensitized nanocrystalline TiO2 solar cells (DSSCs). The electrochemical and photovoltaic features of modeled dyes are investigated by performing DFT insights, i.e. FMOs, absorption maxima, DOS, TDM, NBO, exciton and binding energy, radiative lifetime analysis (ꚍ), electron-injection (Δ G inject ) and regeneration analysis ( Δ G dye regen )@TiO2. FMO analysis confirmed the better electron injection as HOMO of designed dyes was found to be more positive than redox potential I/I3 (-4.8 eV), and the LUMO appeared more negative than the conduction band of TiO2 (-4.0 eV). The modeled photosensitizers exhibited red shift λmax from 338-494 nm with a lower energy gap from 5.62 eV in FZB (R) to 5.17 eV in FZB9. Bridging modification reduces the exciton and binding energy for designed dye FZB9 and FZB7 compared to reference FZB. The designed dyes appeared with a lower radiative lifetime of up to 1.32 than the reference dye of 1.63, better light harvesting efficiency (LHE), and the highest NBO charge on bridges of designed photosensitizers for enhanced light emitting efficiency. The investigated dyes exhibited more negative values for electron injection, i.e. −0.003 and the highest values of dye regeneration ( Δ G regedye regen ) up to 11.717, which unveils innovative and effective injection of electrons toward semiconductor TiO2. Among all dyes, FZB8 proved best with the novel bridging modification that enables quick charge transfer as exhibited the lowest gap (5.17 eV), lowest excitation energy, better LHE, highest charge on LUMO and more negative electron injection (Δ G inject ) . The outcomes of this computational study confirmed that this research established a new benchmark for achieving novel and efficient photosensitizers, thus recommending them for future DSSC applications.

Exhaustive computational studies on pyrimidine derivatives as GPR119 agonist for the development of compounds against NIDDM

BackgroundType-2 Diabetes (T2DM) is a long-term medical disorder characterized by Insulin deficiency and high blood glucose levels. Among other medications to cure T2DM, the review of the literature found that various Pyrimidine derivatives act as an agonist for G-protein-coupled receptor 119 (GPR119) was proposed to control blood glucose levels by enhancing the function of pancreatic Beta-cells and its mechanism of action with fewer adverse effects. In the present research work, In-silico investigations were carried out to investigate the potential of the Pyrimidine analog as an agonist to the protein target GPR119 receptor. We performed exhaustive molecular modeling and protein modeling methodologies such as homology modeling, and molecular docking along with various drug designing tools such as 3D-QSAR and Pharmacophore Mapping to ascertain the design of better GPR119 agonists.ResultsBased on in-depth computational studies, we designed new pyrimidine moiety and analyzed them for GPR119 receptor agonist and further explored the ADMET properties. Designed compounds were found to exhibit better-predicted activities as compared to reference compound.ConclusionsThe current research on pyrimidine derivatives, using molecular docking, 3D-QSAR and Pharmacophore mapping demonstrated that the obtained computational model has significant properties and the designed molecules and Dataset from this model, produced antidiabetic compound against the target GPR119 i.e., compound 1S, 1Z and 1D with the docking score of − 11.696, − 9.314 and − 8.721, respectively. The pharmacokinetics and drug-likeness studies revealed that these compounds may be the future candidates for the treatment of diabetes acting via the GPR119 agonist mechanism.

Red blood cell passage through deformable interendothelial slits in the spleen: Insights into splenic filtration and hemodynamics

The spleen constantly clears altered red blood cells (RBCs) from the circulation, tuning the balance between RBC formation (erythropoiesis) and removal. The retention and elimination of RBCs occur predominantly in the open circulation of the spleen, where RBCs must cross submicron-wide inter-endothelial slits (IES). Several experimental and computational studies have illustrated the role of IES in filtrating the biomechanically and morphologically altered RBCs based on a rigid wall assumption. However, these studies also reported that when the size of IES is close to the lower end of clinically observed sizes (less than 0.5 μm), an unphysiologically large pressure difference across the IES is required to drive the passage of normal RBCs, sparking debates on the feasibility of the rigid wall assumption. In this work, We propose two deformable IES models, namely the passive model and the active model, aiming to explore the impact of the deformability of IES on the filtration function of the spleen. In the passive model, we implement the worm-like string model to depict the IES’s deformation as it interacts with blood plasma and allows RBC to traverse. In contrast, the active model involved regulating the IES deformation based on the local pressure surrounding the slit. To demonstrate the validity of the deformable model, we simulate the filtration of RBCs with varied size and stiffness by IES under three scenarios: (1) a single RBC traversing a single slit; (2) a suspension of RBCs traversing an array of slits, mimicking in vitro spleen-on-a-chip experiments; (3) RBC suspension passing through the 3D spleen filtration unit known as’the splenon’. Our simulation results of RBC passing through a single slit show that the deformable IES model offers more accurate predictions of the critical cell surface area to volume ratio that dictate the removal of aged RBCs from circulation compared to prior rigid-wall models. Our biophysical models of the spleen-on-a-chip indicate a hierarchy of filtration function stringency: rigid model > passive model > active model, providing a possible explanation of the filtration function of IES. We also illustrate that the biophysical model of ‘the splenon’ enables us to replicate the ex vivo experiments involving spleen filtration of malaria-infected RBCs. Taken together, our simulation findings indicate that the deformable IES model could serve as a mesoscopic representation of spleen filtration function closer to physiological reality, addressing questions beyond the scope of current experimental and computational models and enhancing our understanding of the fundamental flow dynamics and mechanical clearance processes within in the human spleen.

Robust lipid scrambling by TMEM16 proteins requires an open groove and thin membrane.

Biological membranes are complex and dynamic structures with different populations of lipids on their inner and outer leaflets. The Ca<2+/>-activated TMEM16 family of membrane proteins play an important role in collapsing this asymmetric lipid distribution by spontaneously, and bidirectionally, scrambling phospholipids between the two leaflets, which can initiate signaling and alter the physical properties of the membrane. While evidence shows that lipid scrambling occurs via an open hydrophilic pathway ("groove") that spans the membrane, it remains unclear if all family members facilitate lipid movement in this manner. Here we present a comprehensive computational study of lipid scrambling by all TMEM16 members with experimentally solved structures. We performed coarse-grained molecular dynamics (MD) simulations of 27 structures from five different family members solved under activating and non-activating conditions, and we captured over 700 scrambling events in aggregate. This enabled us to directly compare scrambling rates, mechanisms, and protein-lipid interactions for fungal and mammalian TMEM16s, in both open (Ca<2+/>-bound) and closed (Ca<2+/>-free) conformations with statistical rigor. We show that nearly all (>90%) scrambling occurs in the dilated groove and the degree of induced membrane thinning positively correlates with the scrambling rate. Surprisingly, we also observed 60 scrambling events that occurred outside the canonical groove, over 90% of which took place at the dimer-dimer interface in mammalian TMEM16s. This new site suggests an alternative mechanism for lipid scrambling in the absence of an open groove.

How pairs of insertion mutations impact protein structure: An exhaustive computational study

How pairs of insertion mutations impact protein structure: An exhaustive computational study

Synthesis, antimicrobial activity and computational studies on (E)-N-(2((4-chlorobenzylidine)amino)ethyl)napthalen-1-amine

The novel Schiff bases were synthesized by combining N1-(Napthalen-1-yl)ethane 1,2-diamine with chlorine-substituted benzaldehyde. The compound is designated as (E)-N-(2((4-chlorobenzylidine)amino)ethyl)napthalen-1-amine (4CLB). This structure was verified by experimental techniques including infrared, NMR, fluorescence, UV, and theoretical methods. Using the B3LYP functional the titled compound computational study was executed. The results for infrared and NMR analysis of the molecule exhibited a significant degree of agreement in both observed and simulated. The reactivity characteristics of 4CLB were computed. The microbiological efficacy of the compound was assessed against multiple Gram-positive bacteria S. aureus, S pneumonia, and Bacillus subtilis. The compound was tested against the following Gram-negative bacteria: Klebsiella pneumonia, E coli, and Proteus vulgaris. The compound Schiff base exhibits the most effective antibacterial activity against all microbes. The 4CLB compound quantum calculations have a strong correlation with antibacterial activity. The compound has non-covalent Hydrogens, these Hydrogens are bonded with the corresponding proteins. It is checked by molecular docking in the Auto Dock software.

Potential Role of Tarantula Venom Peptides in Targeting Human Death Receptors: A Computational Study

Potential Role of Tarantula Venom Peptides in Targeting Human Death Receptors: A Computational Study

The effect of torus tubarius size on upper airway aerodynamics in children: a computational fluid dynamics study.

Some children with sleep-disordered breathing (SDB) continue to experience symptoms after adenotonsillectomy. One possible cause is the excessive size of the torus tubarius. In this study, the relationship between torus tubarius size and surgical outcome in 24 children with SDB who underwent adenotonsillectomy was retrospectively analyzed based on cone beam computed tomography (CBCT) imaging measurements and medical records. A computational fluid dynamics (CFD) approach was used to quantitatively compare the effects of different torus tubarius sizes on upper airway (UA) aerodynamics in children. The percentage of UA area occupied by the torus tubarius (TTA%) was significantly different between the excellent and poor groups (10.4 ± 3.58% vs. 17.71 ± 4.7%, p < 0.001). The results of CFD simulation showed that the mean airflow velocity, wall shear stress (WSS) and pressure drop (ΔP) in the nasopharynx significantly increased when the TTA% was > 15%. Our study confirmed the effect of round pillow size on the aerodynamics of the UA in children. When the TTA% exceeds 15%, it causes change in aerodynamics, which may affect the outcome of children with SDB.

Prediction of Turbulent Boundary Layer Flow Dynamics with Transformers

Time-marching of turbulent flow fields is computationally expensive using traditional Computational Fluid Dynamics (CFD) solvers. Machine Learning (ML) techniques can be used as an acceleration strategy to offload a few time-marching steps of a CFD solver. In this study, the Transformer (TR) architecture, which has been widely used in the Natural Language Processing (NLP) community for prediction and generative tasks, is utilized to predict future velocity flow fields in an actuated Turbulent Boundary Layer (TBL) flow. A unique data pre-processing step is proposed to reduce the dimensionality of the velocity fields, allowing the processing of full velocity fields of the actuated TBL flow while taking advantage of distributed training in a High Performance Computing (HPC) environment. The trained model is tested at various prediction times using the Dynamic Mode Decomposition (DMD) method. It is found that under five future prediction time steps with the TR, the model is able to achieve a relative Frobenius norm error of less than 5%, compared to fields predicted with a Large Eddy Simulation (LES). Finally, a computational study shows that the TR achieves a significant speed-up, offering computational savings approximately 53 times greater than those of the baseline LES solver. This study demonstrates one of the first applications of TRs on actuated TBL flow intended towards reducing the computational effort of time-marching. The application of this model is envisioned in a coupled manner with the LES solver to provide few time-marching steps, which will accelerate the overall computational process.

Ebola Virus Matrix Protein VP40 Single Mutations G198R and G201R Significantly Enhance Plasma Membrane Localization.

Viral proteins frequently undergo single or multiple amino acid mutations during replication, which can significantly alter their functionality. The Ebola virus matrix protein VP40 is multifunctional but primarily responsible for creating the viral envelope by binding to the inner leaflet of the host cell plasma membrane (PM). Changes to the VP40 surface cationic charge via mutations can influence PM interactions, resulting in altered viral assembly and budding. A recent mutagenesis study evaluated the effects of several mutations and found that mutations G198R and G201R enhanced VP40 assembly at the PM and virus-like particle budding. These two mutations lie in the loop region of the C-terminal domain (CTD), which directly interacts with the PM. To understand the role of these mutations in PM localization at the molecular level, we performed both all-atom and coarse-grained molecular dynamics simulations using a dimer-dimer configuration of VP40, which contains the CTD-CTD interface. Our studies indicate that the location of mutations on the outer surface of the CTD regions can lead to changes in membrane binding orientation and degree of membrane penetration. Direct PI(4,5)P2 interactions with the mutated residues seem to further stabilize and pull VP40 into the PM, thereby enhancing interactions with numerous amino acids that were otherwise infrequently or completely inaccessible. These multiscale computational studies provide new insights at the atomic and molecular level as to how VP40-PM interactions are altered through single amino acid mutations. Given the high case fatality rates associated with Ebola virus disease in humans, it is essential to explore the mechanisms of viral assembly in the presence of mutations to mitigate the severity of the disease and understand the potential of future outbreaks.

Synthesis and computational studies for halide‐free, neutral, and bifunctional one‐component ferrocene‐based catalysts for the coupling of carbon dioxide and epoxides

Synthesis and computational studies for halide‐free, neutral, and bifunctional one‐component ferrocene‐based catalysts for the coupling of carbon dioxide and epoxides

Computational study of Rubidium-Rb based cubic Rb2TlCoF6 double perovskite material for photocatalytic water degradation applications: A DFT investigations

The fascinating characteristics, such as straightforward and stable crystal structure, and double perovskites are currently popular materials for applications in renewable energy. In our study, we applied CASTEP and DFT, called density functional theory, to theoretically investigate the mechanical, optical, and thermoelectric characteristics of cubic Rb2TlCoF6. Calculations of the compound Rb2TlCoF6's structural, electrical, optical, mechanical, and thermodynamic properties are made using the GGA-PBE exchange correlational functional and the Fm3m with space group no.225 vol and compound lattice constant are 9.08 Å and 748.613 Å3, respectively. For Rb2TlCoF6, the measured energy band gaps are 1.45 eV. The mechanical and elastic constants are calculated to confirm the ductile properties of Rb2TlCoF6. The brittle characteristics have been verified using Passion and Pugh's ratios, which are 1.67 and 0.25, according to elastic constants. Vickers compound hardness Hv and anisotropy factor “A” are 4.19 and 0.77, respectively. The compounds' optical characteristics reveal significant conductivity and absorption. The compound exhibits high-efficiency photocatalytic activity based on its optical characteristics. Based on mechanical stability, such as Debye temperature, melting temperature, minimum thermal conductivity, average sound velocity, free energy, and other variables, the thermodynamic and structural stabilities are calculated. These materials controlled electrical and other properties make them potentially useful in photocatalytic applications. According to the outcomes, Rb2TlCoF6 is appropriate for photocatalytic water-splitting applications and water deterioration.

Elucidating the binding dynamics and structural impacts of Pt(II) and Pd(II) complexes on human serum albumin: A comprehensive spectroscopic and computational study

The binding of drugs to plasma proteins, such as human serum albumin (HSA), encompasses two main functions: depot and transport, which are performed by these proteins. This binding has significant pharmacodynamic and pharmacokinetic consequences. 2-(furan-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline 1,2-diamino cyclohexane platinum (Pt(II)) or palladium (Pd(II)) complexes, have a similar structure. These new synthetic complexes have desirable anticancer activity, and the binding of these complexes with HSA was investigated. Spectroscopic and thermodynamic analyses indicate that the interactions between HSA and the complexes occur spontaneously with the static-dynamic quenching mechanism. However, the interactions are primarily driven by noncovalent forces such as hydrophobic interactions and π–π stacking, as evidenced by the positive enthalpy and entropy values associated with these complexes. In the circular dichroism (CD) results, HSA had fewer structural changes with the addition of the Pt(II) than the Pd(II) complex. Docking studies were performed at three Sudlow sites, I, II, and III, to identify the complex’s binding site on HSA. The reactive sites of HSA to Pt(II) and Pd(II) complexes mainly reside within its hydrophobic cavity in domain II (site II). Furthermore, molecular dynamics simulations showed low RMSD, Rg, and binding energy values during the 400 ns for the Pt(II) complex. The results suggest that the connection between the Pt(II) complex and HSA is reversible. The Pt(II) complex was a more desirable candidate than the Pd(II) complex. The results of the experimental methods are consistent with those of dynamic simulation and molecular docking methods, indicating that HSA is more stable in the presence of the Pt(II) complex.

Comprehensive structural investigation of a potent and selective CXCR4 antagonist via crosslink modification

Macrocyclization presents a valuable strategy for enhancing the pharmacokinetic and pharmacodynamic profiles of short bioactive peptides. The exploration of various macrocyclic characteristics, such as crosslinking tethers, ring size, and orientation, is generally conducted during the early stages of development. Herein, starting from a potent and selective C-X-C chemokine receptor 4 (CXCR4) cyclic heptapeptide antagonist mimicking the N-terminal region of CXCL12, we demonstrated that the disulfide bridge could be successfully replaced with a side-chain to side-chain lactam bond, which is commonly not enlisted among the conventional disulfide mimetics. An extensive investigation was carried out to explore the chemical space of the resulting peptides, including macrocyclization width, stereochemical configuration, and lactam orientation, all of which were correlated with biochemical activity. We identified a novel heptapeptide that fully replicates the pharmacological profile of the parent peptide on CXCR4, including its potency, selectivity, and antagonistic activity, while demonstrating enhanced stability in a reductive environment. At this stage, computational studies were instructed to shed light on how the lactam cyclization features influenced the overall structure of 21 and, in turn, its ability to interact with the receptor. We envisage that these findings can give new momentum to the use of lactam cyclization as a disulfide bond mimetic and contribute to the enhancement of the repertoire for peptide-based drug development, thereby paving the way for novel avenues in therapeutic innovation.