Number Of Hydrogen Bonds Research Articles

A Bio-Based Polybenzoxazine Derived from Diphenolic Acid with Intrinsic Flame Retardancy, High Glass Transition Temperature and Dielectric Properties.

A bio-based benzoxazine monomer, diphenolic methyl ester hexafluoro diamino benzoxazine (DPME-HFBz), was successfully synthesized from diphenolic acid (DPA), and the chemical structure was successfully verified. The curing kinetics were studied via non-isothermal differential scanning calorimetry (DSC). The activation energies of DPME-HFBz were calculated by Kissinger and Ozawa methods to be 136.15 and 139.92 kJ/mol, respectively, and the reaction order was calculated to be first order. Owing to the large number of hydrogen bonds after polymerization, poly(DPME-HFBz) presented an ultra-high glass transition temperature of 312 °C and a high initial decomposition temperature (350 °C under air and 345 °C under nitrogen). Because of the excellent charring ability (50.2% residue under nitrogen), the LOI value of poly(DPME-HFBz) was as high as 38%. Poly(DPME-HFBz) also exhibited a very low heat release capacity (HRC) of 90 J/(g·K). In addition, poly(DPME-HFBz) had a dielectric constant (Dk) of 1.88 at 1.5 MHz, which was much lower than the Dk of the reported low-dielectric polymers. This work provides an efficient and sustainable strategy for the synthesis of benzoxazine thermosetting materials with excellent comprehensive properties.

Nuclear Magnetic Resonance (NMR) and Density Functional Theory (DFT) Study of Water Clusters of Hydrogen-Rich Water (HRW)

The present study investigated the 1H Nuclear Magnetic Resonance (NMR) spectra of hydrogen-rich water (HRW) produced using the EVObooster device. The analyzed HRW has pH = 7.1 ± 0.11, oxidation–reduction potential (ORP) of (−450 ± 11) mV, and a dissolved hydrogen concentration of 1.2 ppm. The control sample was tap water filtered by patented technology. A 600 NMR spectrometer was used to measure NMR spectra. Isotropic 1H nuclear magnetic shielding constants of the most stable clusters (H2O)n with n from 3 to 28 have been calculated by employing the gauge-including-atomic-orbital (GIAO) method at the MPW1PW91/6-311+G(2d,p) density function level of theory (DFT). The HRW chemical shift is downfield (higher chemical shifts) due to increased hydrogen bonding. More extensive formations were formed in HRW than in control filtered tap water. The exchange of protons between water molecules is rapid in HRW, and the 1H NMR spectra are in fast exchange mode. Therefore, we averaged the calculated chemical shifts of the investigated water clusters. As the size of the clusters increases, the number of hydrogen bonds increases, which leads to an increase in the chemical shift. The dependence is an exponential saturation that occurs at about N = 10. The modeled clusters in HRW are structurally stabilized, suggesting well-ordered hydrogen bonds. In the article, different processes are described for the transport of water molecules and clusters. These processes are with aquaporins, fusion pores, gap-junction channels, and WAT FOUR model. The exponential trend of saturation shows the dynamics of water molecules in clusters. In our research, the chemical shift of 4.257 ppm indicates stable water clusters of 4–5 water molecules. The pentagonal rings in dodecahedron cage H3O+(H2O)20 allow for an optimal arrangement of hydrogen bonds that minimizes the potential energy.

Investigation of Adsorption and Young’s Modulus of Epoxy Resin–Sand Interfaces Using Molecular Dynamics Simulation

Epoxy resins exhibit outstanding curability, durability, and environmental compatibility, rendering them extensively utilized in the realm of engineering curing. Nevertheless, the current curing mechanism of epoxy-based resins in cohesion with sand remains inadequately elucidated, significantly impeding their applicability within the domain of soil curing. This study employed molecular dynamics simulations to investigate the adsorption behavior of three distinct types of epoxy resins on the sand surface: diglycidyl ether of bisphenol-A epoxy resin (DGEBA), diglycidyl ether 4,4′-dihydroxy diphenyl sulfone (DGEDDS), and aliphatic epoxidation of olefin resin (AEOR). The objective was to gain insights into the interactions between the sand surface and the epoxy resin polymers. The results demonstrated that DGEDDS formed a higher number of hydrogen bonds on the sand surface, leading to stronger intermolecular interactions compared to the other two resins. Furthermore, the mechanical properties of the adsorbed models of the three epoxy resins with sand were found to be relatively similar. This similarity can be attributed to their comparable chemical structures. Finally, analysis of the radius of gyration for the adsorbed epoxy resins revealed that AEOR exhibited a rigid structure due to strong molecular interactions, while DGEDDS displayed a flexible structure owing to weaker interactions.

A molecular insight into asphalt-aggregate interfacial debonding: The role of hydrogen bonds in water molecule migration

In this study, molecular dynamics were employed to compare the angles, lengths, and numbers of hydrogen bonds between water molecules and different aggregates. Compared to quartz, calcite has shorter bond lengths, larger bond angles, and a greater number of bonds with water molecules. The differences in hydrogen bonds lead to the formation of a three-layer structure on the calcite surface by water molecules: ordered, relatively ordered, and disordered, while a two-layer structure—relatively ordered and disordered—is formed on the quartz surface. In the ordered layer, water molecules experience the strongest hydrogen bonding, are neatly arranged, and have low diffusion coefficients. In contrast, the disordered layer is characterized by weaker hydrogen bonding, random arrangement, and higher diffusion coefficients. The movement path of water molecules shows that the debonding of asphalt and aggregate is jointly influenced by the migration behavior of both the underlying and upper-layer water molecules. These findings reveal the microscopic mechanism of water molecules forming a wedge shape at the asphalt-aggregate interface from the perspective of hydrogen bonds, explaining why the constraint of water on the Calcite {214} and Calcite {018} surfaces is stronger compared to Calcite {1 0 4}, but the bonding energy with asphalt decays more rapidly.

Identification and anticoagulant mechanisms of novel factor XIa inhibitory peptides by virtual screening of a in silico generated deep-sea peptide database

The objective of this study was to identify novel anticoagulant peptides from the deep-sea using multiple in silico methods, and to investigate their inhibitory activity and molecular mechanisms. A deep-sea peptide database was firstly constructed by performing virtual proteolysis on protein sequences from animals inhabiting deep-sea hydrothermal vents and cold seeps. Candidate anticoagulant peptides were identified through molecular docking and binding free energy screening against FXIa as the target. Two novel anticoagulant peptides, PRNIF (IC50 = 0.67 mM) and GNDRCL (IC50 = 1.52 mM), were identified, and their anticoagulant activities were verified in vitro. PRNIF was demonstrated to be a noncompetitive inhibitor of FXIa, and caused significant prolongation of the thrombin time (TT) and the activated partial thromboplastin time (APTT), whereas GNDRCL markedly prolonged only APTT. Molecular dynamics simulations demonstrated considerable conformational shifts of both anticoagulant peptides when bound to the active sites of FXIa. The lowest energy binding poses of the FXIa-peptide complexes for PRNIF and GNDRCL exhibited comparable numbers of hydrogen bonds and binding free energies. However, occupancy analysis revealed completely distinct stability characteristics of the hydrogen bond interactions. The conserved residue Asp569 in the S1 pocket of FXIa formed strong and stable hydrogen bonds as well as a salt bridge with the arginine residues of PRNIF, which were not observed in the FXIa-GNDRCL complex. To our knowledge, PRNIF represented the first FXIa inhibitory peptide derived from the deep-sea, which may contribute to the development and utilization of deep-sea peptides resources. Two deep-sea peptides may potentially serve as an alternative food-derived ingredient that could be utilized for thrombosis prevention.

Dynamics of impure CO2 and composite oil in mineral nanopores: Implications for shale oil recovery and gas storage performance

Evaluating the application effectiveness of impure CO2 in shale reservoirs is a prerequisite for reducing CO2 purification costs. Therefore, molecular dynamics simulations were applied to study the influential mechanisms of impurity gases, mineral types and oil components on impure CO2 enhanced oil recovery (impure CO2-EOR) and gas storage (GS). The orientation force between H2S and polar oil components and the strong adsorption of H2S on mineral walls improve the solubility and diffusivity of impure CO2 in shale oil. Moreover, the induction force between H2S and CO2 carry additional CO2 to walls, and the hydrogen bonds formed between H2S and walls further enhance oil–gas competitive adsorption, resulting in more adsorbed oil being stripped and more H2S/CO2 being sequestered. N2 hinders the dissolution of H2S/CO2 into shale oil and the diffusion of desorbed oil towards the center of nanopores. Therefore, the EOR and GS performances in nanopores are positively and negatively correlated with the proportion of H2S and N2 in impure CO2, respectively. Both EOR and GS performances of impure CO2 decrease sequentially in illite, quartz, and kerogen nanopores, because the strong adsorption of shale oil on kerogen walls causes oil molecules to arrange tightly and dissolve in kerogen. It weakens the solubility and diffusivity of impure CO2 in shale oil, and also increases the resistance of impure CO2 to displace adsorbed and dissolved oil. By contrast, illite walls have the weakest adsorption on shale oil and the largest number of hydrogen bonds formed with H2S. The increase of heavy component content further enhances the interaction between oil molecules and the adsorption of shale oil on wall, thereby weakening the effects of various impure CO2-EOR mechanisms.

Formation and Dynamics of Imidazole Supramolecular Chains Investigated by Deep Potential Molecular Dynamics Simulation.

Imidazole-based materials have attracted considerable attention due to their promising potential for facilitating anhydrous proton transport at high temperatures. Herein, a machine learning-based deep potential (DP) model for bulk imidazole with first-principles accuracy is developed. The trained model exhibits remarkable accuracy in predicting energies and forces, with minor errors of 4.71 × 10-4 eV/atom and 3.23 × 10-2 eV/Å, respectively. Utilizing DP molecular dynamics simulations, we have systematically investigated the temperature-dependent formation and dynamics of imidazole supramolecular chains through the partial radial distribution function, quantification of hydrogen bond numbers, incoherent intermediate scattering function, and diffusion coefficient. The findings reveal the influence of temperature on the proton transport path following either the "Grotthuss" and "vehicle" mechanism.

In silico sequential mutagenesis of the Carbohydrate Binding Module Family 32 (CBM32) enhances ligand binding affinity

Alginate lyase is a promising target for genetic modification for its degrading biofilm, contributing to bacterial proliferation and antimicrobial resistance. Apart from the main enzyme, the carbohydrate binding module (CBM) component can also be modified to enhance alginate lyase’s activity. This study aimed to perform sequential in silico mutagenesis, molecular docking of selected amino acid residues of Vibrio splendidus CBM32 and performed molecular dynamics (MD) simulations of the mutated structure to validate its ligand-binding efficacy. Seven residues were selected for mutagenesis based on the predicted bonds that formed between the CBM32 and the glucuronic acid ligand (LGU9). Four of seven sequential residue substitutions increased the ligand binding affinity cumulatively from -5.4 Kcal/mol to -6.9 Kcal/mol. The mutated CBM32 had similar MolProbity scores to the original V. splendidus CBM32 structure. From the post-MD simulation analysis, the mutated CBM32 had higher structural stability in a solvent system, a greater number of hydrogen bonds formed with ligand but a lower solvent-accessible surface area than the original structure. The sequential mutagenesis process significantly increased the ligand binding affinity of CBM32 while incurring a minimal change in the overall CBM32 structure. The information on these substituted residues would be beneficial for designing subsequent in vitro mutagenesis and enzymatic assays.

Ab Initio Molecular Dynamics Studies of Stacked Adenine–Thymine and Guanine–Cytosine Nucleic Acid Base Pairs in Aqueous Solution

Ab initio MD studies have been performed on stacked adenine–thymine (A–T) and guanine–cytosine (G–C) nucleobase pairs solvated in water using Born–Oppenheimer molecular dynamics. These two systems have been analyzed using RDF, SDF, angle–distance CDF (combined distribution functions), plane projection analysis, hydrogen bond analysis, and non–covalent interaction (NCI) plots. The stacking property studies have shown that the molecular orientation of the A–T pair is completely opposite to that of the G–C pair though the center of mass distance between the two molecules is similar. The G–C pair shows significantly more stability in water than the A–T system does. RDF analyses show that the –NH– group and carbonyl groups show predominant interaction with water molecules. Water molecules are found to be most in numbers around the cytosine molecule and least around the adenine molecule. Hydrogen bonding studies show that the guanine molecule forms the highest number of hydrogen bonds with water molecules. On the other hand, the hydrogen atom attached to the –NH– group of adenine molecule shows the longest mean H–bond lifetime with water oxygen atoms. NCI interactions calculated through the ab initio method help us to visualize the [Formula: see text]-electron stacking and H–bonding between aromatic nucleobases and water molecules. A great shift in bond polarity and interaction intensity in different functional groups is observed for the nucleobases going from individually solvated molecules to paired states.

Deciphering the 4',7-Dihydroxy-3'-Methylflavone from Boerhavia, Agonist/Antagonist Interactions Against 5-HT2 Receptors using Homology Modeling, Molecular Docking, and Dynamic Simulation Studies.

Seizures, depression, and anxiety are neurological disorders that affected innumerable people worldwide. Recent research has revealed that targeting 5-hydroxytryptamine 2 (5-HT2) receptors can help suppress these conditions. An in-depth literature study has identified that phytocompounds from the Boerhavia genus could reduce seizures. Therefore, homology models of 5-HT2 receptors were generated and validated using techniques such as the alignment of amino acid sequences and the Ramachandran plot. Later, a comparison of modeled structures was made with a non-redundant set of PDB structures. The pharmacokinetics, drug-likeness, blood-brain barrier (BBB) permeability, and Lipinski's rule of five shed light on 22 phytocompounds, which are the potential candidates for molecular docking among 127 Boerhavia's bioactive. Notably, molecular docking analysis revealed 4',7-dihydroxy-3'-methylflavone as the most potent lead compound, which has a strong binding affinity to all modeled receptors. Additionally, with a remarkably high docking score of -9.1 kcal/mol, 4',7-dihydroxy-3'-methylflavone showed promising interactions, particularly with 5-HT2A receptor, as seen from the RMSD, SASA, Rg, and number of hydrogen bonds during 100 ns molecular dynamic (MD) simulation. Principal component analysis (PCA) and Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) further confirmed that 4',7-dihydroxy-3'-methylflavone is the best novel phytocompound in Boerhavia genus for 5-HT2 receptor as agonist/antagonist activity against seizures.

Study on the Influence Mechanism of Hot Flue Gas Injection Pressure on the Wettability of Anthracite Coal: From the Perspective of Molecular Dynamics.

A multicomponent wetting model of coal-water-methane-hot flue gas was hereby constructed to investigate the influence of complex components of hot flue gas on coal wettability. Besides, whether it is feasible to use the NIST method to capture the system pressure was verified from a microscopic perspective. Moreover, how the interaction energy and hydrogen bonds between water and coal, the spreading length of water nanodroplets in the X-direction, and the three-phase contact angle vary with the hot flue gas injection pressure were discussed. Here are the findings: (1) The absolute value of interaction energy between water and coal is negatively correlated with the pressure. In addition, the gradient of decrease shrinks continuously when the pressure rises. (2) As the pressure rises, a decline is monitored in both the number of hydrogen bonds and the spreading length of water nanodroplets in the X-direction, and a critical pressure value exists around 32.64 MPa, which divides the variation into two stages, i.e., rapid decrease and slow decrease. (3) The three-phase contact angle grows with the rise of pressure, and its critical pressure value is similar to that of number of hydrogen bonds and spreading length. In addition, it is found that the density of the gas adsorption layer augments as the pressure rises, which can be seen that a higher injection pressure is favorable for gas wetting. These research observations brought to light that appropriately raising the hot flue gas injection pressure can promote the transition of wetting mode from water wetting to gas wetting, which is of great benefit for relieving the water lock effect and effectively improving the transportation environment of gas.

Research on the Synergistic Inhibition of Angiotensin-Converting Enzyme (ACE) by the Gastrointestinal Digestion Products of the ACE Inhibitory Peptide FPPDVA.

To gain a deeper understanding of the ACE inhibition effect, the inhibitory effect of ACE-inhibiting peptide (ACEIP) FPPDVA's digestive products on ACE was further investigated. Two novel peptides, PD (IC50 = 161.1 ± 1.10 μM) and DV (IC50 = 66.51 ± 0.99 μM) were identified in the digestive products of FPPDVA using LC-MS/MS. The Peptide Mix (FPPDVA, PD, and DV) exhibited a remarkable synergistic effect on ACE inhibition by significantly enhancing it by up to 508% compared to the individual peptides alone. Furthermore, theoretical simulations suggest that the Peptide Mix synergistically inhibits ACE activity by forming more stable complexes with the active site of ACE, facilitated by an increased number of hydrogen bonds. Additionally, Lineweaver-Burk plot analysis and spectroscopic studies further verified the presence of these stable complexes. ITC results show that the combination of Peptides Mix and ACE is a spontaneous exothermic process driven by entropy. The study showed that FPPDVA has a stronger inhibitory effect on ACE after digestion, making it suitable as an antihypertensive peptide in functional foods.

Determining the Identity of Nucleotides and the Energy of Binding of tRNAs to Their Aminoacyl-tRNA Synthetases Using a Simple Logistic Model

This study showed that the predictor in logistic regression can be applied to estimating the Gibbs free energy of tRNAs’ recognition of and binding to their aminoacyl-tRNA synthetases. Then, 24 linear logistic regression models predicting different classes of tRNAs loaded with a corresponding amino acid were trained in a machine learning classification method, reducing the misclassification error to zero. The models were based on minimal subsets of Boolean explanatory variables describing the favorite presence of nucleotides or nucleosides localized in the different parts of the tRNA. In 90% of cases, they agree with the components of the consensus strand in a class of tRNAs loaded by a given amino acid. According to the proposed theoretical model, the values of the free energy for the entry of the recognition state in the process of tRNA charging were obtained, and the inputs from identity nucleotides and the tRNA strand backbone were distinguished. Almost all the resulting models indicated leading anticodon tandems defining the first and second positions of the anticodon (positions 35 and 36 of the tRNA strand) and the small sets (up to six positions) of the other nucleotides as the natural identity nucleotides most influential in the free energy balance. The magnitude of their input to this energy depends on the position in the strand, favoring positions −1, 35, and 36. The role of position 34 is relatively smaller. These identity attributes may not always be fully arranged in a real single adaptor molecule but were comprehensively present in a given tRNA class. A detailed analysis of the resulting models showed that the absolute value of the energy of binding the tandem 35–36 decreases with the number of identity positions, as well as with the decreasing number of possible hydrogen bonds. On the other hand, in these conditions, the absolute value of the energy of binding of other identity nucleotides increases. All the models indicate that the nucleotide-independent energy of the repulsion tRNA backbone decreases with the number of identity nucleotides. It was also shown that the total free energy change in entering the recognition state increases with the amino acid mass, making this process less spontaneous, which may have an evolutionary reference.

Effect of external force on the dispersion of particles and permeability of substances via carbon nanotubes in reverse electrodialysis using molecular dynamics simulation

BackgroundUsing novel technologies and solutions is crucial for producing clean water. There are different ways to remove dissolved salts from water. MethodsThis study aimed to analyze the effect of an external force (EF) on the morphology of channels, the dispersion of particles, and the permeability of substances via carbon nanotubes in reverse electrodialysis. It was done using a computer simulation that studied the movement of molecules. This research aimed to study the effect of EF on the dispersion of particles and permeability of substances via carbon nanotubes using a reverse electrodialysis approach. The results show that increasing the EF from 0.0001 to 0.0005 eV/Å increased the electric current and fluid flow intensity from 5.31 e/ns and 211.31 atom/ns to 5.62 e/ns and 263.01 atom/ns. Moreover, the density decreased from 4.83 to 4.66 atom/nm3. Furthermore, the number of broken hydrogen bonds increased from 116 to 166. Significant findingsBy understanding the effect of EF on particle movement and material passage through carbon nanotubes, researchers can optimize the design of reverse electrodialysis systems to enhance their performance. This can lead to more effective and cost-efficient water treatment solutions, crucial for producing clean water.

A novel and sustainable approach to efficiently modify cotton material via a physical flash-explosion with sub- or SCF-CO2 as medium

A novel and eco-friendly approach to modify natural cotton fiber by flash-explosion with a sub- or supercritical fluid of carbon dioxide (sub- or SCF-CO2) for improving its structure and properties was constructed for the first time. The achieved results demonstrate that remarkable improvements in the coloration performance of cotton fiber by 71.1 % and the water retention by 1001.2 % against the control could be readily available by employing the flashily-explosion method at a recommended condition with 4-cycle explosion in sub- or SCF-CO2, and system temperature, fluid treatment duration and explosion number exhibited much more pronounced positive influences among all parameters. Additionally, minimal influences from the supercritical explosion on cotton fiber micronaire value, thermal property and tensile breaking strength were also observed. The scanning electron microscopy (SEM) and porosity investigations clearly show that plenty of micropores and/or strip fissures were formed on the fiber surfaces and their inner phases, and notably improved fiber surface area, pore volume and size were also obtained after a subsupercritical flash-explosion. Nuclear magnetic resonance hydrogen spectroscopy (1H NMR) and Fourier transform infrared spectroscopy (FT-IR) analysis disclose that numbers of hydrogen bonds between the fiber macrochains and/or from their intramolecular chains were broken by generating numerous free hydroxyl groups, which reasonably supported the improvements of the dye uptake behaviors and water retention properties, etc. The Energy-dispersive X-ray spectroscopy (EDS) analysis on the fiber cross-sections further confirms that a loosening of the inner aggregation structure of the cotton fiber was achieved after a flash explosion by significantly enhancing its coloration performance, etc. This innovative approach provides a promising idea and possibility as an alternative to chemical methods via mechanically and physically modifying fiber or other materials with sub- or SCF-CO2 fluid in an eco-friendly and sustainable manner.

Eco-friendly and flexible polysaccharide-based packaging films for fruit preservation

Food safety and wastage caused by fruit deterioration is a serious global problem. Effective packaging systems for extending the freshness period of fruit play a key role in food safety. In this work, we constructed an eco-friendly and flexible polysaccharide-based packaging film based on hydroxypropyl guar (HPG), cellulose nanocrystals (CNCs), deep eutectic solvents (DES) and anthocyanin (Anth). DES could endow polysaccharide films with multiple hydrogen bond numbers and good stability. Hydroxypropyl guar/cellulose nanocrystals/anthocyanin with 0.2 g deep eutectic solvents (HCA-DES0.2) had good tensile properties, oxygen barrier properties (3.01 cm3/m2·day·Pa), water resistance (WCA 111.97°), antibacterial (CFU ˂ 103), and transparency (55.4 %). The preservation tests of grape and blueberry showed that the shelf life of these two fruits was 12–20 days, and the polysaccharide film had great application potential in fruit preservation.

Molecular Insights into the Potential Anticancer Property of a Diimine-Diazo Molecule: A Molecular Docking and Molecular Dynamics Simulations Perspective

Cancer is a disease in which cells grow abnormally and uncontrollably and destroy body tissue, and it is one of the most important threats to human health. In this study, the interaction of a molecule containing imine and azo groups (DIDA) with tumor growth-related VEGFR2 (PDB ID: 2XIR) and EGFR (PDB ID: 1M17) proteins was investigated by molecular docking and molecular dynamics simulation methods. The molecular docking study revealed that the best binding occurred between DIDA-2XIR with a binding energy of -12.4 kcal/mol. Molecular dynamics simulation was used to verify the stability of the DIDA-2XIR complex. RMSD, RMSF, SASA, Rg parameters and number of hydrogen bonds obtained during molecular dynamics simulations showed that the DIDA-2XIR complex was stable at the molecular level. Our findings have made an important contribution to the understanding of the mechanism of interaction of the DIDA with VEGFR2 and support its availability as a potential VEGFR2 inhibitor.

Lineage-specific pathogenicity, immune evasion, and virological features of SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3.

SARS-CoV-2 JN.1 with an additional L455S mutation on spike when compared with its parental variant BA.2.86 has outcompeted all earlier variants to become the dominant circulating variant. Recent studies investigated the immune resistance of SARS-CoV-2 JN.1 but additional factors are speculated to contribute to its global dominance, which remain elusive until today. Here, we find that SARS-CoV-2 JN.1 has a higher infectivity than BA.2.86 in differentiated primary human nasal epithelial cells (hNECs). Mechanistically, we demonstrate that the gained infectivity of SARS-CoV-2 JN.1 over BA.2.86 associates with increased entry efficiency conferred by L455S and better spike cleavage in hNECs. Structurally, S455 altered the mode of binding of JN.1 spike protein to ACE2 when compared to BA.2.86 spike at ACE2H34, and modified the internal structure of JN.1 spike protein by increasing the number of hydrogen bonds with neighboring residues. These findings indicate that a single mutation (L455S) enhances virus entry in hNECs and increases immune evasiveness, which contribute to the robust transmissibility of SARS-CoV-2 JN.1. We further evaluate the in vitro and in vivo virological characteristics between SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3, and identify key lineage-specific features of the two Omicron sublineages that contribute to our understanding on Omicron antigenicity, transmissibility, and pathogenicity.

On the Role of the Interlayer Interactions in Atomistic Simulations of Kaolinite Clay

A systematic simulation study was performed to investigate the interlayer interactions in a 1:1 layered phyllosilicate clay, kaolinite. Atomistic simulations with classical realistic force fields (INTERFACE and ClayFF) were used to examine the influence of the individual non-bonded interactions on the interlayer binding in the kaolinite model system. By switching off selected pairwise interactions in the applied force fields (leaving the intralayer interactions intact), it was confirmed that the tetrahedral–octahedral-type pairwise interactions held the kaolinite plates together and that interlayer hydrogen bonding, modeled by Coulombic forces, played a dominant role in this. Furthermore, it was observed that the number of hydrogen bonds formed had a significant influence on the basal spacing, and thus there was a striking change in the layer–layer interaction strength when there were only two kaolinite plates in the system, rather than several plates, as in real kaolinite particles. Contrary to expectations, the dispersion forces of the studied force fields alone were found to be strong enough to hold the kaolinite plates together.

Dy-SheHeRASADe: A representation of the [formula omitted] sheet dynamics through surface descriptors

Molecular dynamics (MD) simulations are important tools for studying the dynamic motions of macromolecules at the atomic level. With the increasing capabilities of high performance computing, MD simulations are becoming more widely used. This allows molecular modelers to simulate the molecular behavior of large molecular architectures for much longer trajectories. Appropriate visualization of MD trajectories is becoming essential to provide an immediate and intuitive understanding of a molecule’s dynamics and function. In this study, we implement a novel 3D graphical representation, Dynamical Sheets Helper for RepresentAtion of SurfAce Descriptors (Dy-SheHeRASADe), to visualize the β sheet secondary structures of proteins in the context of molecular dynamics. Dy-SheHeRASADe is developed in UnityMol, an open source molecular viewer and prototyping platform. We considered β sheet fluctuations and hydrogen bond formation during molecular dynamics simulations to characterize the parts of β sheets with large motions or with labile bonds. We propose two visualization modes based on a surface representation of the β sheets calculated according to the positions of the α carbons and the hydrogen bonds between the β strands. The volumetric mode, in which this surface is enclosed in a semi-transparent volume that represents the fluctuation zone of the sheet during dynamics. The heatmap mode, in which the surface is colored according to the amplitude values of the α carbons. In addition, we quantify the β sheet fluctuations by displaying the values of the largest and smallest movements of the β sheets, the surface area of the sheets, and the number of hydrogen bonds.