Search Results (59)

Classical thermodynamics omits rigidity, which property distinguishes solids from gases and liquids. By accounting for rigidity (i.e., Young’s elastic modulus, ϒ), we recently amended historical formulae and moreover linked heat capacity, thermal expansivity, and ϒ. Further exploration is motivation by the importance of classical thermodynamics to various applied sciences. Based on heat performing work, we show here, theoretically, that density times sublimation enthalpy divided by the molar mass (ρΔH_sub/M, energy per volume), depends linearly on ϒ (1 GPa = 10⁹ J m⁻³). Data on diverse metals, non-metallic elements, chalcogenides, simple oxides, alkali halides, and fluorides with cubic structures validate this relationship at ambient conditions. Furthermore, data on hcp metals and molecular solids show that ρΔH_sub/M is proportional to ϒ for anisotropic materials. Proportionality constants vary only from 0.1 to 0.7 among these different material types (>100 substances), which shows that the elastic energy reservoir of solids is large. Proportionality constants depend on whether molecules or atoms are sublimated and are somewhat affected by structure. We show that ductility of refractory, high-ϒ metals affect high-temperature determinations of their ΔH_sub. Our results provide information on sublimation processes and subsequent gas phase reactions, while showing that elasticity of solids is the key parameter needed to assessing their energetics. Implications are highlighted. Full article

Epoxy polymers modified with nanoparticles are increasingly employed due to their enhanced performance in aggressive environments, characterized by mechanical stress, radiation exposure, and extreme temperatures. The mechanical failure of these polymers is attributed to the fracturing of atomic and molecular bonds, that subsequently excites electrons having the capability to be emitted from the nanolayer of the material. The present study demonstrates that the relationship between mechanical loading and electron emission over time serves as an indicator of surface loading and durability. By utilizing the Kinetic Nature of Solid Material Strength (KSMS) theory alongside near-threshold electron emission measurements, the article presents the behavior of epoxy polymers modified with SiO₂ nanoparticles under tensile loading. The results indicate that as mechanical load is applied, photoelectron emission (PE) pulses emerge. Notably, the pulse spectrum highest frequency (fmax) correlates with the time of atomic fluctuations (τ), defined by τ = 1/fmax. Furthermore, ultraviolet (UV) irradiation of the nanoparticles prior to mixing with the polymer is shown to influence the parameter of KSMS responsible for local stress concentration. This suggests that PE is connected with the homogeneity of the composite too. The achieved results demonstrate that PE contactless measurements can be used to detect mechanical destruction of the epoxy polymer composite surface nanolayer, as well as to assess its durability and corresponding activation energy. The results presented in the article may contribute to the development of more reliable epoxy polymer composites and durability measurements of their mechanically loaded surface layer or nanofilms. Full article

Silicon–lithium clusters are promising candidates for hydrogen storage due to their lightweight composition, high gravimetric capacities, and favorable non-covalent binding characteristics. In this study, we employ density functional theory (DFT), global optimization (AUTOMATON and Kick–MEP), and Born–Oppenheimer molecular dynamics (BOMD) simulations to evaluate the structural stability and hydrogen storage performance of key Li–Si systems. The exploration of their potential energy surface (PES) reveals that the true global minima of Li₆Si₆ and Li₁₀Si₁₀ differ markedly from those of the earlier Si–Li structures proposed as structural analogs of aromatic hydrocarbons such as benzene and naphthalene. Instead, these clusters adopt compact geometries composed of one or two Si₄ (T_d) units and a Si₂ dimer, all stabilized by surrounding Li atoms. Motivated by the recurrence of the Si₄–T_d motif, we explore oligomers of Li₄Si₄, which can be viewed as electronically transmuted analogues of P₄, confirming the additive H₂ uptake across dimer, trimer, and tetramer assemblies. Within the series of Si–Li clusters evaluated, the Li₁₂Si₅ sandwich complex, featuring a σ-aromatic Si₅¹⁰⁻ ring encapsulated by two Li₆⁵⁺ moieties, achieves the highest hydrogen capacity, adsorbing 34 H₂ molecules with a gravimetric density of 23.45 wt%. Its enhanced performance arises from the high density of accessible Li⁺ adsorption sites and the electronic stabilization afforded by delocalized σ-bonding. BOMD simulations at 300 and 400 K confirm their dynamic stability and reversible storage behavior, while analysis of the interaction regions confirms that hydrogen adsorption proceeds via weak, dispersion-driven physisorption. These findings clarify the structure–property relationships in Si–Li clusters and provide a basis for designing modular, lightweight, and thermally stable hydrogen storage materials. Full article

Metal–organic frameworks (MOFs) based on the pressure swing adsorption (PSA) process show great promise in separating argon from air. As research burgeons, the number of MOFs has grown exponentially, rendering the experimental identification of materials with significant gas separation potential impractical. This study introduced a high-throughput screening through a two-step strategy based on structure–property relationships, which leveraged Grand Canonical Monte Carlo (GCMC) simulations, to swiftly and precisely identify high-performance MOF adsorbents capable of separating argon from air among a vast array of MOFs. Compared to traditional approaches for material development and screening, this method significantly reduced both experimental and computational resource requirements. This research pre-screened 12,020 experimental MOFs from a computationally ready experimental MOF (CoRE MOF) database down to 7328 and then selected 4083 promising candidates through structure–performance correlation. These MOFs underwent GCMC simulation assessments, showing superior adsorption performance to traditional molecular sieves. In addition, an in-depth discussion was conducted on the structural characteristics and metal atoms among the best-performing MOFs, as well as the effects of temperature, pressure, and real gas conditions on their adsorption properties. This work provides a new direction for synthesizing next-generation MOFs for efficient argon separation in labs, contributing to energy conservation and consumption reduction in the production of high-purity argon gas. Full article

Nanocomposites composed of Cu and Mo were investigated by means of molecular dynamics (MD) simulations to study the incoherent interface between Cu and Mo. In order to select an appropriate potential capable of accurately describing the Cu-Mo system, five many-body potentials were compared: three Embedded Atom Method (EAM) potentials, a Tight Binding Second Moment Approximation (TB-SMA) potential, and a Modified Embedded Atom Method (MEAM) potential. Among these, the EAM potential proposed by Zhou in 2001 was determined to provide the best compromise for the current study. The simulated system was constructed with two layers of Cu and Mo forming an incoherent fcc-Cu(111)/bcc-Mo(110) interface, based on the Nishiyama–Wassermann (NW) and Kurdjumov–Sachs (KS) orientation relationships (OR). The interfacial energies were calculated for each orientation relationship. The NW configuration emerged as the most stable, with an interfacial energy of 1.83 J/m², compared to 1.97 J/m² for the KS orientation. Subsequent simulations were dedicated to modeling Cu atomic deposition onto a Mo(110) substrate at 300 K. These simulations resulted in the formation of a dense layer with only a few defects in the two Cu planes closest to the interface. The interfacial structures were characterized by computing selected area electron diffraction (SAED) patterns. A direct comparison of theoretical and numerical SAED patterns confirmed the presence of the NW orientation relationship in the nanocomposites formed during deposition, corroborating the results obtained with the model fcc-Cu(111)/bcc-Mo(110) interfaces. Full article

Al-Li alloys are widely used in aerospace applications due to their high strength, high fracture toughness, and strong resistance to stress corrosion. However, the lack of interatomic potentials has hindered systematic investigations of the relationship between structures and properties. To address this issue, we apply a neural network-based neuroevolutionary machine learning potential (NEP) and use evolutionary strategies to train it for large-scale molecular dynamics (MD) simulations. The results obtained from this potential function are compared with those from Density Functional Theory (DFT) calculations, with training errors of 2.1 meV/atom for energy, 47.4 meV/Å for force, and 14.8 meV/atom for virial, demonstrating high training accuracy. Using this potential, we simulate cluster formation and the high-temperature stability of the T1 phase, with results consistent with previous experimental findings, confirming the accurate predictive capability of this potential. This approach provides a simple and efficient method for predicting atomic motion, offering a promising tool for the thermal treatment of Al-Li alloys. Full article

This theoretical study investigates the high molecular weight (Mw) production in copolymerization of ethylene and 1-octene using heteroatom-substituted constrained geometry catalysts (CGCs). The research explores the correlation between chain termination reactions and polymer molecular weight, revealing that the Gibbs free energy barrier of the chain termination reactions is positively linked to the molecular weight. Quantitative structure–property relationship models were constructed, indicating that molecular descriptors such as atom charge, orbital energy, and buried volume significantly influence the polymer molecular weight. Full article

During this study, a molecular system was modeled: a nimesulide, β-cyclodextrin, inclusion complex. The use of the Gaussian 16W software package allowed us to optimize geometry and determine the thermochemical characteristics of molecular systems without considering a solvent. And this was also carried out in water media, accounted for by the polarized continuum model (PCM). To confirm the accuracy of the geometry of the β-cyclodextrin molecule, a structural alignment of 46 β-cyclodextrin molecules, accessible by a corresponding search query in the RCSB database, was performed. The RSMD values of carbon and oxygen atom deviations, as well as the total number of atoms aligned, were calculated. This calculation showed a complete conformational coincidence between the β-cyclodextrin structure designed by us and the RCSB database structures. This ensures the correct approach to subsequent calculations involving this structure. Quantum-mechanical modeling of the relationship was carried out in several stages with a gradual complexity of the basic set. The hybrid method of functional density B3LYP and 6-31G(d) was used. At the end of the calculation stage, on the surface of the studied complex, the potential energy of several minimal elements was detected. This means that there are several conformational forms of the molecular system with likely differences. The change in potential energies of the investigated compounds, caused by their application to optimize the in vacuum molecules of the PCM, allowed us to determine the values of the solvatization energies. The greater magnitude of these values in the complex under consideration indicates its better solubility in water compared to nimesulide. Full article

The hydrogen embrittlement (HE) phenomenon occurring in drawn pearlitic steel wires sometimes results in dangerous delayed fracture and has been an important issue for a long time. HE is very sensitive to the amount of plastic deformation applied in the drawing process. Hydrogen (H) atom diffusion is affected by ambient thermal and mechanical conditions such as stress, pressure, and temperature. In addition, the influence of stress gradient (SG) on atomic diffusion is supposed to be crucial but is still unclear. Metallic materials undergoing plastic deformation naturally have SG, such as residual stresses, especially in inhomogeneous regions (e.g., surface or grain boundary). In this study, we performed molecular dynamics (MD) simulation using EAM potentials for Fe and H atoms and investigated the behavior of H atoms diffusing in pure iron (α-Fe) with the SG condition. Two types of SG conditions were investigated: an overall gradient established by a bending deformation of the specimen and an atomic-scale local gradient caused by the grain boundary (GB) structure. A bi-crystal model with H atoms and a GB structure was subjected to bending deformation. For a moderate flexure, bending stress is distributed linearly along the thickness of the specimen. The diffusion coefficient of H atoms in the bulk region increased with an increase in the SG value. In addition, it was clearly observed that the direction of diffusion was affected by the existence of the SG. It was found that diffusivity of the H atom is promoted by the reduction in its cohesive energy. From these MD results, we recognize an exponential relationship between the amount of H atom diffusion and the intensity of the SG in nano-sized bending deformation. Full article

Background: Disinfection by-products used to obtain drinking water, including halomethanes (HMs) such as CH₂Cl₂, CHCl₃, and BrCHCl₂, induce cytotoxicity and hyperproliferation in human lung fibroblasts (MRC-5). Enzymes such as superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) modulate these damages through their biotransformation processes, potentially generating toxic metabolites. However, the role of the oxidative stress response in cellular hyperproliferation, modulated by nuclear factor-kappa B (NF-κB), remains unclear. Methods: In this study, MRC-5 cells were treated with these compounds to evaluate reactive oxygen species (ROS) production, lipid peroxidation, phospho-NF-κB/p65 (Ser536) levels, and the activities of SOD, CAT, and GPx. Additionally, the interactions between HMs and ROS with the IκBα/NF-κB/p65 complex were analyzed using molecular docking. Results: Correlation analysis among biomarkers revealed positive relationships between pro-oxidant damage and antioxidant responses, particularly in cells treated with CH₂Cl₂ and BrCHCl₂. Conversely, negative relationships were observed between ROS levels and NF-κB/p65 levels in cells treated with CH₂Cl₂ and CHCl₃. The estimated relative free energy of binding using thermodynamic integration with the p65 subunit of NF-κB was −3.3 kcal/mol for BrCHCl₂, −3.5 kcal/mol for both CHCl₃ and O₂^•, and −3.6 kcal/mol for H₂O₂. Conclusions: Chloride and bromide atoms were found in close contact with IPT domain residues, particularly in the RHD region involved in DNA binding. Ser281 is located within this domain, facilitating the phosphorylation of this protein. Similarly, both ROS interacted with the IPT domain in the RHD region, with H₂O₂ forming a side-chain oxygen interaction with Leu280 adjacent to the phosphorylation site of p65. However, the negative correlation between ROS and phospho-NF-κB/p65 suggests that steric hindrance by ROS on the C-terminal domain of NF-κB/p65 may play a role in the antioxidant response. Full article

Multiple intermolecular H-bonding interactions play a pivotal role in determining the macroscopic state of ionic liquids (ILs). Hence, the relationship between the microscopic and the macroscopic properties is key for a rational design of new imidazolium ILs. In the present work, we investigated how the physicochemical property of hydroxyl-functionalized imidazolium chloride is connected to the molecular structure and intermolecular interactions. In the isolated ion pair, strong N-H···Cl H-bonding interactions are observed rather than H-bonding interactions at the acidic C₂-H site and alkyl-OH···Cl of the hydroxyl-functionalized imidazolium chloride. However, the N-H···Cl H-bonding interaction of the cation plays a significant role in ion-pair formations and polymeric clusters. For 3-(2-Hydroxy)-1H-imidazolium chloride (EtOHImCl), the oxygen atom (O) engages in two significant interactions within its homodimeric ion-pair cluster: N-H···O and alkyl OH···Cl. Vibrational spectroscopy and DFT calculations reveal that the chloride ion (Cl⁻) forms a hydrogen bond with the C2-H group via a C2-H···Cl interaction site. Natural Bond Orbital (NBO) analysis indicates that the O-H···Cl hydrogen-bonding interaction is crucial for the stability of the IL, with a second-order perturbation energy of approximately 133.8 kJ/mol. Additional computational studies using Atoms in Molecules (AIMs), non-covalent interaction (NCI) analysis, Electron Localization Function (ELF), and Localized Orbital Locator (LOL) provide significant insights into the properties and nature of non-covalent interactions in ILs. Ab initio molecular dynamics (AIMD) simulations of the IL demonstrate its stable states with relatively low energy values around −1680.6510 atomic units (a.u.) at both 100 fs and 400 fs due to O-H···Cl and C-H···Cl interactions. Full article

The COVID-19 pandemic, instigated by the emergence of the novel coronavirus, SARS-CoV-2, created an incomparable global health crisis. Due to its highly virulent nature, identifying potential therapeutic agents against this lethal virus is crucial. PLpro is a key protein involved in viral polyprotein processing and immune system evasion, making it a prime target for the development of antiviral drugs to combat COVID-19. To expedite the search for potential therapeutic candidates, this review delved into computational studies. Recent investigations have harnessed computational methods to identify promising inhibitors targeting PLpro, aiming to suppress the viral activity. Molecular docking techniques were employed by researchers to explore the binding sites for antiviral drugs within the catalytic region of PLpro. The review elucidates the functional and structural properties of SARS-CoV-2 PLpro, underscoring its significance in viral pathogenicity and replication. Through comprehensive all-atom molecular dynamics (MD) simulations, the stability of drug–PLpro complexes was assessed, providing dynamic insights into their interactions. By evaluating binding energy estimates from MD simulations, stable drug–PLpro complexes with potential antiviral properties were identified. This review offers a comprehensive overview of the potential drug/lead candidates discovered thus far against PLpro using diverse in silico methodologies, encompassing drug repurposing, structure-based, and ligand-based virtual screenings. Additionally, the identified drugs are listed based on their chemical structures and meticulously examined according to various structural parameters, such as the estimated binding free energy (ΔG), types of intermolecular interactions, and structural stability of PLpro–ligand complexes, as determined from the outcomes of the MD simulations. Underscoring the pivotal role of targeting SARS-CoV-2 PLpro in the battle against COVID-19, this review establishes a robust foundation for identifying promising antiviral drug candidates by integrating molecular dynamics simulations, structural modeling, and computational insights. The continual imperative for the improvement of existing drugs and exploring novel compounds remains paramount in the global efforts to combat COVID-19. The evolution and management of COVID-19 hinge on the symbiotic relationship between computational insights and experimental validation, underscoring the interdisciplinary synergy crucial to this endeavor. Full article

Much work has been dedicated to the quest to determine the structure–activity relationship in synthetic brassinosteroid (BR) analogs. Recently, it has been reported that analogs with phenyl or benzoate groups in the alkyl chain present activities comparable to those shown by natural BRs, depending on the nature of the substituent in the aromatic ring. However, as it is well known that the activity depends on the structure of the whole molecule, in this work, we have synthesized a series of compounds with the same substituted benzoate in the alkyl chain and a hydroxyl group at C3. The main goal was to compare the activities with analogs with -OH at C2 and C3. Additionally, a molecular-docking study and molecular dynamics simulations were performed to establish a correlation between the experimental and theoretical results. The synthesis of eight new BR analogs was described. All the analogs were fully characterized by spectroscopical methods. The bioactivity of these analogs was assessed using the rice lamina inclination test (RLIT) and the inhibition of the root and hypocotyl elongation of Arabidopsis thaliana. The results of the RLIT indicate that at the lowest tested concentration (1 × 10⁻⁸ M), in the BR analogs in which the aromatic ring was substituted at the para position with methoxy, the I and CN substituents were more active than brassinolide (50–72%) and 2–3 times more active than those analogs in which the substituent group was F, Cl or Br atoms. However, at the highest concentrations, brassinolide was the most active compound, and the structure–activity relationship changed. On the other hand, the results of the A. thaliana root sensitivity assay show that brassinolide and the analogs with I and CN as substituents on the benzoyl group were the most active compounds. These results are in line with those obtained via the RLIT. A comparison of these results with those obtained for similar analogs that had a hydroxyl group at C2 indicates the importance of considering the whole structure. The molecular-docking results indicate that all the analogs adopted a brassinolide-like orientation, while the stabilizing effect of the benzoate group on the interactions with the receptor complex provided energy binding values ranging between −10.17 and −13.17 kcal mol⁻¹, where the analog with a nitrile group was the compound that achieved better contact with the amino acids present in the active site. Full article

This study aimed to address the issue of the low solubility in the model drug probenecid (PRO) and its impact on bioavailability. Two salts of probenecid (PRO), 4-aminopyridine (4AMP), and 4-dimethylaminopyridine (4DAP) were synthesized and characterized by PXRD, DSC, TGA, FTIR, and SEM. The crystal structures of the two salts were determined by SCXRD, demonstrating that the two salts exhibited different hydrogen bond networks, stacking modes, and molecular conformations of PRO. The solubility of PRO and its salts in a phosphate-buffered solution (pH = 6.8) at 37 °C was determined, the results showed that the solubility of PRO salts increased to 142.83 and 7.75 times of the raw drug, respectively. Accelerated stability experiments (40 °C, 75% RH) showed that the salts had good phase stability over 8 weeks. Subsequently, Hirshfeld surface (HS), atom in molecules (AIM), and independent gradient model (IGM) were employed for the assessment of intermolecular interactions. The analyses of salt-forming sites and principles were conducted using molecular electrostatic potential surfaces (MEPs) and pK_a rules. The lattice energy (E_L) and hydration-free energy (E_HF) of PRO and its salts were calculated, and the relationships between these parameters and melting points and the solubility changes were analyzed. Full article

The effect of La, Ce, Pr and Nd ions on four Ln(ligand)₃ complexes and at three DFT levels of calculation was analyzed. Four ligands were chosen, three of which were based on the 1,2,3-triazole ring. The DFT methods used were B3LYP, CAM-B3LYP and M06-2X. The relationships established were between the geometric parameters, atomic charges, HOMO-LUMO energies and other molecular properties. These comparisons and trends will facilitate the synthesis of new complexes by selecting the ligand and lanthanide ion best suited to the desired property of the complex. The experimental IR and Raman spectra of Ln(2b′)₃ complexes where Ln = La, Ce, Pr, Nd, Sm, Gd, Dy, Ho and Er ions have been recorded and compared to know the effect of the lanthanide ion on the complex. The hydration in these complexes was also analyzed. Additionally, the effect of the type of coordination center on the ability of an Ln(ligand)₃ complex to participate in electron exchange and hydrogen transfer was investigated using two in vitro model systems—DPPH and ABTS. Full article