Journal of Molecular Modeling最新文献

{"title":"Mechanical and thermo-mechanical behavior of h-BNNS-reinforced polyurethane nanocomposites: a molecular dynamics and experimental analysis","authors":"Mithilesh K. Dikshit,&nbsp;Neetu Chaudhary,&nbsp;Vimal Kumar Pathak","doi":"10.1007/s00894-026-06752-1","DOIUrl":"10.1007/s00894-026-06752-1","url":null,"abstract":"<div><h3>Context</h3><p>The present research systematically investigates polyurethane (PU)/hexagonal boron nitride nanosheet (h-BNNS) nanocomposites with varying h-BNNS loadings using a molecular dynamics (MD) simulation-driven framework, complemented by experimental validation based on the solvent-casting technique. The work aims to elucidate the fundamental structure–property–performance relationships governing the mechanical and thermo-mechanical behavior of PU in the presence of h-BNNS reinforcement.</p><h3>Method</h3><p>Atomistic models of PU were constructed in Materials Studio software, and nanocomposite systems containing 0.3, 0.5, and 0.7 wt.% h-BNNS were developed. Structural equilibration was achieved through energy minimization followed by dynamic simulations using the Forcite module with the DREIDING force field. Elastic, shear, and bulk moduli were determined using the constant strain approach with six independent deformation modes. Temperature-dependent behavior was investigated in the range of 300–600 K with 25 K increments. The simulation results demonstrated a monotonic enhancement in elastic, shear, and bulk moduli with increasing h-BNNS content, with the 0.7 wt.% system exhibiting the highest stiffness and resistance to deformation in ambient conditions. Thermo-mechanical analysis revealed gradual modulus degradation with temperature for all compositions; however, h-BNNS-reinforced systems consistently maintained superior stiffness, indicating enhanced thermal stability and delayed softening. Experimental validation was conducted by fabricating PU/h-BNNS nanocomposites via a solvent-casting method using identical filler concentrations. Experimentally, the elastic modulus increased up to 0.5 wt.% reinforcement of h-BNNS due to improved dispersion and strong interfacial bonding, followed by a reduction at 0.7 wt.% attributed to nanosheet agglomeration and stress concentration effects. In contrast, MD simulations predicted a continuous modulus increase with filler loading and yielded higher absolute values due to idealized assumptions such as defect-free interfaces and uniform dispersion. Despite quantitative discrepancies, both experimental and computational results exhibited strong qualitative agreement, identifying 0.5 wt.% h-BNNS as the optimal reinforcement level.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147830010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Theoretical analysis of Curcuma longa polyphenols as eco-friendly corrosion inhibitors for copper in acidic medium","authors":"Zakaria Ait El Caid,&nbsp;Omar Dagdag,&nbsp;Driss Benmessaoud Left,&nbsp;Mustapha Zertoubi","doi":"10.1007/s00894-026-06753-0","DOIUrl":"10.1007/s00894-026-06753-0","url":null,"abstract":"<div><h3>Context</h3><p>Protecting copper against corrosion in harsh acidic conditions continues to be a significant challenge in materials research. This study examined three natural curcuminoids from <i>Curcuma longa</i>: curcumin (CUR), demethoxycurcumin (DEM), and bisdemethoxycurcumin (BIS), as environmentally benign corrosion inhibitors. Density functional theory (DFT) studies indicated that CUR possesses the shortest <i>HOMO–LUMO</i> energy gap (<i>3.606</i> eV), the highest global softness, and the highest electrophilicity index, signifying increased chemical reactivity and robust donor–acceptor interactions. DEM exhibited a notable capacity to receive back-donated electrons. Adsorption studies indicated that all molecules assume a planar form on the copper surface, promoting π–surface interactions. Among the examined compounds, CUR had the greatest binding affinity with the lowest adsorption energy (<b><i>−</i></b>41.494 <i>kJ.mol⁻</i>^<i>1</i><i>).</i> These findings underscore that <i>C. longa</i> constituents are viable, sustainable, and eco-friendly alternatives to synthetic corrosion inhibitors for copper in acidic environments.</p><h3>Methods</h3><p>ORCA and Quantum ESPRESSO were employed to conduct all calculations within the context of density functional theory (DFT). Geometry optimizations and electronic structure calculations were conducted under strict self-consistent field (SCF) convergence criteria using the B3LYP functional, def2-SVP basis set, and def2/J auxiliary basis set. Periodic DFT calculations were conducted in Quantum ESPRESSO to investigate the adsorption properties. The wave functions were subjected to plane-wave cutoff energies of 30 Ry, while the charge density was subjected to 240 Ry.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147830009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First-principles insights on the mechanical, electronic and optical properties of cubic TlXY3 (X = Mg, Ca, Sr, Ba; Y = Br, I) for optoelectronic applications","authors":"Jing Wang,&nbsp;Yuanwei Liu,&nbsp;Shuting Guo,&nbsp;Qiqiao Zhong,&nbsp;Yan Chen,&nbsp;Shanjun Chen","doi":"10.1007/s00894-026-06756-x","DOIUrl":"10.1007/s00894-026-06756-x","url":null,"abstract":"<div><h3>Context</h3><p>Halide perovskite materials have broad application prospects in fields, such as solar cells, sensors, and light-emitting diodes (LEDs). Employing the density-functional theory, this study explored the mechanical, electronic and optical properties of TlXY₃ (X = Mg, Ca, Sr, Ba; Y = Br, I). All cubic TlXY₃ crystals are mechanically, structurally and thermodynamically stable, as shown by the elastic constants and the Gold-Schmidt tolerance factor. Mechanical properties prove that they are all ductile compounds. TlXY₃ (X = Mg, Ca; Y = Br, I) are ionic bond materials, while TlXY₃ (X = Sr, Ba; Y = Br, I) are metallic bond compounds. The electronic properties indicate that TlXY₃ are all wide-bandgap semiconductor materials using HSE06 functional. The optical properties indicate that TlXY₃ all exhibit strong absorption and broad absorption peak within the UV spectral ranges and substantial transmission within the visible and infrared spectral ranges. Hence, these materials are well-suited as candidate materials for UV absorbers and ultraviolet-operating radiation detectors.</p><h3>Methods</h3><p>Density-functional theory (DFT) calculations were performed using CASTEP software. The GGA-PBE functional and the ultrasoft pseudopotential were employed to account for exchange–correlation. The elastic constants were determined via the stress–strain method. The electronic properties were calculated using the PBE and HSE06 hybrid functional, and the optical properties were calculated using the HSE06 hybrid functional.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147829929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated xTB and simplified Tamm–Dancoff analysis of composition-dependent electronic structure in GaInZnP/ZnSeyS1-y core/shell quantum dots with DFT and TDDFPT benchmarking","authors":"Oluwasesan Adegoke,&nbsp;Ojodomo J. Achadu","doi":"10.1007/s00894-026-06728-1","DOIUrl":"10.1007/s00894-026-06728-1","url":null,"abstract":"<div><h3>Context</h3><p>Alloyed core/shell quantum dots (QDs) provide a platform for composition-controlled modulation of electronic structure and optical response. Using an integrated extended tight binding (xTB) and simplified Tamm Dancoff approximation (sTDA) framework, a composition-defined GaInZnP/ZnSe_yS_1-y core/shell QD series (<i>y</i> = 0.00, 0.25, 0.50, 0.75, 1.00) revealed a distinctly nonlinear dependence of electronic and excited-state behaviour on shell composition. Relative stability favoured S-rich shells, while mixed-shell compositions showed non-ideal energetic behaviour with a pronounced deviation at <i>y</i> = 0.75. The frontier electronic structure did not vary monotonically with Se content, while the optical response showed composition-dependent redistribution of low-energy transitions. Benchmark comparison with density functional theory (DFT) and time-dependent density functional perturbation theory (TDDFPT) confirmed that the nonlinear evolution of frontier-level separation and absorption behaviour was an intrinsic feature of the alloy series, although the exact magnitude and position of the extrema remain method dependent. A distinct anomaly at <i>y</i> = 0.75 indicated enhanced frontier state reorganisation within the mixed-shell environment.</p><h3>Method</h3><p>Atomistic GaInZnP/ZnSe_yS_1-y QDs spanning <i>y</i> = 0.00 to 1.00 were analysed under identical structural constraints to isolate shell anion substitution effects. Ground-state electronic structure and excited-state properties were evaluated using xTB and sTDA, with DFT and TDDFPT used as independent benchmarks for frontier electronic structure and optical absorption trends. Composition-dependent changes in energetic stability, frontier-orbital separation, density-of-states like distributions, absorption onset, and frontier-orbital localisation were then compared across the full alloy series using a consistent analysis framework.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-026-06728-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147830011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Shock-induced detonation mechanism of NH3OH+N5ˉ: a deep potential molecular dynamics study with and without nuclear quantum effect","authors":"Jikai Zhao,&nbsp;Jidong Zhang,&nbsp;Weijing Zhang","doi":"10.1007/s00894-026-06737-0","DOIUrl":"10.1007/s00894-026-06737-0","url":null,"abstract":"<div><h3>Context</h3><p>As a novel type of high-energy-density, environmentally friendly, and low-sensitivity energetic materials (EMs), <i>cyclo</i>-pentazolate salts are being extensively studied. However, their detonation mechanism remains unclear. This study developed a neural network potential (NNP) to simulate the shock-induced detonation process of NH₃OH⁺N₅ˉ, a representative salt of the pentazolate anion (N₅ˉ). The well-trained NNP exhibits high precision comparable to DFT, as well as high efficiency. The NNP-based large-scale molecular dynamics (MD) simulations for NH₃OH⁺N₅ˉ produced an ideal <i>C-J</i> detonation velocity of 9.4 km/s, which is in agreement with the value estimated by the Cheetah 7.0 program (9.93 km/s). The simulation demonstrates that the proton transfer from NH₃OH⁺ to N₅ˉ is the initial reaction, while the primary decomposition pathway of N₅ˉ is a ring-opening reaction, or the bimolecular reactions with its initial decomposition intermediate azide anion N₃ˉ resulting in the formation of N₈ ring. Quantum chemical calculations show that these pathways possess low activation barriers. The influence of nuclear quantum effects on shock-induced chemical reactions was also studied, which shows that nuclear quantum corrections not only improve the accuracy of predicted ideal detonation velocity but also improve temperature in simulations, which results in the different reaction mechanism of shock-induced detonation reaction of NH₃OH⁺N₅ˉ, facilitating the ring-opening reaction of N₅ˉ ring and preventing its reaction with N₃. This study enhances the understanding of the detonation mechanism of <i>cyclo</i>-pentazolate salts.</p><h3>Methods</h3><p>In this work, NNP potential was trained by the DeePMD-kit package and homemade FORTRAN code. The density functional theory (DFT) calculation of structural energies and atomic forces, as well as ab initio molecular dynamics (AIMD), was conducted using the Vienna Ab initio Simulation Package (VASP) software. The PAW method and the GGA-PBE functional were adopted. The shock wave response MD simulations were conducted by LAMMPS with the multiscale shock technique (MSST) and QB-MSST methods. Quantum chemical calculations were carried out at the M06-2X/TZVP level using the Gaussian 09 program.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147829544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of Fe(III) and water in the oxidation of chalcopyrite","authors":"Selma Fabiana Bazan,&nbsp;Hélio Anderson Duarte,&nbsp;Guilherme Ferreira de Lima","doi":"10.1007/s00894-026-06747-y","DOIUrl":"10.1007/s00894-026-06747-y","url":null,"abstract":"<div><h3>Context</h3><p>Chalcopyrite is the most abundant copper sulfide mineral and is becoming increasingly important for meeting the growing demand for copper. However, its slow dissolution during the leaching process remains a technological challenge, in which the key step is the oxidation of chalcopyrite. The initial stages of chalcopyrite oxidation by Fe³⁺(aq) were investigated on the sulfur-terminated (001) and (112) surfaces. Adsorption of the [Fe(OH)₃(H₂O)₂] complex is stronger on the (001)-S surface (−18.8 kcal mol⁻¹) than on (112)-S (−13.4 kcal mol⁻¹), forming bidentate bonds that promote electron transfer from the surface to the oxidizing agent. The subsequent redox step proceeds through a hydrogen-transfer mechanism, in which water undergoes homolytic dissociation to yield Fe²⁺–OH₂ and an ∙OH radical that attacks surface sulfur atoms, forming S–OH species. This process is both thermodynamically and kinetically favorable on (001)-S (Δ<i>E</i> = −6 kcal mol⁻¹; <i>E</i>_<i>a</i> = 11 kcal mol⁻¹) but strongly hindered on (112)-S (<i>E</i>_<i>a</i> ≈ 80 kcal mol⁻¹). The high stabilization of reaction products on (112)-S likely promotes surface passivation, which may explain the kinetic limitations observed experimentally during chalcopyrite leaching. Comparatively, although O₂ is a stronger oxidant, its low solubility in aqueous media limits its effectiveness relative to Fe³⁺.</p><h3>Methods</h3><p>Density functional theory (DFT) calculations were performed under periodic boundary conditions using the PW91 exchange–correlation functional and plane-wave basis sets and Vanderbilt ultrasoft pseudopotentials. A Hubbard U correction of 2 eV was applied to surface Fe atoms. Calculations were carried out using the Quantum ESPRESSO 6.2.1 package. Activation barriers were computed using the nudged elastic band method, and atomic charges were obtained through Löwdin population analysis.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture><span>The alternative text for this image may have been generated using AI.</span></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-026-06747-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147829543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First-principles investigation of half-metallic, optical and thermoelectric properties in CaX₂Se₄ (X = Mn, V) spinels","authors":"Ashiq Ramzan,&nbsp;Mudasir Younis Sofi,&nbsp;Mohd. Shahid Khan,&nbsp;M. Ajmal Khan","doi":"10.1007/s00894-026-06744-1","DOIUrl":"10.1007/s00894-026-06744-1","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Context&lt;/h3&gt;&lt;p&gt;Spinel chalcogenides of the type CaX₂Se₄ (X = Mn, V) represent a class of transition-metal compounds in which magnetic ordering, electronic structure, and lattice dynamics are strongly interrelated, making them attractive for spin-dependent transport and thermoelectric applications. In particular, the coexistence of partially filled transition-metal 3&lt;i&gt;d&lt;/i&gt; states and chalcogen p states provides a favorable platform for exchange-driven spin polarization and tunable carrier transport. In this study, a comprehensive first-principles investigation based on density functional theory is carried out to examine the structural stability and magnetic ground state along with the electronic structure elastic response lattice vibrations optical characteristics and thermoelectric behavior of CaMn₂Se₄ and CaV₂Se₄. The calculated negative formation enthalpies together with the absence of imaginary phonon modes confirm both thermodynamic and dynamical stability. Total-energy analysis identifies the ferromagnetic phase as the ground state for both systems. The spin-resolved electronic band structures indicate half-metallic behavior, characterized by a metallic majority-spin channel and minority-spin band gaps of 2.44 eV for CaMn₂Se₄ and 2.05 eV for CaV₂Se₄. The computed elastic constants satisfy the mechanical stability criteria for cubic crystals and indicate a ductile mechanical response. Within the constant relaxation time approximation, n-type transport calculations predict large Seebeck coefficients and enhanced thermoelectric performance at elevated temperatures up to 800 K. Optical analysis further reveals strong dielectric polarization and pronounced absorption extending from the visible to the ultraviolet region. Collectively, these results establish CaMn₂Se₄ and CaV₂Se₄ as stable, spin-polarized chalcogenide spinels with coupled magnetic, transport, and optical functionalities.&lt;/p&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;p&gt;All calculations are performed within the framework of density functional theory using the WIEN2k package, which implements the full-potential linearized augmented plane-wave (FP-LAPW) method. Structural optimization is carried out using the generalized gradient approximation in the Perdew–Burke–Ernzerhof form for the exchange–correlation functional. To achieve an improved description of the electronic structure and band gaps, the modified Becke–Johnson exchange potential is employed. The valence states are treated semi-relativistically, while the core states are treated fully relativistically. Spin–orbit coupling is neglected after test calculations confirm its negligible influence on the electronic structure near the Fermi level. The plane-wave cutoff parameter &lt;span&gt;({R}_{MT}{K}_{max})&lt;/span&gt; is set to 8.0, and appropriate muffin-tin radii are chosen for Ca, Mn/V, and Se atoms. Brillouin-zone integrations are performed using a Monkhorst–Pack k-point mesh corresponding to a 10 × 10 × 10 grid for self-consistent calculations, and t","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147829545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A quantum-chemical study of synthesis and stability of glycine on olivine surface","authors":"Abu Asaduzzaman","doi":"10.1007/s00894-026-06745-0","DOIUrl":"10.1007/s00894-026-06745-0","url":null,"abstract":"<div><h3>Context</h3><p>Using glycine as a model system, this study examines the surface assisted reaction between methylamine and formic acid on an olivine (010) surface. A comparative analysis of co-adsorbed, mixed phase, and gas phase pathways of methyl amine and formic acid to form glycine shows that a surface assisted pathway exists that connects adsorbed formic acid and methylamine to a surface stabilized glycine configuration with significantly reduced reaction energetics relative to gas phase, suggesting a plausible role for silicate minerals in facilitating complex organic synthesis under astro-physically relevant conditions.</p><h3>Methods</h3><p>First-principles density functional theory calculations were performed using the Vienna Ab initio Simulation Package (VASP) with the Perdew–Burke–Ernzerhof (PBE) exchange correlation functional and the projector augmented wave (PAW) method. Minimum energy reaction pathways and activation barriers were determined using the nudged elastic band (NEB) method, with all energies referenced to clearly defined initial states. Short time thermal stability of surface-bound glycine was assessed using ab initio molecular dynamics (AIMD) simulations at 1200 K to probe high temperature persistence on picosecond timescales.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-026-06745-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147829255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Halogen bond-driven azo–hydrazone tautomerisation: a computational study","authors":"Antti Siiskonen,&nbsp;Arri Priimagi","doi":"10.1007/s00894-026-06740-5","DOIUrl":"10.1007/s00894-026-06740-5","url":null,"abstract":"<div><h3>Context</h3><p>Azo–hydrazone tautomerisation affects the photoswitching behaviour and physical properties of tautomerisable azobenzenes. Non-covalent interactions, such as halogen bonding, can shift the tautomeric equilibrium by stabilising one tautomer over the other. Here, we have used computational methods to study how halogen bonding affects the azo–hydrazone tautomerisation of 2-hydroxy- and 4-hydroxyazobenzenes and their azonaphthalene derivatives. We also studied the effect of alkoxy groups, commonly employed as attachment points when incorporating azobenzenes into functional polymeric systems, on tautomerisation and halogen bonding by systematically replacing ring hydrogens with methoxy groups. In addition, self-complementary halogen-bonded dimers based on 2′-iodo-2-hydroxyazonaphthalene bearing methoxy and nitro groups were studied. Our results show that halogen bonding generally shifts the tautomeric equilibrium towards the hydrazone form. When the azo tautomer is only slightly more stable (∆<i>G</i> = 0–2 kcal mol⁻¹), halogen bonding can invert the tautomeric preference. External factors such as temperature affect the halogen bonding strength and thereby the tautomeric equilibrium, suggesting that these halogen-bonded systems may offer a tunable platform for sensing applications.</p><h3>Methods</h3><p>The Gaussian 16 program was used for geometry optimisations, interaction energy calculations, and to generate the wavefunctions. All calculations were performed using the M06-2X/DGDZVP density functional theory method. The counterpoise correction method by Boys and Bernardi was used to correct for the basis set superposition error. The AIMAll program was used to perform the interacting quantum atoms analyses of the wavefunctions.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00894-026-06740-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147829662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular simulation insights into glycerol extraction from biodiesel using deep eutectic solvents","authors":"Neha,&nbsp;Anand Bharti,&nbsp;Padmini Padmanabhan","doi":"10.1007/s00894-026-06732-5","DOIUrl":"10.1007/s00894-026-06732-5","url":null,"abstract":"<div><h3>Context</h3><p>Biodiesel has emerged as a sustainable and viable alternative to fossil fuels to meet the growing global energy demand. However, crude biodiesel produces glycerol as a major byproduct, which adversely affects its quality and engine performance. Additionally, the combustion of biodiesel in the presence of glycerol emits harmful pollutants, making the effective removal of glycerol a critical step in biodiesel purification. Liquid–liquid extraction using conventional organic solvents has been explored for glycerol removal from biodiesel, but its applicability is limited by high volatility, flammability, poor selectivity, and losses of biodiesel, which compromise process safety and energy efficiency. Consequently, recent attention has shifted toward sustainable solvents, including deep eutectic solvents, which offer low volatility, reusability, and improved separation performance. In this study, deep eutectic solvents are explored as promising extraction solvents for the selective removal of glycerol from biodiesel.</p><h3>Methods</h3><p>In this study, classical molecular dynamics simulations were performed with the GROMACS package and the OLPS-AA force field to investigate the molecular interactions governing glycerol extraction from biodiesel using deep eutectic solvents. The DESs studied included choline chloride:urea (1:2), choline chloride:ethylene glycol (1:2), and choline chloride:ethylene glycol (1:3). Structural and dynamical properties were analyzed using radial distribution functions, hydrogen-bond analysis, and density profiles to quantify intermolecular interactions and preferential solvation behavior. The molecular-level insights obtained from these simulations were used to assess the affinity of deep eutectic solvents for glycerol by determining the glycerol distribution coefficient between the DES-rich and biodiesel-rich phases.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"32 6","pages":""},"PeriodicalIF":2.5,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147827017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}