Atoms In Molecules Research Articles

Vibrational Spectra and Computational Study of Amyl Acetate: MEP, AIM, RDG, NCI, ELF and LOL Analysis

This work is focused on biologically active neat amyl acetate and its solutions in ethanol/heptane. According to the experimental results, when the concentration of amyl acetate in the amyl acetate-ethanol solution decreases, the additional band appears on the low-frequency side. The primary reason for the formation of such additional band is the intermolecular hydrogen bonding between amyl acetate and ethanol. In the amyl acetate-heptane solution, as the concentration of amyl acetate in the solution decreases, the band corresponding to the C=O stretching vibrations shifted to a higher frequency. This is explained by the fact that heptane breaks intermolecular interactions in solution, resulting in a simpler spectral band corresponding to the C=O stretching vibrations. Calculations are also used to study interactions in amyl acetateethanol complexes and their spectral manifestations. When the complex formation energies are calculated, this energy increases with the number of molecules, but the average hydrogen bond energy per one bond remains unchanged. The density functional theory (DFT) method is used to analyze molecular structural parameters: Mulliken atomic charge distribution; thermodynamic parameters; molecular electrostatic potential (MEP) surface; atoms in molecules (AIM) analysis; quantum chemical parameters such as reduced density gradient (RDG) and noncovalent interaction (NCI) analysis; electron localization functions (ELF) analysis; and localized orbital locator (LOL) analysis.

The facile preparation of polydopamine-modified sepiolite and its adsorption properties and microscopic mechanism for cadmium ion

Natural sepiolite (SEP) has the characteristics of cation exchange, abundant reserves, low cost, and environmental friendliness, but its adsorption capacity for heavy metal pollutants is limited. Because polydopamine (PDA) molecules contain rich functional groups such as phenolic and amino groups, in the present work, dopamine and natural sepiolite were utilized as raw materials to prepare polydopamine-modified sepiolite composite (SEP/PDA) by simple co-precipitation method. According to Langmuir isotherm model, the maximum adsorption capacity of SEP/PDA for Cd2+ can reach 203.21 mg/g at 298 K. At the initial concentration of 100 mg/L, the adsorption capacity was 2.9 times that of natural sepiolite. The composite material has good reusability and anti-cationic interference performance and has 100 % removal ability of low concentration Cd2+ in actual electroplating wastewater. Density Functional Theory (DFT) calculations were performed to obtain the electronic structure information. To elucidate the microscopic mechanism, molecular surface analyses, Interaction Region Indicator (IRI), Atom In Molecules (AIM) theory, Bond Order Density (BOD), and Electron Localization Function (ELF) were conducted. These analyses revealed that the amino nitrogen and phenolic oxygen atoms in the dopamine molecules donate lone pair electrons to coordinate with cadmium ions. Polydopamine, which possesses multiple oxidation states, contains catechol, quinone, and indole or a lesser extend pyrrole groups that can complex with cadmium ions, resulting in the formation of a surface complex. This coordination significantly enhances the adsorption properties of the SEP/PDA composite.

Empirical, computational studies and non-covalent interactions analysis of a novel salt with cadmium transition metal precursor

In this research paper, (C3H5N2)6[CdCl4][CdCl6] was successfully synthesized using a slow evaporation process. The structure was confirmed through single-crystal X-ray crystallography, FT-IR, and thermal analysis. The material was found to crystallize in the tetragonal system (space group I41/a) and the following parameters a = b = 12.0872 (8) Å; c = 24.6985 (16) Å, the crystal packing shows parallel layers of cations and stacks of discrete anions positioned at y = 1/4 and 3/4. The junction between the monoprotonated imidazolium cations and the anions, along with the crystal structure stability, relies on Cl···H−N, and Cl···H−C hydrogen bonds. Computational investigations, conducted using the B3LYP method with 6–311++G(d,p) and LANL2DZ mixed basis set, demonstrated close alignment between the computed and the experimental data, providing insights into the material's geometrical and vibrational properties. The non-covalent interactions were studied through Atoms-In-Molecule (AIM) and Reduced Density Gradient (RDG) analysis and quantitatively using the Hirshfeld surfaces associated with 2D fingerprint plots. Furthermore, thermal stability was assessed through Thermogravimetric and Differential Scanning Calorimetry (TG–DSC) analysis.

Hirshfeld Atom Refinement (HAR) and Complementary Bonding Analysis of Lithium m-Terphenylhydridoborates Containing B-H···Li Linkages.

The synthesis and characterization of the lithium m-terphenylhydridoborates [Li(2,6-Mes2C6H3)BH3]2 (1), Li(2,6-Mes2C6H3)2BH2 (2) and Li(OEt2)(2,6-Mes2C6H3)2BH2 (3) are reported. Hirshfeld Atom Refinement (HAR) of the experimentally obtained molecular structures by single-crystal X-ray crystallography allowed the determination of the exact positions of the hydrogen atoms. The bond situations of the various B-H···Li linkages were investigated by a complementary bonding analysis using various methods including atoms in molecules (AIM), electron localizability indicator (ELI-D), non-covalent interaction (NCI) index and the compliance matrix.

Effect of non-covalent interactions on the stability and structural properties of 2,4-dioxo-4-phenylbutanoic complex: a computational analysis.

The 2,4-dioxo-4-phenylbutanoic acid (DPBA) is a subject of interest in pharmaceutical research, particularly in developing new drugs targeting viral and bacterial infections. Complexation with metal ions can improve the stability and solubility of organic compounds. The present study uses quantum chemical calculations to explore the structural and electronic results arising from the interaction between the metal cation (Fe2+) and the π-system of DPBA in different solvents. For this purpose, the analyses of atoms in molecules (AIM) and natural bond orbital (NBO) are employed to comprehend the interaction features and the charge delocalization during the process of complexation. The results demonstrate that the strongest/weakest interactions are evident when the complex is situated in non-polar/polar solvents, respectively. In addition, the investigated complex exhibits two intramolecular hydrogen bonds (IMHBs) characterized by the O-H···O motif. The results indicate that the HBs present in the complex fall within the category of weak to medium HBs. Moreover, the O-H···O HBs are influenced by cation-π interactions, which can increase/decrease their strength in polar/non-polar solvents. To enhance understanding of the interactions above, an examination is conducted on various physical properties including the energy gap, electronic chemical potential, chemical hardness, softness, and electrophilicity power. All calculations are conducted within the density functional theory (DFT) using the ωB97XD functional and 6-311 + + G(d,p) basis set. The computations are performed using the quantum chemistry package GAMESS, and the obtained results are visualized by employing the GaussView program.

Mechanisms for forming methylglyoxal complexes with benzene and ethanol molecules. Nonempirical calculations

The formation mechanism of methylglyoxal monomers, dimers, trimers, methylglyoxal+benzene, and methylglyoxal+ethanol complexes was investigated using the density functional theory (DFT) approach and the B3LYP/6-311++G(d, p) functional set. Methylglyoxal has two C=O stretching vibrations, and in solvents, the intensity of the first C=O vibration band increased sharply, and the intensity of the second C=O vibration band decreased. This is due to the C=O···H hydrogen bond formed between methylglyoxal+benzene/ethanol solvents. Also, the calculations showed that among the molecules of methyglyoxal+benzene/ethanol mainly weak interactions, i.e. Van der Waals interactions, play a dominant role. Calculations are shown the complex formation energy increases as the number of molecules increases, but the average hydrogen bond energy corresponding to each bond remains unchanged. Also, the DFT method was used to study molecular structure, quantum chemical parameters such as Mulliken atomic charge distribution, atoms in molecules (AIM), reduced density gradient (RDG) and noncovalent interaction (NCI), electron localization functions (ELF), and localized orbital locator (LOL).

Crystal Growth, Structural Elucidation, Chemical Reactivity, Topology Exploration (ELF, LOL, AIM, RDG) and NLO Activity of 4-Cumyl Phenol Crystal Using Quantum Chemical Calculation

The main objective of the study is to analyze the structural behavior and NLO activity of 4-cumyl phenol by experimental and theoretical spectroscopic techniques. Its computational result is compared with the cumene compound. The optimized structural parameters of the title compound were computationally obtained at the B3LYP/6-31G (d, p) basis set. The fundamental modes of vibration were examined by experimental FT-IR, and FT-Raman techniques. The distribution of the vibrational bands was carried out with the help of normal coordinate analysis (NCA). The resulting harmonic wavenumbers were scaled by using NCA method. Topological analysis, such as Electron localization function (ELF), natural bond orbital analysis (NBO), reduced density gradient (RDG) and atoms in molecule (AIM) analysis, molecular electrostatic potential (MEP) have been used to evaluate the intermolecular interaction, especially the hydrogen bonds. UV-visible spectrum of the compound was recorded in the region 200–900 nm and the electronic properties and HOMO-LUMO energies were calculated by time dependent density functional theory approach.

Synthesis, Crystal Structure and Antifungal Activity of (E)-1-(4-Methylbenzylidene)-4-(3-Isopropylphenyl) Thiosemicarbazone: Quantum Chemical and Experimental Studies.

A novel (E)-1-(4-methylbenzylidene)-4-(3-isopropylphenyl) thiosemicarbazone was synthesized in a one-pot four-step synthetic route. Fourier transform infrared spectroscopy (FTIR), 1H and 13C nuclear magnetic resonances (NMR), single-crystal X-ray diffraction, and UV-visible absorption spectroscopy were utilized to confirm the successful preparation of the title compound. Single-crystal data indicated that the intramolecular hydrogen bond N(3)-H(3)···N(1) and intermolecular hydrogen bond N(2)-H(2)···S(1) (1 - x, 1 - y, 1 - z) existed in the crystal structure and packing of the title compound. Besides the covalent interaction, the non-covalent weak intramolecular hydrogen bond N(3)-H(3)···N(1) discussed by atoms in molecules (AIM) theory also functioned in maintaining the title compound's crystal structure. The strong intermolecular hydrogen bond N(2)-H(2)···S(1) (1 - x, 1 - y, 1 - z) discussed by Hirshfeld surface analysis played a major role in maintaining the title compound's crystal packing. The local maximum and minimum electrostatic potential of the title compound was predicted by electrostatic potential (ESP) analysis. The UV-visible spectra and HOMO-LUMO analysis revealed that the title compound has a low ΔEHOMO-LUMO energy gap (3.86 eV), which implied its high chemical reactivity due to the easy occurrence of charge transfer interactions within the molecule. Molecular docking and in vitro antifungal assays evidenced that its antifungal activity is comparable to the reported pyrimethanil, indicating its usage as a potential candidate for future antifungal drugs.

Synthesis, vibrational, thermal, topological, electronic, electrochemical stability and DFT studies of new DABCO based ionic liquids

The design of new ILs with different anions could provide interesting physico-chemical properties and for these reasons, the knowledge about the synthesis, the thermal, vibrational, topological, electronic, electrochemical properties and interaction between the selected cation-anion in these ILs are important subjects. Therefore, the understanding about these properties of these compounds is an important subject of study. In this work, we studied three ionic liquids based on the 1-decyl-1,4-diazabicyclo[2.2.2]octane, DABCO-cation, where the corresponding anions were [Br]-, [PF6]-, and [N(SO₂CF₃)₂]-. The syntheses of these bicyclic DABCO ionic liquids are based on an alkylation reaction of 1,4-diazabicyclo[2.2.2] octane and 1-bromodecanefollowed by anion exchange. The obtained ILs are characterized by 1H, 13C, 19F and 31P-NMR spectroscopy. Vibrational spectroscopy studies are conducted by infrared (FTIR/ATR) and Raman spectroscopy in the wavenumber range 600–4000 cm-1 and 45–3500 cm-1, respectively. Furthermore, the thermal stabilities were investigated using the thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) methods. Results indicate that the thermal stability follow the order [C10DABCO][Br]<[C10DABCO][PF6]<[C10DABCO][N(SO₂CF₃)₂]. Additionally, the structural parameters, electrostatic potential (ESP) maps, interaction energies, non-covalent interaction (NCI), atoms in molecule (AIM) analysis, natural bond orbital (NBO), frontier molecular orbital (FMO) analysis and Electrochemical window (ECW) are studied and analyzed by means of DFT calculations at the M06–2X-GD3/AUG–cc–pVDZ level of theory.

Cooperativity and halonium transfer in the ternary NCI···CH3I···-CN halogen-bonded complex: An ab initio gas phase study.

The strength and nature of the two halogen bonds in the NCI···CH3I···-CN halogen-bonded ternary complex are studied in the gas phase via ab initio calculations. Different indicators of halogen bond strength were employed to examine the interactions including geometries, complexation energies, Natural Bond Order (NBO) Wiberg bond indices, and Atoms in Molecules (AIM)-based charge density topological properties. The results show that the halogen bond is strong and partly covalent in nature when CH3I donates the halogen bond, but weak and noncovalent in nature when CH3I accepts the halogen bond. Significant halogen bond cooperativity emerges in the ternary complex relative to the corresponding heterodimer complexes, NCI···CH3I and CH3I···-CN, respectively. For example, the CCSD(T) complexation energy of the ternary complex (-18.27kcal/mol) is about twice the sum of the complexation energies of the component dimers (-9.54kcal/mol). The halonium transfer reaction that converts the ternary complex into an equivalent one was also investigated. The electronic barrier for the halonium transfer was calculated to be 6.70kcal/mol at the CCSD(T) level. Although the MP2 level underestimates and the MP3 overestimates the barrier, their calculated MP2.5 average barrier (6.44kcal/mol) is close to that of the more robust CCSD(T) level. Insights on the halonium ion transfer reaction was obtained by examining the reaction energy and force profiles along the intrinsic reaction coordinate, IRC. The corresponding evolution of other properties such as bond lengths, Wiberg bond indices, and Mulliken charges provides specific insight on the extent of structural rearrangements and electronic redistribution throughout the entire IRC space. The MP2 method was used for geometry optimizations. Energy calculations were performed using the CCSD(T) method. The aug-cc-pVTZ basis set was employed for all atoms other than iodine for which the aug-cc-pVTZ-PP basis set was used instead.

Exploring Polymorphism in Quinoline‐4‐Carbaldoxime: Experimental Validation and Computational Insights into Hydrogen Bonding and Structural Variations

AbstractThis study identifies and characterizes a second polymorph (Poly‐II) of quinoline‐4‐carbaldoxime (HQ), isolated from an acetone‐acetonitrile mixture. Poly‐II was compared to the previously known Poly‐I using PXRD, DSC, IR, and Raman spectroscopy. Poly‐I forms a 1D supramolecular assembly, whereas Poly‐II exhibits a 2D assembly with additional hydrogen bonds. Hirshfeld surface analysis reveals the presence of different non‐covalent interactions in Poly‐I and Poly‐II, and atom‐in‐molecule (AIM) analysis identifies their strength. AIM analysis, along with Espinosa's relation, was used to calculate the strength of O─H···N and C─H···N interactions in Poly‐I and Poly‐II. The values are −30.0 and −6.17 kJ/mol for Poly‐I, whereas the values for Poly‐II are −36.18 and −3.66 kJ/mol. The plane wave periodic DFT calculations determined the lattice energies of Poly‐I and Poly‐II to be −1.52 and −1.53 eV, respectively, indicating that both polymorphs have comparable stability. The crystal parameters of Poly‐I and Poly‐II obtained from theoretical simulations and the experiment are comparable, indicating the similar stability of Poly‐I and Poly‐II. Computational simulations confirmed experimental data, showing both polymorphs have similar stability and melting points despite different unit cell volumes.

Exploiting macrocyclic polylactam for sensing V-series nerve agents: A computational study

The nerve agents are organophosphorus compounds (OPs) developed as chemical warfare agents (CWAs) that inhibit acetylcholinesterase (AChE) and lead to impeding neurological signals in mammals. Therefore, detecting such nerve agents is important, and efforts to study the fundamental interactions of host systems with CWAs are scarce in the literature. In this report, the cyclic 18-membered tetralactam [Ⅰ] as a host molecule has been chosen to sense V-series nerve agents. The DFT calculated results reveal that VM, VG, and VX, bind strongly with the core unit of the host molecule tetralactam [Ⅰ] with a preference for VM. The remarkably higher binding affinity of VM is governed by more hydrogen bonding interactions with the core of the cyclic 18-membered tetralactam [Ⅰ]. The nerve agent Russian VX has been found to bind weakly with the receptor molecule. The hydrogen bonding interactions of these nerve agents have further been analyzed with non-covalent interactions (NCI) and atoms in molecule (AIM) calculations. The tetralactam moiety exhibits the binding with V-series nerve agents and the absorption spectral results can be used as diagnostic signatures for sensing of such nerve agents in useful applications.

Supramolecular assembly mediated through NH···OX (X = C, N, P) hydrogen bonds and Y···π (Y = Br, π) contacts: Structural/computational studies of the P(O)(NHC(O)C6H4-3-NO2)(NHC6H4-3-Br)2 phosphoric triamide

Supramolecular assembly is studied in the structure of N,N'-bis(3‑bromo-phenyl)-N"-(3-nitro-benzoyl)phosphoric triamide, P(O)(NHC(O)C6H4-3-NO2)(NHC6H4-3-Br)2, I, by X-ray crystallography combined with quantum chemical calculations. The asymmetric unit of I is composed of two symmetry-independent molecules that show differences in some torsion angles, especially the ones related to the rotation of amine moieties. The conformations of amine moieties in two molecules are considered based on the resembling P—N—C—C/OP—N—C torsion angles, which associate with the ±sp/+sc conformations in one molecule and –sc/+sp and –sp/–sc conformations in the other molecule (sp = synperiplanar and sc = synclinal). In the crystal structure, the molecules are connected through N—H···OX (X = P, C, N) hydrogen bonds, forming a two-dimensional architecture along the bc plane. The C—H···O/π···π interactions do not change the dimensionality made by N—H···O hydrogen bonds, while the participation of Br···π interactions creates a three-dimensional network. The title structure represents the first observation of Br···π interaction in the C(O)NHP(O)-based family. The methods of Atoms in Molecules (AIM), Natural Bond Orbital (NBO) and Reduced Density Gradient (RDG) are used for the study of noncovalent interactions.

A detailed TD-DFT and intermolecular interaction study of vitamin K in soluble, poorly soluble and insoluble solvents, as well as an ADME and molecular docking study

Vitamin K is one of the most important fat-soluble vitamins and while there are two main types of vitamin K in nature, known as K1 (phylloquinone) and K2 (menaquinones), there is also a synthetic type of vitamin K known as K3 (menadione). Recent studies have shown that it is crucial to know the non-covalent interactions, ADME and molecular docking of molecules in different solvent media. Therefore, we have performed some quantum chemical calculations, ADME and intra-and intermolecular interaction calculations of a number of K1, K2 and K3 such as K1-water (K1 + W), K1-methanol (K1 + M), K1-triacetin (K1 + T), K2-water (K2 + W), K2-methanol (K2 + M), K2-triacetin (K2 + T), K3-water (K3 + W), K3-methanol (K3 + M), K3-triacetin (K3 + T) performed by Density Functional Theory (DFT) and Multiwfn: A multifunctional wavefunction analyzer. Molecular structures, HOMO-LUMO energies, MEP and electronic properties have been calculated and described using DFT at the level of B3LYP/6-311G (d,p) level. The nature of the molecular interactions between vitamin K and solvents such as water, methanol and triacetin were also investigated using topological analyses such as atoms in molecule (AIM), non-covalent interaction index (NCI), reduced density gradient (RDG), Localized orbital locator (LOL) and electron localization function (ELF). In addition, FMO for electronic transitions, MEP for electrophilic and nucleophilic attack, ADME to investigate how a chemical is processed by a living organism, and Fukui functions to determine electron density are explained. Finally, molecular docking was used to determine the biological activity of the vitamin K.

AIM/NBO Analysis of the Geminal Coupling Constants in the Stabilization of A-Type Dimeric Proanthocyanidin: Angular Dependence.

The angular dependence of the indirect short-range spin-spin coupling constants (SSCC), the geminal , , and in A-type dimeric proanthocyanidin, was investigated using density functional theory. We studied the rotation of ring B around the bond. Therefore, we calculated hyperconjugative charge transfers and bond polarizations within the natural bond orbital (NBO) approach, performing a topological study based on Bader's theory, AIM (atoms in molecules), and analyzing the angular dependence of AIM/NBO parameters. The results describe a relationship between the geminal coupling that changes with angular variation and NBO charge transfers to the bonds involved in the coupling pathways that can explain the behavior of the former property. Based on AIM/NBO data, inductive and mesomeric effects were described and quantified, showing a clear correlation with the stabilization of the structure, demonstrating a resonance-assisted inductive effect. We also set out strong hyperconjugative interactions (anomeric effect) involving nonbonding electron pairs of oxygen atoms. This analysis of coupling constants supports previous models by other authors and shows the application in this particular case. Moreover, the SSCCs studied herein are used for identifying stable structures and conformational search analysis of flavonoids. Finally, our results show the relationship between SSCCs and the structure stabilization and charge delocalization effects.

The curious case of S4N4 − A reinvestigation

This work employs quantum chemical methods to explore electronic properties and bonding of the S4N4 molecule. We utilized calculations of multidimensional off-nucleus magnetic shielding, anisotropy of the induced current density (ACID), natural bond orbitals (NBOs), and atoms in molecules (AIM). The unique S4N4 system comprises bent bonding, absence of NN, weakness in the centers of SS bonds, and polar SN bonds. Our findings uncover coexisting of both electron localization and delocalization in S4N4. The magnetic analysis discloses curved connections between the nitrogen atoms and the SS bonds, drawing possible electron delocalization pathways as two pyramid-like regions of magnetic activity. Our magnetic calculations were performed at DFT/GIAO-B3LYP using Jorge-TZP-DKH and 6-311++G(2d,2p) basis sets. No remarkable qualitative differences were noticed between the obtained magnetic features from these two basis sets. Capturing the magnetic details associated with structural features shows superiority of ZZ component of the magnetic shielding tensor (σzz(r)) over the isotropic magnetic shielding (σiso(r)).

2D hydrogen bonded organic framework (2D-HOF) in benzodioxane-coupled-pyridine as a charge carrier: Synthesis, structural, quantum computational investigation

This research presents a comprehensive investigation into the synthesis, structural features, and charge carrier properties of a novel 2D Hydrogen-Bonded Organic Framework (2D-HOF) formed by Benzodioxane-Coupled-Pyridine. The synthesis involves the reaction of 2,3-dihydrobenzo[b][1,4]dioxin-6-carbaldehyde with pyridine-2-carbohydrazide in the presence of acetic acid and ethanol solvent, leading to the formation of (E)-2-(2-((2,3-dihydrobenzo[b][1,4]dioxin-6-yl)methylene)hydrazinyl)pyridine (DDMP). Single crystal X-ray diffraction analysis reveals the monoclinic crystal system with the P21/n space group, showcasing a non-planar structure due to a distinctive twisting motion in the dioxane ring. The crystal packing is governed by a complex network of intermolecular interactions, including hydrogen bonds, short contacts, and π-stacking, ultimately forming a stable 2D-HOF. Hirshfeld Surface (HS) analysis provides insights into key interactions, emphasizing the significance of hydrogen bonding, short contacts, and stacking interactions in molecular packing. The 2D fingerprint (FP) plots quantitatively highlight crucial interatomic contacts, with hydrogen bonding, CH…H, and O…H interactions dominating. Molecular Electrostatic Potential (MEP) analysis reveals potential sites for electrophilic and nucleophilic attacks, aiding in predicting reactive sites and charge carrier behavior. Energy framework analysis sheds light on the pairwise interaction energies within the crystal structure, emphasizing the role of dispersive forces in stabilizing the crystal lattice. Density functional theory calculations indicate the molecule's charge transfer capabilities, suggesting its suitability for applications such as batteries, supercapacitors, and solar cells. Additionally, global reactivity parameters suggest that the 2D HOF material has electron and proton conduction capabilities, making it versatile for various applications. Atoms-in-molecules (AIM) topology analysis, particularly non-covalent interaction (NCI) analysis, provides a detailed understanding of intra and intermolecular interactions, highlighting hydrogen bonding and π…π interactions. H-bond binding energy analysis confirms the non-covalent nature of identified interactions, emphasizing their strength and significance.

Simultaneous desulfurization and dearomatization of simulated straight-run diesel with novel green DBN-based ionic liquids

Given the surplus of diesel fuel in China and the extensive utilization of renewable energy sources, there is a growing inclination to eliminate organic sulphur and aromatic hydrocarbons from diesel fuel for its application as high-quality ethylene cracking feedstock. In this study, a series of 1,5-diazabicyclo[4.3.0]non-5-ene (DBN)-based ionic liquids with [DBNH]+ as the cation and imidazole as the anion were designed and synthesized for the simultaneous desulfurization and dearomatization of straight-run diesel fuel. Considering factors such as extractant stability, residue content in oil, and separation performance, [DBNH][Tr], exhibiting excellent performance characteristics, was screened as the optimal extractant. Following three-stage cross-flow extraction with an extractant/oil ratio of 3:1 at 30 °C, complete removals of sulfides (benzothiophene) and polycyclic aromatic hydrocarbons (1-methylnaphthalene) were achieved while saturated alkanes reached up to 95.8 wt%, making it suitable for ethylene cracking applications. The interaction mechanisms between ionic liquids and oil components were revealed by atoms in molecules (AIM) topology analysis, independent gradient model based on Hirshfeld partition (IGMH) analysis, and symmetric adaptive perturbation theory energy decomposition techniques, revealing that dispersion-dominated van der Waals (VDW) forces primarily govern interactions due to π-π stacking.

Investigating the potential of NH2-Functionalized MIL-53(Fe) nanoparticle as a carrier for 5-fluorouracil through molecular dynamics simulation

This study investigates the role of the NH2-functionalized MIL-53(Fe) nanoparticle as a carrier for the anti-cancer drug 5-fluorouracil (5-Fu) through molecular dynamics (MD) simulation. The Atom in Molecules (AIM) method was used to determine the interaction type between 5-Fu and NH2-MIL-53(Fe). The Steered Molecular Dynamics (SMD) approach was employed to calculate the free energy of drug encapsulation. The simulation included the NH2-MIL-53(Fe) nanoparticle containing 5-FU molecules and water molecules at different temperatures and 1 atm pressure. The properties analyzed included density, radial distribution functions, displacement, diffusion, and binding energy of the drug with NH2-MIL-55(Fe). It is shown that the drug was encapsulated in the framework channels and the variation of density of the system with temperature in the presence of nanoparticles decreased. The drug's mean square displacement, total self-diffusion coefficient, and diffusion coefficient in channel direction increased with time as temperature rose. The drug was aligned to have its oxygen atoms towards the metal nodes of the framework. However, The nitrogen atom of the amine functional group in NH2-MIL-53(Fe) interacts more with the F atom of 5-Fu which shows the effect of this functional group on the adsorption of the 5-Fu. The drug's adsorption percentage increased from 298 K to 328 K. The calculated binding energy increased with temperatures and was desirable as it countered the drug's repulsive forces with atoms of NH2-MIL-53(Fe). The results of the molecular docking simulation confirmed MD simulation.

Selective detection of food contaminants using engineered gallium-organic frameworks with MD and metadynamics simulations

The exclusion mechanism of food contaminants such as bisphenol A (BPA), Flavonoids (FLA), and Goitrin (GOI) onto the novel gallium–metal organic framework (MOF) and functionalized MOF with oxalamide group (MOF-OX) is evaluated by utilizing molecular dynamics (MD) and Metadynamics simulations. The atoms in molecules (AIM) analysis detected different types of atomic interactions between contaminant molecules and substrates. To assess this procedure, a range of descriptors including interaction energies, root mean square displacement, radial distribution function (RDF), density, hydrogen bond count (HB), and contact numbers are examined across the simulation trajectories. The most important elements in the stability of the systems under examination are found to be stacking π–π and HB interactions. It was confirmed by a significant value of total interaction energy for BPA/MOF-OX (− 338.21 kJ mol−1) and BPA/MOF (− 389.95 kJ mol−1) complexes. Evaluation of interaction energies reveals that L–J interaction plays an essential role in the adsorption of food contaminants on the substrates. The free energy values for the stability systems of BPA/MOF and BPA/MOF-OX complexes at their global minima reached about BPA/MOF = − 254.29 kJ mol−1 and BPA/MOF-OX = − 187.62 kJ mol−1, respectively. Nevertheless, this work provides a new strategy for the preparation of a new hierarchical tree-dimensional of the Ga-MOF hybrid material for the adsorption and exclusion of food contaminates and their effect on human health.