Including Van Der Waals Interactions Research Articles

Polyaromatic Hydrocarbon Inclusion Complexes with 2-Hydroxylpropyl-β/γ-Cyclodextrin: Molecular Dynamic Simulation and Spectroscopic Studies.

In aqueous and solid media, 2-HP-β/γ-CD inclusion complexes with poly aromatic hydrocarbon (PAH) Phenanthrene (PHN), Anthracene (ANT), Benz(a)pyrene (BaP), and Fluoranthene (FLT) were investigated for the first time. The inclusion complexes were characterized and investigated using fluorescence and 1HNMR spectroscopy. The most prevalent complexes consisting of both guests and hosts were those with a 1:1 guest-to-host ratio. The stability constants for the complexes of PHN with 2-HP-β-CD and 2-HP-γ-CD were 85 ± 12 M-1 and 49 ± 29 M-1, respectively. Moreover, the stability constants were found to be 502 ± 46 M-1 and 289 ± 44 M-1 for the complexes of ANT with both hosts. The stability constants for the complexes of BaP with 2-HP-β-CD and 2-HP-γ-CD were (1.5 ± 0.02) × 103 M-1 and (9.41 ± 0.03) × 103 M-1, respectively. The stability constant for the complexes of FLT with 2-HP-β-CD was (1.06 ± 0.06) × 103 M-1. However, FLT was observed to form a weak complex with 2-HP-γ-CD. Molecular dynamic (MD) simulations were used to investigate the mechanism and mode of inclusion processes, and to monitor the atomic-level stability of these complexes. The analysis of MD trajectories demonstrated that all guests formed stable inclusion complexes with both hosts throughout the duration of the simulation time, confirming the experimental findings. However, the flexible Hydroxypropyl arms prevented the PAHs from being encapsulated within the cavity; however, a stable exclusion complex was observed. The main forces that influenced the complexation included van der Waals interactions, hydrophobic forces, and C-H⋯π interaction, which contribute to the stability of these complexes.

Synthesis and Characterization of Propofol‐Like Compounds, Anticancer Activities and Investigation of Their Anesthetic Effects by Molecular Docking

AbstractThis study was designed to synthesize hybrid molecules starting from 2,6‐diisopropyl aniline (1), which is similar to Propofol (2,6‐diisopropyl phenol), by increasing its biological activity with other heterocycles and to determine the anesthetic activity of the obtained compounds. For this purpose, commercially available 2,6‐diisopropylaniline (1) was used as a starting compound. Then, ester (2), hydrazide (3), carbothioamide (5, 6) and Schiff bases derivatives (4 a–f) were synthesized, respectively. To achieve the etomidate‐like target compound 8, compound 7 containing chloroacetamide group was firstly synthesized from starting compound 1, and this compound reacted with ethyl‐1H‐imidazole‐5‐carboxylate. The structures of the newyl synthesized 12 compounds were characterized and confirmed by FT‐IR, MALDI‐TOF/MS, 1H NMR, 13C NMR.Within the scope of in silico study, ligand binding status of all compounds on the GABAA receptor was revealed. Molecular docking studies of them with GABAA found out that the interaction modes, including van der Waals interactions, hydrogen bonds, and pi‐pi interactions, are similar to that of the cocrystalline ligand Propofol. For the compounds 1, 2, 3, 4 d, 5, 7 have micromolar (μM) level, for the compounds 4 a, 4 b, 4 c, 4 e, 4 f, 6 and 8 have nanomolar (nM) level of inhibition has been estimated. When all data such as active localization, interacting residues, bond types formed, estimated Ki values, docking scores are evaluated together, compounds 1, 2, 3 and 7 which can be considered as synthesis starting or intermediate material, may be less effective.On the other hand the anticancer activities of the synthesized compounds were investigated against A549 (non‐small cell lung carcinoma) and BEAS‐2B cell line (normal bronchial epithelial) cell lines using Resazurin cell viability assay. It has been revealed that the compounds 4, 5, 6 and 8 may be more active in terms of anesthetic activity, whereas only compound 6 showed anti‐cancer activity.

Novel formulated alumina-silica hybrid sol for the entire consolidation of waterlogged decayed ivory from Sanxingdui ruin site

Large amount of ivory was excavated from Sanxingdui site which was waterlogged, severely degraded and in urgent need for conservation. There has been much effort for the conservation of waterlogged ivory by scientists. However, due to a lack of appropriate conservation material and the need to use non-destructive methods, no satisfactory results have been achieved previously. In this work, a novel formulated water-based Al–Si hybrid sol of size about 20 nm was prepared and introduced through a quasi-dynamic equilibrium method to waterlogged ivory tusk for the purpose of conservation. Good conservation performance could be achieved, since Al–Si sol gradually permeates into the interior of the ivory, distributes homogeneously and connects the loose components of ivory. Samples treated with appropriate amount of Al–Si sol displayed satisfactory compressive strength and porous intact structure. It was found that the fluidity of Al–Si sol had a significant influence on the conservation effect. Moreover, Al–Si sol not only consolidated HAP but also worked well on the soil embedded in unearthed ivory, which was beneficial to conserve ivory intactly. Slightly negatively charged Al–Si hybrid gel could interact with ivory matrix through multiple interactions including van der Waals force, electrostatic interaction, chemical and hydrogen bonding.

Theoretical prediction of proteins network-induced nonlocal response in molecules-resonator biosensor with hydrogen bonds including van der waals interactions

The present study investigates the adsorption-induced resonance frequency shift of a biomolecule-resonator system, considering the shear distortion effect, distributed adatoms, and small-scale effects using nonlocal elasticity theory. The adsorption-induced energy is modeled using a distributional approach for both the bio-receptor and spike protein. The dynamic behavior model for a microbeam resonator is derived, incorporating surface stress. The functional microbeam approach and the localized biomolecule approach are employed, along with van der Waals (vdW) interactions using the Lennard-Jones (6–12) potential to calculate the influence of all applied conditions. Explicit inertia moment and shear force are determined based on the nonlocal Timoshenko beam equations, with residual stress applied as an additive axial load. Numerical results demonstrate that the computed frequency shift depends on the active surface parameters, adsorbed adatoms, as well as the localized receptor and spike. The evaluation of results indicates that interatomic phenomena make the microsystem softer, emphasizing the importance of considering it in computations. Thus, the derived model is suitable for investigating the dynamic behavior of the biomolecule-resonator, applicable for determining both mass and density of spike and virus in the presence of adatom bonds.

Regulation Mechanism of Phenolic Hydroxyl Number on Self-Assembly and Interaction between Edible Dock Protein and Hydrophobic Flavonoids.

In this study, galangin (Gal), kaempferol (Kae), quercetin (Que), and myricetin (Myr) were chosen as the representative flavonoids with different phenolic hydroxyl numbers in the B-ring. The edible dock protein (EDP) was chosen as the new plant protein. Based on this, the regulation mechanism of the phenolic hydroxyl number on the self-assembly behavior and molecular interaction between EDP and flavonoid components were investigated. Results indicated that the loading capacity order of flavonoids within the EDP nanomicelles was Myr (10.92%) > Que (9.56%) > Kae (6.63%) > Gal (5.55%). Moreover, this order was consistent with the order of the hydroxyl number in the flavonoid's B ring: Myr (3) > Que (2) > Kae (1) > Gal (0). The micro morphology exhibited that four flavonoid-EDP nanomicelles had a core-shell structure. In the meantime, the EDP encapsulation remarkably improved the flavonoids' water solubility, storage stability, and sustained release characteristics. During the interaction of EDP and flavonoids, the noncovalent interactions including van der Waals forces, hydrophobic interaction, and hydrogen bonding were the main binding forces. All of the results demonstrated that the hydroxyl number of bioactive compounds is a critical factor for developing a delivery system with high loading ability and stability.

Tuning Gaps and Schottky Contacts of Graphene/Phosphorene Heterostructures by Vertical Electric Field and Strain.

We present a comprehensive study of the structural and electronic properties of a graphene/phosphorene (G/P) heterostructure in the framework of density functional theory, including van der Waals interaction in the exchange-correlation functional. While the G(4 × 1)/P(3 × 1) superlattice usually used in the literature is subject to a strain as high as about 7%, the in-plane strain could be drastically reduced to under 1% in the G(4 × 13)/P(3 × 12) heterostructure investigated here. Adapting the lattice constants of the rectangular lattices, the equilibrium configuration in the xy plane of phosphorene relative to the graphene layer is optimized. This results in an equilibrium interlayer distance of 3.5 Å and a binding energy per carbon atom of 37 meV, confirming the presence of weak van der Waals interaction between the graphene and the phosphorene layers. The electronic properties of the heterostructure are evaluated under different values of interlayer distance, strain and applied vertical electric field. We demonstrate that G/P heterostructures form an n-type Schottky contact, which can be transformed into p-type under external perturbations. These findings, together with the possibility to control the gaps and barrier heights, suggest that G/P heterostructures are promising for novel applications in electronics and may open a new avenue for the realization of innovative optoelectronic devices.

Molecular Dynamics study on buckling behavior of vertically aligned carbon nanotube (VACNT) bundles with characterized waviness

The buckling behavior of vertically aligned carbon nanotube (VACNT) bundles with a characterized waviness ratio was studied using the principle of sinusoidal waves. A MATLAB algorithm was used to generate bundles with a user-specified waviness ratio, and 12 VACNT models were used under a constant strain of 0.01/ps uniaxial compression with three variable parameters: waviness ratio, number of VACNTs within the bundle, and presence of van der Waals interactions; moreover, the findings suggest that these parameters significantly influenced the critical buckling stress (σcomp) and buckling behavior of the bundle. Increasing the waviness resulted in a significant reduction of approximately 59.96% between a bundle with no waviness and a bundle with a waviness ratio of 0.33. Including van der Waals interactions played a critical role in strengthening the overall VACNT bundle, whereas eliminating them changed the buckling pattern and behavior of the bundles, furthermore, increasing the number of VACNTs in a bundle increased the critical buckling stress of the overall bundle. This study provides insight into the structural behavior of VACNT bundles, which is expected to impact the design of any system in which the collective mechanical behavior of the VACNT bundles is critical. These findings can improve the study of composite materials in lithium-ion batteries for high-capacity CNT composite anodes.

High throughput calculations for a dataset of bilayer materials

Bilayer materials made of 2D monolayers are emerging as new systems creating diverse opportunities for basic research and applications in optoelectronics, thermoelectrics, and topological science among others. Herein, we present a computational bilayer materials dataset containing 760 structures with their structural, electronic, and transport properties. Different stacking patterns of each bilayer have been framed by analyzing their monolayer symmetries. Density functional theory calculations including van der Waals interactions are carried out for each stacking pattern to evaluate the corresponding ground states, which are correctly identified for experimentally synthesized transition metal dichalcogenides, graphene, boron nitride, and silicene. Binding energies and interlayer charge transfer are evaluated to analyze the interlayer coupling strength. Our dataset can be used for materials screening and data-assisted modeling for desired thermoelectric or optoelectronic applications.

Exploring the aggregation of amyloid-β 42 through Monte Carlo simulations

Coarse-grained Monte Carlo simulations are performed for a disordered protein, amyloid-β 42 to identify the interactions and understand the mechanism of its aggregation. A statistical potential is developed from a selected dataset of intrinsically disordered proteins, which accounts for the respective contributions of the bonded and non-bonded potentials. While, the bonded potential comprises the bond, bend, and dihedral constraints, the nonbonded interactions include van der Waals interactions, hydrogen bonds, and the two-body potential. The two-body potential captures the features of both hydrophobic and electrostatic interactions that brings the chains at a contact distance, while the repulsive van der Waals interactions prevent them from a collapse. Increased two-body hydrophobic interactions facilitate the formation of amorphous aggregates rather than the fibrillar ones. The formation of aggregates is validated from the interchain distances, and the total energy of the system. The aggregate is structurally characterized by the root-mean-square deviation, root-mean-square fluctuation and the radius of gyration. The aggregates are characterized by a decrease in SASA, an increase in the non-local interactions and a distinct free energy minimum relative to that of the monomeric state of amyloid-β 42. The hydrophobic residues help in nucleation, while the charged residues help in oligomerization and aggregation.

The quantitative study of methane adsorption on the Pt(997) step surface as the initial process for reforming reactions

The adsorption states and thermal process of methane on a stepped Pt surface were investigated using temperature-programmed desorption (TPD), infrared reflection absorption spectroscopy (IRAS), and density functional theory (DFT) calculations including van der Waals interactions. By estimating the activation energies of methane desorption from the TPD data, it was revealed that the adsorption energy for methane on the step site (0.19 eV) was higher than that on the terrace site (0.15 eV). The IRAS spectrum after multilayer adsorption and subsequent 70 K heating showed two peaks at 3009 and 1305 cm−1, which were assigned to the antisymmetric stretching and the deformation modes for adsorbed methane on the step site, respectively. The present DFT calculations show that the most stable adsorption structure for methane on the step site is a “2H” structure, where two C-H bonds point toward Pt atoms. Based on the electronic structure analysis, we conclude that the stability of the 2H structure originates from the mixing between the methane molecular orbitals and the orbitals of step Pt atoms. As a result, the length of the C-H bond pointing toward the Pt step atom is elongated compared with that of other C-H bonds. Thus, the Pt step site already activates the adsorbed methane slightly.

Review of Colloid (Nano‐ and Micro‐Particle) Transport and Surface Interaction in Groundwater. William P. Johnson and Eddy F. Pazmino. The Groundwater Project. 111 pp. ISBN: 978‐1‐77470‐070‐9. DOI: https://doi.org/10.21083/978‐1‐77470‐070‐9

Review of <i>Colloid (Nano‐ and Micro‐Particle) Transport and Surface Interaction in Groundwater</i>. William P. Johnson and Eddy F. Pazmino. The Groundwater Project. 111 pp. ISBN: 978‐1‐77470‐070‐9. DOI: https://doi.org/10.21083/978‐1‐77470‐070‐9

A density functional theory study of thiophene and pyridine adsorption on Pt/Rh-doped Cu (100) surface

The adsorption of pyridine and thiophene molecules on clean, doped Rh-Cu (100) and Pt-Cu (100) surfaces was investigated using density functional theory calculations including van der Waals interactions (optB86b-vdW). Various Rh-Cu and Pt-Cu slabs, in which the Cu surface atoms are substituted by a monomer, dimer, and tetramer, were tested by adsorbing pyridine and thiophene molecules. The adsorption properties of these systems were examined regarding their adsorption energy, adsorption heights, electron density difference (EDD), and density of states (DOS). Our results indicate that, for the thiophene molecule, the adsorption energy was increased from 0.98 to 3.55 eV after alloying the Cu surface with an Rh tetramer. Concerning the adsorption of pyridine, the adsorption energy is increased from 0.96 to 3.06 eV after substituting the Cu atoms with an Rh tetramer. Therefore, the Rh-Cu (100) doped surface was found to be more suitable for the adsorption of thiophene and pyridine in comparison with the clean surface. Bader charge analysis shows that the charge transfer was from surface atoms to the thiophene molecule for all systems except the case of the adsorption on the Pt4-Cu (100) surface. However, concerning the adsorption of pyridine on doped surfaces, all charge transfers are moved from the surface to the molecule and attained 0.34 electron charge when the Cu atoms are substituted by Rh dimer. Furthermore, the electron density difference (EDD) calculations for doped surfaces display a charge accumulation on the thiophene molecule. The EDD confirmed the results of the charge transfer obtained for the pure and doped Cu (100) surface with Pt tetramer and Rh tetramers. The results of PDOS of four metal atoms in the top layer making a 4-fold hollow site indicate an upshift of the d orbitals, which can explain the redistribution of charge between the surface and both molecules.

How are Hydroxyl Groups Localized on a Graphene Sheet?

Arrangements of hydroxyl groups on graphene sheets were systematically investigated using density functional theory calculations that included van der Waals interactions. Results show that hydroxyl groups tend to gather at para-positions on graphene sheets to generate perfect ring-like hexahydroxyl group adsorption. The close proximity of hydroxyl groups is in good agreement with the experimental separation between unoxidized, aromatic and oxidized, saturated regions in graphene oxide. The orientation of hydrogen atoms in hydroxyl groups creates both O–H···O and O–H···π hydrogen bonds. Calculations also indicated that the binding energy per hydroxyl group follows a logarithmic function with respect to the number of hydroxyl groups. Besides, the opening band gap was observed for several derivatives, and the relationship between the band gap and O/C ratio was found to be nonmonotonic. Analysis of the density of states showed that bands around the Fermi levels of derivatives between graphene and hydroxyl groups are mainly composed of 2pz orbitals of carbon and oxygen atoms.

Structural and elastic behaviour of aragonite at high-pressure: A contribution from first-principle simulations

Aragonite (CaCO3, space group Pmcn) is an important mineral for both geological and biological reasons, being one of the phases that recycles carbon in deep Earth conditions and the product of biomineralization of several terrestrial and marine organisms, respectively. Because of its ubiquity, aragonite has been the subject of several investigations to understand its elastic behaviour and stability at different P-T conditions, but the results reported in literature are still very scattered. Aiming at providing further details on this topic, in the present work we determined the structural and elastic properties of aragonite at absolute zero (0 K) within the Density Functional Theory framework, using a posteriori correction to include the weak long-range interactions. The equation of state parameters for this mineral phase, calculated between 0 GPa – 25 GPa, were K0 = 80.2(7) GPa, K’ = 4.37(10) and V0 = 223.00(6) Å3, in good agreement with the bulk modulus calculated from the elastic moduli (KR = 78.49 GPa). The results were compared to previous experimental and theoretical data, finding them in line with some specific studies, and show that some structural features (e.g., the carbonate ion aplanarity) could be related to the mechanism of phase transition to the post-aragonite phase at high pressure. The present work highlights the importance of including van der Waals interactions in the physical treatment of the structural and elastic properties of aragonite, and further extends the knowledge of the behaviour of this mineral as a function of pressure.

ZnC3-2D a new material for hydrogen reversible storage predicted by first-principles calculations

In order to improve the transport, electronics and storage properties of graphene layers, we have constructed compact structures with graphene sheets. With the Use of the density functional theory (DFT) and ab-initio molecular dynamics (AIMD) calculations including van der Waals interactions, the structural stability and hydrogen storage properties of the neat ZnC3 monolayer have been systematically investigated, the adsorption of H2 molecules on ZnC3 shows good results. A high binding energy up to 0.3169 eV with 3.30 Å as equilibrium distance. A low activation energy allows the molecule to migrate on the surface so easily up to 0.022 eV. The investigation revealed a high gravimetric (GC) and volumetric (Vc) capacities up to 7.73 wt% and 98.44 g/l as a new 2D material for hydrogen storage. The hydrogenation/dehydrogenation (desorption) temperature is expected to be 215.55 K. The desorption temperature (TD) proved to be significantly greater as compared to the critical point of hydrogen (33 K). Furthermore, the TD calculations were confirmed with AIMD simulations of the adsorption of 17 H2 molecule on ZnC3. Thus, the monolayer ZnC3 could function as a reversible hydrogen storage substrate under feasible conditions.

XEDA, a fast and multipurpose energy decomposition analysis program.

A fast and multipurpose energy decomposition analysis (EDA) program, called XEDA, is introduced for quantitative analysis of intermolecular interactions. This program contains a series of variational EDA methods, including LMO-EDA, GKS-EDA and their extensions, to analyze non-covalent interactions and strong chemical bonds in various environments. XEDA is highly efficient with a similar computational scaling of single point energy calculations. Its efficiency and universality are validated by a series of test examples including van der Waals interactions, hydrogen bonds, radical-radical interactions and strong covalent bonds.

Density functional study on formic acid decomposition on Pd(111) surface: a revisit and comparison with other density functional methods.

The mechanism of formic acid decomposition on the Pd(111) surface has been investigated by several theoretical methods in previous studies, including PBE and PW91. These results indicated that the mechanism is different from different methods, and even by using the same method (i.e., PBE), the mechanism is also different. In this study, we have revisited the formic acid decomposition on Pd(111) surface by using another density functional RPBE and by including van der Waals interaction which is neglected in the previous studies. Our results showed that the formic acid is decomposed via O-H bond cleavage to form bi-HCOO*, and the most favorable pathway is HCOOH* → bi-HCOO* + H* → CO2* + 2H*. The energy barrier is 0.55eV at the rate-determining step. This conclusion is consistent with one of the PBE study. This demonstrated that computational methods have a great influence on the reaction mechanism, and care should be taken in selecting the appropriate computational methods.

Accurate Quantification of Sulfonamide Metabolites in Goat Meat: A New Strategy for Minimizing Interaction between Sheep Serum Albumin and Sulfonamide Metabolites.

To date, the determination of sulfonamide metabolites in animal-derived food has universal disadvantages of low throughput and no integrated metabolites involved. In this study, a powerful and reliable strategy for high-throughput screening of sulfonamide metabolites in goat meat was proposed based on an aqueous two-phase separation procedure (ATPS) combined with ultrahigh-performance liquid chromatography quadrupole-Orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap). Noncovalent interactions including van der Waals force, hydrogen bonding, and hydrophobic effect were determined to be staple interactions between the sulfonamide metabolites and sheep serum albumin by fluorescence spectroscopy and molecular docking technology, and an 80% acetonitrile-water solution/(NH4)2SO4 was used as ATPS in order to release combined sulfonamide metabolites and minimize the influence of sheep serum albumin. Sulfonamide metabolites in the matrix were screened based on a mechanism of mass natural loss and core structure followed by identification combined with the pharmacokinetic. The developed strategy was validated according to EU standard 2002/657/EC with CCα ranging from 0.07 to 0.98 μg kg-1, accuracy recovery with 84-107%, and RSDs lower than 8.9%. Eighty seven goat meat samples were used for determination of 26 sulfonamides and 8 potential metabolites. On the basis of the established innovative process, this study has successfully implemented the comprehensive detection of sulfonamide metabolites, including N4-acetylated substitution, N4-hydroxylation, 4-nitroso, azo dimers, oxidized nitro, N4 monoglucose conjugation, β-d-glucuronide, and N-4-aminobenzenesulfonyl metabolites, which were shown to undergo oxidation, hydrogenation, sulfation, glucuronidation, glucosylation, and O-aminomethylation.

Derjaguin-Landau-Verwey-Overbeek energy landscape of a Janus particle with a nonuniform cap.

A colloidal particle is often termed "Janus" when some portion of its surface is coated by a second material which has distinct properties from the native particle. The anisotropy of Janus particles enables unique behavior at interfaces. However, rigorous methodologies to predict Janus particle dynamics at interfaces are required to implement these particles in complex fluid applications. Previous work studying Janus particle dynamics does not consider van der Waals interactions and realistic, nonuniform coating morphology. Here we develop semianalytic equations to accurately calculate the potential landscape, including van der Waals interactions, of a Janus particle with nonuniform coating thickness above a solid boundary. The effects of both nonuniform coating thickness and van der Waals interactions significantly influence the potential landscape of the particle, particularly in high ionic strength solutions, where the particle samples positions very close to the solid boundary. The equations developed herein facilitate more simple, accurate, and less computationally expensive characterization of conservative interactions experienced by a confined Janus particle than previous methods.

Interfacial film formation and film stability of high hydrostatic pressure-treated β-lactoglobulin

The mechanical stability of interfacial protein films is limited through the intermolecular interaction of the adsorbed proteins. Since the intermolecular interactions vary in dependence of the protein structure, the investigation of intentionally induced structural modifications (i.e., through high hydrostatic pressure) of interfacial active proteins is required to mechanistically understand their structure-function-relationship. The aim of this study was to link the structural analysis of pressure-treated whey protein β-lactoglobulin at the oil/water-interface with the formation of the interfacial protein film and the resulting film stability against mechanical stress. For this purpose, we treated β-lactoglobulin in water at pH 7 with hydrostatic pressures of 600 MPa for 10 min at 20 °C and analyzed the protein structure in oil/water-emulsion with Fourier-transform-infrared-spectroscopy, extrinsic fluorescence, and ζ-potential. We characterized the molecular density and interfacial film properties via Langmuir trough analysis, electron-paramagnetic-resonance-spectroscopy, interfacial shear and dilatational rheology. The structural flexibility of pressure-treated β-lactoglobulin favored its unfolding and a fast interfacial protein film formation that resulted in pronounced intermolecular interactions, including van der Waals interactions, hydrophobic associations and disulfide bonds. The high interfacial molecule density combined with many and strong intermolecular interactions stabilized the pressure-treated protein film against shear deformation and small dilatational deformation. However, against high dilatational deformation, the pressure-treated β-lactoglobulin film showed a lower stability due to a slow migration towards unoccupied interfacial area. Hence, our research contributes to the control of the mechanical protein film stability, and thus the colloidal stability of emulsions in dependence of the protein structure at the oil/water-interface.