Van Der Waals Type Research Articles

Binding of the anticancer drug BI-2536 to human serum albumin. A spectroscopic and theoretical study

BI-2536 is a potent Polo-like kinase inhibitor which induces apoptosis in diverse human cancer cell lines. The binding affinity of BI-2536 for human serum albumin (HSA) protein may define its pharmacokinetic and pharmacodynamic profile. We have studied the binding of BI-2536 to HSA by means of different spectroscopic techniques and docking calculations. We have experimentally observed that the affinity of BI-2536 for HSA is higher than that of other common HSA binding drugs. Therefore, it can be postulated that the drug dose should be increased to achieve a certain concentration of free drug in plasma, although BI-2536 could also reach tumour tissues by uptaking HSA/BI-2536 complex. Only a single binding site on HSA has been observed for BI-2536 which seems to correspond to the subdomain IIA pocket. The formation of the HSA/BI-2536 complex is a spontaneous and entropy-driven process that does not cause a significant change of the secondary structure of the protein. Its endothermic character could be related to proton release. Thermodynamic analysis showed that the main protein-drug interactions are of the van der Waals type although the presence of amide and ether groups in BI-2536 could also allow H-bonding with some residues in the subdomain IIA pocket.

DFT and TD-DFT theoretical studies on photo-induced electron transfer process on [Cefamandole].C60 nano-complex

The C60 fullerene displays a considerable electronegativity. It has a unique photophysical and electrochemical behavior that can be used as a suitable drug carrier. In the present study, the interaction of C60 fullerene as an electron recipient with the Cefamandole antibiotic was investigated in both ground and excited states using DFT and TD-DFT methods. The study of the interaction of C60 and Cefamandole via electron localization function (ELF) and reduced density gradient (RDG) revealed that the complex formation is of van der Waals type. The data from natural bonding orbitals (NBO) analysis also confirmed the interaction type. The study of absorption and emission spectrum via CAM-B3LYP in the TD-SCF state showed that the emission peak of C60 fullerene in the 591.73nm after the complex formation results in the extinction of this emission spectrum due to charge transfer (CT) from chelator to fluorophore. The photoinduced electron transfer (PET) process was investigated using the electron hole theory.

Weak Interactions under Pressure: hp-CuBi and Its Analogues.

The metastable binary compound hp-CuBi was obtained from the direct chemical reaction between copper and bismuth at a pressure of 5 GPa and a temperature of 720 K. The atomic arrangement comprises slabs of puckered Cu layers sandwiched between Bi planes. The QTAIM charges calculated for compounds of bismuth with transition metals reveal negligible charge transfer for hp-CuBi. Analysis of the chemical bonding with position-space techniques discloses multicenter interactions within the Bi-Cu-Bi slabs and lone-pair interactions of the van der Waals type between these entities. hp-CuBi exhibits metal-type electrical conductivity with superconductivity below Tc =1.3 K.

Vermicompost Incorporation into Soil Contaminated with Deltamethrin as an Attempt to Reduce the Toxicity Caused by this Pyrethroid: A Structural Study of Soil

The use of vermicompost for remediating soil contaminated with the commercial formulation containing deltamethrin was proposed. Biotoxicity tests with the goal of evaluating the potential remediation degree of the vermicompost after its addition to contaminated soils were performed. The tests lasted 56 days and involved Eisenia foetida earthworms. Possible structural changes in humic acids from these soils were evaluated by means of FTIR spectroscopy. The soil contaminated with deltamethrin offers toxicity to the earthworms. However, the vermicompost addition caused great positive impact on soil contamination level, which became quite similar to the reference soil. The vermicompost remedial effect depends on the source material. In this study the vermicompost were from filter cake and orange peel. The results obtained by FTIR pointed out for a weak interaction such as van der Waals type between the pyretroid and humic acids.

G-C3N4/SnS2 Heterostructure: a Promising Water Splitting Photocatalyst

Graphite-like carbon nitride (g-C3N4) based heterostrutures has attracted intensive attention due to their prominent photocatalytic performance. Here, we explore the g-C3N4/SnS2 coupling effect on the electronic structures and optical absorption of the proposed g-C3N4/SnS2 heterostructure through performing extensive hybrid functional calculations. The obtained geometric structure, band structures, band edge positions and optical absorptions clearly reveal that the g-C3N4 monolayer weakly couples to SnS2 sheet, and forms a typical van der Waals heterojunction. The g-C3N4/SnS2 heterostructure can effectively harvest visible light, and its valence band maximum and conduction band minimum locate in energetically favorable positions for both water oxidation and reduction reactions. Remarkably, the charge transfer from the g-C3N4 monolayer to SnS2 sheet leads to the built-in interface polarized electric field, which is desirable for the photogenerated carrier separation. The built-in interface polarized electric field as well as the nice band edge alignment implys that the g-C3N4/SnS2 heterostructure is a promising g-C3N4 based water splitting photocatalyst with good performance.

Unexpected Ge-Ge Contacts in the Two-Dimensional Ge4 Se3 Te Phase and Analysis of Their Chemical Cause with the Density of Energy (DOE) Function.

A hexagonal phase in the ternary Ge-Se-Te system with an approximate composition of GeSe0.75 Te0.25 has been known since the 1960s but its structure has remained unknown. We have succeeded in growing single crystals by chemical transport as a prerequisite to solve and refine the Ge4 Se3 Te structure. It consists of layers that are held together by van der Waals type weak chalcogenide-chalcogenide interactions but also display unexpected Ge-Ge contacts, as confirmed by electron microscopy analysis. The nature of the electronic structure of Ge4 Se3 Te was characterized by chemical bonding analysis, in particular by the newly introduced density of energy (DOE) function. The Ge-Ge bonding interactions serve to hold electrons that would otherwise go into antibonding Ge-Te contacts.

Comparing van der Waals DFT methods for water on NaCl(001) and MgO(001).

In this work, a range of van der Waals type density functionals are applied to the H2O/NaCl(001) and H2O/MgO(001) interface systems to explore the effect of an explicit dispersion treatment. The functionals we use are the self-consistent vdW functionals vdW-DF, vdW-DF2, optPBE-vdW, optB88-vdW, optB86b-vdW, and vdW-DF-cx, as well as the dispersion-corrected PBE-TS and PBE-D2 methods; they are all compared with the standard PBE functional. For both NaCl(001) and MgO(001), we find that the dispersion-flavoured functionals stabilize the water-surface interface by approximately 20%-40% compared to the PBE results. For NaCl(001), where the water molecules remain intact for all overlayers, the dominant contribution to the adsorption energy from "density functional theory dispersion" stems from the water-surface interactions rather than the water-water interactions. The optPBE-vdW and vdW-DF-cx functionals yield adsorption energies in good agreement with available experimental values for both NaCl and MgO. To probe the strengths of the perturbations of the adsorbed water molecules, we also calculated water dipole moments and found an increase up to 85% for water at the MgO(001) surface and 70% at the NaCl(001) surface, compared to the gas-phase dipole moment.

Trapping of organophosphorus chemical nerve agents by pillar[5]arene: A DFT, AIM, NCI and EDA analysis

The encapsulation of organophosphorus (OP) nerve agents by pillar[5]arene (P5) molecule, shows that adsorption occurs with a larger structural reorganization of the host molecule. The computed binding energies shows that the complexes formed are more stable inside the cavity. Tabun was found to have the highest binding energy among the studied OPs. The computed Gibbs free energy is negative for Dimethyl methylphosphonate, sarin and tabun, and are positive for soman (GD) and ethyl-S-dimethylaminoethyl methylphosphonothiolate (VX). The inclusion complexes were found to have lower band gap. The quantum theory of Atoms-in-molecules analysis shows that ρ values were positive which implies the existence of noncovalent interactions. The Laplacian of the charge density ∇2ρ for bond critical points bonds are small and are negative which indicates the depletion of electronic charge along the bond paths and existence of an electrostatic nature of bonding between the guest and host molecule. The noncovalent interactions analysis clearly shows the existence of hydrogen bonding and van der Waals bonding in these inclusion complexes. The energy decomposition analysis shows that the, interaction between the P5 and the larger guest molecules VX and GD are mainly due to electrostatic interaction and for small guest, the interactions are mostly of van der Waals type.

First-principles modeling of GaN/MoSe$_{2}$ van der Waals heterobilayer

We investigate structural and electronic properties of the graphene-like gallium nitride (GaN) monolayer deposited on a MoSe$_{2}$ monolayer by using density functional theory with the inclusion of the nonlocal van der Waals correction. The GaN is bound weakly to the MoSe$_{2}$ monolayer with adsorption energy of 49 meV/atom. We find that the heterobilayer is energetically favorable with the interlayer distance of 3.302 {\AA} indicating van der Waals (vdW) type interaction and the most stable stacking configuration is verified with different deposition sequences. The heterostructure of GaN/MoSe$_{2}$ is found to be indirect band gap semiconductor with gap value of 1.371 eV. Our results demonstrate the potential design of new two-dimensional nanoelectronic devices based on the vdW heterostructure.

Understanding interactions in the adsorption of gaseous organic compounds to indoor materials.

We studied adsorption of organic compounds to a wide range of indoor materials, including plastics, gypsum board, carpet, and many others, under various relative humidity conditions by applying a conceptual model of the free energy of interfacial interactions of both van der Waals and Lewis acid-base (e-donor/acceptor) types. Data used for the analyses were partitioning coefficients of adsorbates between surface and gas phase obtained from three sources: our sorption experiments and two other published studies. Target organic compounds included apolars, monopolars, and bipolars. We established correlations of partitioning coefficients of adsorbates for a considered surface with the corresponding hexadecane/air partitioning coefficients of the adsorbates which are used as representative of a van der Waals descriptor instead of vapor pressure. The logarithmic adsorption coefficients of the apolars and weak bases, e.g., aliphatics and aromatics, to indoor materials linearly correlates well with the logarithmic hexadecane/air partitioning coefficients regardless of the surface polarity. The surface polarity in terms of e-donor/acceptor interactions becomes important for adsorption of the strong bases and bipolars, e.g., amines, phenols, and alcohols, to unpainted gypsum board. Under dry or humid conditions, the adsorption to flat plastic materials still linearly correlates well with the van der Waals interactions of the adsorbates, but no correlations were observed for the adsorption to fleecy or plush materials, e.g., carpet. Adsorption of highly bipolar compounds, e.g., phenol and isopropanol, is strongly affected by humidity, attributed to Lewis acid-base interactions with modified surfaces.

Phase diagram of crushed powders

Compression of monodisperse powder samples in quasistatic conditions is addressed in a pressure range such that particles fragmentation occurs while the solid remains incompressible (typical pressure range of 1–300 MPa for glass powders). For a granular bed made of particles of given size, the existence of three stages is observed during compression and crush up. First, classical compression occurs and the pressure of the granular bed increases along a characteristic curve as the volume decreases. Then, a critical pressure is reached for which fragmentation begins. During the fragmentation process, the granular pressure stays constant in a given volume range. At the end of this second stage, 20%–50% of initial grains are reduced to finer particles, depending on the initial size. Then the compression undergoes the third stage and the pressure increases along another characteristic curve, in the absence of extra fragmentation. The present paper analyses the analogies between the phase transition in liquid-vapour systems and powder compression with crush-up. Fragmentation diagram for a soda lime glass is determined by experimental means. The analogues of the saturation pressure and latent heat of phase change are determined. Two thermodynamic models are then examined to represent the crush-up diagram. The first one uses piecewise functions while the second one is of van der Waals type. Both equations of state relate granular pressure, solid volume fraction, and initial particle diameter. The piecewise functions approach provides reasonable representations of the phase diagram while the van der Waals one fails.

Predicting PR EOS binary interaction parameter using readily available molecular properties

The proper design, operation, simulation and optimization of numerous chemical processes require the knowledge of phase behavior of coexisting phases over wide ranges of pressure and temperature. A convenient method for describing equilibrium phase behavior is use of analytic equations of state. The most widely used equations of state (EOS) are the cubic van der Waals type equations such as the Soave–Redlich–Kwong (SRK) and Peng–Robinson (PR) EOS. These equations utilize one or two empirical binary interaction parameters (BIPs) for each binary pair in a mixture. These BIPs can have a significant effect on the predicted properties of mixtures and are generally required for accurate predictions.In a recent work, we developed generalized models to estimate the BIPs in the PR EOS for non-ideal, low-pressure systems using a quantitative structure–property relationship (QSPR) modeling approach. In a departure from our earlier work, we present in this study a different modeling approach which utilizes only readily available molecular properties of the components involved in a mixture. This greatly simplifies application of our new models, since they do not require elaborate computational methods for generation of molecular descriptors.To develop the present generalized model, a VLE database consisting of 1010 binary systems comprised of non-ideal, low-pressure binary systems as well as asymmetric, high-pressure binary systems was utilized. Using this database, the BIPs for the PR EOS were first determined by regressing the VLE experimental data for each system. Then, the BIPs were generalized in terms of molecular properties of components in a mixture. Results indicate that the generalized model provides bubble-point pressure predictions with an average absolute deviation (AAD) of 9% when compared with an AAD of 4.7% through direct regressions of the BIPs. Further, the model developed in this study was compared to our previous model by predicting bubble-point pressures of non-ideal, low-pressure binary systems. The predictions from the model developed in this study were comparable to our previous results (9.2% compared to 8.3% AAD), thus demonstrating the usefulness of the simpler approach presented in this work.

Mg(OH)2−WS2 van der Waals heterobilayer: Electric field tunable band-gap crossover

Magnesium hydroxide $[\mathrm{Mg}{(\mathrm{OH})}_{2}]$ has a layered brucitelike structure in its bulk form and was recently isolated as a new member of two-dimensional monolayer materials. We investigated the electronic and optical properties of monolayer crystals of $\mathrm{Mg}{(\mathrm{OH})}_{2}$ and ${\mathrm{WS}}_{2}$ and their possible heterobilayer structure by means of first-principles calculations. It was found that both monolayers of $\mathrm{Mg}{(\mathrm{OH})}_{2}$ and ${\mathrm{WS}}_{2}$ are direct-gap semiconductors and these two monolayers form a typical van der Waals heterostructure with a weak interlayer interaction and a type-II band alignment with a staggered gap that spatially separates electrons and holes. We also showed that an out-of-plane electric field induces a transition from a staggered to a straddling-type heterojunction. Moreover, by solving the Bethe-Salpeter equation on top of single-shot ${\mathrm{G}}_{0}{\mathrm{W}}_{0}$ calculations, we show that the low-energy spectrum of the heterobilayer is dominated by the intralyer excitons of the ${\mathrm{WS}}_{2}$ monolayer. Because of the staggered interfacial gap and the field-tunable energy-band structure, the $\mathrm{Mg}{(\mathrm{OH})}_{2}\ensuremath{-}{\mathrm{WS}}_{2}$ heterobilayer can become an important candidate for various optoelectronic device applications in nanoscale.

Sequestration of Catechol and Pentachlorophenol by Mechanochemically Treated Kaolinite

AbstractThe pollution of soils by organic contaminants, such as phenols, is a serious problem because of the high toxicity and persistence in the environment. Mechanochemical treatments (MTs) of polluted soils with minerals, such as clays and oxides, which have surfaces that exhibit catalytic properties, have been suggested to be a new useful strategy to promote both organic and inorganic pollutant degradation. Nevertheless, much still remains to be studied about the capability of clays to promote pollutant removal by means of the mechanochemical activation of the mineral surfaces. This work investigates the efficiency of the mineral kaolinite in promoting the sequestration of catechol (CAT) and pentachlorophenol (PCP) by MT. A well crystallized kaolinite (KGa-1b) was milled for prolonged times with different amounts of organic molecules so as to obtain two different clay:organic compound ratios. Prolonged grinding and a higher clay mineral:organic compound ratio were found to be more effective in promoting a stronger removal than simple contact. After 1 h of mechanochemical treatment, the PCP and CAT removal percentages were 32% and 20%, respectively. Additionally, a 7-day undisturbed incubation of the milled mixtures produced a trend for increased CAT removal (up to 40%). The interaction mechanism between kaolinite and each organic compound (i.e. CAT and PCP) after a MT was inferred by integrating information from spectroscopic, diffractometric, and chromatographic analyses. X-ray diffraction and Fourier-transform infrared data suggested a strong interaction between CAT and KGa-1b. This interaction mechanism likely occurs through the formation of an inner-sphere complex by H-bonding between the organic molecules and the oxygens of the kaolinite tetrahedral sheet. On the other hand, a weak interaction (i.e. van der Waals type) can occur between the KGa-1b O-planes and the PCP molecules, which likely bind to the external surfaces of KGa-1b.

Effects of carbon nanofiller characteristics on PTT chain conformation and dynamics: A computational study

The effects of nanofiller chemistry and geometry on static and dynamic properties of an aromatic polyester, poly (trimethylene terephthalate), were addressed thanks to long-run classical molecular dynamics simulation. Two carbon nanofillers, graphene and carbon nanotube, were employed, where graphene was used in pristine and functionalized forms and carbon nanotube was used in two different diameters. The nanofiller geometry and chemistry were found to exert significant effects on conformation and dynamic behavior of PTT chain at the interface within the time scale the simulation was performed. It was found that PTT chain underwent interaction of van der Waals type with nanofiller via two subsequent phases, adsorption and orientation. The former stage, with definite characteristic time, involved translation of polymer chain toward interface while the latter was controlled by vibrational motions of chain atoms. The consequence of interaction was an increase in conformational order of polymer chain by transition to folded shape being favorable for any subsequent structural ordering (crystallization). The interaction of polymer with nanofiller gave rise to a reduction in overall mobility of polymer chain characterized by crossover from normal diffusive motion to subdiffusive mode.

Structural Stability and High Temperature Tolerance of Bilayer Nanoribbons Composited with Graphene and Borophene#

Background: It has been found that the bilayer structure, especially the bilayer graphenes, can markedly weaken the anisotropy of elastic properties. For tri-layer systems, such as a monolayer grapheme sandwiched in bilayer graphenes and boron nitride nanosheets. The BN-G-BN achieves a more stable combined structure than G-G-G. The results further indicated that the high-temperature distortion resistance of interlayer graphene in the tri-layer complex is related to both material type and constrain conditions at the up-down layers. Methods: The structural stability and high temperature tolerance of bilayer complex nanoribbons are analyzed using the molecular dynamics method. By calculating a variety of potential functions between nanosheets and optimal interlayer distances, the differences in structural stability are examined. By simulating structural performance at high temperatures and analyzing the radial distribution function (RDF) and deformation electron density, the hightemperature distortion resistance is researched. Results: The optimal distances between layers are approximately 0.359 nm for bilayer borophene (B/B), 0.340 nm for bilayer graphene (G/G) and 0.348 nm for the hybrid bilayer (B/G). Analyzing of the results of the binding energy, interaction energy and van der Waals energies between nanosheets revealed that the structural stability of the bilayer complexes from high to low in turn are B/G, B/B and G/G. The dominant interaction sustaining complex stability is a typical van der Waals interaction. The structural analyses on the above complexes at high temperature (1500 K) indicated that the hybrid bilayer nanosheet B/G, in the three bilayer complexes, has the highest temperature tolerance, followed by G/G and then B/B. Conclusion: The results indicated that the bilayer borophene, especially for hybrid bilayer nanosheets, can help to improve the structural stability. The results revealed that the excitation of a greater number of local electrons in borophene results in the high temperature deformation resistance of B/B being inferior to that of G/G. The B/G, in three bilayer complexes composited with graphene and borophene, has the best structural stability and the highest temperature tolerance. Keywords: Bilayer nanosheets, graphenes and borophene, high-temperature deformation, molecular dynamics, structural stability.

Systematic Generation of Anisotropic Coarse-Grained Lennard-Jones Potentials and Their Application to Ordered Soft Matter.

We have developed an approach to coarse-grained (CG) modeling of the van der Waals (vdW) type of interactions among molecules by representing groups of atoms within those molecules in terms of ellipsoids (rather than spheres). Our approach systematically translates an arbitrary underlying all-atom (AA) representation of a molecular system to a multisite ellipsoidal potential within the family of Gay-Berne type potentials. As the method enables arbitrary levels of coarse-graining, or even multiple levels of coarse-graining within a single simulation, we describe the method as a Level of Detail (LoD) model. The LoD model, as integrated into our group's Metropolis Monte Carlo computational package, is also capable of reducing the complexity of the molecular electrostatics by means of a multipole expansion of charges obtained from an AA force field (or directly from electronic structure calculations) of the charges within each ellipsoid. Electronic polarizability may additionally be included. The present CG representation does not include transformation of bonded interactions; ellipsoids are connected at the fully atomistic bond sites by freely rotating links that are constrained to maintain a constant distance. The accuracy of the method is demonstrated for three distinct types of self-assembling or self-organizing molecular systems: (1) the interaction between benzene and perfluorobenzene (dispersion interactions), (2) linear hydrocarbon chains (a system with large conformational flexibility), and (3) the self-organization of ethylene carbonate (a highly polar liquid). Lastly, the method is applied to the interaction of large (∼100 atom) molecules, which are typical of organic nonlinear optical chromophores, to demonstrate the effect of different CG models on molecular assembly.

Casimir-Polder effect for a stack of conductive planes

The Casimir-Polder interaction between an atom and a multilayered system composed of infinitely thin planes is considered using the zeta-function regularization approach with summation of the zero-point energies. As a prototype material, each plane is represented by a graphene sheet whose optical response is described by a constant conductivity or Drude-Lorentz model conductivity. Asymptotic expressions for various separations are derived and compared to numerical calculations. We distinguish between large atom/plane limit, where retardation effects are prominent, and small atom/plane limit, where the typical van der Waals coefficient is found to be dependent on the number of graphenes and characteristic distances. The calculated energies for different atoms and graphene conductivity models brings forward the basic science of the Casimir-Polder effect and suggests ways to manipulate this interaction experimentally.

Effects of Exposure to Pulsed Light on Surface and Structural Properties of Edible Films Made from Cassava and Taro Starch

Edible films derived from starch have been proposed as packaging materials. However, they may suffer physicochemical changes due to a variety of factors, such as pulsed light (PL) treatments. In this study, the effect of PL treatment as a crosslinking method on films made from cassava (Manihot esculenta C.) and taro (Colocasia esculenta L. Schott) starch, plasticized with glycerol was evaluated. The average molecular weight, contact angle, moisture content, X-ray diffraction pattern, color, and mechanical and microstructural properties were evaluated. Films subjected to PL showed deterioration compared with control films as demonstrated by an increase in the contact angle, surface roughness, and crystallinity, and a decrease in the tensile strength, transparency, and water content, independent of the amylose content of the starches evaluated. Finally, the surface properties of these materials are defined by intermolecular interactions such as van der Waals-type force interactions (hydrogen bond), new bonds (crosslinking) formed between the biopolymeric chains (starch), and by breakage of covalent bonds.

Attractive Coulomb interaction of two-dimensional Rydberg excitons

We analyze theoretically the Coulomb scattering processes of highly excited excitons in the direct bandgap semiconductor quantum wells. We find that contrary to the interaction of ground state excitons the electron and hole exchange interaction between excited excitons has an attractive character both for $s$- and $p$-type 2D excitons. Moreover, we show that similarly to the three-dimensional (3D) highly excited excitons, the direct interaction of 2D Rydberg excitons exhibits van der Waals type long-range interaction. The results predict the linear growth of the absolute value of exchange interaction strength with an exciton principal quantum number, and point the way towards enhancement of optical nonlinearity in 2D excitonic systems.