Van Der Waals Type Interactions Research Articles

Phase transitions and composite order in U(1)N lattice London models

The phase diagrams and the nature of the phase transitions in multicomponent gauge theories with an Abelian gauge field are important topics with various physical applications. While an early renormalization-group-based study indicated that the direct transition from a fully ordered to a fully disordered state is continuous for N=1 and N>183, recently it was demonstrated that the transition is discontinuous for N=2. We quantitatively study the dependence on N of the degree of discontinuity of this transition. Our results suggest that the transition is discontinuous at least up to N=7. Furthermore, we demonstrate that, at increased coupling strength, the phase transitions of the neutral and charged sectors of the model split, which for N>2 yields a new phase with composite order. The transition from the composite-order phase to the fully disordered phase is then also discontinuous, at least for N=3 and N=4. Via a duality argument, this indicates that van der Waals–type interaction between directed loops may be responsible for the discontinuous phase transitions in these models. Published by the American Physical Society 2024

Weakly bound complexes of 1,2,3-triazole with nitrogen and carbon dioxide isolated in solid argon: A combined FT-IR matrix isolation and theoretical investigation

Matrix isolation FT-IR spectroscopy was combined with quantum-chemical calculations in order to characterize complexes of 1,2,3-triazole (3TR) with nitrogen and carbon dioxide. Geometries of the possible 1:1 and 1:2 complexes, as well as 3TR dimers, were optimized at the DFT (B3LYP-D3) level of theory with the 6–311++G(3df,3pd) basis set. Six different 3TR⋯N2 structures of the 1:1 stoichiometry were optimized which are characterized by weak hydrogen bonds (N-H⋯N and C-H⋯N) and/or Van der Waals type interactions (N⋯C, N⋯N, N⋯π). Two the most stable geometries, both containing a N-H⋯N bridge, were identified experimentally in solid argon. As for 3TR⋯CO2 complexes, out of two minima located on the potential energy surface, only one with a strongly bent N-H⋯O hydrogen bond was detected in the matrix after deposition. In both cases, only annealing experiments at 32 K resulted in the formation of small amounts of 1:2 structures.

Triel tris(aminoaryl)aluminum, gallium, and indium complexes and their homocoupling reactions mediated by NiBr2

Here, we present the synthesis, spectroscopic characterization, structural analysis, and studies on the bonding situation of group 13 tris(o-aminoaryl) complexes, [M(C6H4(o-NMe2))3] (1–3) and [M(C10H6(o-NMe2))3] (4–6) where M = Al, Ga, In. X-ray and DFT structural parameters, in conjunction with the inspection of the molecular electrostatic potential (MEP) of related triaryl, MAr3, models where Ar = C6H4, C10H6, suggest for 1–6 the presence of two partially polar covalent intramolecular M–N triel bonds. Interestingly, indium complexes 3 and 6 bind a third nitrogen atom with a Van der Waals type interaction. Stoichiometrical reactions of 1–3 with NiBr2 at 25 °C afforded the homocoupling product bi-o-dimethylaminophenyl (7) in up to 73 % isolated yield with 1 and 3 as the nucleophile. While 4–6 performed poorly under the same reaction conditions or at 100 °C providing either traces or at most 13 % of bi-o-dimethylaminonaphtyl (8) with 4 according to GC–MS. Hypothetical DFT bimetallic species [BrNi(μ-Br)M{C6H4(o-NMe2)}3] and [Ni(Br)2M{C10H6(o-NMe2}3] where M = Al (9, 12), Ga (10, 13), In (11, 14) are proposed reaction intermediates implied in the transmetalation/reductive elimination process that affords diaromatic amines 7 and 8.

Binding of Mammea A/AA (MA) to calf thymus DNA revealed by the ratiometric absorbance of MA in the UV-visible range molecular dynamic simulations and TD-DFT calculations

The in vitro anti-proliferative activity of MA ( 5,7-dihydroxy-8-(3-methylbut-2-enyl)-6-(3-methyl-1-oxobutyl)-4-phenyl[1]2H-[1]benzopyran-2-one)on a variety of cancer cells was previously demonstrated. This work strives to understand the mechanisms by which MA exerts this biological activity. Thereafter, the binding of MA to calf thymus DNA was studied by monitoring the change in the UV-visible absorbance of MA. It was found that, the response of MA to binding with calf thymus DNA is characterised by an increase in the AS/AL ratio of the absorbance of the longest wavelength absorption band to the shortest one, and the appearance of a new band at about 377 nm assigned to S0→S1 transition, which is red shifted as compared to free MA. From the bands ratio, the binding constant is found to be 4.3x105 M−1, indicating strong binding. The deduced binding free energy, enthalpy and entropy are −7.7 kcal/mol, −10.89 ± 0.28 kcal/mol and −54.46 ± 4 J/K, respectively, indicating that MA binds to DNA by a non-bonding Van der Waals type interactions and hydrogen bonds. Further study with classical molecular dynamics shows that MA binds to DNA by intercalation, where it is positioned between two AT base pairs. Unlike isolated MA, TDDFT calculations on ten images extracted from the MD trajectory show that, the frontier molecular orbitals of the complex are distributed over the DNA and MA. This indicates a strong stacking interaction and then explains the hypochromism and the red shift of the S0→S1 transition. The present work demonstrates the potency of MA as antitumor compound and as absorbance-based molecular probe. Communicated by Ramaswamy H. Sarma

Particle Ratios in a Multicomponent Nonideal Hadron Resonance Gas

We have considered formation of a multicomponent nonideal hot and dense gas of hadronic resonances in the ultrarelativistic heavy ion collisions. In the statistical thermal model approach, the equation of state (EoS) of the noninteracting ideal hadron resonance gas (IHRG) does not incorporate either the attractive part or the short-range repulsive part of the baryonic interaction. On the other hand, in the nonideal hadron resonance gas (NIHRG) model, we can incorporate these interactions using the van der Waals (VDW) type approach. Studies have been made to see its effect on the critical parameters of the quark-hadron phase transition. However, it can also lead to modifications in the calculated relative particle yields. In this paper, we have attempted to understand the effect of such van der Waals-type interactions on the relative particle yields and also studied their dependences on the system’s thermal parameters, such as the temperature and baryon chemical potential μ B . We have also taken into account the decay contributions of the heavier resonances. These results on particle ratios are compared with the corresponding results obtained from the point-like, i.e., noninteracting IHRG model. It is found that the particle ratios get modified by incorporating the van der Waals-type interactions, especially in a baryon-rich system which is expected to be formed at lower RHIC energies, SPS energies, and in the forthcoming CBM experiments due to high degree of nuclear stopping in these experiments.

Microplastics and organics - A comparative study of sorption of triclosan and malachite green onto polyethylene.

This study aims to elucidate interaction of organics with microplastics in a comparative manner via the use of two model compounds (i.e., triclosan (TCS) and malachite green (MG)) having different physicochemical properties, onto polyethylene (PE). TCS, is hydrophobic with low solubility, while MG is hydrophilic with high aqueous solubility. Kinetic studies indicate faster sorption (teq = 24 h) and equilibrium studies show much higher capacity (qe = 6,921 μg/g) for TCS, when compared to those of MG (teq = 5 d, qe = 221 μg/g). While pseudo-kinetic model fits sorption of both organics to PE, equilibrium isotherms as well as the results on effect of particle size and pH indicate dissimilar sorption mechanisms. Considering pHPZC = 2, observation of favourable sorption of TCS in acidic regions and sorption being unaffected by particle size was explained by TCS sorption to be dominated by hydrophobic interactions in amorph regions of PE. Higher removal of MG was observed at lower surface charge of PE, and a clear favourable impact of surface area on MG sorptive capacity pointed to the presence of non-specific van der Waals type interactions on the surface of PE. Mechanistic evaluations presented here contribute to our understanding of interaction of MPs with organics in aquatic ecosystems.

Electromagnetically induced transparency and absorption cross-over with a four-level Rydberg system

Electromagnetically induced transparency (EIT) and absorption (EIA) are quantum coherence phenomena which result from the interference of excitation pathways. Combining these with Rydberg atoms have opened up many possibilities for various applications. We introduce a theoretical model to study Rydberg-EIT and Rydberg-EIA effects in cold Cs and Rb atomic ensembles in a four-level ladder type scheme taking into account van der Waals type interactions between the atoms. The proposed many-body method for analysis of such systems involves a self-consistent mean field approach and it produces results which display a very good agreement with recent experiments. Our calculations also successfully demonstrate experimentally observed EIT-EIA cross-over in the Rb case. Being able to simulate the interaction effects in such systems has significant importance, especially for controlling the optical response of these.

A computational investigation on the adsorption of amoxycillin on graphene oxide nanosheet

ABSTRACT Graphene-based nanomaterials have demonstrated significant potential in environmental applications and more particularly in water treatment, especially with the extensive use of emerging pollutants (EP). These pollutants originate either from wastewater treatment plants or agricultural activities. This study focused on the antibiotic amoxycillin which is most commonly administered to humans, livestock, and aquaculture to fight a multitude of infectious diseases. In order to understand the use of graphene oxide as an adsorbent in the removal of amoxycillin and to clarify the interfacial interaction at the molecular level, a Density Function Theory study at the B3PW91/cc-pVDZ level of theory, molecular dynamics simulation, and independent gradient model were performed to determine the structural and energetic properties, and to analyse the different interactions involved in the approach. The obtained results shows that AMX exhibits a nucleophilic behaviour whereas GO acts as an electrophile, and that the adsorption process occurs spontaneously via a parallel mode indicating strong interactions. It was established that the stability of the formed complexes is mainly due to the existence of both hydrogen bonds and Van der Waals type interactions.

DNA-Mimicking Metal-Organic Frameworks with Accessible Adenine Faces for Complementary Base Pairing.

Biologically derived metal–organic frameworks (Bio-MOFs) are significant, as they can be used in cutting-edge biomedical applications such as targeted gene delivery. Herein, adenine (Ade) and unnatural amino acids coordinate with Zn2+ to produce biocompatible frameworks, KBM-1 and KBM-2, with extremely defined porous channels. They feature an accessible Watson–Crick Ade face that is available for further hydrogen bonding and can load single-stranded DNA (ssDNA) with 13 and 41% efficiency for KBM-1 and KBM-2, respectively. Treatment of these frameworks with thymine (Thy), as a competitive guest for base pairing with the Ade open sites, led to more than 50% reduction of ssDNA loading. Moreover, KBM-2 loaded Thy-rich ssDNA more efficiently than Thy-free ssDNA. These findings support the role of the Thy-Ade base pairing in promoting ssDNA loading. Furthermore, theoretical calculations using the self-consistent charge density functional tight-binding (SCC-DFTB) method verified the role of hydrogen bonding and van der Waals type interactions in this host–guest interface. KBM-1 and KBM-2 can protect ssDNA from enzymatic degradation and release it at acidic pH. Most importantly, these biocompatible frameworks can efficiently deliver genetic cargo with retained activity to the cell nucleus. We envisage that this class of Bio-MOFs can find immediate applicability as biomimics for sensing, stabilizing, and delivering genetic materials.

Synthesis, X-ray molecular structure and QTAIM and NCI-RDG theoretic studies of a new cadmium (II) (4′4 diaminodiphenylmethane) (meso-arylporphyrin) coordination compound

In this study, a new five-coordinated cadmium porphyrin complex axially ligated with 4,4′-diaminodiphenylmethane (4,4′-mda) with the formula [Cd(TClPP)(4,4′-mda)]•CHCl3•(4,4′-mda)•2H2O (complex (1)) where TClPP is the meso-tetra(para-chlorophenyl)porphyrinate was prepared and characterized by FT-IR,1H NMR, and UV/Vis spectroscopy. The crystal structure was determined using single crystal X-ray diffraction. This complex crystallizes in the monoclinic crystal system with the space group P-1. The coordination sphere around the cadmium center is shown as a distorted square pyramidal coordination environment and the porphyrin core presents a dome-type deformation due to the large size of the central cadmium(II) ion. The crystal lattice of (1) is mainly stabilized by classic and non-conventional hydrogen bonds as indicated by the experimental data explored by the PLATON program. To obtain an insight into the physical nature of these intermolecular bonds, we extensively used Bader's quantum theory of atoms-in-molecules (QTAIM). This analysis proved that the coordinated 4,4′-mda (ligand I) stabilizes the structure of (1) by the formation of Van der Waals (VdW) type interactions. Additionally, the non-covalent interaction via the reduced density gradient (NCI-RDG) analysis established nicely the presence of such intermolecular interactions type hydrogen bonding interactions between ligands I and II, from one side, and (iii) hydrogen bonding and Van der Waal interactions, from the other side, with involving [Cd(TClPP)(4,4′-mda)], ligand I and II and the neighboring [Cd(TClPP)(4,4′-mda)] molecules.

Theoretical study of Au20/WS2 composite material as a potential candidate for the capture of XO (X=C, N, S) gases

In this study, density functional theory (DFT) calculations were carried out to understand the structural stability of the interaction of Au20 pyramidal cluster on the tungsten disulfide (WS2) monolayer. According to the adsorption energy values, the predominant interaction in this system (Au20/WS2) corresponds to chemisorption (−4.68 eV). This behavior is also reproduced by small gold clusters (Aun, n = 3, 5, 9, 13 and 16). The Au20/WS2 composite system presents a mechanism of interaction influenced by the charge transfer from the Au20 cluster to the WS2 monolayer. The structural stability was corroborated by ab-initio molecular dynamics (AIMD) calculations, which exhibits how the WS2 monolayer is a good support for transition metals such as Au clusters. According to the analysis of the electronic and optical properties, the Au20/WS2 composite system has a semi-metallic behavior, based on to the band spectrum (0.65 eV). The optical properties of the Au20/WS2 composite system exhibits a broad absorption spectrum of visible light, in contrast to the isolated Au20 cluster and the WS2 monolayer. The performance of this composite material in the adsorption process of the XO (X = C, N, and S) molecule was also evaluated. The interaction between the XO molecule and the Au atoms shows a favorable formation of bonding with a van der Waals (vdW) type interaction, according to the critical points analysis. Our results show high adsorption energy values in all active sites of the Au20 cluster. This kind of composite system provide a structural idea, about the use of the WS2 monolayer as a support of transition metals at the nanoscale level for the capture of polluting gases.

High-Strength, Strongly Bonded Nanocomposite Hydrogels for Cartilage Repair

Polyacrylamide-based hydrogels are widely used as potential candidates for cartilage replacement. However, their bioapplicability is sternly hampered due to their limited mechanical strength and puncture resistance. In the present work, the strength of polyacrylamide (PAM) hydrogels was increased using titanium oxide (TiO2) and carbon nanotubes (CNTs) separately and a combination of TiO2 with CNTs in a PAM matrix, which was interlinked by the bonding between nanoparticles and polymers with the deployment of density functional theory (DFT) approach. The synergistic effect and strong interfacial bonding of TiO2 and CNT nanoparticles with PAM are attributed to high compressive strength, elastic modulus (>0.43 and 2.340 MPa, respectively), and puncture resistance (estimated using the needle insertion test) for the PAM-TiO2-CNT hydrogel. The PAM-TiO2-CNT composite hydrogel revealed a significant self-healing phenomenon along with a sign toward the bioactivity and cytocompatibility by forming the apatite crystals in simulated body fluid as well as showing a cell viability of ∼99%, respectively. Furthermore, for new insights on interfacial bonding and structural and electronic features involved in the hydrogels, DFT was used. The PAM-TiO2-CNT composite model, constructed by two interfaces (PAM-TiO2 and PAM-CNT), was stabilized by H-bonding and van der Waals-type interactions. Employing the NCI plot, HOMO-LUMO gap, and natural population analysis tools, the PAM-TiO2-CNT composite has been found to be most stable. Therefore, the prepared polyacrylamide hydrogels in combination with the TiO2 and CNT can be a remarkable nanocomposite hydrogel for cartilage repair applications.

Insights into the interaction dynamics between volatile anesthetics and tubulin through computational molecular modelling

General anesthetics, able to reversibly suppress all conscious brain activity, have baffled medical science for decades, and little is known about their exact molecular mechanism of action. Given the recent scientific interest in the exploration of microtubules as putative functional targets of anesthetics, and the involvement thereof in neurodegenerative disorders, the present work focuses on the investigation of the interaction between human tubulin and four volatile anesthetics: ethylene, desflurane, halothane and methoxyflurane. Interaction sites on different tubulin isotypes are predicted through docking, along with an estimate of the binding affinity ranking. The analysis is expanded by Molecular Dynamics simulations, where the dimers are allowed to freely interact with anesthetics in the surrounding medium. This allowed for the determination of interaction hotspots on tubulin dimers, which could be linked to different functional consequences on the microtubule architecture, and confirmed the weak, Van der Waals-type interaction, occurring within hydrophobic pockets on the dimer. Both docking and MD simulations highlighted significantly weaker interactions of ethylene, consistent with its far lower potency as a general anesthetic. Overall, simulations suggest a transient interaction between anesthetics and microtubules in general anesthesia, and contact probability analysis shows interaction strengths consistent with the potencies of the four compounds. Communicated by Ramaswamy H. Sarma

On the hydrogen storage performance of Cu-doped and Cu-decorated graphene quantum dots: a computational study

Hydrogen gas is a promising renewable energy source. The hydrogen storage performance of two differently modified graphene surfaces, particularly Cu-doped and Cu-decorated circumcoronene (CC), is investigated using density functional theory, 6-311G* basis set and Bader's quantum theory of atoms in molecules (QTAIM). It is found that the Cu-doped CC is able to bind three H2 molecules on one Cu atom, while the Cu-decorated CC is able to bind up to five H2 molecules on one Cu atom. Changes in the topology of charge density upon the H2 adsorption are evaluated under the formalism of QTAIM analysis. The QTAIM analysis of bond critical points as well as the density of states analysis show that the interaction between Cu and adsorbed H2 molecules can be considered as a physisorption (a van der Waals type interaction). Overall, the results presented in this study point out that the Cu-decorated graphene surfaces are more suitable potential candidates for hydrogen storage than the Cu-doped ones. Furthermore, the inclusion of diffuse functions in the basis set is critically considered.

Van der Waals heterostructures of MoS2 and Janus MoSSe monolayers on graphitic boron-carbon-nitride (BC3, C3N, C3N4 and C4N3) nanosheets: a first-principles study

In this work, we extensively investigate the structural and electronic properties of van der Waals heterostructures (HTs) constructed by MoS2/BC3, MoS2/C3N, MoS2/, MoS2/ and those using Janus MoSSe instead of MoS2 by performing density functional theory calculations. The electronic band structure calculations and the corresponding partial density of states reveal that the significant changes are driven by a quite strong layer–layer interaction between the constitutive layers. Our results show that although all monolayers are semiconductors as free-standing layers, the MoS2/C3N and MoS2/ bilayer HTs display metallic behavior as a consequence of the transfer of charge carriers between two constituent layers. In addition, it is found that in the MoSSe/C3N bilayer HT, the degree of metallicity is affected by the interface chalcogen atom type when Se atoms face the C3N layer, and the overlap of the bands around the Fermi level is smaller. Moreover, the half-metallic magnetic is shown to form a magnetic half-metallic trilayer HT with MoS2 independent of the stacking sequence, i.e. whether it is sandwiched or a two layer encapsulate MoS2 layer. We further analyze the trilayer HTs in which MoS2 is encapsulated by two different monolayers and it is revealed that at least with one magnetic monolayer, it is possible to construct a magnetic trilayer. While the trilayer of /MoS2/BC3 and /MoS2/ exhibit half-metallic characteristics, /MoS2/C3N possesses a magnetic metallic ground state. Overall, our results reveal that holly structures of BCN crystals are suitable for heterostructure formation even over a van der Waals-type interaction, which significantly changes the electronic nature of the constituent layers.

Density functional calculations of organic pollutants adsorbed on Hittorf's violet phosphorene

Abstract Hittorf's violet phosphorene with large specific surface area and high hole mobility is a potential candidate for gas sensing. Here, a case about adsorption behavior of organic chemicals on violet phosphorene has been systematically studied based on density functional theory. From our results, all seven considered organic chemicals (benzoapyrene, benzene, methylbenzene, formaldehyde, m-xylene, o-xylene and p-xylene) on violet phosphorene show molecular adsorption with exothermic process. Among them, the adsorption of benzopyrene with −0.881 eV adsorption energy is most conducive for complete adsorption-desorption cycles, which is an essential feature of reversible gas sensors. Small amounts of charge transfer indicate that the adsorption mechanism is mainly van der Waals type interaction. In particular, further work function and electronic structure analysis indicates that the electrical conductivity changes significantly after benzoapyrene exposure. That makes it possible to transmit gas sensing signals using electrical strategy. We also found that violet phosphorene multilayer maintains consistent benzoapyrene adsorption performance with its monolayer, which is conducive to practical application. Our simulations could provide theoretical basis for the exploration of two-dimensional organics sensing materials.

Benchmarking van der Waals-treated DFT: The case of hexagonal boron nitride and graphene on Ir(111)

There is enormous recent interest in weak, van der Waals-type (vdW) interactions due to their fundamental relevance for two-dimensional materials and the so-called vdW heterostructures. Tackling this problem using computer simulation is very challenging due to the non-trivial, non-local nature of these interactions. We benchmark different treatments of London dispersion forces within the density functional theory (DFT) framework on hexagonal boron nitride or graphene monolayers on Ir(111) by comparing the calculated geometries to a comprehensive set of experimental data. The geometry of these systems crucially depends on the interplay between vdW interactions and wave function hybridisation, making them excellent test cases for vdW-treated DFT. Our results show strong variations in the calculated atomic geometry. While some of the approximations reproduce the experimental structure, this is rather based on \textit{a posteriori} comparison with the ``target results''. General predictive power in vdW-treated DFT is not achieved yet and might require new approaches.

Geometry Optimization Skills of DFTB: Simple to Complex Molecular Systems

As the Density-functional theory (DFT) is an exact theory in principle for computing ground state electronic structures of the multi-electron and many-body systems, it's approximate variants currently being used are far from fail-safe. One of the very fundamental problem that has become apparent is its inability to account the substantial effect of van der Waals (vdW) type interactions exist in large molecular assemblies. To overcome such problem, a density functional tight binding (DFTB) theory whose fundamental formulation is based on the DFT but implements Slater−Kirkwood model and Slater−Koster files with a focus on solid state systems having vdW interactions as a binding force has been widely used recently. Its self-consistent charge ( SCC) approach is more promising theoretical model due to introducing self-consistent calculation of Mulliken charges. Present work is aimed at evaluating the geometry optimization skills of such DFTB method while applying to very simple to quite complex molecular systems of the order: water, benzene, crystalline 1,4-bis (tri-methylsilyl) benzene, and crystalline siloxaalkane. We fully optimized the isolated molecules of each of them as well as the unit cell geometries of the last two specimens and measured the dimensions of the particular sets of bond lengths, bond angles, and torsional angles in each optimized geometry. These values are found to be in an excellent agreement with the concerned experimental values. It makes the DFTB method very versatile and superb quantum mechanical model for computing ground state electronic structures.

Arsine adsorption on the surface of palladium-doped carbon nanotubes

Density functional theory was used to investigate arsine interactions with palladium-doped single-walled carbon nanotubes (Pd/SWCNTs). Adsorption energies, quantum descriptors, bond order, atomic charge, optical properties, and electrostatic potential of Pd/SWCNTs, arsine and arsine-Pd/SWCNT complexes were calculated. The results show arsine is weakly bonded to Pd/SWCNTs through van der Waals type interactions. The interaction between Pd and Pd/SWCNT is physisorption as the binding energy and charge transfer are small, and adsorption distance is large. The electronic transitions from the highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO) (H→L) have the maximal wavelength and the lowest oscillator strength.

Krypton-methanol spectroscopic study: Assessment of the complexation dynamics and the role of the van der Waals interaction

The Kr–CH3OH (Krypton–Methanol) system has several technological applications, such as the determination of diffusivity coefficients, their use in the development of detectors and combustion techniques among others. We report an extensive theoretical study concerning the stability of such complex. A mix between molecular dynamics, electronic structure calculations and solution of the nuclear Schrodinger equation lead to investigation of spectroscopic constants, lifetime of the complex and its Quantum Theory Atom in Molecules (QTAIM) properties. The study of the Potential Energy Curves (PEC) suggested three configurations to be stable as their potential well were able to harbor 9 vibrational levels. Properties from the curves also allowed us to obtain the lifetime of the complex, whose values were >1 ps regardless of the conformation. Furthermore, topological investigations of the charge density profile of the complex, in the scope of QTAIM properties, show that van der Waals type interactions takes place between the noble gas and the methanol molecule. These features are in consonance to the experimental fact that this complex is stable.