Van Der Waals Dispersion Correction Research Articles

Detection of nucleobases using 2D germanane nanosheet: A first-principles study

The electronic properties and geometric stability of germanane nanosheet is explored using first-principle studies. The germanane nanosheet exhibits semiconducting properties and stability of germanane sheet is ensured with formation energy. The adsorption behavior of deoxyribo nucleic acid (DNA)/ribo nucleic acid (RNA) nucleobases on monolayer germanane nanosheet have been investigated using density functional theory with van der Waals dispersion correction. The adsorption of nucleobases is found to be physisorbed on germanane nanosheet with the van der Waals type of interaction. The order of adsorption of nucleobases with germanane nanosheet is known to be C > G > A > T > U. We observed the changes in the energy band structure and the density of states variation due to the adsorption of nucleobases on germanane nanosheet. Our results confirm that apart from graphene, germanane monolayer can be used to detect nucleotides in the field of biotechnology and medical science.

Tunable Band Gaps of InxGa1–xN Alloys: From Bulk to Two-Dimensional Limit

Using first-principles calculations combined with a semiempirical van der Waals dispersion correction, we have investigated structural parameters, mixing enthalpies, and band gaps of buckled and planar few-layer InxGa1–xN alloys. We predict that the band gaps of buckled InxGa1–xN alloys with hydrogen passivation can be tuned from 5.6 to 0.7 eV with preservation of direct band gap and well-defined Bloch character, making them promising candidate materials for future light-emitting applications. Unlike that in their bulk counterparts, the phase separation could be suppressed in these two-dimensional systems because of reduced geometrical constraints. The disordered planar thin films undergo severe lattice distortion, nearly losing the Bloch character for valence bands, whereas the ordered planar ones maintain the Bloch character yet with the highest mixing enthalpies.

An experimental and computational study of CO2 adsorption in the sodalite-type M-BTT (M = Cr, Mn, Fe, Cu) metal-organic frameworks featuring open metal sites.

We present a comprehensive investigation of the CO2 adsorption properties of an isostructural series of metal-organic frameworks, M-BTT (M = Cr, Mn, Fe, Cu; BTT3- = 1,3,5-benzenetristetrazolate), which exhibit a high density of open metal sites capable of polarizing and binding guest molecules. Coupling gas adsorption measurements with in situ neutron and X-ray diffraction experiments provides molecular-level insight into the adsorption process and enables rationalization of the observed adsorption isotherms. In particular, structural data confirms that the high initial isosteric heats of CO2 adsorption for the series are directly correlated with the presence of open metal sites and further reveals the positions and orientations of as many as three additional adsorption sites. Density functional theory calculations that include van der Waals dispersion corrections quantitatively support the observed structural features associated with the primary and secondary CO2 binding sites, including CO2 positions and orientations, as well as the experimentally determined isosteric heats of CO2 adsorption.

Towards accurate models for amorphous GeTe: Crucial effect of dispersive van der Waals corrections on the structural properties involved in the phase-change mechanism

The effect of van der Waals dispersion correction in combination with density functional theory is investigated on a canonical amorphous phase-change material. Density functional theory (DFT), using the generalized gradient approximation, usually fails to reproduce the structure of amorphous tellurides, which manifests by an overestimation of the interatomic bond distances, and particularly the Ge-Te one involved in local geometries (tetrahedral or defect octahedral). Here, we take into account dispersion forces in a semiempirical way and apply such DFT simulations to amorphous GeTe. We obtain a substantial improvement of the simulated structure factor and pair-correlation function, which now reproduce the experimental counterparts with an unprecedented accuracy, including on a recent partial contribution from anomalous x-ray scattering and from x-ray absorption. A detailed analysis of the corresponding structures indicates that the dispersion correction reduces the Ge-Te bond length, increases the fraction of tetrahedral germanium, and reduces the presence of heteropolar so-called fourfold ABAB rings. Given that these structural features have been stressed to be central for the understanding of the phase-change mechanism, the present results challenge our current understanding of the crystal to amorphous transformation at play.

Lattice Defects and the Mechanical Anisotropy of Borophene

Using density functional theory combined with a semi-empirical van der Waals dispersion correction, we have investigated the stability of lattice defects including boron vacancy, substitutional and interstitial X (X=H, C, B, N, O) and $\Sigma$5 tilt grain boundaries in borophene and their influence on the anisotropic mechanical properties of this two-dimensional system. The pristine borophene has significant in-plane Young's moduli and Poisson's ratio anisotropy due to its strong and highly coordinated B-B bonds. The concentration of B vacancy and $\Sigma$5 grain boundary could be rather high given that their formation energies are as low as 0.10 eV and 0.06 eV/$\AA$ respectively. In addition, our results also suggest that borophene can react easily with H$_2$, O$_2$ and N$_2$ when exposed to these molecules. We find that the mechanical properties of borophene are remarkably degraded by these defects. The anisotropy in Poisson's ratio, however, can be tuned by some of them. Furthermore, the adsorbed H or substitutional C may induce remarkably negative Poisson's ratio in borophene, and the substitutional C or N can significantly increase the Poisson's ratio by contrast.

Electronic Properties of Acetaminophen Adsorbed on 2D Clusters: A First Principles Density Functional Study

AbstractThe interaction of acetaminophen (N‐acetyl‐para‐aminophenol), a prominent analgesic and antipyretic, with 2D clusters was investigated using density functional theory with inclusion of van der Waals dispersion correction. The implicit solvation model with three different solvents; water, ethanol and carbon tetrachloride were utilized to observe the trends in binding energy as a function of solvent polarity. The calculated results demonstrate that interactions are not solely dependent on solvent polarity, but inherent properties of the 2D clusters drive the nature of the interaction; i. e. physisorbed states were favored for graphene, boron nitride (BN), and phosphorene, whereas a chemisorbed state is preferred for silicene. Analysis of the frontier orbitals and density of states (DOS) show that the acetaminophen functionalization induces mid‐gap energy states in BN. Chemisorbed acetaminophen on silicene induces a 2p core level shift in silicon. The calculated results provide atomistic insights on the nature of interactions of acetaminophen with the new class of 2D materials beyond graphene for potential sensing applications.

Effects of Vanadium Substitution in the Layered LiFeSO4OH: A First Principles Investigation

This work aims to investigate effects of vanadium substitution on structural and electronic properties of the pristine LiFeSO4OH compound using GGA, GGA+U and GGA + van der Waals (vDW) dispersion corrections. Upon vanadium substitution, the band gap of substituted vanadium on LiFeSO4OH decreased implying the increase in electronic conductivity, thus a good property for a cathode material. Moreover, the volume of substituted material also increased suggesting ease movement of lithium ions within the host structure thus increasing the ionic conductivity. Since no experimental structure of this material has been reported, therefore the structure of current layered LiFeSO4OH is adopted. Furthermore, electronic properties viz. the lattice parameter, density of state (DOS), bond length (BL), bond order (BO) and charge density were also determined using the first principles approach.

Stability and Electronic Properties of 2D Nanomaterials Conjugated with Pyrazinamide Chemotherapeutic: A First-Principles Cluster Study

Electronic and optical properties of 2D models of graphene, boron nitride (BN), silicene, SiC, and phosphorene functionalized with pyrazinamide (PZA), a front line antitubercular chemotherapeutic, are investigated using cluster models and density functional theory with van der Waals dispersion corrections and including solvent effects. PZA favors covalent functionalization onto silicene and SiC whereas it is physisorbed onto graphene, BN, and phosphorene at a nearest-neighbor distance >3.0 A and binding energies between −0.7 and −0.8 eV. The analysis of orbital energies, frontier orbitals, density of states, and absorption spectra shows that the HOMO–LUMO gaps for graphene, silicene, and phosphorene remain virtually unchanged upon adsorption, whereas midgap states appear in the BN and SiC clusters. For silicene, Si 2p core level photoemission spectroscopy is the better tool to analyze the chemisorption of PZA. Our study brings atomistic insight into the structural, electronic, and optical response of 2D m...

The energetic of (CH2F2)2 investigated by TDL IR spectroscopy and DFT computations: From collision induced relaxation of ro-vibrational transitions to non-covalent interactions.

Difluoromethane (CH2F2) is an atmospheric pollutant presenting strong absorptions within the 8-12 μm atmospheric window, hence it can contribute to global warming. Its dimer, (CH2F2)2, is bound through weak hydrogen bonds (wHBs). Theoretically, wHBs are of paramount importance in biological systems, though their modeling at density functional theory (DFT) level requires dispersion correlations to be accounted for. In this work, the binding energy (3.1 ± 0.5 kcal mol(-1)) of (CH2F2)2 is experimentally derived from the foreign broadening coefficients of the monomer compound, collisionally perturbed by a range of damping gases. Measurements are carried out on CH2F2 ro-vibrational transitions by means of tunable diode laser spectroscopy. Six stationary points on the potential energy surface (PES) of the dimer are investigated at DFT level by using some of the last generation density functionals (DFs). The Minnesota M06 suite of functionals as well as range separated DFs and DFs augmented by the non-local (NL) van der Waals (vdW) dispersion corrections are considered. DFT results are compared to reference values at the estimated complete basis set (CBS) limit of CCSD(T) theory (coupled cluster with singles and doubles augmented by a perturbational estimate of connected triples) and to the experimental binding energy. The M06-2X, M06-HF, VV10, BLYP-NL, and B3LYP-NL DFs reproduce CCSD(T)/CBS binding energies with a mean absolute deviation <0.4 kcal mol(-1) and about the same deviation from the experimental value. The present results are of twofold relevance: (i) they show that binding energy of homodimers can be conveniently obtained from the monomer's foreign broadening coefficients and that the correct simulation of hydrogen bonds involved in (CH2F2)2 needs non-covalent interactions to be included into DFT; (ii) O2- and N2-pressure broadening parameters represent fundamental data for exploiting the efficacy of remote sensing measurements employed to retrieve temperature and concentration profiles of our atmosphere.

Beyond Energies: Geometries of Nonbonded Molecular Complexes as Metrics for Assessing Electronic Structure Approaches.

Electronic structure approaches for calculating intermolecular interactions have traditionally been benchmarked almost exclusively on the basis of energy-centric metrics. Herein, we explore the idea of utilizing a metric related to geometry. On a diverse series of noncovalently interacting systems of different sizes, from the water dimer to the coronene dimer, we evaluate a variety of electronic structure approximations with respect to their abilities to reproduce coupled-cluster-level geometries. Specifically, we examine Hartree-Fock, second-order Møller-Plesset perturbation theory (MP2), attenuated MP2, scaled MP2, and a number of density functionals, many of which include empirical or nonempirical van der Waals dispersion corrections. We find a number of trends that transcend system size and interaction type. For instance, functionals incorporating VV10 nonlocal correlation tend to yield highly accurate geometries; ωB97X-V and B97M-V, in particular, stand out. We establish that intermolecular distance, as measured by, e.g., the center-of-mass separation of two molecules, is the geometric parameter that deviates most profoundly among the various methods. This property of the equilibrium intermolecular separation, coupled with its accessibility via a small series of well-defined single-point calculations, makes it an ideal metric for the development and evaluation of electronic structure methods.

Native point defects in few-layer phosphorene

Using hybrid density functional theory combined with a semiempirical van der Waals dispersion correction, we have investigated the structural and electronic properties of vacancies and self-interstitials in defective few-layer phosphorene. We find that both a vacancy and a self-interstitial defect are more stable in the outer layer than in the inner layer. The formation energy and transition energy of both a vacancy and a self-interstitial P defect decrease with increasing film thickness, mainly due to the upward shift of the host valence band maximum in reference to the vacuum level. Consequently, both vacancies and self-interstitials could act as shallow acceptors, and this well explains the experimentally observed p-type conductivity in few-layer phosphorene. On the other hand, since these native point defects have moderate formation energies and are stable in negatively charged states, they could also serve as electron compensating centers in n-type few-layer phosphorene.

Layered uranium(VI) hydroxides: structural and thermodynamic properties of dehydrated schoepite α-UO₂(OH)₂.

The structure of dehydrated schoepite, α-UO2(OH)2, was investigated using computational approaches that go beyond standard density functional theory and include van der Waals dispersion corrections (DFT-D). Thermal properties of α-UO2(OH)2, were also obtained from phonon frequencies calculated with density functional perturbation theory (DFPT) including van der Waals dispersion corrections. While the isobaric heat capacity computed from first-principles reproduces available calorimetric data to within 5% up to 500 K, some entropy estimates based on calorimetric measurements for UO3·0.85H2O were found to overestimate by up to 23% the values computed in this study.

Metal adatoms-decorated silicene as hydrogen storage media

Hydrogen storage properties of 10 different adatom decorated silicene are carried out using density functional theory calculations with long-range van der Waals dispersion correction. It is found that the binding energy between metal adatoms and the silicene is greater than the cohesive energy of bulk metal so that clustering of adatom will not occur once it is bonded with silicene. The adsorption of H2 on Li, Na, K, Mg, Ca, and Au decorated silicene is a weak physisorption. Differently, a weaker chemisorption is responsible for the adsorption of H2 on Be, Sc, Ti, and V decorated silicene. In particular, silicene with Na, K, Mg, and Ca decorating on both sides leads to 7.31–9.40 wt% hydrogen storage capacity with desirable adsorption energy, indicating that the metal-decorated silicene can serve as a high capacity hydrogen storage medium.

Structural and Electronic Properties of Monolayer 1T-MoS2 Phase, and Its Interaction with Water Adsorbed on Perfect, Single S-Vacated and MoS2-Unit-Vacated Surface: Density Functional Theory Calculations

Using density functional theory calculations with van der Waals dispersion corrections, we studied the structural and electronic properties of monolayer 1T-MoS2, and how it interacts with water on perfect and vacancy-doped cases, which include single sulfur and MoS2-unit vacancies. We first optimized and calculated its structural parameters and electronic properties and confirmed earlier reports suggesting its metastable state and metallic electronic structure. Results show that adsorption sites on perfect surface bind water weakly while the opposite is true for vacancy sites adsorption. Climbing nudged elastic band calculations revealed that sulfur vacancy site could favorably dissociate water and evolve hydrogen with moderate energy cost, while significantly high energies are required for the same processes on MoS2 unit vacancy. The results are important in supplementing efforts to find clean and renewable energy sources.

Noncovalent functionalization of single-walled carbon nanotubes by aromatic diisocyanate molecules: A computational study

We investigate the noncovalent functionalization of metallic single-walled carbon nanotubes (SWCNT) (6,0) by 4,4′-methylene diphenyl diisocyanate (MDI) and toluene-2,4-diisocyanate (TDI) molecules using the density functional theory (DFT) method with van der Waals dispersion correction. The obtained local minima show the dependence between the molecular arrangement of the adsorbates on SWCNT surface and their binding energies. We analyze the interplay between the π–π stacking interactions and isocyanate functional groups. For the analysis of the changes in the electronic structure we calculate the density of states (DOS) and charge density plots.

Comparison of van der Waals corrected and sparse-matter density functionals for the metal-free phthalocyanine/gold interface

In this paper, we report a systematic study on the effect of different van der Waals dispersion correction methods in conjunction with Density Functional Theory on the adsorption characteristics of a monolayer of metal-free phthalocyanine on Au(111). The chosen dispersion corrections were DFT-D2, the Tkatchenko-Scheffler method with and without self-consistent screening, and four sparse-matter density functionals. A comparison among different dispersion corrections was performed and the results are related to available experimental scanning tunnel microscopy and x-ray standing-wave measurements for similar molecules on Au(111). We found that the Tkatchenko-Scheffler method as well as a sparse-matter density functional which employs the exchange potential of optB86b and the nonlocal correlation of Dion describe the adsorbed system, e.g., electronic and geometric structure with an adsorption distance of $3.3$ \AA{}, reasonably well within moderate computational costs.

Energetics of formation and hydration of functionalized silica nanoparticles: An atomistic computational study

The energetics of formation and hydration of functionalized silica nanoparticles were studied using a combination of first-principles calculations based on density functional theory with van der Waals dispersion correction and molecular dynamics. The energetics and effects of group density were evaluated in both; hydrophilic (ethylene-glycol) and hydrophobic (sulfonic) organosilane functional groups, and the optimum group density were obtained in vacuum and aqueous environment. The functional group bounded in a geminal silanol site was found to be more stable than silanol one, by ∼1.30 and ∼1.32eV for hydrophilic and hydrophobic groups, respectively. In vacuum, an optimum graft density of 4.2 and 4.5groups/nm2 was obtained for hydrophobic and hydrophilic coverage, based on molecular dynamics calculations. Interestingly, a double well energy profile is obtained when functionalized nanoparticles are placed within aqueous media, and those minima for hydrophilic groups appear at lower coverage compared to hydrophobic one. The double energy minima is explained by the H2O molecules arrangement as function of the group density on nanoparticles surface. At low coverage, H2O molecules surround the groups while at high coverage, the functional groups shield the molecules to penetrate within the groups and the size effect of the functional group studied here was found to be negligible on the stability.

Graphyne and Graphdiyne: Versatile Catalysts for Dehydrogenation of Light Metal Complex Hydrides

The interaction between new two-dimensional carbon allotropes, i.e. graphyne (GP) and graphdiyne (GD), and light metal complex hydrides LiAlH4, LiBH4, and NaAlH4 was studied using density functional theory (DFT) incorporating long range van der Waals dispersion correction. The light metal complex hydrides show much stronger interaction with GP and GP than that with fullerene due to the well defined pore structure. Such strong interactions greatly affect the degree of charge donation from the alkali metal atom to AlH4 or BH4, consequently destabilizing the Al-H or B-H bonds. Compared to the isolated light metal complex hydride, the presence of GP or GD can lead to a significant reduction of the hydrogen removal energy. Most interestingly, the hydrogen removal energies for LiBHx on GP and with GD are found to be lowered at all the stages (x from 4 to 1) whereas the H-removal energy in the third stage is increased for LiBH4 on fullerene. In addition, the presence of uniformly distributed pores on GP and GD is expected to facilitate the dehydrogenation of light metal complex hydrides. The present results highlight new interesting materials to catalyze light metal complex hydrides for potential application as media for hydrogen storage. Since GD has been successfully synthesized in a recent experiment, we hope the present work will stimulate further experimental investigations in this direction.

Equations of state for crystalline zirconium iodide: The role of dispersion

We present the first-principle equations of state of several zirconium iodides, ZrI2, ZrI3, and ZrI4, computed using density functional theory methods that apply various methods for introducing the dispersion correction. Iodides formed due to reaction of molecular or atomic iodine with zirconium and zircaloys are of particular interest due to their application to the cladding material used in the fabrication of nuclear fuel rods. Stress corrosion cracking (SCC), associated with fission product chemistry with the clad material, is a major concern in the life cycle of nuclear fuels, as many of the observed rod failures have occurred due to pellet–cladding chemical interactions (PCCI) [A. Atrens, G. Dannhäuser, G. Bäro, Stress-corrosion-cracking of zircaloy-4 cladding tubes, Journal of Nuclear Materials 126 (1984) 91–102; P. Rudling, R. Adamson, B. Cox, F. Garzarolli, A. Strasser, High burn-up fuel issues, Nuclear Engineering and Technology 40 (2008) 1–8]. A proper understanding of the physical properties of the corrosion products is, therefore, required for the development of a comprehensive SCC model. In this particular work, we emphasize that, while existing modeling techniques include methods to compute crystal structures and associated properties, it is important to capture intermolecular forces not traditionally included, such as van der Waals (dispersion) correction. Furthermore, crystal structures with stoichiometries favoring a high I:Zr ratio are found to be particularly sensitive, such that traditional density functional theory approaches that do not incorporate dispersion incorrectly predict significantly larger volumes of the lattice. This latter point is related to the diffuse nature of the iodide electron cloud.

Assembly of cyclic hydrocarbons from ethene and propene in acid zeolite catalysis to produce active catalytic sites for MTO conversion

The formation of cyclic hydrocarbons from smaller building blocks such as ethene and propene is investigated in protonated ZSM-5, using a 2-layered ONIOM(B3LYP/6-31+g(d):HF/6-31+g(d)) approach and an additional Grimme-type van der Waals dispersion correction term to account for the long-range dispersion interactions. These cyclic species form precursors for active hydrocarbon pool species and play a key role in activating the acidic zeolite host for successful methanol-to-olefin (MTO) conversion. Starting from trace amounts of ethene and propene that are formed during an initial induction period or during the active phase, dimerization reactions allow for rapid chain growth. The products of these reactions can be neutral alkenes, framework-bound alkoxide species or intermediate carbenium ions, depending on the zeolite environment taken into account. On the basis of rate constants for successive reaction steps, a viable route toward cyclization is proposed, which starts from the formation of a framework-bound propoxide from propene, followed by dimerization with an additional propene molecule to form the 2-hexyl carbenium ion which finally undergoes ring closure to yield methylcyclopentane. This cyclic species in turn forms a precursor for either an active hydrocarbon pool compound or for deactivating coke deposit.