DFT-D Calculations Research Articles

Calculations of adsorption, coadsorption, diffusion, and reaction barriers of H atoms in the H2 formation on a positively charged coronene

DFT-D calculations of adsorption, diffusion and reaction barriers of atomic hydrogen radicals (H) to form H2 on positively charged coronene (Cor+) were studied for cis dimers (ortho, meta, and para) of H on central and edge rings. Results show, by comparison with the neutral system, that cationic polycyclic aromatic hydrocarbons (PAH) are more efficient for hydrogen recombination because these systems have a lower diffusion and reaction barriers. In some cases, hydrogen recombination does not take place because H desorption occurs. However, the adsorption of a third H leads to lower reaction barriers than in the dimer systems.

A first-principles DFT dispersion-corrected C60/Au(111) Raman study

We present an extensive density functional theory (DFT) study on the interaction of C60 molecules with Au(111), involving both periodic metal surfaces and clusters. The aim of this work is 2-fold: First, to quantify the adsorption energies per molecule (Eads) of the C60/Au(111) system from periodic calculations using a dispersion-corrected functional (DFT-D3). Secondly, to determine the effect of the metal substrate on the adsorbed C60 molecule via calculated non-resonant Raman vibrational frequencies. Using a commensurate (23×23) R30° phase – as proposed by experimental work as a stable C60/Au(111) monolayer – our DFT-D3 periodic calculations show a slight C60 molecule preference to adsorb on its hexagonal facet, with a calculated adsorption energy value of 2.40 eV. Our DFT-D3 calculations further reveal an energetic gain when the C60 molecule is adsorbed on an HCP surface (2.40 eV) site compared to an FCC one (2.31 eV). Using a variety of finite-size, slab-type Au clusters (e.g.Au24, Au32 and Au50), our DFT-D3 calculated Raman intensity profile shows a strong interaction between the C60 fullerene molecule and the gold substrate. This influences new vibrational modes over a wide range of frequencies, compared to those active modes for the isolated C60 gas-phase single molecule, and an overall shift of frequencies and symmetries. The DFT-D3 calculated Raman spectra of the C60 molecule supported on Au clusters are in good agreement when confronted to those recently obtained experimentally under ultra-high vacuum (UHV) conditions using tip-enhanced Raman spectroscopy (TERS).

Molecular simulation of efficient removal of H2S pollutant by cyclodextrine functionalized CNTs

DFT-D3 calculations were carried out to investigate interaction of H2S and CH4 between numerous functionalized CNTs (f-CNTs), including hydroxyl, carboxyl, and cyclodextrin groups as potential candidates for selective adsorption and elimination of toxic pollutants. It was found that pristine CNTs as well as nanotube surface of functionalized CNTs cannot stably adsorb the H2S molecule (adsorption energy of −0.17 eV). However, H2S adsorption was significantly enhanced with different magnitudes upon the functionalization of CNT. For f-CNTs, H2S adsorption was accompanied by releasing energies in the range between −0.34 to −0.54 eV where the upper limit of this range belongs to the cyclodextrin-functionalized CNT (CD-CNT) as the consequence of the existence of both dispersion and electrostatic interactions between the adsorbate and substrate. Findings also demonstrated a significantly weaker interaction between CH4 and CD-CNT in comparison to the H2S molecule with adsorption energy of −0.14 eV. Electronic properties of the selected substrates revealed no significant changes in the inherent electronic properties of the CNTs after functionalizing and adsorbing the gas molecules. Moreover, DFTB-MD simulation demonstrated high adsorption capacity as well as CD-CNT ability for H2S molecules against the CH4 one under ambient condition.

RNA aptasensor based on gold nanoparticles for selective detection of neomycin B, molecular approach

In this article, immobilized RNA aptamer on the gold nanoparticle surface was theoretically designed for selective detection of the neomycin B, neomycin C and paromomycin. Several molecular dynamic simulations on the pure aptamer, aptamer with –S(CH2)6– linker and immobilized aptamer on the gold nanoparticles surface were performed in the presence of different analytes. The obtained results indicate that the linker does not perturb the structure of the RNA aptamer. Also, full atomistic MD simulations on the immobilized RNA aptamer, as a biosensor, reveal a good sensing ability toward neomycin B in the presence of paromomycin and neomycin C. Due to complex formation, the distance of the aptamer and gold nanoparticles decreases. Moreover, the analysis of the electrostatic interactions between the aptamer and neomycin B shows a reduction in the tendency of the aptamer to interact with the gold nanoparticles, significantly. On the basis of the DFT-D3 calculations, neomycin B forms the most stable complex with the aptamer binding site, due to the strong hydrogen bond formation. Moreover, the obtained results indicate that electrostatic interactions are the driving forces of complex formation. On the basis of QM/MD results, the proposed aptasensor is a good candidate for the detection of neomycin B.

DFT study of the electronic and structural properties of single Al and N atoms and Al-N co-doped graphyne toward hydrogen storage

Abstract In this work, electronic and structural properties of single Al or N atom doped and Al-N co-doped graphyne (GY) toward hydrogen storage were investigated using DFT-D calculations. Results show that N and Al atoms energetically prefer to lie instead of Csp in the chain and Csp2 in the hexagonal ring, respectively. Al or N doping changes conducting nature of GY from semiconductor to metallic. Pristine GY and more stable structures of Al doped, N doped and Al-N co-doped GY were examined for H2 adsorption. Adsorption energies for the first H2 molecule are about −0.140, −0.224, −0.141 and −0.288 eV/H2, respectively. They can hold 4, 9, 7 and 16 H2 molecules with average adsorption energy of ~−0.089, −0.158, −0.144 and −0.161 eV/H2, respectively. Also, the calculated corresponding hydrogen storage capacities reach up to 5.26, 10.17, 8.75 and 16.67 wt%, respectively. Although, effect of Al atom is more than N atom, when both of them co-doped in GY, its electronic and structural properties, as well as hydrogen storage capacity improve, extremely and they have a synergistic effect onto hydrogen adsorption. These findings show that N-Al co-doped GY can be used for designing new hydrogen storage materials in the future.

Sensing and elimination of the hazardous materials such as Sarin by metal functionalized γ-graphyne surface: A DFT study

Sarin is an organophosphorus compound, poisonous and deadly, which is used in the preparation of chemical weapons. We are looking for materials for using as sensing and capturing of Sarin, so the effect of Li, Ti, Fe and Ni single atoms on the structural and electronic properties of graphyne (GY) toward Sarin adsorption was investigated by DFT-D calculations. Seven sites of GY and different distances from GY plane were investigated to gain the best structure of M-decorated GY. Then, adsorption of Sarin on the pristine and M-decorated GY was considered. The results showed that H1 is the best site for metal decoration and Sarin adsorption. Pristine GY is a semiconductor with direct band gap about 0.431 eV. Metal intern causes to change GY character into semi-metallic and decrease GY band gap. Decoration with all metals improves adsorption energy of Sarin, extremely, e.g. up to 4.5 times for Ti-decoration. Among six examined sites of Sarin, for Ni-decoration, etheric oxygen and for others, oxygen of carbonyl group is the best site for adsorption. In all systems, charge transfer happens from Sarin and metal to GY sheet. Also, in presence of the Sarin molecule, the band gap values decrease. Adsorption energies, location of metal atoms, metal and Sarin charges, band structure and partial density of state (PDOS) diagrams were brought and discussed. Ultimately, our study shows that Li, Ti, Fe and Ni-decorated GY can be used as a promising candidate for sensing and capturing applications of CWAs such as Sarin.

Removing phenol contaminants from wastewater using graphene nanobuds: DFT and reactive MD simulation investigations

Phenol and phenolic compounds are extensively found in effluents and are toxic even at low concentrations hence their elimination from aqueous solutions is necessary. In the present work, the interaction of phenol and water molecules with graphene and graphene nanobud (GNB) was investigated using DFT-D3 calculations with revPBE/def2-TZVP model of theory. Various binding sites and ways of approach for phenol/water molecule approaching the selected adsorbents were evaluated. We found that water molecule tends to interact weakly with both graphene and GNB compared with the phenol molecule. The strength of adsorption for GNB at the top of the fullerene cage as well as near the neck site and onto the graphene surface was found to be stronger for phenol rather than water molecule. This can be attributed to the existence of simultaneous π-π stacking and electrostatic attractions for phenol/adsorbent system. Our first-principles calculations showed that binding nature of interacting molecules depends strongly on the long-range non-local dispersion forces but slightly to the solvent entity. The obtained binding energies compared with the experimental and highly accurate quantum-mechanical values available in literature for water/benzene adsorbed onto the graphene surface. Moreover, the adsorption ability and capacity of GNB was verified by reactive MD simulation carrying out at ambient condition. The desirable binding strength obtained accompanied with high specific surface area of GNB (due to fastened buckyballs) compared with the graphene lead to practically arrest these novel hybrid nano-materials as superior adsorbents for phenol adsorption and remediation from water-contaminated environment.

Metal-Organic Framework Containing Planar Metal-Binding Sites: Efficiently and Cost-Effectively Enhancing the Kinetic Separation of C2H2/C2H4.

One of the emerging problems plaguing the chemical industry today is the efficient and cost-effective separation of C2 hydrocarbons. In order to help address this problem, we report a new material, NbU-1, constructed by extremely cheap starting materials. The special structural characteristics of NbU-1 such as the planar, mixed-valence copper clusters and Lewis-basic adsorption channels enforce interactions with acetylene molecules that lead to the highest kinetic separation efficiency for C2H2/C2H4. Via DFT-D calculations, it is indicated that C2H2 molecules are adsorbed onto the two adjacent Cu(I) centers, but not the usual single open metal sites of Cu centers. The reported results not only provide information for a deep investigation into the separation mechanism but also offer an alternative strategy for preparing cost-effective materials that can perform highly efficient separations of light hydrocarbons.

Influence of the aromatic surface on the capacity of adsorption of VOCs by magnetite supported organic-inorganic hybrids.

It has been recently evidenced that hybrid magnetic nanomaterials based on perylene diimide (PDI) dopamine and iron oxide nanoparticles are useful for the adsorption and determination of volatile organic compounds (VOCs). However, NDI compounds are expensive and difficult to handle compared to smaller size diimides. Therefore, in this manuscript a combined experimental and theoretical investigation is reported including the analysis of the effect of changing the aromatic surface on the ability of these magnetite supported organic–inorganic hybrid nanoparticles (NPs) to adsorb several aromatic and non-aromatic VOCs. In particular, two new hybrid Fe3O4NPs are synthesized and characterized where the size of organic PDI dopamine linker is progressively reduced to naphthalene diimide (NDI) and pyromellitic diimide (PMDI). These materials were utilized to fill two sorbent tubes in series. Thermal desorption (TD) combined with capillary gas chromatography (GC)/flame detector (FID) was used to analyze both front and back tubes. Adsorption values (defined as % VOCs found in the front tube) were determined for a series of VOCs. The binding energies (DFT-D3 calculations) of VOC–Fe3O4NP complexes were also computed to correlate the electron-accepting ability of the arylene diimide (PDI, NDI or PMDI) with the adsorption capacity of the different tubes. The prepared hybrids can be easily separated magnetically and showed great reusability.

Interrogation of fractional crystallization behavior of a newly exploited chiral resolution method for racemic 1-(pyridin-2-yl)ethylamine via DFT-D3 calculations of cohesive energy

A novel chiral separation method for 1-(pyridin-2-yl)ethylamine is developed and the underlying energetics is investigated by DFT-D3.

The quantum mechanics-based polarizable force field for water simulations.

We report here a new force field for water based solely on quantum mechanics (QM) calculations with no empirical data. The QM was at a high level, coupled cluster single double triple, for all orientations and distances for water dimer plus X3LYP density functional theory (DFT) on 19 larger water clusters. In addition, we included charge and polarization based on the polarizable charge equilibration method and nonbond interactions from DFT-D3 calculations on the H2 and O2 crystal. This model, denoted as RexPoN, provides quite excellent agreement with experimental (expr) data for the solid and liquid phase of water: T melt = 273.3 K (expr = 273.15 K) and properties at 298 K: ΔH vap = 10.36 kcal/mol (expr = 10.52), density = 0.9965 gr/cm3 (expr = 0.9965), entropy = 68.4 (J/mol)/K (expr = 69.9), dielectric constant = 76.1 (expr = 78.4), and ln D s (self-diffusion coef) = -10.08 (expr = -11.24). Such an accurate force field for water will, we believe, be useful for full solvent calculations of electrocatalysis, where we can restrict QM water to just the first one or two layers involving reactions, using RexPoN to provide the polarization for a more distant solvent. Also, RexPoN may provide a better description of the solvent for proteins, DNA, polymers, and inorganic systems for applications to biomolecular, pharma, electrocatalysis (fuel cells and water splitting), and batteries where interaction with explicit water molecules plays a significant role.

Structure determination of oxamic acid from laboratory powder X-Ray diffraction data and energy minimization by DFT-D

The structure determination from laboratory X-ray powder diffraction data of oxamic acid, a derivative of the biologically active oxalic acid and the simplest organic acid containing an amide group, is presented in this contribution. An energy minimization analysis by DFT-D was carried out. The structure was determined with the program TALP and refined by the Rietveld method with GSAS-II in space group Cc (No. 9). The final unit-cell parameters are a = 9.4989 (6), b = 5.43796 (9), c = 6.8637 (9) Å, β = 107.152 (5)°, V = 338.772 (10) Å3, Z = 4. The refinement converged to the figures of merit: Re = 0.01674, Rp = 0.03270, Rwp = 0.05652 and GoF = 3.378 with a good fit between the calculated pattern of the structural model and the experimental pattern. The DFT-D calculations show an excellent reproduction of the experimental structure, validating the correctness of the structure. The non-centrosymmetric nature of the structure was confirmed by SHG measurements. In the crystal structure, the molecules are close to planar and form a complex 2D hydrogen-bonding pattern based on the cyclic amide-acid heterosynthon.

Adsorption and Quantification of Volatile Organic Compounds (VOCs) by using Hybrid Magnetic Nanoparticles.

The ability of Fe3 O4 magnetic nanoparticles decorated with perylene bisimides to adsorb aromatic volatile organic compounds (VOCs) is reported. We have used DFT-D3 calculations to anticipate the strong ability of the electron-poor perylene bisimide to form noncovalent complexes with electron-rich aromatic rings belonging to the VOC family. Subsequently, we synthesized a hybrid magnetic nanomaterial based on bisimide perylene dopamine and iron oxide nanoparticles. This material was used to fill a sorbent tube to study its ability to adsorb aromatic VOCs. We connected two tubes in series filled with the hybrid nanoparticles. The analysis of the front and back tubes was performed by thermal desorption (TD) coupled with capillary gas chromatography (GC)/flame ionization detector (FID). Adsorption values (defined as %VOCs found in the back tube) were determined for a series of aromatic VOCs and compared with the DFT binding energies. The tubes can be desorbed and reutilized more than 200 times without losing their properties.

DFT study of single-walled carbon hollows as media for hydrogen storage

Understanding the interaction of hydrogen molecules with hollow materials is crucial in the fields of hydrogen storage, sensors, catalysis, and fuel cells. In this paper, we studied hydrogen adsorption on single-walled carbon hollows by means of DFT-D3 calculations. These structures adsorb H2 molecules significantly stronger (adsorption energy, Ea, of −12.55 to −20.56 kJ/mol) than coronene (−4.15 kJ/mol), the representative of graphene, and corannulene (−7.83 kJ/mol), a slightly bent polyaromatic molecule. The reduced density gradient analysis was involved to visualize interacting regions between hydrogen and a series of adsorbents. Energy decomposition analysis was used to divide the total interaction energy into constituents. It is founded that the dispersion term is dominating in all studied cases. The present results should broaden our understanding of the mechanisms of hydrogen storage using carbon hollows.

Quantum chemical exploration of formaldehyde clusters (H2 CO)n (n = 2-4).

Global exploration of equilibrium structures and interconversion pathways on the quantum chemical potential energy surface (PES) is performed for (H2 CO)n (n = 2-4) by using the Scaled Hypersphere Search-Anharmonic Downward Distortion Following (SHS-ADDF) method. Density functional theoretical (DFT) calculations with empirical dispersion corrections (D3) yielded comparable results for formaldehyde dimer in comparison with recent detailed studies at CCSD(T) levels. Based on DFT-D3 calculations, trimer and tetramer structures and their stabilities were studied. For tetramer, a highly symmetrical S4 structure was found as the most stable form in good accordance with experimentally determined tetramer unit in the formaldehyde crystal. © 2018 Wiley Periodicals, Inc.

Benchmarking the Effective Fragment Potential Dispersion Correction on the S22 Test Set.

The usual modeling of dispersion interactions in density functional theory (DFT) is often limited by the use of empirically fitted parameters. In this study, the accuracies of the popular empirical dispersion corrections and the first-principles derived effective fragment potential (EFP) dispersion correction are compared by computing the DFT-D and HF-D equilibria interaction energies and intermolecular distances of the S22 test set dimers. Functionals based on the local density approximation (LDA) and generalized gradient approximation (GGA), as well as hybrid functionals, are compared for the DFT-D calculations using coupled cluster CCSD(T) at the complete basis set (CBS) limit as the reference method. In general, the HF-D(EFP) method provides accurate equilibrium dimerization energies and intermolecular distances for hydrogen-bonded systems compared to the CCSD(T)/CBS reference data without using any empirical parameters. For dispersion-dominant and mixed systems, the structures and interaction energies obtained with the B3LYP-D(EFP) method are similar to or better than those obtained with the other DFT-D and HF-D methods. Overall, the first-principles derived -D(EFP) correction presents a robust alternative to the empirical -D corrections when used with the B3LYP functional for dispersion-dominant and mixed systems or with Hartree-Fock for hydrogen-bonded systems.

Tuning the Dirac Cone of Bilayer and Bulk Structure Graphene by Intercalating First Row Transition Metals Using First-Principles Calculations

Modern nanoscience has focused on two-dimensional (2D) layer structure materials which have garnered tremendous attention due to their unique physical, chemical, and electronic properties since the discovery of graphene in 2004. A recent advancement in graphene nanotechnology opens a new avenue of creating 2D bilayer graphene (BLG) intercalates. Using first-principles dispersion-corrected DFT techniques, we have designed 20 new materials in silico by intercalating first-row transition metals (TMs) with BLG, i.e., 10-layered structure and 10 bulk crystal structures of TM intercalated in BLG. More specifically, we investigated the equilibrium structure and electronic properties of layered and bulk structure BLG intercalated with first-row TMs (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, and Zn). The present DFT-D calculations show that the 2pz subshells of C atoms in graphene and the 3dyz subshells of the TM atoms provide the electron density near the Fermi energy level, controlling the material properties of the BLG-intercalated materials. This article highlights how the Dirac point moves in both the BLG and bulk-BLG given different TM-intercalated materials. The implications of controllable electronic structure and properties of intercalated BLG-TM materials for future device applications are discussed. This work opens up new avenues for the efficient production of two-dimensional and three-dimensional carbon-based intercalated materials with promising future applications in nanomaterial science.

Corrosion protection of Al(111) by 8-hydroxyquinoline: a comprehensive DFT study.

8-Hydroxyquinoline (8HQ) is a new green corrosion inhibitor. DFT-D calculations are performed to investigate the adsorption of 8HQ and derivatives on the Al(111) surface from low to high coverage. From θ = 0.20 to 0.66, the adsorption energies are -1.12, -2.41, -1.66 and -3.44 eV per molecule for 8HQ, and its tautomer, its hydrogenated and its dehydrogenated species, independently of the coverage. In contrast, the geometry of the adsorbates changes between coverage up to 0.66 and the full monolayer (θ = 1). The creation of a dipole at the molecule/metal interface reduces the work function of aluminum. To further evaluate the modification of the reactivity of the surface, adsorption of O2 on the Al(111) surface covered by the organic layer is investigated. O2 dissociation takes place for θ = 0.66. When the Al surface is fully covered (θ = 1), the reduction of O2 and the oxidation of Al atoms do not occur.

Cocrystals Help Break the “Rules” of Isostructurality: Solid Solutions and Polymorphism in the Malic/Tartaric Acid System

Crystalline solid solutions have the potential to afford tunable materials for pharmaceutical and technological applications. Unfortunately, these poorly understood phases are difficult to obtain and, hence, to study. In fact, commonly accepted empirical rules prescribe that only molecules of similar size and electron distribution are mutually soluble in the solid state. Here, despite the evident structural and electronic differences, the enantiomers of malic acid and tartaric acid are crystallized together in a variable stoichiometric ratio to produce both cocrystals and solid solutions. In some cases, physical mixtures are observed. The composition and polymorphism of the crystalline products are explained by DFT-d molecular substitution calculations for the cocrystallized molecules in different (known) structures. At the same time, from a crystal engineering perspective, the behavior of this complex system is rationalized thanks to the existence of intermediate cocrystal forms that merge the structural...

Labile Low-Valent Tin Azides: Syntheses, Structural Characterization, and Thermal Properties.

The first two examples of the class of tetracoordinate low-valent, mixed-ligand tin azido complexes, Sn(N3)2(L)2, are shown to form upon reaction of SnCl2 with NaN3 and SnF2 with Me3SiN3 in either pyridine or 4-picoline (2, L = py; 3, L = pic). These adducts of Sn(N3)2 are shock- and friction-insensitive and stable at r.t. under an atmosphere of pyridine or picoline, respectively. A new, fast, and efficient method for the preparation of Sn(N3)2 (1) directly from SnF2, and by the stepwise de-coordination of py from 2 at r.t., is reported that yields 1 in microcrystalline form, permitting powder X-ray diffraction studies. Reaction of 1 with a nonbulky cationic H-bond donor forms the salt-like compound {C(NH2)3}Sn(N3)3 (4) which is comparably stable despite its high nitrogen content (55%) and the absence of bulky weakly coordinating cations that are conventionally deemed essential in related systems of homoleptic azido metallates. The spectroscopic and crystallographic characterization of the polyazides 1-4 provides insight into azide-based H-bonded networks and unravels the previously unknown structure of 1 as an important lighter binary azide homologue of Pb(N3)2. The atomic coordinates for 1 and 2-4 were derived from powder and single crystal XRD data, respectively; those for 1 are consistent with predictions made by DFT-D calculations under periodic boundary conditions.