Inclusion Of Dispersion Interactions Research Articles

Searching for DFT-based methods that include dispersion interactions to calculate the physisorption of H2 on benzene and graphene.

Simulations of the hydrogen storage capacities of nanoporous carbons require an accurate treatment of the interaction of the hydrogen molecule with the graphite-like surfaces of the carbon pores, which is dominated by the dispersion forces. These interactions are described accurately by high level quantum chemistry methods, like the Coupled Cluster method with single and double excitations and a non-iterative correction for triple excitations (CCSD(T)), but those methods are computationally very expensive for large systems and for massive simulations. Density functional theory (DFT)-based methods that include dispersion interactions at different levels of complexity are less accurate, but computationally less expensive. In order to find DFT-methods that include dispersion interactions to calculate the physisorption of H2 on benzene and graphene, with a reasonable compromise between accuracy and computational cost, CCSD(T), Møller-Plesset second-order perturbation theory method, and several DFT-methods have been used to calculate the interaction energy curves of H2 on benzene and graphene. DFT calculations are compared with CCSD(T) calculations, in the case of H2 on benzene, and with experimental data, in the case of H2 on graphene. Among the DFT methods studied, the B97D, RVV10, and PBE+DCACP methods yield interaction energy curves of H2-benzene in remarkable agreement with the interaction energy curve obtained with the CCSD(T) method. With regards to graphene, the rev-vdW-DF2, PBE-XDM, PBE-D2, and RVV10 methods yield adsorption energies of the lowest level of H2 on graphene, very close to the experimental data.

Adsorption of methylene blue and its N-demethylated derivatives on the (111) face of coinage metals: The importance of dispersion interactions.

The adsorption of methylene blue and its N-demethylated derivatives on the (111) surface of three coinage metals is investigated using density functional theory with and without the inclusion of dispersion interactions. It is shown that the adsorption of these dye molecules on the metal surfaces can be largely classified as physisorption as the adsorption energy is dominated by dispersion interactions. While the molecules are found to adsorb on Au and Ag parallel to the surface with molecular geometries basically unaltered, the adsorption on Cu(111) features a butterfly configuration, accompanied by the largest adsorption energies among the three metal surfaces. The significant covalent character on Cu(111) is analyzed from the perspective of electronic structure.

A theoretical study of confinement effect of zeolite on the ethylene dimerization reaction

The influences of pore confinement and topology effect on ethylene dimerization over a series of zeolite, like HMOR, HZSM-5, HBEA and HMCM-22, have been systematically studied by density functional theory including dispersion interaction (DFT-D). Both of the stepwise and the concerted mechanisms are considered. Compared to the corresponding 8T models, the calculated activation energies are considerably reduced in the large models of zeolite due to the pore confinement effect. Moreover, the manners of ethylene dimerization are found to be related to the pore structure of zeolite catalyst. In stepwise mechanism, HMCM-22 shows better activity as suggested by the calculated activation energies. In concerted mechanism, the energy barriers in HBEA and HMCM-22 are much lower than that in HMOR and HZMS-5, indicting a better catalytic performance. By comparing the two mechanisms happened in one zeolite, we suggest that the concerted mechanism is preferable in HBEA, HMCM-22 and HMOR zeolite with large pores, while two mechanisms compete to each other in HZSM-5 with medium-size pores.

Revisiting the hydration structure of aqueous Na.

A combination of theory, X-ray diffraction (XRD) and extended x-ray absorption fine structure (EXAFS) are used to probe the hydration structure of aqueous Na+. The high spatial resolution of the XRD measurements corresponds to Qmax = 24 Å-1 while the first-reported Na K-edge EXAFS measurements have a spatial resolution corresponding to 2k = Qmax = 16 Å-1. Both provide an accurate measure of the shape and position of the first peak in the Na-O pair distribution function, gNaO(r). The measured Na-O distances of 2.384 ± 0.003 Å (XRD) and 2.37 ± 0.024 Å (EXAFS) are in excellent agreement. These measurements show a much shorter Na-O distance than generally reported in the experimental literature (Na-Oavg ∼ 2.44 Å) although the current measurements are in agreement with recent neutron diffraction measurements. The measured Na-O coordination number from XRD is 5.5 ± 0.3. The measured structure is compared with both classical and first-principles density functional theory (DFT) simulations. Both of the DFT-based methods, revPBE and BLYP, predict a Na-O distance that is too long by about 0.05 Å with respect to the experimental data (EXAFS and XRD). The inclusion of dispersion interactions (-D3 and -D2) significantly worsens the agreement with experiment by further increasing the Na-O distance by 0.07 Å. In contrast, the use of a classical Na-O Lennard-Jones potential with SPC/E water accurately predicts the Na-O distance as 2.39 Å although the Na-O peak is over-structured with respect to experiment.

The role of London dispersion interactions in strong and moderate intermolecular hydrogen bonds in the crystal and in the gas phase

Two variants of density functional theory computations have been applied to characterization of hydrogen bonds of the 1-(2-hydroxylethyl)-3-methylimidazolium acetate ([C2OHmim][OAc]), i.e. with and without inclusion of dispersion interactions. A comparison of the results demonstrates that London dispersion interactions have very little impact on the energetical, geometrical, infrared spectroscopic and electron density parameters of charge-assisted intermolecular hydrogen bonds functioning both in the crystal of the [C2OHmim][OAc] and in the isolated [C2OHmim]+ [OAc]− ion pairs.

A DFT study of (WO3)3nanoclusters adsorption on defective MgO ultrathin films on Ag(001)

The structures and electronic properties of (WO3)3nanocluster adsorption on defective MgO ultrathin films supported on Ag(001) metal surfaces have been investigated by means of density functional theory (DFT) calculations including dispersion interactions.

Reducibility of ZrO2/Pt3Zr and ZrO2/Pt 2D films compared to bulk zirconia: a DFT+U study of oxygen removal and H2 adsorption.

Oxide reducibility is an important property that determines the chemical and physical behavior of the materials under working conditions. Zirconia is a non-reducible oxide that exhibits high resistance to the loss of oxygen and low reactivity towards hydrogen, two typical processes involved in oxide reduction. Oxide reducibility can change substantially by nanostructuring (e.g. formation of nanoparticles). In this study, we investigate theoretically by means of DFT+U calculations including dispersion interactions the properties of 2D zirconia films supported on a Pt3Zr alloy and Pt metal surfaces, two systems recently prepared experimentally. The results show that the supported ZrO2 ultrathin films behave very differently from the corresponding bulk oxide, with a low formation energy of oxygen vacancies, and a clear tendency to split the H2 molecule homolytically with direct reduction of the oxide. The comparison of free-standing and supported ZrO2 films shows that these peculiar properties are not due to the formation of a 2D nanostructure, but rather to the presence of the metal support and of a metal/oxide interface. The results provide evidence for the uncommon properties of supported 2D oxides.

Can dispersion corrections annihilate the dispersion-driven nano-aggregation of non-polar groups? An ab initio molecular dynamics study of ionic liquid systems.

In this study, we aim at understanding the influence of dispersion correction on the ab initio molecular dynamics simulations of ionic liquid (IL) systems. We investigated a large bulk system of the 1-butyl-3-methylimidazolium triflate IL and a small cluster system of ethylamine in ethylammonium nitrate both under periodic boundary conditions. The large system displays several changes upon neglect of dispersion correction, the most striking one is the surprising decrease of the well-known microheterogeneity which is accompanied by an increase of side chain hydrogen atom-anion interplay. For the diffusion coefficient, we observe a correction towards experimental behavior in terms of the cation becoming faster than the anion with dispersion correction. Changes in the electronic structure upon dispersion correction are reflected in larger/smaller dipole moments for anions/cations also seen in the calculated IR spectrum. The energetics of different ion pair dimer subsystems (polar and non-polar) are in accordance with the analysis of the trajectories: A detailed balance in the ionic liquid system determines its particular behavior. While the overall interaction terms for dispersion-corrected calculations are higher, the decrease in microheterogeneity upon inclusion of dispersion interaction becomes obvious due to the relation between all contributions to polar-polar terms. For the small system, we clearly observe the well known behavior that the hybrid functionals show higher reaction barriers than the pure generalized gradient approximation (GGA) functionals. The correction of dispersion reduces the discrepancies in some cases. Accounting for the number of jumps, we observe that dispersion correction reduces the discrepancies from 50% to less than 10%.

Electronic Structure of the (Undoped and Fe-Doped) NiOOH O2 Evolution Electrocatalyst

A DFT study was carried out on the atomic and electronic structure of bulk β-NiOOH, with and without substitution of Ni by Fe, examining different stackings and proton distributions in the constituent sheets. The energies of different NiOOH configurations, evaluated at the DFT + U level including dispersion interactions, have very similar values for different stackings and proton distributions, justifying the observed fact that NiOOH is usually obtained in highly disordered form and supporting the assumption that local structures might depend on the synthesis method. Ni ions seem to prefer centrosymmetric coordinations, even if this implies inhomogeneous numbers of OH groups around them; these inhomogeneities can even induce disproportionation of Ni3+ into Ni2+ and Ni4+. The electronic structure, computed with a hybrid DFT functional able to give accurate band gaps for different materials, always shows semiconducting character, with band gaps having widths varying in the 0.8–1.5 eV range and edges formed ...

Theoretical insights into the relative bonding of normal and abnormal N‐heterocyclic carbenes in [PdCl2(NHCR)2] and [PdCl2(NHCR)(aNHCR)] (R = H, Ph, Mes)

Quantum chemical insights into normal Pd‐C2(NHCR) and abnormal Pd‐C5(aNHCR) bonding, dominated by dispersion interactions in N‐hetereocyclic carbene complexes [PdCl2(NHCR)2] (I, R = H; II, R = Ph; III, R = Mes (2,4,6‐trimethyl)phenyl)) and [PdCl2(NHCR)(aNHCR] (IV, R = H; V, R = Ph; VI, R = Mes) have been investigated at DFT and DFT‐D3(BJ) level of theory with particular emphasis on the effects of the noncovalent interactions on the structures and the nature of Pd‐C2(NHCR) and Pd‐C5(aNHCR) bonds. The optimized geometries are good agreement with the experimental values. The Pd‐C bonds are essentially single bond. Hirshfeld charge distributions indicate that the abnormal aNHCR carbene ligand is relatively better electron donor than the normal NHCR carbene ligand. The C2 atom has larger %s contribution along Pd‐C2 bond than the C5 atom along Pd‐C5 bond. As a consequence the Pd‐C2(NHCR) bonds are relative stronger than the Pd‐C5(aNHCR) bonds. Thus, the results of natural hybrid orbital analysis support the key point of the present study. Calculations predict that for bulky substituent (R = Ph, Mes) at carbene, the Pd‐C2(NHCR) bond is stronger than Pd‐C5(aNHCR) bond due to large dispersion energy in [PdCl2(NHCR)2] than in [PdCl2(NHCR)(aNHCR)]. However, in case of non‐bulky substituent with small and almost equal contribution of dispersion energy, the Pd‐C2(NHCR) bond is relative weaker than Pd‐C5(aNHCR) bond. The bond dissociation energies are dependent on the R substituent, the DFT functional and the inclusion of dispersion interactions. Major point of this study is that the abnormal aNHCs are not always strongly bonded with metal center than the normal NHCs. Effects of dispersion interaction of substituent at nitrogen atoms of carbene ligand are found to play a crucial role on estimation of relative bonding strengths of the normal and abnormal aNHCs with metal center. © 2016 Wiley Periodicals, Inc.

Structural investigations on a linear isolated depsipeptide: the importance of dispersion interactions.

In this paper we present the first investigations on an isolated linear depsipetide CyCO-Gly-Lac-NH-PhOMe (cyclohexylcarbonyl-glycine-lactate-2-anisidine abbreviated as MOC) in a molecular beam experiment. Depsipeptides are a special subclass of peptides which contain at least one ester bond replacing a peptide bond. This leads to a different folding behavior and a different biological activity compared to a "normal" peptide. In order to analyze the folding of an isolated depsipeptide on a molecular level a variety of combined IR/UV methods including IR/IR/UV experiments are applied to MOC. Three different isomers are identified in combination with DFT calculations using the hybrid functional B3LYP-D3 with a TZVP basis set. The most stable structure shows a tweezer-like arrangement between the aromatic chromophore and the aliphatic cyclohexyl ring. A characteristic feature of this structure is that it is stabilized by dispersion interactions resulting from CH/π interactions. If dispersion is not taken into account this structural arrangement is no longer a minimum on the potential energy surface indicating the importance of dispersion interactions.

Effect of graphene support on large Pt nanoparticles.

State-of-the-art catalysts are often created via deposition of monolayers, sub-monolayers or nanoparticles of the catalytic material over supports, aiming to increase the surface area and decrease the loading of the catalytic material and therefore the overall cost. Here, we employ large-scale DFT calculations to simulate platinum clusters with up to 309 atoms interacting with single layer graphene supports with up to 880 carbon atoms. We compute the adsorption, cohesion and formation energies of two and three-dimensional Pt clusters interacting with the support, including dispersion interactions via a semi-empirical dispersion correction and a vdW functional. We find that three-dimensional Pt clusters are more stable than the two-dimensional when interacting with the support, and that the difference between their stabilities increases with the system size. Also, the dispersion interactions are more pronounced as we increase the nanoparticle size, being essential to a reliable description of larger systems. We observe inter-atomic expansion (contraction) on the closest (farthest) Pt facets from the graphene sheet and charge redistribution with overall charge being transferred from the platinum clusters to the support. The Pt-Pt expansion, which is related to the charge transfer in the system, correlates with the adsorption energy per Pt atom in contact with the graphene. These, and other electronic and structural observations show that the effect of the support cannot be neglected. Our study provides for the first time, to the best of our knowledge, quantitative results on the non-trivial combination of size and support effects for nanoparticles sizes which are relevant to catalyst design.

Dispersion and Solvation Effects on the Structure and Dynamics of N719 Adsorbed to Anatase Titania (101) Surfaces in Room-Temperature Ionic Liquids: An ab Initio Molecular Simulation Study

Ab initio, density functional theory (DFT)-based molecular dynamics (MD) has been carried out to investigate the effect of explicit solvation on the dynamical and structural properties of a [bmim][NTf2] room-temperature ionic liquid (RTIL), solvating a N719 sensitizing dye adsorbed onto an anatase titania (101) surface. The effect of explicit dispersion on the properties of this dye-sensitized solar cell (DSC) interface has also been studied. Upon inclusion of dispersion interactions in simulations of the solvated system, the average separation between the cations and anions decreases by 0.6 A; the mean distance between the cations and the surface decreases by about 0.5 A; and the layering of the RTIL is significantly altered in the first layer surrounding the dye, with the cation being on average 1.5 A further from the center of the dye. Inclusion of dispersion effects when a solvent is not explicitly included (to dampen longer-range interactions) can result in unphysical “kinking” of the adsorbed dye’s ...

Time-dependent density functional theory study of the luminescence properties of gold phosphine thiolate complexes.

The origin of the emission of the gold phosphine thiolate complex (TPA)AuSCH(CH3)2 (TPA = 1,3,5-triaza-7-phosphaadamantanetriylphosphine) is investigated using time-dependent density functional theory (TDDFT). This system absorbs light at 3.6 eV, which corresponds mostly to a ligand-to-metal transition with some interligand character. The P-Au-S angle decreases upon relaxation in the S1 and T1 states. Our calculations show that these two states are strongly spin-orbit coupled at the ground state geometry. Ligand effects on the optical properties of this complex are also discussed by looking at the simple AuP(CH3)3SCH3 complex. The excitation energies differ by several tenths of an electronvolt. Excited state optimizations show that the excited singlet and triplet of the (TPA)AuSCH(CH3)2 complex are bent. On the other hand, the Au-S bond breaks in the excited state for the simple complex, and TDDFT is no longer an adequate method. The excited state energy landscape of gold phosphine thiolate systems is very complex, with several state crossings. This study also shows that the formation of the [(TPA)AuSCH(CH3)2]2 dimer is favorable in the ground state. The inclusion of dispersion interactions in the calculations affects the optimized geometries of both ground and excited states. Upon excitation, the formation of a Au-Au bond occurs, which results in an increase in energy of the low energy excited states in comparison to the monomer. The experimentally observed emission of the (TPA)AuSCH(CH3)2 complex at 1.86 eV cannot be unambiguously assigned and may originate from several excited states.

Effect of Palladium Surface Structure on the Hydrodeoxygenation of Propanoic Acid: Identification of Active Sites

The effect of palladium surface structure on the hydrodeoxygenation of propanoic acid has been investigated by studying the mechanism over Pd(111) and Pd(211) model surfaces. We developed a microkinetic model based on parameters obtained from density functional theory and harmonic transition state theory and studied the reaction mechanism at a characteristic experimental reaction temperature of 473 K. The activity of active sites on flat surface models was found to be 3–8 times higher than the activity of stepped surface models, suggesting that the hydrodeoxygenation of propanoic acid over a palladium catalyst is not very sensitive to surface structure. Very good agreement between computations and experiments could be obtained for our Pd(111) model if we include dispersion interactions between the gas species and the metal surface approximately by using the PBE-D3 functional for adsorption/desorption processes. Our model calculations predict that on both stepped and flat surfaces, the dominant deoxygenation mechanism proceeds by a decarbonylation pathway; however, on stepped surface models, decarboxylation and decarbonylation are essentially competitive. A sensitivity analysis of our models suggests that C–OH and C–H bond cleavages control the overall rate over both Pd(111) and (211) catalyst surface models. In addition, on Pd(211) the C–C bond dissociation of propionate to CH3CH2 and CO2, a key step in the decarboxylation mechanism, is also partially rate controlling.

Dynamics of ultrathin gold layers on vitreous silica probed by density functional theory.

The structure and properties of Au ultrathin films on hydroxyl-free and hydroxylated silica glass surfaces are investigated using ab initio molecular dynamics simulations. Substantial surface structure dependence of Au agglomeration behavior (solid-state dewetting) is found. On hydroxyl-free surfaces, the Au film virtually undergoes instantaneous agglomeration accompanied by the formation of voids exposing a bare silica glass surface. In contrast, simulated annealing of the Au film on hydroxylated surface models leaves its structure unchanged within the simulation time. This points to a key role of reactive defect sites in the kinetics of solid-state dewetting processes of metals deposited on the glass surface. Such sites are important for initial void nucleation and formation of metal clusters. In addition, our calculations demonstrate the crucial role of the appropriate inclusion of dispersion interactions in density functional theory simulations of metals deposited on glass surfaces. For defective, hydroxyl-free glass surfaces the dispersion correction accounts for 35% of the total adhesion energy. The effect is even more dramatic for hydroxylated glass surfaces, where adhesion energies are almost entirely due to dispersion interactions. The Au adhesion energies of 200 and 160 kJ (mol nm(2))(-1) calculated for hydroxylated glass surfaces are in good agreement with the experimental data.

The challenge of linear (E)-enones in the Rh-catalyzed, asymmetric 1,4-addition reaction of phenylboronic acid: a DFT computational analysis.

Why are linear (E)-enones such challenging substrates in the Rh-catalyzed asymmetric arylation with boronic acids, which is one of the most important asymmetric catalysis methods? DFT computations show that these substrates adopt a specific conformation in which the largest substituent is antiperiplanar to Rh(I) π-complexed with the C = C bond within the enantioselectivity-determining carborhodation transition state. Additionally, for such structures, there is a strong, but not exclusive, preference for s-cis enone conformation. This folding minimizes steric interactions between the substrate and the ligand, and hence reduces the enantioselectivity. This idea is further confirmed by investigating three computation-only substrate "probes", one of which is capable of double asymmetric induction, and a recent computationally designed 1,5-diene ligand. On average, excellent agreement between predicted and experimental enantioselectivity was attained by a three-pronged approach: 1) thorough conformational search within ligand and substrate subunits to locate the most preferred carborhodation transition state; 2) including dispersion interaction and long-range corrections by SMD/ωB97xD/DGDZVP level of theory; and 3) full substrate and ligand modeling. Based on the results, a theory-enhanced enantioselectivity model that is applicable to both chiral diene and diphosphane ligands is proposed.

Do Ag(n) (up to n = 8) clusters retain their identity on graphite? Insights from first-principles calculations including dispersion interactions.

Adsorption of pre-formed Agn clusters for n = 1 - 8 on a graphite substrate is studied within the density functional theory employing the vdW-DF2 functional to treat dispersion interactions. Top sites above surface layer carbon atoms turn out to be most favorable for a Ag adatom, in agreement with experimental observations. The same feature is observed for clusters of almost all sizes which have the lowest energies when the Ag atoms are positioned over top sites. Most gas phase isomers retain their structures over the substrate, though a couple of them undergo significant distortions. Energetics of the adsorption can be understood in terms of a competition between energy cost of disturbing Ag-Ag bonds in the cluster and energy gain from Ag-C interactions at the surface. Ag3 turns out to be an exceptional candidate in this regard that undergoes significant structural distortion and has only two of the Ag atoms close to surface C atoms in its lowest energy structure.

Enthalpy-Entropy Tuning in the Adsorption of Nucleobases at the Au(111) Surface.

The interaction of DNA molecules with hard substrates is of paramount importance both for the study of DNA itself and for the variety of possible technological applications. Interaction with inorganic surfaces strongly modifies the helical shape of DNA. Hence, an accurate understanding of DNA structure and function at interfaces is a fundamental question with enormous impact in science and society. This work sets the fundamentals for the simulation of entire DNA oligomers on gold surfaces in dry and wet conditions. Thanks to the new GolDNA-AMBER force field, which was derived from first principles and includes dispersion interactions and polarization effects, we simulated self-assembled guanine and adenine monolayers on Au(111) in vacuo and the adsorption of all nucleobases on the same substrate in aqueous conditions. The periodic monolayers obtained from classical simulations match very well those from first principle calculations and experiments, assessing the robustness of the force field and motivating the application to more complex systems for which quantum calculations are not affordable and experiments are elusive. The energetics of nucleobases on Au(111) in solution reveal fundamental physicochemical effects: we find that the adsorption paradigm shifts from purely enthalpic to dominantly entropic by changing the environment and aggregation phase.

A dominant homolytic O–Cl bond cleavage with low-spin triplet-state Fe(iv)O formed is revealed in the mechanism of heme-dependent chlorite dismutase

Chlorite dismutase (Cld) is a heme-dependent enzyme that catalyzes the decomposition of toxic chlorite (ClO2(-)) into innocuous chloride and O2. In this paper, using the hybrid B3LYP density functional theory (DFT) method including dispersion interactions, the Cld reaction mechanism has been studied with a chemical model constructed on the X-ray crystal structure. The calculations indicate that the reaction proceeds along a stepwise pathway in the doublet state, i.e. a homolytic O-Cl bond cleavage of the substrate leading to an O-Fe(heme) species and a ClO˙ radical, followed by a rebinding O-O bond formation between them. The O-Fe(heme) species is demonstrated to be a low-spin triplet-state Fe(IV)=O diradicaloid. A low-spin singlet-state Fe(IV)=O is much less stable than the former, with an energy difference of 9.2 kcal mol(-1). The O-Cl bond cleavage is rate-limiting with a barrier of 10.6 kcal mol(-1), in good agreement with the experimental reaction rate of 2.0 × 10(5) s(-1). Furthermore, a heterolytic O-Cl bond dissociation in the initial step is shown to be unreachable, which ensures the high efficiency of the Cld enzyme by avoiding the generation of chlorate byproduct observed in the reactions of synthetic Fe porphyrins. Also, the pathways in the quartet and sextet states are unfavorable for the Cld reaction. The present results reveal a detailed mechanism III (defined in the text) including an interesting di-radical intermediate composed of a low-spin triplet-state Fe(IV)=O and a ClO˙ radical. Compared to a competitive heterolytic Cl-O cleavage in synthetic Fe porphyrins, the revelation of the domination of homolysis in Cld indicates not only the high efficiency of enzyme, but also the sensitivity of a heme and the significance of the enzymatic active-site surroundings (the His170 and Arg183 residues in the present case), which gives more insights into heme chemistry.