Long-range Dispersion Research Articles

Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding.

Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.

Unique adsorption behaviors of NO and O2 at hydrogenated anatase TiO2(101)

Titanium dioxide (TiO2) is one of the most widely studied transition metal oxides, especially for its unique performances in heterogeneous photocatalysis. Different phases of TiO2 have been found to exhibit different photo-activities, though the origins are still not fully understood. In this work, we use the density functional theory (DFT) calculations, corrected by on-site Coulomb and long-range dispersion interactions, to study the adsorptions of nitric oxide (NO) and oxygen (O2) molecules on the clean and hydrogenated anatase TiO2(101) surfaces. We also compare the detailed calculated results regarding their structural, energetic and electronic properties with those obtained at rutile TiO2(110). It has been found that the behaviors of the surface localized electrons being transferred from adsorbed H, as well as the adsorption behaviors of NO and O2 are quite different at the two surfaces, which can be attributed to their characteristic local bonding structures around the surface hydroxyl. These results may also help explain the different photocatalytic activities of these two main facets of anatase and rutile TiO2

Analysis of the Impact of African Dust Storms on the Presence of Enteric Viruses in the Atmosphere in Tenerife, Spain

ABSTRACT Airborne viruses and their relation to dust storms, as a possible route for dispersion, have not been widely investigated. There are, however, studies that have described the airborne dispersal of pathogenic viruses and their potential impact on public and agronomical health. Atmospheric samples were collected in an urban area of Tenerife during 2009, 2010, 2012 and 2013 and screened for the presence of enteric viruses using PCR and sequencing. The potential relationship of viral data with African dust storms and other climatic variables (viz., the seasonality, origin of the air mass and PM levels) was analyzed. Enteroviruses and Rotaviruses were detected in 15.4% (20/130) and 36.9% (48/130) of the samples, respectively. No significant statistical relationships were observed with African dust storms or the origin of the air masses, although higher percentages of positives were obtained for dust storm days. Enterovirus detection was significantly linked to warmer seasons, and PM2.5 levels showed an inverse correlation with a rotaviral presence. This is the first multi-year report to describe the presence of Enterovirus and Rotavirus genetic sequences in air samples collected in an outdoor urban environment. The data illustrates the need for source region sampling to determine links and the influence of the weather and climatic and regional wind patterns on long-range atmospheric dispersion of viruses in future research efforts.

How Does Nonlocal Dispersal Affect the Selection and Stability of Periodic Traveling Waves?

In ecology a number of spatiotemporal datasets on cyclic populations reveal periodic traveling waves of abundance. This calls for studies of periodic traveling wave solutions of ecologically realistic mathematical models. For many species, such models must include long-range dispersal. However, mathematical theory on periodic traveling waves is almost entirely restricted to reaction-diffusion equations, which assume purely local dispersal. I study integrodifferential equation models in which dispersal is represented via a convolution. The dispersal kernel is assumed to be of either Gaussian or Laplace form; in either case it contains a parameter scaling the width of the kernel. I show that as this parameter tends to zero, the integrodifferential equation asymptotically approaches a reaction-diffusion model. I exploit this limit to determine the effect of a small degree of nonlocality in dispersal on periodic traveling wave properties and on the selection of a periodic traveling wave solution by localized perturbation of an unstable steady state. My analysis concerns equations of “$\lambda$--$\omega$” type, which are the normal form of a large class of oscillatory systems close to a Hopf bifurcation point. I finish the paper by showing how my results can be used to determine the effect of nonlocal dispersal on spatiotemporal dynamics in a predator-prey system.

The RbSr 2Σ+ ground state investigated via spectroscopy of hot and ultracold molecules.

We report on spectroscopic studies of hot and ultracold RbSr molecules, and combine the results in an analysis that allows us to fit a potential energy curve (PEC) for the X(1)2Σ+ ground state bridging the short-to-long-range domains. The ultracold RbSr molecules are created in a μK sample of Rb and Sr atoms and probed by two-colour photoassociation spectroscopy. The data yield the long-range dispersion coefficients C6 and C8, along with the total number of supported bound levels. The hot RbSr molecules are created in a 1000 K gas mixture of Rb and Sr in a heat-pipe oven and probed by thermoluminescence and laser-induced fluorescence spectroscopy. We compare the hot molecule data with spectra we simulated using previously published PECs determined by three different ab initio theoretical methods. We identify several band heads corresponding to radiative decay from the B(2)2Σ+ state to the deepest bound levels of X(1)2Σ+. We determine a mass-scaled high-precision model for X(1)2Σ+ by fitting all data using a single fit procedure. The corresponding PEC is consistent with all data, thus spanning short-to-long internuclear distances and bridging an energy gap of about 75% of the potential well depth, still uncharted by any experiment. We benchmark previous ab initio PECs against our results, and give the PEC fit parameters for both X(1)2Σ+ and B(2)2Σ+ states. As first outcomes of our analysis, we calculate the s-wave scattering properties for all stable isotopic combinations and corroborate the locations of Fano-Feshbach resonances between alkali Rb and closed-shell Sr atoms recently observed [V. Barbéet al., Nat. Phys., 2018, 14, 881]. These results and more generally our strategy should greatly contribute to the generation of ultracold alkali-alkaline-earth dimers, whose applications range from quantum simulation to state-controlled quantum chemistry.

Amphi-Pacific tropical disjunctions in the bryophyte floras of Asia and the New World

Disjunctions between tropical America and tropical Asia, commonly called amphi-Pacific tropical disjunctions, have frequently been discussed among flowering plants but have received very little attention in bryology. A screening of the literature revealed nine species and sixteen genera or infrageneric taxa of bryophytes with amphi-Pacific tropical (or subtropical) ranges. They include Austinia tenuinervis, Diphyscium chiapense, D. longiflorum, Elmerobryum, Fissidens sect. Sarawakia, Ganguleea angulosa, Hydrogonium arcuatum, Hymenostyliella, Hymenostylium aurantiacum, Luisierella barbula, Mniomalia, Rozea, Sphaerotheciella and Sorapilla among the mosses and Ceratolejeunea grandiloba, Drepanolejeunea subg. Rhaphidolejeunea, Lejeunea sect. Echinocolea, Lobatiriccardia, Myriocoleopsis sect. Myriocoleopsis, Phycolepidozia, Pictolejeunea, Rectolejeunea, Southbya organensis and Vitalianthus among liverworts. All of them occur in tropical or subtropical Asia and the Neotropics but are not known from Africa. The causes of the amphi-Pacific tropical disjunctions in bryophytes are still unclear. In flowering plants, molecular analyses indicate that amphi-Pacific tropical ranges frequently resulted from past migration across Eurasia and the northern Atlantic Ocean, followed by local extinction. This scenario may also have operated in amphi-Pacific bryophytes but some might have reached South America via the southern Pacific migration route. The possibility of direct long-range dispersal across the Pacific Ocean cannot be ruled out and this scenario seems likely for Southbya organensis, which occurs on Hawaii and freely produces spores and small gemmae. The possibility that the disjunctive ranges reflect insufficient collecting and that some taxa also occur in Africa should also be taken into account. There is no strong evidence for human introduction of amphi-Pacific tropical bryophytes. The new combinations Lejeunea sect. Echinocolea (R.M.Schust.) Gradst. comb. nov. and Myriocoleopsis sect. Protocolea (R.M.Schust.) Gradst. comb. nov. are proposed.

CO2 interaction with violarite (FeNi2S4) surfaces: a dispersion-corrected DFT study.

The unbridled emissions of gases derived from the use of fossil fuels have led to an excessive concentration of carbon dioxide (CO2) in the atmosphere with concomitant problems to the environment. It is therefore imperative that new cost-effective catalysts are developed to mitigate the resulting harmful effects through the activation and conversion of CO2 molecules. In this paper, we have used calculations based on the density functional theory (DFT), including two semi-empirical approaches for the long-range dispersion interactions (-D2 and -D3), to explore the interaction of CO2 with the surfaces of spinel-structured violarite (FeNi2S4). This ternary sulfide contains iron ions in the highest possible oxidation state, while the nickel atoms are in the mixed 2+/3+ valence state. We found that CO2 interaction with violarite is only moderate due to the repulsion between the oxygen lone pairs and the electronic clouds of the sulfur surface atoms. This suggests that the CO2 activation is not dictated by the presence of nickel, as compared to the pure iron-isomorph greigite (Fe3S4). These results differ from findings in (Ni,Fe) ferredoxin enzymes, where the Ni/Fe ratio influences the redox potential, which suggests that the periodic crystal structure of violarite may hinder its redox capability.

Trends in Adhesion Energies of Gold on MgO(100), Rutile TiO2(110), and CeO2(111) Surfaces: A Comparative DFT Study

The adhesion of gold on three oxide surfaces (magnesia, titania, and ceria) is studied by means of dispersion-corrected DFT+U calculations, considering in a systematic approach an isolated Au atom, Au20 clusters, and periodic extended interfaces to model large nanoparticles. The results show that for a Au1 monomer the adhesion energy on the three oxides is similar: 0.83 eV (TiO2), 0.99 eV (CeO2), and 1.09 eV (MgO). The picture is more complex for nanoclusters and extended interfaces, where morphological factors largely determine the binding capability of these oxides toward Au. For Au20, the adhesion on rutile TiO2 is smaller and dominated by long-range dispersion contributions, while the better match between Au atoms and surface oxygen anions leads to a larger binding on magnesia and ceria. Overall, a CeO2 > MgO > TiO2 trend is observed. For the extended interfaces, the trend is CeO2 ≈ MgO > TiO2. Notice that the adhesion energies of a 20-atom cluster are 2–3 times larger than those of the extended inter...

Atomic adsorption on pristine graphene along the Periodic Table of Elements – From PBE to non-local functionals

The understanding of atomic adsorption on graphene is of high importance for many advanced technologies. Here we present a complete database of the atomic adsorption energies for the elements of the Periodic Table up to the atomic number 86 (excluding lanthanides) on pristine graphene. The energies have been calculated using the projector augmented wave (PAW) method with PBE, long-range dispersion interaction corrected PBE (PBE+D2, PBE+D3) as well as non-local vdW-DF2 approach. The inclusion of dispersion interactions leads to an exothermic adsorption for all the investigated elements. Dispersion interactions are found to be of particular importance for the adsorption of low atomic weight earth alkaline metals, coinage and s-metals (11th and 12th groups), high atomic weight p-elements and noble gases. We discuss the observed adsorption trends along the groups and rows of the Periodic Table as well some computational aspects of modelling atomic adsorption on graphene.

Short-range second order screened exchange correction to RPA correlation energies.

Direct random phase approximation (RPA) correlation energies have become increasingly popular as a post-Kohn-Sham correction, due to significant improvements over DFT calculations for properties such as long-range dispersion effects, which are problematic in conventional density functional theory. On the other hand, RPA still has various weaknesses, such as unsatisfactory results for non-isogyric processes. This can in parts be attributed to the self-correlation present in RPA correlation energies, leading to significant self-interaction errors. Therefore a variety of schemes have been devised to include exchange in the calculation of RPA correlation energies in order to correct this shortcoming. One of the most popular RPA plus exchange schemes is the second order screened exchange (SOSEX) correction. RPA + SOSEX delivers more accurate absolute correlation energies and also improves upon RPA for non-isogyric processes. On the other hand, RPA + SOSEX barrier heights are worse than those obtained from plain RPA calculations. To combine the benefits of RPA correlation energies and the SOSEX correction, we introduce a short-range RPA + SOSEX correction. Proof of concept calculations and benchmarks showing the advantages of our method are presented.

Long-range dipolar order and dispersion forces in polar liquids.

Complex solvation phenomena, such as specific ion effects, occur in polar liquids. Interpretation of these effects in terms of structure and dispersion forces will lead to a greater understanding of solvation. Herein, using molecular dynamics, we probe the structure of polar liquids through specific dipolar pair correlation functions that contribute to the potential of mean force that is "felt" between thermally rotating dipole moments. It is shown that unique dipolar order exists at separations at least up to 20 Å for all liquids studied. When the structural order is compared with a dipolar dispersion force that arises from local co-operative enhancement of dipole moments, a strong agreement is found. Lifshitz theory of dispersion forces was compared with the structural order, where the theory is validated for all liquids that do not have significant local dipole correlations. For liquids that do have significant local dipole correlations, specifically liquid water, Lifshitz theory underestimates the dispersion force by a factor of 5-10, demonstrating that the force that leads to the increased structure in liquid water is missed by Lifshitz theory of van der Waals forces. We apply similar correlation functions to an ionic aqueous system, where long-range order between water's dipole moment and a single chloride ion is found to exist at 20 Å of separation, revealing a long-range perturbation of water's structure by an ion. Furthermore, we found that waters within the 1st, 2nd, and 3rd solvation shells of a chloride ion exhibit significantly enhanced dipolar interactions, particularly with waters at larger distances of separation. Our results provide a link between structures, dispersion forces, and specific ion effects, which may lead to a more robust understanding of solvation.

Casimir-Polder Size Consistency: A Constraint Violated by Some Dispersion Theories.

A key goal in quantum chemistry methods, whether ab initio or otherwise, is to achieve size consistency. In this work we formulate the related idea of "Casimir-Polder size consistency" that manifests in long-range dispersion energetics. We show that local approximations in time-dependent density functional theory dispersion energy calculations violate the consistency condition because of incorrect treatment of highly nonlocal "xc kernel" physics, by up to 10% in our tests on closed-shell atoms.

The nature of the noncovalent interactions between fullerene C60 and aromatic hydrocarbons

To better understand the solubility of fullerenes in common aromatic organic solvents such as benzene, toluene, tetralin, 1,2,4-trimethylbenzene and 1-methylnaphthalene, the structures, energies and electronic properties of the complexes formed by fullerene C60 with benzene, toluene, tetralin, 1,2,4-trimethylbenzene and 1-methylnaphthalene, respectively, have been investigated by the density functional theory with long-range dispersion correction. It was found that the solubility of C60 in these solvents is generally proportional to the intermolecular force between solute molecule and solvent molecule. In order to further understand the nature of the noncovalent interactions between C60 and these aromatic hydrocarbons, interaction energy decomposition analyses were performed with the symmetry adapted perturbation theory. The results clearly show that the noncovalent interactions between C60 and the aromatic hydrocarbons are mainly dependent on both electrostatic and dispersion components, with dispersion playing the dominant role. The other important finding is that the nature of the noncovalent interactions between C60 and alkylbenzene or alkylnaphthalene is almost the same as the nature of the noncovalent interactions between C60 and benzene.

Comparative phylogeography of a vulnerable bat and its ectoparasite reveals dispersal of a non-mobile parasite among distinct evolutionarily significant units of the host

Knowledge about phylogeographical structuring and genetic diversity is of key importance for the conservation of endangered species. Comparative phylogeography of a host and its parasite has the potential to reveal cryptic dispersal and behaviour in both species, and can thus be used to guide conservation management. In this study, we investigate the phylogeographic structure of the Bechstein’s bat, Myotis bechsteinii, and its ectoparasitic bat fly, Basilia nana, at 12 sites across their entire distribution. For both species, a mitochondrial sequence fragment (ND1 and COI respectively) and nuclear microsatellite genotypes (14 and 10 loci respectively) were generated and used to compare the phylogeography of host and parasite. Our findings confirm the presence of three distinct genetic subpopulations of the Bechstein’s bat in (1) Europe, (2) the Caucasus and (3) Iran, which remain isolated from one another. The genetic distinctiveness of host populations in the Caucasus region and Iran emphasize that these populations must be managed as distinct evolutionarily significant units. This phylogeographical pattern is however not reflected in its parasite, B. nana, which shows evidence for more recent dispersal between host subpopulations. The discordant genetic pattern between host and parasite suggest that despite the long-term genetic isolation of the different host subpopulations, long-range dispersal of the parasite has occurred more recently, either as the result of secondary contact in the primary host or via secondary host species. This indicates that a novel pathogenic threat to one host subpopulation may be able to disperse, and thus have important consequences for all subpopulations.

Phylogeography and connectivity of molluscan parasites: Perkinsus spp. in Panama and beyond

Panama is a major hub for commercial shipping between two oceans, making it an ideal location to examine parasite biogeography, potential invasions, and the spread of infectious agents. Our goals were to (i) characterise the diversity and genetic connectivity of Perkinsus spp. haplotypes across the Panamanian Isthmus and (ii) combine these data with sequences from around the world to evaluate the current phylogeography and genetic connectivity of these widespread molluscan parasites. We collected 752 bivalves from 12 locations along the coast of Panama including locations around the Bocas del Toro archipelago and the Caribbean and Pacific entrances to the Panama Canal, from December 2012 to February 2013. We used molecular genetic methods to screen for Perkinsus spp. and obtained internal transcribed spacer region (ITS) ribosomal DNA (rDNA) sequences for all positive samples. Our sequence data were used to evaluate regional haplotype diversity and distribution across both coasts of Panama, and were then combined with publicly available sequences to create global haplotype networks. We found 26 ITS haplotypes from four Perkinsus spp. (1–12 haplotypes per species) in Panama. Perkinsus beihaiensis haplotypes had the highest genetic diversity, were the most regionally widespread, and were associated with the greatest number of hosts. On a global scale, network analyses demonstrated that some haplotypes found in Panama were cosmopolitan (Perkinsus chesapeaki, Perkinsus marinus), while others were more geographically restricted (Perkinsus olseni, P. beihaiensis), indicating different levels of genetic connectivity and dispersal. We found some Perkinsus haplotypes were shared across the Isthmus of Panama and several regions around the world, including across ocean basins. We also found that haplotype diversity is currently underestimated and directly related to the number of sequences. Nevertheless, our results demonstrate long-range dispersal and global connectivity for many haplotypes, suggesting that dispersal through shipping probably contributes to these biogeographical patterns.

Benchmark CCSD-SAPT study of rare gas dimers with comparison to MP-SAPT and DFT-SAPT.

Symmetry-adapted perturbation theory (SAPT) based on coupled cluster approach with single and double excitations (CCSD) treatment of intramonomer electron correlation effects was applied to study rare gas homodimers from He2 to Kr2. The obtained benchmark CCSD-SAPT energies, including cumulant contributions to first order exchange and second-order exchange-induction terms, were then compared to their counterparts found using other methods-Møller-Plesset-SAPT based on many-body Møller-Plesset perturbation theory and DFT-SAPT based on density functional theory. The SAPT terms up to the second-order were calculated with the basis sets close to the complete basis set at the large range of interatomic distances R. It was shown that overestimation of the binding energies De found with DFT-SAPT reported in the work of Shirkov and Makarewicz [J. Chem. Phys. 142, 064102 (2015)] for Ar2 and Kr2 is mostly due to underestimation of the exchange energy Eexch(1) when comparing to the CCSD-SAPT benchmark. The CCSD-SAPT potentials were found to give the following values of the dissociation energies D0: 0.0006 cm-1 for He2, 16.71 cm-1 for Ne2, 85.03 cm-1 for Ar2, and 129.81 cm-1 for Kr2, which agree well with the values found from previously reported highly accurate ab initio supermolecular potentials and experimental data. The long-range dispersion coefficients C2n up to n = 6 that give the dispersion energy asymptotically equivalent to its SAPT counterpart were calculated from dynamic multipole polarizabilities at different levels of theory.

Molecular dynamics simulation of ZnO wurtzite phase under high and low pressures and temperatures

Isothermal and isobaric ensembles behaviours of ZnO wurtzite phase have been investigated, by parallel molecular dynamics method and using Buckingham potential, which contains long-range Coulomb, repulsive exponential, and attractive dispersion terms. To conduct our calculations, we have used dl_poly 4 software, under which the method is implemented. We have examined the influence of the temperature and pressure on molar volume in the ranges of 300–3000 K and 0–200 GPa. Isothermal-isobaric relationships, fluctuations, standard error, equilibrium time, molar volume and its variation versus time are predicted and analyzed. Our results are close to available experimental data and theoretical results.

The 2016 Al-Mishraq sulphur plant fire: Source and health risk area estimation

On October 20, 2016, Daesh (Islamic State) set fire to the sulphur production site Al-Mishraq as the battle of Mosul in northern Iraq became more intense. An extensive plume of toxic sulphur dioxide and hydrogen sulphide caused comprehensive casualties. The intensity of the SO2 release was reaching levels of minor volcanic eruptions and the plume was observed by several satellites. By investigation of the measurement data from instruments on the MetOp-A, MetOp-B, Aura and Soumi satellites we have estimated the time-dependent source term to 161 kilotonnes sulphur dioxide released into the atmosphere during seven days. A long-range dispersion model was utilized to simulate the atmospheric transport over the Middle East. The ground level concentrations predicted by the simulation were compared with observation from the Turkey National Air Quality Monitoring Network. Finally, the simulation data provided, using a probit analysis of the simulated data, an estimate of the health risk area that was compared to reported urgent medical treatments.

Density functional theory (DFT) study of O3 molecules adsorbed on nitrogen-doped TiO2/MoS2 nanocomposites: applications to gas sensor devices

Density functional theory calculations were carried out to investigate the adsorption behaviors of O3 molecules on the undoped and N-doped TiO2/MoS2 nanocomposites. With the inclusion of vdW interactions, which correctly account the long-range dispersion energy, the adsorption energies and final geometries of O3 molecules on the nanocomposite surfaces were improved. For O3 molecules on the considered nanocomposites, the binding sites were located on the fivefold coordinated titanium atoms of the TiO2 anatase. The structural properties of the adsorption systems were examined in view of the bond lengths and bond angles. The variation of electronic structures was also discussed in view of the density of states, molecular orbitals and distribution of spin densities. The results suggest that the adsorption of the O3 molecule on the N-doped TiO2/MoS2 nanocomposite is more favorable in energy than that on the pristine one, indicating that the N-doped nanocomposite has higher sensing capability than the pristine one. This implies that the N-doped TiO2/MoS2 nanocomposite would be an ideal O3 gas sensor. However, our calculations thus provide a theoretical basis for the potential applications of TiO2/MoS2 nanocomposites as efficient O3 sensors, leading to very interesting results in the context of air quality measurement.

Assessment of the announced North Korean nuclear test using long-range atmospheric transport and dispersion modelling

On 6 January 2016, the Democratic People’s Republic of Korea announced to have conducted its fourth nuclear test. Analysis of the corresponding seismic waves from the Punggye-ri nuclear test site showed indeed that an underground man-made explosion took place, although the nuclear origin of the explosion needs confirmation. Seven weeks after the announced nuclear test, radioactive xenon was observed in Japan by a noble gas measurement station of the International Monitoring System. In this paper, atmospheric transport modelling is used to show that the measured radioactive xenon is compatible with a delayed release from the Punggye-ri nuclear test site. An uncertainty quantification on the modelling results is given by using the ensemble method. The latter is important for policy makers and helps advance data fusion, where different nuclear Test-Ban-Treaty monitoring techniques are combined.