Comparing the performance of density functionals in describing the adsorption of atoms and small molecules on Ni(111)

Molecular Simulations of Nanoscale Transformations in Ionic Semiconductor Nanocrystals

Density functional theory (DFT) calculations have played a pivotal role in identifying and understanding different coordination modes of carbon monoxide adsorbed in zeolites: Previous studies combining IR spectroscopic measurements and DFT have firmly established that an adsorbed CO molecule can interact either with a single cation (single-site interaction), or with two or more cations simultaneously (dual-site or multiple-site interaction). However, one aspect that has been scarcely addressed so far is the dependence of the DFT equilibrium structures on the choice of the functional. With the ongoing development of DFT, exemplified by the more widespread use of dispersion-corrected DFT, this question becomes increasingly relevant. The present study investigates whether the inclusion of an empirical dispersion correction leads to qualitatively different predictions in comparison with dispersion-uncorrected DFT, taking CO adsorbed in sodium-exchanged chabazite having two different Si/Al ratios (Si/Al = 11:1 and Si/Al = 2:1) as a model system. Equilibrium structures obtained with the PBE functional and with the dispersion-corrected PBE-D functional are compared, revealing a tendency of dispersion-corrected DFT to favour a stronger interaction of CO with dual sites. This is indicated by a short contact between the oxygen atom of the CO molecule (already coordinated through its carbon atom to a primary Na+ cation) and a secondary Na+ cation. In addition to these qualitative findings, the quantitative agreement of calculated adsorption enthalpies and C–O stretching frequencies with experimental values obtained from variable-temperature IR spectroscopy is evaluated. While neither functional is particularly successful in predicting accurate adsorption enthalpies, the range of C–O stretching frequency values delivered by the PBE-D functional shows a better agreement with the experimental measurements.

Density functional theory (DFT) calculations were carried out to understand the structural stability of 2D nanosheets of gold and silver in hexagonal phase of 2H by the adsorption of small molecules. In this work, we have obtained the bonding and adsorption properties of such small molecules as H2O, H2O2, and C2H5OH on 2H phase of gold and silver nanosurfaces, through DFT method using Quantum Expresso (QE) code. The high absorption energy values of (-2.45 eV, -2,46 eV, -2, 41 eV) for H2O, H2O2, and C2H5OH molecules on 2H-Au surfaces, respectively obtained than that of 2H-silver surfaces that the interaction between small molecules and both 2H nanosurfaces corresponds to physisorption. However, during the adsorption, the gold surface in the 2H phase (2H-Au) seems to preserve its atomic structure, while 2H-Ag surface changes from 2H to the fcc structure. Based on the analysis of electronic and physicochemical properties, the composite systems of 2H-gold/2H-silver-small molecules exhibit semiconductor behaviour. While 2H-Ag surfaces have short recovery time values for hydrogen peroxide (H2O2), this time is quite long for 2H-Au surfaces. Because of the long recovery time, Au-2H reported surfaces can be a candidate for possible applications of viral capture. Thus, the reported results are significant, and they would stimulate the experimental and further studies.

Clusters and nanoparticles of gold have received considerable attention during the past decade. The exceptional catalytic properties of small gold aggregates have motivated research aimed at providing insights into the molecular origins of this unexpected reactivity. The experimental observations have stimulated many theoretical studies of the electronic, structural, and chemical properties of gold clusters. Since it is not practical to calculate gold clusters using high-level ab initio correlation methods, density functional theory (DFT)-based approaches have usually been employed in such calculations, but it is not clear which functionals provide the best performance. Herein we report the results of calculations on the structure and stability of Au2 and Au8, as a model study, using various density functionals. To the best of our knowledge, there has been no previous systematic study for DFT performance on the structure and stability of gold clusters. Although the performance of density functionals is widely known for light element systems, certain functionals successful in light element chemistry may not work effectively in heavy element chemistry. This is due to the strikingly different bonding nature of heavy element systems from their light element analogues. Thus, the results of this work may be useful for future work in choosing the most appropriate density functional for gold clusters when performing DFT calculations. Kohn-Sham DFT calculations were performed with 16 different exchange correlation functionals, namely, the local density approximation (LDA:SVWN), the generalized gradient approximation (GGA:BLYP, BP86, BPW91, PW91, PBE, HCTH, tHCTH, LC-BPW91, LC-PW91 and LCPBE), and the hybrid GGA functionals (B3LYP, B3PW91, mPW1PW91, PBE0 and X3LYP). We used the relativistic effective core potentials derived by Stevens et al. and valence basis sets employed in previous works. All the calculations were carried out using the program package GAUSSIAN 09. Au2 Cluster. We compare the calculated spectroscopic constants, bond length (Re), vibrational frequency (ωe), and dissociation energy (De) with the experimental data 20 in Table 1. Overall, the LDA and several GGA functionals provide good performance for bond length (and vibrational frequency) and dissociation energy, respectively. The use of hybrid GGA functionals, i.e., the inclusion of Hartree-Fock exchange, does not improve the pure GGA results. These observations are in contrast to the known performance of functionals in light element chemistry: in general, LDA < GGA < hybrid GGA. It was reported, for instance, that the performance of the pure BP86 functional is very poor for light element systems, but its performance is observed to be one of the most effective for Au2. It is evident from our calculations that any one functional could not provide reliable spectroscopic constants of Au2. The poor performance of hybrid GGA functionals may be partly ascribed to the functional parameterization optimal to light-element systems only. Intriguingly, the long range correction to the GGA functionals (LC-GGA) improves the performance for bond lengths. Au8 Cluster. There are no experimental data for the structures and energies of Au8. Han 10 reported the relative

A new theoretical model for inelastic tunneling in realistic systems : comparing STM simulations with experiments

Surfaces of simple fcc metals such as Cu with nonzero and unequal Miller indices are intrinsically chiral. Density functional theory (DFT) calculations are a useful way to study the enantiospecific adsorption of small chiral molecules on these chiral metal surfaces. We report DFT calculations of seven chiral molecules on several structurally distinct chiral Cu surfaces. These surfaces include two surfaces with (111)-oriented terraces and one with (100)-oriented terraces. Calculations are also described on a surface that was modified to mimic the surface structures that typically appear on real metal surfaces following thermally driven fluctuations in step edges. Our results provide initial information on how variation in the surface structure of intrinsically chiral metal surfaces can affect the enantiospecific adsorption of small molecules on these surfaces.

The letter presents the adsorption properties of CO, NH3, CH4, SO2, and H2S molecules over niobium doped graphene sheet (Nb/G). Using density functional theory, the optimum configuration and orientation of adsorbent molecules over the Nb/G surface are geometrically optimized, and adsorption energy, adsorption distance, Hirshfeld charge transfer, electron localization function, and the work function of Nb/G-molecule systems are calculated. CO and SO2 molecules over Nb/G show chemisorption, hence they have high reactivity towards Nb/G. Adsorption of NH3, CH4, and H2S on Nb/G shows physisorption as they are weakly adsorbed. The adsorption of these molecules indicates the suitability of Nb/G as a sensor. To understand the superiority of Nb/G over pristine graphene, comparison of adsorption properties was made between the two systems. The work function of Nb/G with adsorbed molecule suggests that the Fermi level of Nb/G surface may be controlled by the selection of appropriate adsorbent molecules. Therefore, Nb/G could be a good candidate for gas sensing application.

ConspectusDensity functional theory (DFT) calculations are used in over 40,000 scientific papers each year, in chemistry, materials science, and far beyond. DFT is extremely useful because it is computationally much less expensive than ab initio electronic structure methods and allows systems of considerably larger size to be treated. However, the accuracy of any Kohn-Sham DFT calculation is limited by the approximation chosen for the exchange-correlation (XC) energy. For more than half a century, humans have developed the art of such approximations, using general principles, empirical data, or a combination of both, typically yielding useful results, but with errors well above the chemical accuracy limit (1 kcal/mol). Over the last 15 years, machine learning (ML) has made major breakthroughs in many applications and is now being applied to electronic structure calculations. This recent rise of ML begs the question: Can ML propose or improve density functional approximations? Success could greatly enhance the accuracy and usefulness of DFT calculations without increasing the cost.In this work, we detail efforts in this direction, beginning with an elementary proof of principle from 2012, namely, finding the kinetic energy of several Fermions in a box using kernel ridge regression. This is an example of orbital-free DFT, for which a successful general-purpose scheme could make even DFT calculations run much faster. We trace the development of that work to state-of-the-art molecular dynamics simulations of resorcinol with chemical accuracy. By training on ab initio examples, one bypasses the need to find the XC functional explicitly. We also discuss how the exchange-correlation energy itself can be modeled with such methods, especially for strongly correlated materials. Finally, we show how deep neural networks with differentiable programming can be used to construct accurate density functionals from very few data points by using the Kohn-Sham equations themselves as a regularizer. All these cases show that ML can create approximations of greater accuracy than humans, and is capable of finding approximations that can deal with difficult cases such as strong correlation. However, such ML-designed functionals have not been implemented in standard codes because of one last great challenge: generalization. We discuss how effortlessly human-designed functionals can be applied to a wide range of situations, and how difficult that is for ML.

We present a combined experimental and theoretical quantification of the adsorption enthalpies of seven organic molecules (acetone, acetonitrile, dichloromethane, ethanol, ethyl acetate, hexane, and toluene) on graphene. Adsorption enthalpies were measured by inverse gas chromatography and ranged from -5.9 kcal/mol for dichloromethane to -13.5 kcal/mol for toluene. The strength of interaction between graphene and the organic molecules was estimated by density functional theory (PBE, B97D, M06-2X, and optB88-vdW), wave function theory (MP2, SCS(MI)-MP2, MP2.5, MP2.X, and CCSD(T)), and empirical calculations (OPLS-AA) using two graphene models: coronene and infinite graphene. Symmetry-adapted perturbation theory calculations indicated that the interactions were governed by London dispersive forces (amounting to ∼60% of attractive interactions), even for the polar molecules. The results also showed that the adsorption enthalpies were largely controlled by the interaction energy. Adsorption enthalpies obtained from ab initio molecular dynamics employing non-local optB88-vdW functional were in excellent agreement with the experimental data, indicating that the functional can cover physical phenomena behind adsorption of organic molecules on graphene sufficiently well.

We use a periodic density functional theory (DFT) code to study the adsorption of CH3 and H, as well as their co-adsorption on a Ni(111) surface with and without Ni ad-atom, at a surface coverage of 0.25 monolayer (ML). We systematically investigate the site preference for CH3 and H. Then we combine CH3 and H in many co-adsorbed configurations on both surfaces. Methyl and hydrogen adsorption on a flat Ni(111) surface favours the hollow site over the top site. The presence of a Ni ad-atom stabilizes the adsorption of CH3 better than a flat surface, while hydrogen is more stable on a flat Ni(111) surface. When H and CH3 are co-adsorbed at nearest Ni neighbours on the (111) surface, their interaction is always repulsive. However, the dissociative adsorption of CH4 is stabilised when the fragments are infinitely separated. For the co-adsorbed fragments CH3 and H, in the presence of an ad-atom, the repulsive interaction is lowered, so that the dissociative form of CH4 is locally stable.

Effect of oxygen-containing groups in functionalized graphene on its gas sensing properties

The crucial role of dispersion force in correctly describing the adsorption of some typical small-size gas molecules (e.g., CO2, N2, and CH4) in ion-exchanged chabazites has been investigated at different levels of theory, including the standard density functional theory calculation using the Perdew, Burke, and Ernzerhof (PBE) exchange-correlation functional and van der Waals density functional theory (vdWDFT) calculations using different exchange-correlation models - vdW_DF2, optB86b, optB88, and optPBE. Our results show that the usage of different vdWDFT functionals does not significantly change the adsorption configuration or the profile of static charge rearrangement of the gas-chabazite complexes, in comparison with the results obtained using the PBE. The calculated values of adsorption enthalpy using different functionals are compared with our experimental results. We conclude that the incorporation of dispersion interaction is imperative to correctly predict the trend of adsorption enthalpy values, in terms of different gas molecules and Cs(+) cation densities in the adsorbents, even though the absolute values of adsorption enthalpy are overestimated by approximate 10 kJ/mol compared with experiments.

Adsorption of C2H2 and C2H4 on Pt-decorated graphene nanostructure: Ab-initio study

In the context of the recovery of agricultural waste, many researches have focused on the preparation of adsorbents from natural waste from fruit trees, egg shells, palm waste or sawdust. This work aims to optimize the preparation of a biosorbent from rubber hulls by studying its ability to adsorb small and medium molecules. The influence of parameters such as drying temperature (X1), particle size (X2), stirring time (X3) and sodium hypochloride mass (X4) was studied. The results indicate that the model used for biosorbent optimization on methylene blue and iodine index is significant. In addition, this model has greater adsorption capabilities on small molecules than with large molecules. Statistical analysis of the data shows that temperature is the most influential factor in the adsorption of small molecules. On the other hand, particle size has a significant influence on the adsorption of large molecules. The optimum biosorbent preparation values are 1.0 for drying temperature (X1), −1.0 for biosorbent grain size (X2), 1.0 for stirring time (X3) and 1.0 for sodium hypochloride mass (X4).

Optical Trapping of a Single Molecule of Length Sub-1 nm in Solution