Gradient-corrected Density Functional Theory Research Articles

A computational study of a light-driven artificial device: a third generation rotational photo-molecular motor in dilute solutions.

A third-generation artificial photo-molecular motor, featuring two photo-switchable rotating moieties in connection with a pseudoasymmetric molecular centre, is investigated by combining quantum-mechanics (QM) algorithms with classical molecular dynamics (MD) propagators. In particular, in the present contribution we have addressed such a molecular motor in different rotational isomers following the experimental observations arising from the application of multiple spectroscopic techniques in dilute solutions. At first, we focused our attention on the reproduction of the UV/Vis absorption spectrum in two solvents (acetonitrile and cyclohexane) with different gradient-corrected density functional theory (B3LYP, Cam-B3LYP, PBE, PBE0) functionals in conjunction with the conductor-like and polarizable continuum model (C-PCM). Furthermore, we refined the absorption signals by combining a classical MD sampling at room-temperature with DFT-based electronic degrees of freedom to compute perturbed excitation wavelengths driven by thermal fluctuation and solvation effects. In this respect, we have modelled the investigated artificial motor within solution nanodroplets with solvent molecules treated contextually at atomistic level and via a dielectric and polarizable continuum model.

Understanding the role of oxygen-vacancy defects in Cu2O(111) from first-principle calculations

The presence of defects, such as copper and oxygen vacancies, in cuprous oxide films determines their characteristic carrier conductivity and consequently their application as semiconducting systems. There are still open questions on the induced electronic re-distribution, including the formation of polarons. Indeed, to accurately reproduce the structural and electronic properties at the cuprous oxide surface, very large slab models and theoretical approaches that go beyond the standard generalized gradient corrected density functional theory are needed. In this work we investigate oxygen vacancies formed in proximity of a reconstructed Cu2O(111) surface, where the outermost unsaturated copper atoms are removed, thus forming non-stoichiometric surface layers with copper vacancies. We address simultaneously surface and bulk properties by modelling a thick and symmetric slab, to find that hybrid exchange-correlation functionals are needed to describe the oxygen vacancy in this system. Our simulations show that the formation of oxygen vacancies is favoured in the sub-surface layer. Moreover, the oxygen vacancy leads to a splitting and left-shift of the shallow hole states in the gap, which are associated with the deficiency of copper at the surface. These findings suggest that surface electronic structure and reactivity are sensitive to the presence of oxygen vacancies, also when the latter are formed deeper within the film.

Converting CO2 to formic acid by tuning quantum states in metal chalcogenide clusters

The catalytic conversion of CO2 into valuable chemicals is an effective strategy for reducing its adverse impact on the environment. In this work, the formation of formic acid via CO2 hydrogenation on bare and ligated Ti6Se8 clusters is investigated with gradient-corrected density functional theory. It is shown that attaching suitable ligands (i.e., PMe3, CO) to a metal-chalcogenide cluster transforms it into an effective donor/acceptor enabling it to serve as an efficient catalyst. Furthermore, by controlling the ratio of the attached donor/acceptor ligands, it is possible to predictably alter the barrier heights of the CO2 hydrogenation reaction and, thereby, the rate of CO2 conversion. Our calculation further reveals that by using this strategy, the barrier heights of CO2 hydrogenation can be reduced to ~0.12 eV or possibly even lower, providing unique opportunities to control the reaction rates by using different combinations of donor/acceptor ligands.

Developing Efficient Suzuki Cross-Coupling Catalysts by Doping Palladium Clusters with Silver

It is shown that doping of a Pd cluster by Ag atoms can provide an efficient catalyst for the Suzuki–Miyaura cross-coupling reactions. We demonstrate this intriguing possibility by considering a model reaction involving bromobenzene and phenylboronic acid as reagents where the reaction involves oxidation, transmetallation, and reduction steps. We have examined the reaction barriers of all three steps for a conventional ligated Pd catalyst, a nearly icosahedral Pd13 cluster, and a monosilver-doped Pd12Ag cluster using gradient-corrected density functional theory. It is observed that the reaction carried out on the Pd sites adjacent to an Ag atom in a Pd12Ag cluster shows substantially lower barriers for the oxidation and reduction steps compared to the conventional ligated Pd catalyst and the pure Pd13 cluster. A detailed analysis indicates that the Ag site donates charge to the neighboring Pd site. While such a donation may have been expected to reduce the barrier for the oxidative step, the lowering of the barrier for the reduction step indicates that the respective sites not only act as a donor but can also serve as an acceptor for the reduction step. Furthermore, because of the differential donor–acceptor characteristic of the Ag and Pd atoms, it is observed that the barrier heights of the redox steps are primarily dependent on the chosen active site. The calculated results show that by altering the atom (Ag or Pd) at the active site of the reaction, the activation energies of the redox steps can either be reduced or increased. This shows that the active sites of a bimetallic cluster-like Pd12Ag can be utilized to control the barrier heights of suitable chemical reactions. The relative trend of the barrier heights for both clusters is also observed to be predictable by the conceptual density functional theory. Previous studies in our group have indicated that the reaction barriers for Pdn clusters can be lowered by supporting them on reduced graphene. We, therefore, propose that silver-doped Pdn clusters may provide an even better catalyst.

Vibrational response and motion of carbon monoxide on Cu(100) driven by femtosecond laser pulses: Molecular dynamics with electronic friction

Carbon monoxide on copper surfaces continues to be a fascinating, rich microlab for many questions evolving in surface science. Recently, hot-electron mediated, femtosecond-laser pulse induced dynamics of CO molecules on Cu(100) were the focus of experiments [Inoue et al., Phys. Rev. Lett. 117, 186101 (2016)] and theory [Novko et al., Phys. Rev. Lett. 122, 016806 (2019)], unraveling details of the vibrational nonequilibrium dynamics on ultrashort (subpicoseconds) timescales. In the present work, full-dimensional time-resolved hot-electron driven dynamics are studied by molecular dynamics with electronic friction (MDEF). Dissipation is included by a friction term in a Langevin equation which describes the coupling of molecular degrees of freedom to electron-hole pairs in the copper surface, calculated from gradient-corrected density functional theory (DFT) via a local density friction approximation (LDFA). Relaxation due to surface phonons is included by a generalized Langevin oscillator model. The hot-electron induced excitation is described via a time-dependent electronic temperature, the latter derived from an improved two-temperature model. Our parameter-free simulations on a precomputed potential energy surface allow for excellent statistics, and the observed trends are confirmed by on-the-fly ab initio molecular dynamics with electronic friction (AIMDEF) calculations. By computing time-resolved frequency maps for selected molecular vibrations, instantaneous frequencies, probability distributions, and correlation functions, we gain microscopic insight into hot-electron driven dynamics and we can relate the time evolution of vibrational internal CO stretch-mode frequencies to measured data, notably an observed redshift. Quantitatively, the latter is found to be larger in MDEF than in experiment and possible reasons are discussed for this observation. In our model, in addition we observe the excitation and time evolution of large-amplitude low-frequency modes, lateral CO surface diffusion, and molecular desorption. Effects of surface atom motion and of the laser fluence are also discussed.

Influence of the exchange-correlation potential and magnetic properties on the Li2FeSiO4 cathode materials

Seen the interest in the application of the density-functional theory (DFT) calculations to reproduce the experimentally observed properties of the potential electrode materials, we consider the electronic structure, electrochemical properties, mechanical and thermodynamic properties of the Li2FeSiO4 compound using magnetic or non-magnetic gradient-corrected density-functional theory (GGA + SP, GGA) and magnetic or non-magnetic DFT corrected for on-site Coulomb interactions (GGA + U + SP, GGA + U) to allow a direct comparison of the four methods. In terms of the structural characteristics, the non-magnetic scheme cannot correctly describe them, but magnetic scheme can. However, like in GGA + SP and GGA + U + SP method, the accuracy is different in the description of the microscopic details for different magnetic schemes. As for electrochemical and electronic properties, only GGA + U + SP results are in line with the experimental values due to the reset of the electronic structure. The results show that both enhanced localization and spin-polarized effects present in the GGA + U + SP approximation are essential to reproduce the experimentally observed properties of the polyanionic compounds. Furthermore, we found that the inductive effect of the exchange correlation potential and magnetic properties also has some effect on the thermodynamic properties of the polyanionic compounds.

On the Possibility of Using the Jellium Model as a Guide To Design Bimetallic Superalkali Cations.

The potential application of the jellium model as guidance in the rational design of bimetallic superalkali cations is examined under gradient-corrected density functional theory for the first time. By using Li, Mg, and Al as atomic building blocks, a series of bimetallic cationic clusters with 2, 8, 20, and 40 valence electrons are obtained and investigated. As the corresponding neutral clusters tend to lose one valence electron to achieve closed-shell states in the jellium model, these studied cations exhibit much lower vertical electron affinities (EAvert , 3.42-4.95 eV) than the ionization energies (IEs) of alkali metal atoms, indicating their superalkali identities. The high stability of these cationic clusters is guaranteed by their considerable HOMO-LUMO gaps and binding energies per atom. Moreover, the feasibility of using the designed superalkalis as efficient reductants to activate CO2 and N2 molecules and as stable building blocks to assemble ionic superatom compounds is explored. Therefore, this study may provide an effective method for obtaining various metallic superatoms with extensive applications on the basis of the simple jellium rule.

Theoretical Surface Science Beyond Gradient-Corrected Density Functional Theory: Water at α-Al2O3(0001) as a Case Study

The quantum chemical description of the adsorption, vibrations, and reactions of molecules at periodic solid surfaces is frequently based on a methodological “standard model”: density functional th...

Density functional theory based probe of the affinity interaction of saccharide ligands with extra-cellular sialic acid residues

Changes in glycosylation pattern leads to malignant transformations among the cells. In combination with upregulated actions of sialyltransferases, it ultimately leads to differential expression of sialic acid (SA) at cell surface. Given its negative charge and localization to extracellular domain, SA has been exploited for the development of targeted theranostics using approaches, such as, cationization and appending recognition saccharides on carrier surface. In this study, we have performed quantum mechanical calculations based on density functional theory (DFT) to study the interaction of saccharides with extracellular SA. Gradient-corrected DFT with the three parameter function (B3) was utilized for the calculation of Lee–Yang–Parr (LYP) correlation function. Atomic charge, vibrational frequencies and energy of the optimized structures were calculated through B3LYP. Our calculations demonstrate a stronger galactose–sialic acid interaction at tumour-relevant low pH and hyperthermic condition. These results support the application of pH responsive delivery vehicles and targeted hyperthermic chemotherapy for eradicating solid tumour deposits. These studies, conducted a priori, can guide the formulation scientists over appropriate choice of ligands and their applications in the design of ‘smart’ theranostic tools.

Ab initio study of CO2 hydrogenation mechanisms on inverse ZnO/Cu catalysts

Methanol formation from CO2 and molecular hydrogen on ZnO/Cu catalysts is studied by gradient corrected density functional theory. The catalytically active region is modeled as a minimum size inverse catalyst represented by ZnXOY(H) clusters of different size and a ZnO nano-ribbon on an extended Cu(111) surface. These systems are chosen as a representative of thermodynamically stable catalyst structures under typical reaction conditions. Comparison to a high level wave function method reveals that density functional theory systematically underestimates reaction barriers, but nevertheless conserves their energetic ordering. In contrast to other metal-supported oxides like ceria and zirconia, the reaction proceeds through the formation of formate on ZnOX/Cu, thus avoiding the CO intermediate. The difference between the oxides is attributed to variance in the initial activation of CO2. The energetics of the formate reaction pathway is insensitive to the exact environment of undercoordinated Zn active sites, which points to a general mechanism for Cu-Zn based catalysts.

A Conducting Poly(N-(1-Naphthyl)ethylenediamine dihydrochloride) Nanofibers for the Sensitive and Interference-Free Detection of Dopamine

This research demonstrated the development of a stable, sensitive, and selective electrochemical method based on poly(N-(1-Naphthyl) ethylenediamine dihydrochloride) nanofibers-modified anodized glassy carbon electrode (PNEDA/AGCE) for the detection of dopamine (DA) in the presence of ascorbic acid (AA) and uric acid (UA). The PNEDA/AGCE sensor could easily separate the oxidation signals of AA, DA, and UA from their mixture solution in PBS (pH 7.0). It showed linear behavior over wide concentration ranges for DA sensing and the detection limits were ca. 0.070 and 0.075 μM in PBS (pH 7.0) and diluted human serum samples respectively, while the sensitivities were ca. 0.085 and 0.080 μA.μM−1, respectively. The high sensitivity for the PNEDA/AGCE sensor can be ascribed to the facile H-bonding interaction between the free –NH2 groups of PNEDA and oxidizable –OH groups of DA, which was verified by Gradient-corrected density functional theory (DFT) calculation. The PNEDA/AGCE sensor showed excellent repeatability and reproducibility with very low RSD (%) and excellent recoveries of DA concentrations in human serum samples.

Layer-controlled band alignment, work function and optical properties of few-layer GeSe

The electronic properties, such as the layer-dependent behavior of the band structure, band gap, work function alignment and dielectric properties of the few-layer GeSe are systematically investigated via gradient-corrected density functional theory computations, inspired by the experimentally observation of two-dimension materials such as graphene, phosphorene, MoS2 and BN. The results indicate that the few-layer GeSe presents a robust direct band gap, which decreases with increasing the thickness from bilayer (1.15eV) to six-layer (1.00eV) around the X point. Furthermore, the work function increases rapidly from monolayer (4.44eV) to trilayer (4.95eV). The robust direct band gap characteristics and the layer-dependent band gap suggest that the few-layer GeSe is a promising material for efficient solar energy harvesting applications. The layer dependence of the GeSe work function offers a practical route to tune the Schottky barrier in GeSe based electronic devices. Our results provide new insights on utilizing the layer-controlled band gap of the atomic layers of GeSe.

On the feasibility of designing hyperalkali cations using superalkali clusters as ligands.

The possibility of using superalkali clusters instead of alkali atoms as ligands to design a class of cationic compounds, referred to as hyperalkali cations, has been examined by using gradient-corrected density functional theory. By taking typical superalkalis (FLi2, OLi3, and NLi4) as examples, a series of hyperalkali cations ML2+ [M = (super)halogen; L = superalkali] have been constructed and investigated. Calculational results show that all the superalkali moieties preserve their geometric and electronic integrity in these proposed cations. The stability of these studied cations is guaranteed by the strong ionic bonds between superalkali ligand and (super)halogen core, as well as their large highest occupied molecular orbital-lowest unoccupied molecular orbital gaps and positive dissociation energies. In particular, all these proposed cations possess lower vertical electron affinities (2.36-3.56 eV) than those of their corresponding cationic superalkali ligands, verifying their hyperalkali nature. We, therefore, hope that this study will provide an approach to obtain new species with excellent reducing capability by utilizing various superalkalis as building blocks.

Femtosecond-laser induced dynamics of CO on Ru(0001): Deep insights from a hot-electron friction model including surface motion

A Langevin model accounting for all six molecular degrees of freedom is applied to femtosecond-laser induced, hot-electron driven dynamics of Ru(0001)($2\ifmmode\times\else\texttimes\fi{}2$):CO. In our molecular dynamics with electronic friction approach, a recently developed potential energy surface based on gradient-corrected density functional theory accounting for van der Waals interactions is adopted. Electronic friction due to the coupling of molecular degrees of freedom to electron-hole pairs in the metal are included via a local density friction approximation, and surface phonons by a generalized Langevin oscillator model. The action of ultrashort laser pulses enters through a substrate-mediated, hot-electron mechanism via a time-dependent electronic temperature (derived from a two-temperature model), causing random forces acting on the molecule. The model is applied to laser induced lateral diffusion of CO on the surface, ``hot adsorbate'' formation, and laser induced desorption. Reaction probabilities are strongly enhanced compared to purely thermal processes, both for diffusion and desorption. Reaction yields depend in a characteristic (nonlinear) fashion on the applied laser fluence, as well as branching ratios for various reaction channels. Computed two-pulse correlation traces for desorption and other indicators suggest that aside from electron-hole pairs, phonons play a non-negligible role for laser induced dynamics in this system, acting on a surprisingly short time scale. Our simulations on precomputed potentials allow for good statistics and the treatment of long-time dynamics (300 ps), giving insight into this system which hitherto has not been reached. We find generally good agreement with experimental data where available and make predictions in addition. A recently proposed laser induced population of physisorbed precursor states could not be observed with the present low-coverage model.

Unraveling the Apparent Dimerization Tendency in Small Mon Clusters with n = 3–10

The geometric, electronic, and magnetic properties of Mon clusters, with n = 3–10, are investigated from a computational point of view. Calculations are carried out using gradient-corrected density functional theory, a small core pseudopotential to represent inner electrons, and a triple-ζ basis set to describe the 4s, 4p, 4d, and 5s valence atomic orbitals. The geometries of the ground states for every cluster size are distorted versions of the familiar structures adopted by transition metal aggregates. Both the average interatomic distance and the atomization energy show a monotonic increase. In most cases metallic aggregates exhibit closed-shell electronic configurations. Only Mo3, Mo8, and Mo10 show open-shell electronic structures. However, several isomers are found to lie within 60 meV/at above the corresponding ground state for all cluster sizes. The apparent tendency to form dimers observed by some authors in small molybdenum clusters from the dimer to the heptamer is revisited using the present m...

Molecular adsorption of NO on free-standing and on graphene-supported Mo3W5 cluster: a density functional theory investigation

The adsorption of molecular NO on the free-standing and graphene-supported Mo3W5 cluster is studied using methods from the gradient-corrected density functional theory. Before, the effect of the graphene support on the properties of the metal cluster was investigated. The interaction between the metal cluster and the graphene sheet takes place mainly through W atoms, which form up to three bonds with the support. Interaction energies are in the range from 0.6 to 1.5 eV. An amount of charge of about 0.4–0.5 e $$^-$$ is transferred from the cluster to the support. Geometric distortions in the metal aggregate are negligible. An important decrease in the magnetic moment of Mo3W5 with respect to its free-standing value is observed after the interaction with the support. Molecular NO adsorbs on sites involving W atoms only, both for the free-standing and the supported metal cluster. Adsorption energies are in a range from 2 to 4 eV. A parallel mode is the preferred mode from an energetic point of view. Moreover, for that parallel adsorption mode, the N–O bond is more effectively activated. Magnetic moments change largely after adsorption indicating important rearrangement in the electronic configuration of the metal cluster. An important amount of electronic charge is transferred both from the free-standing and from the supported metal cluster to NO. The amount of charge transferred seems to be closely related to the activation of the N–O bond. The effect of the graphene sheet on the catalytic properties of Mo3W5 seems to be negligible, with the exception of some changes in the electronic configuration of the cluster.

Electronic Structure and Circular Dichroism of Natural Alboatisins Isolated from Aerial Parts of Isodon Albopilosus: DFT and TDDFT Study

The stable conformations of a series of bioactive molecules, (−)-alboatisins A–C, are identified via Monte Carlo searching with the MMFF94 molecular mechanics force field. Then, the optical rotation (OR) values, vibrational circular dichroism (VCD), and electronic circular dichroism (ECD) spectra were calculated using the gradient-corrected density functional theory method. The vibrational and transition modes of molecular chirality were explored in terms of their microscopic origin. The calculated specific rotations are in agreement with the experimental values. From the OR analysis, it was concluded that optical rotation values are regulated by hydroxyl substitution. Vibrations occurring on the chiral skeleton may cause strong absorption in VCD spectra; VCD spectra are thus the spectral response to deformation vibrations on the chiral carbon skeleton. The lowest-energy negative Cotton effect is caused by σ → π* transition. Frontier molecular orbital analysis showed that strong ECD absorptions are produced when the dominant transition on the chiral skeleton is asymmetric; ECD spectra show the result of transitions lacking asymmetry on the chiral skeleton.

First principles calculations on nitrogen reactivity on tungsten surfaces

Using the spin-polarized gradient-corrected density functional theory we investigate the adsorption and dissociation of nitrogen molecule and hydrogen nitride radicals on two model surfaces of tungsten, W{1 0 0} and W{1 1 0}. The goal of the investigations is to predict the number and nature of the nitrogenized moieties that could be found on a tungsten surface after nitrogen-seeded hydrogen (deuterium) plasma discharge. The surfaces are considered clean or saturated in hydrogen or nitrogen atoms as they are expected to be after nitrogen seeded hydrogen plasma irradiation. We find that the radicals NH, NH2 and NH3 are dissociated by the catalytic action of the metallic surfaces if they are animated with an initial kinetic energy of less than 2.5 eV. The products of the reaction are a nitrogen atom incorporated into the metal surface and an adsorbed proton. The general conclusion is that nitrogen reduces hydrogen retention on the surface and more generally that the nitrided surfaces should be less reactive than the clean tungsten even if the two surfaces we consider behave quite differently.

A theoretical study of imine hydrocyanation catalyzed by halogen-bonding.

A detailed theoretical study of the mechanism and energetics of an organocatalysis based on C=N activation by halogen-bonding is presented for the hydrocyanation of N-benzylidenemethylamine. The calculations at the level of scalar-relativistic gradient-corrected density functional theory give an insight in this catalytic concept and provide information on the characteristics of four different monodentate catalyst candidates acting as halogen-bond donors during the reaction.

Tuning the oxidation states of Au and exploring new superhalogen anions, AuOxFy− (x, y = 1–4; x + y = 2–5)

AuOxFy− species (x+y=2–5) are systematically studied using gradient corrected density functional theory. Their vertical detachment energies are larger than the electron affinity of halogen, suggesting them as a new class of superhalogen anions. Attempts have been made to tune the oxidation states of Au successively from +2 to +8 in AuOxFy−. However, AuOxFy− are stable only up to +5 oxidation state which is predicted to be the highest possible oxidation state of Au. Our calculations clearly show that AuOxFy− become unstable and tend to form (AuOx−2Fy−)O2 complexes when the oxidation state of Au exceeds +5.