van der Waals forces in density functional theory: a review of the vdW-DF method

Modified Density Functional Dispersion Correction for Inorganic Layered MFX Compounds (M = Ca, Sr, Ba, Pb and X = Cl, Br, I)

MFX (M = Ca, Ba, Sr, Pb and X = Cl, Br, I) compounds have received considerable attention due to their technological application as X-ray detectors, pressure sensors, and optical data storage materials, when doped with rare-earth ions. MFX compounds belong to the class of layered materials with a tetragonal Matlockite crystal structure, characterized by weakly stacked double-halide layers along the crystallographic c-axis. These layers predominantly determine phase transitions, elastic, and mechanical properties. However, the correct description of the lattice parameter c is a challenge for most standard DFT functionals, which tend to overestimate the lattice parameter c. Because of the weak interactions between the halide layers, dispersion-corrected functionals seem to be a better choice. We investigated 11 different inorganic layered MFX compounds for which experimental data are available, with standard and dispersion-corrected functionals to assess their performance in reproducing the lattice parameter c, structural, and vibrational properties of the MFX compounds. Our results revealed that these functionals do not describe the weak interactions between the halide layers in a balanced way. Therefore, we modified Grimme's popular DFT-D2 dispersion correction scheme in two different ways by (i) replacing the dispersion coefficients and van der Waals radii with those of noble gas atoms or (ii) increasing the van der Waals radii of the MFX atoms up to 40%. Comparison with the available experimental data revealed that the latter approach applied to the PBE (Perdew-Burke-Ernzerhof)-D2 functional with 30% increased van der Waals radii, which we coined PBE-D2* (S_rvdw 1.30) is best suited to fine-tune the description of the weak interlayer interactions in MFX compounds, thus significantly improving the description of their structural, vibrational, and mechanical properties. Work is in progress applying this new, computationally inexpensive scheme to other inorganic layered compounds and periodic systems with weakly stacked layers.

In Silico Strategies in Tuberculosis Drug Discovery

Tuberculosis (TB) remains a serious threat to global public health, responsible for an estimated 1.5 million mortalities in 2018. While there are available therapeutics for this infection, slow-acting drugs, poor patient compliance, drug toxicity, and drug resistance require the discovery of novel TB drugs. Discovering new and more potent antibiotics that target novel TB protein targets is an attractive strategy towards controlling the global TB epidemic. In silico strategies can be applied at multiple stages of the drug discovery paradigm to expedite the identification of novel anti-TB therapeutics. In this paper, we discuss the current TB treatment, emergence of drug resistance, and the effective application of computational tools to the different stages of TB drug discovery when combined with traditional biochemical methods. We will also highlight the strengths and points of improvement in in silico TB drug discovery research, as well as possible future perspectives in this field.

Physicochemical properties of L- and DL-valine: first-principles calculations

At present, physicochemical properties of amino acid molecular crystals are of the utmost interest. The compounds where molecules have different chirality are the focus of particular interest. This paper, presents a study on the structural and electronic properties of crystalline L- and DL-valine within the framework of density functional theory including van der Waals interactions. The results of this study showed that electronic properties of the two forms of valine are similar at zero pressure. Pressure leads to different responses in these crystals which is manifested as various deformations of molecules. The pressure effect on the infrared spectra and distribution of electron density of L- and DL-valine has been studied.

Oxygen Reduction Reaction at Penta-Coordinated Co Phthalocyanines

From the early 60s, Co complexes, especially Co phthalocyanines (CoPc) have been extensively studied as electrocatalysts for the oxygen reduction reaction (ORR). Generally, they promote the 2-electron reduction of O2 to give peroxide whereas the 4-electron reduction is preferred for fuel cell applications. Still, Co complexes are of interest because depending on the chemical environment of the Co metal centers either promote the 2-electron transfer process or the 4-electron transfer. In this study, we synthetized 3 different Co catalysts where Co is coordinated to 5 N atoms using CoN4 phthalocyanines with a pyridine axial linker anchored to carbon nanotubes. We tested complexes with electro-withdrawing or electro-donating residues on the N4 phthalocyanine ligand. The catalysts were characterized by EPR and XPS spectroscopy. Ab initio calculations, Koutecky-Levich extrapolation and Tafel plots confirm that the pyridine back ligand increases the Co-O2 binding energy, and therefore promotes the 4-electron reduction of O2. But the presence of electron withdrawing residues, in the plane of the tetra N atoms coordinating the Co, does not further increase the activity of the compounds because of pull-push electronic effects.

Inclusion of Van der Waals Interactions in DFT using Wannier Functions without empirical parameters

We describe a method for including van der Waals (vdW) interactions in Density Functional Theory (DFT) using the Maximally-Localized Wannier functions (MLWFs), which is free from empirical parameters. With respect to the previous DFT/vdW-WF2 version, in the present DFT/vdW-WF2-x approach, the empirical, short-range, damping function is replaced by an estimate of the Pauli exchange repulsion, also obtained by the MLWFs properties. Applications to systems contained in the popular S22 molecular database and to the case of adsorption of Ar on graphite, and Xe and water on graphene, indicate that the new method, besides being more physically founded, also leads to a systematic improvement in the description of systems where vdW interactions play a significant role.

Extension and evaluation of the D4 London-dispersion model for periodic systems

We present an extension of the DFT-D4 model [J. Chem. Phys., 2019, 150, 154122] for periodic systems. The main new ingredients are additional reference polarizabilities for highly-coordinated group 1-5 elements derived from pseudo-periodic electrostatically-embedded cluster calculations. To illustrate the performance of the updated method, several test cases are considered, for which we compare D4 to its predecessor D3(BJ), as well as to a comprehensive set of other dispersion-corrected methods. The largest improvements are observed for solid-state polarizabilities of 16 inorganic salts, where the D4 model achieves an unprecedented accuracy, surpassing its predecessor as well as other, computationally much more demanding approaches. For cell volumes and lattice energies of two sets of chemically diverse molecular crystals, the accuracy gain is less pronounced compared to the already excellently performing D3(BJ) method. For the challenging adsorption energies of small organic molecules on metallic as well as on ionic surfaces, DFT-D4 provides values in good agreement with experimental and/or high-level references. These results suggest the application of the proposed D4 model as a physically improved yet computationally efficient dispersion correction for standard DFT calculations as well as low-cost approaches like semi-empirical or even force-field models.

The closed-edge structure of graphite and the effect of electrostatic charging

The properties of graphite, and of few-layer graphene, can be strongly influenced by the edge structure of the graphene planes, but there is still much that we do not understand about the geometry and stability of these edges. We present an experimental and theoretical study of the closed edges of graphite crystals, and of the effect of an electric field on their structure. High-resolution transmission electron microscopy is used to image the edge structure of fresh graphite and of graphite that has been exposed to an electric field, which experiences a separation of the graphene layers. Computer simulations based on density functional theory are used to rationalise and quantify the preference for the formation of multiple concentric loops at the edges. A model is also presented to explain how the application of an electric field leads to the separation of the folded edges.

DFT simulations unravel the thermodynamics of folded edges in graphite, and explain why an electric field can open the loops.

Exploring the Adsorption Mechanism of Tetracene on Ag(110) by STM and Dispersion-Corrected DFT

Self-assembled strategy has been proven to be a promising vista in constructing organized low-dimensional nanostructures with molecular precision and versatile functionalities on solid surfaces. Herein, we investigate by a combination of scanning tunneling microscopy (STM) and dispersion-corrected density functional theory (DFT), the adsorption of tetracene molecules on the silver substrate and the mechanism mediating the self-assembly on Ag(110). As expected, ordered domain is formed on Ag(110) after adsorption with adjacent molecules being imaged with alternating bright or dim pattern regularly. While such behavior has been assigned previously to the difference of molecular adsorption height, herein, it is possible to investigate essentially the mechanism leading to the periodic alternation of brightness and dimness for tetracene adsorbed on Ag(110) thanks to the consideration of Van der Waals (vdW) dispersion force. It is demonstrated that the adsorption height in fact is same for both bright and dim molecules, while the adsorption site and the corresponding interfacial charge transfer play an important role in the formation of such pattern. Our report reveals that vdW dispersion interaction is crucial to appropriately describe the adsorption of tetracene on the silver substrate, and the formation of delicate molecular architectures on metal surfaces might also offers a promising approach towards molecular electronics.

Probing Multiphased Transition in Bulk MoS2 by Direct Electron Injection

Structural phase transitions in layered two-dimensional (2D) materials are of significant interest owing to their ability to exist in multiple metastable states with distinctive properties. However, phase transition in bulk MoS₂ by nondestructive electron infusion has not yet been realized. In this study, we report the 2H to 1T' phase transition and in-between intermediates in bulk MoS₂ using MoS₂/[Ca₂N]⁺·e^- heterostructures, in which kinetic free electrons were directly injected into MoS₂. We observed various phases in MoS₂ ranging from heavily doped 2H to a distorted lattice state and then on to a complete 1T' state. Snapshots of the multiphase transition were captured by extraordinary Raman shift and bandgap reduction and were further elucidated by theoretical calculations. We also observed a weakening in interlayer coupling in the vicinity of the metallic regime, which led to an unusually strong photoluminescence emission, suggesting light-efficient bulk MoS₂. Our results thus suggest the optoelectronic applications that can fully utilize the multiphase transition of bulk 2D materials.

The role played by the molecular geometry on the electronic transport through nanometric organic films

The electronic transport properties in molecular heterojunctions are intimately connected with the molecular conformation between the electrodes, and the electronic structure of the molecule/electrode interface. In this work, we perform an ab initio density-functional-theory investigation of the structural and transport properties through self-assembled CuPc molecules sandwiched between gold contacts with (111) surfaces. We demonstrated (i) a tunneling regime ruled by the π orbitals of the aromatic rings of CuPc molecules; and (ii) a high variation (up to two orders of magnitude) of the current density with the orientation of the CuPc molecules relative to the gold surface. The source of this variation is the geometrical dependence of the energy of the highest-occupied-molecular-orbital with respect to the chemical potential of the metal and the generation of intra-molecular transport channels for a configuration with CuPc molecules tilted with respect to the gold surface.

Theoretical Study on the Aggregation of Copper Clusters on a Liquid Surface

The ground state structures of copper clusters with different sizes along with their aggregation have been systematic investigated using Amsterdam Density Functional (ADF) and Atomistix ToolKit (ATK) programs. On the basis of geometry optimization, some Cu clusters with more stable structures which were not reported previously have been revealed. In most cases, these Cu clusters prefer to adopt icosahedral structures which originate from the 13-atom icosahedron. It has also been demonstrated that the interaction between two Cu clusters is anisotropic, which is attributed to their charge distribution, especially the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of Cu clusters. Moreover, we have carried out the simulation of Cu clusters aggregation on the silicone oil substrate by means of Monte Carlo (MC) method, which shows good consistence with our previous experimental studies.

Synthesis and Characterization of Halloysite/Carbon Nanocomposites for Enhanced NSAIDs Adsorption from Water

The adsorption of ketoprofen, naproxen, and diclofenac (non-steroidal anti-inflammatory drugs, NSAIDs) on halloysite/carbon nanocomposites and non-modified halloysite were investigated in this work. Halloysite/carbon nanocomposites were obtained through liquid phase impregnation and carbonization using halloysite as the template and saccharose as the carbon precursor. Scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier-transform infrared spectrometry (FT-IR), and low-temperature nitrogen adsorption method were employed to study the morphological and structural changes of the halloysite/carbon nanocomposites. The effects of contact time, initial concentration of adsorbates, pH of solution, and mass of adsorbent on the adsorption were studied. Adsorption mechanism was found to fit pseudo-second-order and intra-particle diffusion models. The obtained experimental adsorption data were well represented by the Langmuir multi-center adsorption model. Adsorption ability of halloysite/carbon nanocomposites was much higher for all the studied NSAIDs in comparison to non-modified halloysite. Optimized chemical structures of ketoprofen, naproxen, and diclofenac obtained by Density Functional Theory (DFT) calculation showed that charge distributions of these adsorbate molecules and their ions can be helpful to explain the details of adsorption mechanism of NSAIDs on halloysite/carbon nanocomposites.

Crystal structures and the electronic properties of silicon-rich silicon carbide materials by first principle calculations

Silicon carbide has been used in a variety of applications including solar cells due to its high stability. The high bandgap of pristine SiC, necessitates nonstoichiometric silicon carbide materials to be considered to tune the band gap for efficient solar light absorptions. In this regards, thermodynamically stable Si-rich SixC1-x materials can be used in solar cell applications without requiring the expensive pure grade silicon or pure grade silicon carbide. In this work, we have used density functional theory (DFT) to examine the stability of various polymorphs of silicon carbide such as 2H-SiC, 4H-SiC, 6H-SiC, 8H-SiC, 10H-SiC, wurtzite, naquite, and diamond structures to produce stable structures of Si-rich SixC1-x. We have systematically replaced the carbon atoms by silicon to lower the band gap and found that the configurations of these excess silicon atoms play a significant role in the stability of Si-rich SixC1-x. Hence, we have investigated different configurations of silicon and carbon atoms in these silicon carbide structures to obtain suitable SixC1-x materials with tailored band gaps. The results indicate that 6H-SixC1-x is thermodynamically the most favorable structure within the scope of this study. In addition, Si substitution for C sites in 6H-SiC enhances the solar absorption, as well as shifts the absorption spectra toward the lower photon energy region. In addition, in the visible range the absorption coefficients are much higher than the pristine SiC.

Interaction of CO, O, and CO2 with Cu cluster supported on Cu(1 1 1): a density functional theory study

We performed density functional theory (DFT) based calculations to investigate the interaction of CO₂ and its dissociated species (CO and O) on Cu₃ cluster supported on Cu(1 1 1) (Cu₃/Cu(1 1 1)) surfaces. Similar investigations were conducted on Cu(1 1 1) for purpose of comparison. In general, adsorption of CO and O are stronger on the cluster region than on the terrace region of Cu₃/Cu and on the flat Cu surface. CO₂, on the other hand, is weakly adsorbed on the surfaces. With reference to CO₂ dissociation on Cu(1 1 1), we found that the cluster lowers the activation barrier and provides a more stable adsorption of the dissociated species. The presence of co-adsorbed CO in the cluster, however, will increase the activation energy. The variation in the activation barrier with the amount of CO is influenced by the stability of the O atom from the dissociated CO₂. We further found that the adsorption energy of O atom is a possible descriptor for CO₂ dissociation on the cluster region. The Cu cluster supported on Cu surface could be a promising catalyst for CO₂ related reactions based on the lower activation energy for CO₂ dissociation on the system than on Cu(1 1 1).

Size, Composition, and Support-Doping Effects on Oxygen Reduction Activity of Platinum-Alloy and on Non-platinum Metal-Decorated-Graphene Nanocatalysts

Recent investigations reported in the open literature concerning the functionalization of graphene as a support material for transition metal nanoparticle catalysts have examined isolated systems for their potential Oxygen Reduction Reaction (ORR) activity. In this work we present results which characterize the ability to use functionalized graphene (via dopants B, N) to upshift and downshift the adsorption energy of mono-atomic oxygen, O* (the ORR activity descriptor on ORR Volcano Plots), for various compositions of 4-atom, 7-atom, and 19-atom sub-nanometer binary alloy/intermetallic transition metal nanoparticle catalysts on graphene (TMNP-MDG). Our results show several important and interesting features: (1) that the combination of geometric and electronic effects makes development of simple linear mixing rules for size/composition difficult; (2) that the transition from 4- to 7- to 19-atom TMNP on MDG has pronounced effects on ORR activity for all compositions; (3) that the use of B and N as dopants to modulate the graphene-TMNP electronic structure interaction can cause shifts in the oxygen adsorption energy of 0.5 eV or more; (4) that it might be possible to make specific doped-graphene-Ni_xCu_y TMNP systems which fall close to the Volcano Peak for ORR. Our results point to systems which should be investigated experimentally and may improve the viability of future fuel cell or other ORR applications, and provide new paths for future investigations of more detail for TMNP-MDG screening.

Theoretical studies on the energy structures and optical properties of copper cysteamine - a novel sensitizer

Copper cysteamine (Cu-Cy) is a new type of photosensitizer, which can be activated not only by ultraviolet light, but also by X-rays, microwaves and ultrasound to generate reactive oxygen species for treating cancer and infection diseases. Moreover, copper cysteamine has a strong luminescence, which can be used for both therapeutics and imaging. In addition, it can also be used for solid state lighting, radiation detection and sensing. However, its electronic structures, and particularly its excited states, are not yet clear. Here, we present a computational study aiming to determine the nature of the excited states involved in the photophysical processes that lead to the luminescence of this compound. This study has been conducted using density functional theory (DFT), using both hybrid functionals and time-dependent DFT. It is found that both absorption and emission involve the replacement of an electron among the 3d and 4s orbitals of one or the other of the two types of Cu atoms found in the system. Our computed results compared well with the experimental absorption and emission results. These results are very helpful for the understanding of the experimental observations.

Extending and assessing composite electronic structure methods to the solid state

A hierarchy of simplified Hartree-Fock (HF), density functional theory (DFT) methods, and their combinations has been recently proposed for the fast electronic structure computation of large systems. The covered methods are a minimal basis set Hartree-Fock (HF-3c), a small basis set global hybrid functional (PBEh-3c), and its screened exchange variant (HSE-3c), all augmented with semiclassical correction potentials. Here, we extend their applicability to inorganic covalent and ionic solids as well as layered materials. The new methods have been dubbed HFsol-3c, PBEsol0-3c, and HSEsol-3c, respectively, to indicate their parent functional as well as the correction potentials. They have been implemented in the CRYSTAL code to enable routine application for molecular as well as solid materials. We validate the new methods on diverse sets of solid state benchmarks that cover more than 90 solids ranging from covalent, ionic, semi-ionic, layered, and molecular crystals. While we focus on structural and energetic properties, we also test bandgaps, vibrational frequencies, elastic constants, and dielectric and piezoelectric tensors. HSEsol-3c appears to be most promising with mean absolute error for cohesive energies and unit cell volumes of molecular crystals of 1.5 kcal/mol and 2.8%, respectively. Lattice parameters of inorganic solids deviate by 3% from the references, and vibrational frequencies of α-quartz have standard deviations of 10 cm^-1. Overall, this shows an accuracy competitive to converged basis set dispersion corrected DFT with a substantial increase in computational efficiency.

Adsorption of NO Gas Molecules on Monolayer Arsenene Doped with Al, B, S and Si: A First-Principles Study

The structures and electronic properties of monolayer arsenene doped with Al, B, S and Si have been investigated based on first-principles calculation. The dopants have great influences on the properties of the monolayer arsenene. The electronic properties of the substrate are effectively tuned by substitutional doping. After doping, NO adsorbed on four kinds of substrates were investigated. The results demonstrate that NO exhibits a chemisorption character on Al-, B- and Si-doped arsenene while a physisorption character on S-doped arsenene with moderate adsorption energy. Due to the adsorption of NO, the band structures of the four systems have great changes. It reduces the energy gap of Al- and B-doped arsenene and opens the energy gap of S- and Si-doped arsenene. The large charge depletion between the NO molecule and the dopant demonstrates that there is a strong hybridization of orbitals at the surface of the doped substrate because of the formation of a covalent bond, except for S-doped arsenene. It indicates that Al-, B- and Si-doped arsenene might be good candidates as gas sensors to detect NO gas molecules owning to their high sensitivity.

Evidence for a strain-tuned topological phase transition in ZrTe5

A phase transition between topologically distinct insulating phases involves closing and reopening the bandgap. Near the topological phase transition, the bulk energy spectrum is characterized by a massive Dirac dispersion, where the bandgap plays the role of mass. We report measurements of strain dependence of electrical transport properties of ZrTe₅, which is known to host massive Dirac fermions in the bulk due to its proximity to a topological phase transition. We observe that the resistivity exhibits a pronounced minimum at a critical strain. We further find that the positive longitudinal magnetoconductance becomes maximal at the critical strain. This nonmonotonic strain dependence is consistent with the switching of sign of the Dirac mass and, hence, a strain-tuned topological phase transition in ZrTe₅.

Layer breathing and shear modes in multilayer graphene: a DFT-vdW study

In this work, we study structural and vibrational properties of multilayer graphene using density-functional theory with van der Waals (vdW) functionals. Initially, we analyze how different vdW functionals compare by evaluating the lattice parameters, elastic constants and vibrational frequencies of low energy optical modes of graphite. Our results indicate that the vdW-DF1-optB88 functional has the best overall performance on the description of vibrational properties. Next, we use this functional to study the influence of the vdW interactions on the structural and vibrational properties of multilayer graphene. Specifically, we evaluate binding energies, interlayer distances and phonon frequencies of layer breathing and shear modes. We observe excellent agreement between our calculated results and available experimental data, which suggests that this functional has truly predictive power for layer-breathing and shear frequencies that have not been measured yet. This indicates that careful selected vdW functionals can describe interlayer bonding in graphene-related systems with good accuracy.

Ribosomal RNA-Aminoglycoside Hygromycin B Interaction Energy Calculation within a Density Functional Theory Framework

We intend to investigate the drug-binding energy of each nucleotide inside the aminoglycoside hygromycin B (hygB) binding site of 30S ribosomal RNA (rRNA) subunit by using the molecular fractionation with conjugate caps (MFCC) strategy based on the density functional theory (DFT), considering the functional LDA/PWC, OBS, and the dielectric constant parametrization. Aminoglycosides are bactericidal antibiotics that have high affinity to the prokaryotic rRNA, inhibiting the synthesis of proteins by acting on the main stages of the translation mechanism, whereas binding to rRNA 16S, a component of the 30S ribosomal subunit in prokaryotes. The identification of the nucleotides presenting the most negative binding energies allows us to stabilize hygB in a suitable binding pocket of the 30S ribosomal subunit. In addition, it should be highlighted that mutations in these residues may probably lead to resistance to ribosome-targeting antibiotics. Quantum calculations of aminoglycoside hygromycin B-ribosome complex might contribute to further quantum studies with antibiotics like macrolides and other aminoglycosides.

Energy, Phonon, and Dynamic Stability Criteria of Two-Dimensional Materials

First-principles calculations have become a powerful tool to exclude the Edisonian approach in search of novel two-dimensional (2D) materials. However, no universal first-principles criteria to examine the realizability of hypothetical 2D materials have been established in the literature yet. Because of this, and as the calculations are always performed in an artificial simulation environment, one can unintentionally study compounds that do not exist in experiments. Although investigations of physics and chemistry of unrealizable materials can provide some fundamental knowledge, the discussion of their applications can mislead experimentalists for years and increase the gap between experimental and theoretical research. By analyzing energy convex hull, phonon spectra, and structure evolution during ab initio molecular dynamics simulations for a range of synthesized and recently proposed 2D materials, we construct energy, phonon, and dynamic stability filters that need to be satisfied before proposing novel 2D compounds. We demonstrate the power of the suggested filters for several selected 2D systems, revealing that some of them cannot be ever realized experimentally.

Structure and Dynamics of Water at the Water-Air Interface Using First-Principles Molecular Dynamics Simulations. II. NonLocal vs Empirical van der Waals Corrections

van der Waals (vdW) correction schemes have been recognized to be essential for an accurate description of liquid water in first-principles molecular dynamics simulation. The description of the structure and dynamics of water is governed by the type of the vdW corrections. So far, two vdW correction schemes have been often used: empirical vdW corrections and nonlocal vdW corrections. In this paper, we assess the influence of the empirical vs nonlocal vdW correction schemes on the structure and dynamics of water at the water–air interface. Since the structure of water at the water–air interface is established by a delicate balance of hydrogen bond formation and breaking, the simulation at the water–air interface provides a unique platform to testify as to the heterogeneous interaction of water. We used the metrics [Ohto et al. J. Chem. Theory Comput., 2019, 15, 595−60230468702] which are directly connected with the sum-frequency generation spectroscopic measurement. We find that the overall performance of nonlocal vdW methods is either similar or worse compared to the empirical vdW methods. We also investigated the performance of the optB88-DRSLL functional, which showed slightly less accuracy than the revPBE-D3 method. We conclude that the revPBE-D3 method shows the best performance for describing the interfacial water.

Quasiparticle Levels at Large Interface Systems from Many-Body Perturbation Theory: The XAF-GW Method

We present a fully ab initio approach based on many-body perturbation theory in the GW approximation to compute the quasiparticle levels of large interface systems without significant covalent interactions between the different components of the interface (meaning that the different components can be separated without the creation of dangling bonds). The only assumption in our approach is that the polarizability matrix (chi) of the interface can be given by the sum of the polarizability matrices of individual components of the interface. We show analytically, using a two-state hybridized model, that this assumption is valid even in the presence of interface hybridization to form bonding and antibonding states up to first order in the overlap matrix elements involved in the hybridization. We validate our approach by showing that the band structure obtained in our method is almost identical to that obtained using a regular GW calculation for bilayer black phosphorus, where interlayer hybridization is significant. Significant savings in computational time and memory are obtained by computing chi only for the smallest subunit cell of each component and expanding (unfolding) the chi matrix to that in the unit cell of the interface. To treat interface hybridization, the full wave functions of the interface are used in computing the self-energy. We thus call the method XAF-GW (X, eXpand-chi; A, Add-chi; F, Full wave functions). Compared to GW-embedding type approaches in the literature, the XAF-GW approach is not limited to specific screening environments or to nonhybridized interface systems. XAF-GW can also be applied to systems with different dimensionalities, as well as to Moire superlattices such as in twisted bilayers. We illustrate the generality and usefulness of our approach by applying it to self-assembled PTCDA monolayers on Au(111) and Ag(111) and PTCDA monolayers on graphite-supported monolayer WSe₂. In all cases, the predicted HOMO and LUMO levels agree well with experimental measurements.

Cooperativity and coverage dependent molecular desorption in self-assembled monolayers: computational case study with coronene on Au(111) and HOPG

One of the common practices in the literature of molecular desorption is the comparison of theoretically (mostly using DFT) calculated single molecule adsorption energies with experimental desorption energies from studies like temperature programmed desorption (TPD) etc. Comparisons like those do not consider that the experimental desorption energies are obtained via ensemble techniques while theoretical values are calculated at the single molecule level. Theoretical values are generally based upon desorption of a single molecule from a clean surface, or upon desorption of an entire monolayer. On the other hand, coverage dependent molecule-molecule interactions add to and modify molecule-substrate interactions that contribute to the experimentally determined desorption energies. In this work, we explore the suitability of an additive nearest neighbor model for determining general coverage dependent single molecule desorption energies in non-covalent self-assembled monolayers (SAMs). These coverage dependent values serve as essential input to any model attempting to reproduce coverage dependent desorption or for understanding the time dependent desorption from a partially covered surface. This method is tested using a case study of coronene adsorbed on Au(111) and HOPG substrates with periodic DFT calculations. Calculations show that coronene exhibits coverage and substrate dependence in molecular desorption. We found that intermolecular contact energies in the coronene monolayer are not strongly influenced by the HOPG substrate, while coronene desorption on Au(111) exhibits strong cooperativity where the additive model fails.

Ordered Mesoporous Carbons for Adsorption of Paracetamol and Non-Steroidal Anti-Inflammatory Drugs: Ibuprofen and Naproxen from Aqueous Solutions

The adsorption of paracetamol and non-steroidal anti-inflammatory drugs (ibuprofen and naproxen) on ordered mesoporous carbons (OMC) and, for comparison, on commercial activated carbon, were investigated in this work. OMC adsorbents were obtained by the soft-templating method and were characterized by low-temperature nitrogen adsorption and scanning electron microscopy (SEM). The effects of contact time and initial concentration of organic adsorbates on the adsorption were studied. The contact time to reach equilibrium for maximum adsorption was 360 min for all the studied adsorbates. The adsorption mechanism was found to fit pseudo-second-order and intra particle-diffusion models. Freundlich, Langmuir and Langmuir-Freundlich isotherm models were used to analyze equilibrium adsorption data. Based on the obtained experimental data, the adsorption isotherm in the applied concentration range for all the studied adsorbates was well represented by the Freundlich-Langmuir model. The adsorption ability of ordered mesoporous carbon materials was much higher for paracetamol and naproxen in comparison to commercial activated carbon. The removal efficiency for ibuprofen was significantly lower than for other studied pharmaceuticals and comparable for all adsorbents. Theoretical calculations made it possible to obtain optimized chemical structures of (S)-naproxen, ibuprofen, and paracetamol molecules. Knowledge of charge distributions of these adsorbate molecules can be helpful to explain why paracetamol and naproxen can react more strongly with the surface of adsorbents with a large numbers of acidic groups compared to ibuprofen facilitating more efficient adsorption of these pharmaceuticals on ordered mesoporous carbons.

Molecular Surface Functionalization of Carbon Materials via Radical-Induced Grafting of Terminal Alkenes

Formation of functional monolayers on surfaces of carbon materials is inherently difficult because of the high bond strength of carbon and because common pathways such as SN2 mechanisms cannot take place at surfaces of solid materials. Here, we show that the radical initiators can selectively abstract H atoms from H-terminated carbon surfaces, initiating regioselective grafting of terminal alkenes to surfaces of diamond, glassy carbon, and polymeric carbon dots. Nuclear magnetic resonance (NMR) and X-ray photoelectron spectroscopy (XPS) demonstrate formation of self-terminating organic monolayers linked via the terminal C atom of 1-alkenes. Density functional theory (DFT) calculations suggest that this selectivity is at least partially thermodynamic in origin, as significantly less energy is needed to abstract H atoms from carbon surfaces as compared to typical aliphatic compounds. The regioselectivity favoring binding to the terminal C atom of the reactant alkenes arises from steric hindrance encountered in bond formation at the adjacent carbon atom. Our results demonstrate that carbon surface radical chemistry yields a versatile, selective, and scalable approach to monolayer formation on H-terminated carbon surfaces and provide mechanistic insights into the surface selectivity and regioselectivity of molecular grafting.

Van der Waals Density Functional Theory vdW-DFq for Semihard Materials

There are a large number of materials with mild stiffness, which are not as soft as tissues and not as strong as metals. These semihard materials include energetic materials, molecular crystals, layered materials, and van der Waals crystals. The integrity and mechanical stability are mainly determined by the interactions between instantaneously induced dipoles, the so called London dispersion force or van der Waals force. It is challenging to accurately model the structural and mechanical properties of these semihard materials in the frame of density functional theory where the non-local correlation functionals are not well known. Here, we propose a van der Waals density functional named vdW-DFq to accurately model the density and geometry of semihard materials. Using β -cyclotetramethylene tetranitramine as a prototype, we adjust the enhancement factor of the exchange energy functional with generalized gradient approximations. We find this method to be simple and robust over a wide tuning range when calibrating the functional on-demand with experimental data. With a calibrated value q = 1.05 , the proposed vdW-DFq method shows good performance in predicting the geometries of 11 common energetic material molecular crystals and three typical layered van der Waals crystals. This success could be attributed to the similar electronic charge density gradients, suggesting a wide use in modeling semihard materials. This method could be useful in developing non-empirical density functional theories for semihard and soft materials.

A generally applicable atomic-charge dependent London dispersion correction

The so-called D4 model is presented for the accurate computation of London dispersion interactions in density functional theory approximations (DFT-D4) and generally for atomistic modeling methods. In this successor to the DFT-D3 model, the atomic coordination-dependent dipole polarizabilities are scaled based on atomic partial charges which can be taken from various sources. For this purpose, a new charge-dependent parameter-economic scaling function is designed. Classical charges are obtained from an atomic electronegativity equilibration procedure for which efficient analytical derivatives with respect to nuclear positions are developed. A numerical Casimir-Polder integration of the atom-in-molecule dynamic polarizabilities then yields charge- and geometry-dependent dipole-dipole dispersion coefficients. Similar to the D3 model, the dynamic polarizabilities are precomputed by time-dependent DFT and all elements up to radon (Z = 86) are covered. The two-body dispersion energy expression has the usual sum-over-atom-pairs form and includes dipole-dipole as well as dipole-quadrupole interactions. For a benchmark set of 1225 molecular dipole-dipole dispersion coefficients, the D4 model achieves an unprecedented accuracy with a mean relative deviation of 3.8% compared to 4.7% for D3. In addition to the two-body part, three-body effects are described by an Axilrod-Teller-Muto term. A common many-body dispersion expansion was extensively tested, and an energy correction based on D4 polarizabilities is found to be advantageous for larger systems. Becke-Johnson-type damping parameters for DFT-D4 are determined for more than 60 common density functionals. For various standard energy benchmark sets, DFT-D4 slightly but consistently outperforms DFT-D3. Especially for metal containing systems, the introduced charge dependence of the dispersion coefficients improves thermochemical properties. We suggest (DFT-)D4 as a physically improved and more sophisticated dispersion model in place of DFT-D3 for DFT calculations as well as other low-cost approaches like semi-empirical models.

Performance of van der Waals DFT approaches for helium diffraction on metal surfaces

The ability of the different approaches proposed to date to include the effects of van der Waals (vdW) dispersion forces in density functional theory (DFT) is currently under debate. Here, we used the diffraction of He on a Ru(0 0 0 1) surface as a challenging benchmark system to analyze the suitability of several representative approaches, from the ones correcting the exchange-correlation generalized gradient approximation (GGA) functional, to the ones correcting the DFT energies through pairwise-based methods. To perform our analysis, we have built seven continuous potential energy surfaces (PESs) and carried out quantum dynamics simulations using a multi-configuration time-dependent Hartree method. Our analysis reveals that standard DFT within the PBE-GGA framework, although it overestimates diffraction probabilities, yields the best results in comparison with available experimental measurements. On the other hand, although several of the existing vdW DFT approaches yield physisorption wells in very good agreement with experiment, they all seem to overestimate the long-distance corrugation of the PES, the region probed by He scattering, resulting in a large overestimation of diffraction probabilities.

Tuneable thermal expansion of poly (3,4-ethylenedioxythiophene) polystyrene sulfonate

Linear coefficient of thermal expansion is calculated for a mixture of poly(3,4-ethylenedioxythiophene) and polystyrene sulfonate (PEDOT:PSS) using density functional theory and the Debye-Grüneisen model. The linear coefficient of thermal expansion is a key factor in thermal management (thermal conductivity, thermal stress and thermal fatigue) of microelectronic and energy devices, being common applications of the conjugated polymeric PEDOT:PSS system. The obtained value of 53  ×  10^-6 K^-1 at room temperature can be rationalised based on the electronic structure analysis. The PEDOT and PSS units are bonded by a dipole-dipole interaction between S in PEDOT and H in PSS. A C-C bond in a benzene ring (PSS) or thiophene (PEDOT) is up to 13 times stronger than the S-H bond. By adjusting the population of the S-H bonds by deprotonating PSS, the linear coefficient of thermal expansion can be enhanced by 57%. This allows for tuning the thermal properties of PEDOT:PSS in cutting-edge devices.

DFT Computed Dielectric Response and THz Spectra of Organic Co-Crystals and Their Constituent Components

Terahertz (THz) spectroscopy has been put forth as a non-contact, analytical probe to characterize the intermolecular interactions of biologically active molecules, specifically as a way to understand, better develop, and use active pharmaceutical ingredients. An obstacle towards fully utilizing this technique as a probe is the need to couple features in the THz regions to specific vibrational modes and interactions. One solution is to use density functional theory (DFT) methods to assign specific vibrational modes to signals in the THz region, coupling atomistic insights to spectral features. Here, we use open source planewave DFT packages that employ ultrasoft pseudopotentials to assess the infrared (IR) response of organic compounds and complex co-crystal formulations in the solid state, with and without dispersion corrections. We compare our DFT computed lattice parameters and vibrational modes to experiment and comment on how to improve the agreement between theory and modeling to allow for THz spectroscopy to be used as an analytical probe in complex biologically relevant systems.

ITO Work Function Tunability by Polarizable Chromophore Monolayers

The ability to tune the electronic properties of oxide-bearing semiconductors such as Si/SiO₂ or transparent metal oxides such as indium-tin oxide (ITO) is of great importance in both electronic and optoelectronic device applications. In this work, we describe a process that was conducted on n-type Si/SiO₂ and ITO to induce changes in the substrate work function (WF). The substrates were modified by a two-step synthesis comprising a covalent attachment of coupling agents' monolayer followed by in situ anchoring reactions of polarizable chromophores. The coupling agents and chromophores were chosen with opposite dipole orientations, which enabled the tunability of the substrates' WF. In the first step, two coupling agents with opposite molecular dipole were assembled. The coupling agent with a negative dipole induced a decrease in WF of modified substrates, while the coupling agent with a positive dipole produced an increase in WFs of both ITO and Si substrates. The second modification step consisted of in situ anchoring reaction of polarizable chromophores with opposite dipoles to the coupling layer. This modification led to an additional change in the WFs of both Si/SiO₂ and ITO substrates. The WF was measured by contact potential difference and modeled by density functional theory-based theoretical calculations of the WF for each of the assembly steps. A good fit was obtained between the calculated and experimental trends. This ability to design and tune the WF of ITO substrates was implemented in an organic electronic device with improved I- V characteristics in comparison to a bare ITO-based device.

Determination of the structure and geometry of N-heterocyclic carbenes on Au(111) using high-resolution spectroscopy

N-heterocyclic carbenes (NHCs) bind very strongly to transition metals due to their unique electronic structure featuring a divalent carbon atom with a lone pair in a highly directional sp2-hybridized orbital. As such, they can be assembled into monolayers on metal surfaces that have enhanced stability compared to their thiol-based counterparts. The utility of NHCs to form such robust self-assembled monolayers (SAMs) was only recently recognized and many fundamental questions remain. Here we investigate the structure and geometry of a series of NHCs on Au(111) using high-resolution X-ray photoelectron spectroscopy and density functional theory calculations. We find that the N-substituents on the NHC ring strongly affect the molecule-metal interaction and steer the orientation of molecules in the surface layer. In contrast to previous reports, our experimental and theoretical results provide unequivocal evidence that NHCs with N-methyl substituents bind to undercoordinated adatoms to form flat-lying complexes. In these SAMs, the donor-acceptor interaction between the NHC lone pair and the undercoordinated Au adatom is primarily responsible for the strong bonding of the molecules to the surface. NHCs with bulkier N-substituents prevent the formation of such complexes by forcing the molecules into an upright orientation. Our work provides unique insights into the bonding and geometry of NHC monolayers; more generally, it charts a clear path to manipulating the interaction between NHCs and metal surfaces using traditional coordination chemistry synthetic strategies.

Understanding and Quantifying London Dispersion Effects in Organometallic Complexes

Quantum chemical methods are nowadays able to determine properties of larger chemical systems with high accuracy and Kohn-Sham density functional theory (DFT) in particular has proven to be robust and suitable for everyday applications of electronic structure theory. A clear disadvantage of many established standard density functional approximations like B3LYP is their inability to describe long-range electron correlation effects. The inclusion of such effects, also termed London dispersion, into DFT has been extensively researched in recent years, resulting in some efficient and routinely used correction schemes. The well-established D3 method has demonstrated its efficiency and accuracy in numerous applications since 2010. Recently, it was improved by developing the successor (termed D4) which additionally includes atomic partial charge information for the generation of pairwise dispersion coefficients. These coefficients determine the leading-order (two-body) and higher-order (three- or many-body) terms of the D4 dispersion energy which is simply added to a standard DFT energy. With its excellent accuracy-to-cost ratio, the DFT-D4 method is well suited for the determination of structures and chemical properties for molecules of most kinds. While dispersion effects in organic molecules are nowadays well studied, much less is known for organometallic complexes. For such systems, there has been a growing interest in designing dispersion-controlled reactions especially in the field of homogeneous catalysis. Here, efficient electronic structure methods are necessary for screening of promising model complexes and quantifying dispersion effects. In this Account, we describe the quality of calculated structural and thermodynamic properties in gas-phase obtained with DFT-D4 corrected methods, specifically for organometallic complexes. The physical effects leading to London dispersion interactions are briefly discussed in the picture of second-order perturbation theory. Subsequently, basic theoretical aspects of the D4 method are introduced followed by selected case studies. Several chemical examples are presented starting with the analysis of transition metal thermochemistry and noncovalent interactions for small, heavy element containing main group compounds. Computed reaction energies can only match highly accurate reference values when all energy contributions are included in the DFT treatment, thus highlighting the major role of dispersion interactions for the accurate description of thermochemistry in gas-phase. Furthermore, the correlation between structural and catalytic properties is emphasized where the accessibility of high quality structures is essential for reaction planning and catalyst design. We present calculations for aggregates of organometallic systems with intrinsically large repulsive electrostatic interactions which can be stabilized by London dispersion effects. The newly introduced inclusion of atomic charge information in the DFT-D4 model robustly leads to quantitatively improved dispersion energies in particular for metallic systems. By construction it yields results which are easily understandable due to a clear separation into hybridization and charge (oxidation) state and two- and many-body effects, respectively. Due to its high computational efficiency, the D4 dispersion model is even applicable to low-cost classical and semiempirical theoretical methods.