Geometry optimization of periodic systems using internal coordinates

Reductive Dechlorination of Chlorinated Ethenes at the Sulfidated Zero-Valent Iron Surface: A Mechanistic DFT Study

Sulfidated nano- and microscale zero-valent iron (S-(n)ZVI) has shown enhanced selectivity and reactive lifetime in the degradation of chlorinated ethenes (CEs) compared to pristine (n)ZVI. However, varying effects of sulfidation on the dechlorination rates of structurally similar CEs have been reported, with the underlying mechanisms remaining poorly understood. In this study, we investigated the β-dichloroelimination reactions of tetrachloroethene (PCE), trichloroethene (TCE), cis-1,2-dichloroethene (cis-DCE), and trans-1,2-dichloroethene (trans-DCE) at the S and Fe sites of several S-(n)ZVI surface models by using density functional theory. Dechlorination reactions were both kinetically and thermodynamically more favorable at Fe sites compared to S sites, indicating that maintaining the accessibility of reactive Fe sites is crucial for achieving high S-(n)ZVI reactivity with contaminants. At Fe sites adjacent to S atoms, the reactivity for CE dechlorination followed the order trans-DCE ≈ TCE > cis-DCE > PCE. PCE degradation was hindered at these sites due to the steric effects of S atoms. At the S sites, the energy barriers correlated with the CEs' energy of the lowest unoccupied molecular orbital in the order PCE < TCE < DCE isomers. Our findings reveal that the experimentally observed selectivity of S-(n)ZVI materials for individual CEs can be explained by an interplay of the varying reactivities of Fe and S sites in CE dechlorination reactions.

Clustering of atoms relative to vector space in the Z-matrix coordinate system and 'graphical fingerprint' analysis of 3D pharmacophore structure

The behavior of a molecule within its environment is governed by chemical fields present in 3D space. However, beyond local descriptors in 3D, the conformations a molecule assumes, and the resulting clusters also play a role in influencing structure-activity models. This study focuses on the clustering of atoms according to the vector space of four atoms aligned in the Z-Matrix Reference system for molecular similarity. Using 3D-QSAR analysis, it was aimed to determine the pharmacophore groups as interaction points in the binding region of the β2-adrenoceptor target of fenoterol stereoisomers. Different types of local reactive descriptors of ligands have been used to elucidate points of interaction with the target. Activity values for ligand-receptor interaction energy were determined using the Levenberg-Marquardt algorithm. Using the Molecular Comparative Electron Topology method, the 3D pharmacophore model (3D-PhaM) was obtained after aligning and superimposing the molecules and was further validated by the molecular docking method. Best guesses were calculated with a non-output validation (LOO-CV) method. Finally, the data were calculated using the 'graphic fingerprint' technique. Based on the eLKlopman (Electrostatic LUMO Klopman) descriptor, the Q2 value of this derivative set was calculated as 0.981 and the R2ext value is calculated as 0.998.

Investigating the role of dispersion corrections and anharmonic effects on the phase transition in SrZrS3: A systematic analysis from AIMD free energy calculations

A thermally driven needle-like (NL) to distorted perovskite (DP) phase transition in SrZrS3 was investigated by means of ab initio free energy calculations accelerated by machine learning. As a first step, a systematic screening of the methods to include long-range interactions in semilocal density functional theory Perdew-Burke-Ernzerhof calculations was performed. Out of the ten correction schemes tested, the Tkatchenko-Scheffler method with iterative Hirshfeld partitioning method was found to yield the best match between calculated and experimental lattice geometries, while predicting the correct order of stability of NL and DP phases at zero temperature. This method was then used in free energy calculations, performed using several approaches, so as to determine the effect of various anharmonicity contributions, such as the anisotropic thermal lattice expansion or the thermally induced internal structure changes, on the phase transition temperature (TNP→DP). Accounting for the full anharmonicity by combining the NPT molecular dynamics data with thermodynamic integration with harmonic reference provided our best estimate of TNL→DP = 867 K. Although this result is ∼150 K lower than the experimental value, it still provides an improvement by nearly 300 K compared to the previous theoretical report by Koocher et al. [Inorg. Chem. 62, 11134-11141 (2023)].

Intrinsic Effects of Sulfidation on the Reactivity of Zero-Valent Iron With Trichloroethene: A DFT Study

Sulfidation represents a promising approach to enhance the selectivity and longevity of zero-valent iron (ZVI) in water treatment, particularly for nanoscale ZVI (nZVI). While previous mechanistic studies have primarily concentrated on the impact of sulfidation on the (n)ZVI hydrophobicity, the fundamental effects of sulfidation on the (n)ZVI reactivity with target contaminants remain poorly understood. Herein, we employed density functional theory to elucidate reaction mechanisms of trichloroethene (TCE) dechlorination at various (n)ZVI surface models, ranging from pristine Fe0 to regularly sulfidated Fe surfaces. Our findings indicate that sulfidation intrinsically hinders the TCE dechlorination by (n)ZVI, which aligns with prior observations of sulfur poisoning in transition metal catalysts. We further demonstrate that the positive effects of sulfidation emerge when the surface of (n)ZVI undergoes corrosion. Notably, S sites exhibit higher reactivity compared to the sites typically present on the surface of (n)ZVI oxidized in water. Additionally, S sites protect nearby Fe sites against oxidation and make them more selective for direct electron transfer. Overall, our results reveal that the reactivity of sulfidated (n)ZVI is governed by an interplay of intrinsic inhibitory effects and corrosion protection. A deeper understanding of these phenomena may provide new insights into the selectivity of sulfidated (n)ZVI for specific contaminants.

Lattice Dynamics of Quinacridone Polymorphs: A Combined Raman and Computational Approach

Polarized low-frequency Raman microscopy and a posteriori dispersion-corrected density functional simulations are combined to investigate the lattice vibrations of the αI, β, and γ polymorphs of the model organic semiconductor quinacridone, which are known to display different optical and electronic properties. The comparison between experiments and calculations allows for unambiguous mode assignment and identification of the scattering crystal faces. Conversely, the agreement between simulations and experiments validates the adopted computational methods, which correctly describe the intermolecular interaction of the molecular material. The acquired knowledge of quinacridone lattice dynamics is used to describe the αI to β thermal transition and, most consequentially, to reliably characterize the electron-lattice phonon coupling strength of the three polymorphs, obtaining hints about the electrical transport mechanism of the material.

How the Temperature and Composition Govern the Structure and Band Gap of Zr-Based Chalcogenide Perovskites: Insights from ML Accelerated AIMD

The effects of temperature and composition on the structural and electronic properties of chalcogenide perovskite (CP) materials AZrX3 (A = Ba, Sr, Ca; X = S, Se) in the distorted perovskite (DP) phase are investigated using ab initio molecular dynamics (AIMD) accelerated by machine-learned force fields. Long-range van der Waals (vdW) interactions, incorporated into the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional using the DFT-D3 scheme, are found to be crucial for achieving correct predictions of structural parameters. Our calculations show that the distortion of the DP structure with respect to the parent cubic (C) phase, realized in the form of interoctahedral tilting, decreases with the increasing size of the A cations. The tendency for a gradual transformation of the DP-to-C phase with increasing temperature is shown to be strongly composition-dependent. The transformation temperature decreases with the size of cation A and increases with the size of anion X. Thus, within the range of the temperatures considered here (300-1200 K), a complete transformation is observed only for BaZrS3 (∼600 K) and BaZrSe3 (∼900 K). The computed band gap of CPs is shown to monotonically decrease with increasing temperature, and the magnitude of this decrease is found to be proportional to the extent of the thermally induced changes in the internal structure. Diverse factors affecting the magnitude of band gaps of CP materials are analyzed.

Exploring the Stability and Disorder in the Polymorphs of L-Cysteine through Density Functional Theory and Vibrational Spectroscopy

Static and dynamic density functional calculations are reported for the four known polymorphs of l-cysteine. Static calculations are used to explore the relative free energies (within the harmonic approximation) of the polymorphs as a function of pressure. An important feature of the structural differences between the polymorphs is shown to be the dihedral angle of the C-C-S-H bond. It is shown that, by varying this angle, it is possible to move between hydrogen bonding motifs S-H···S and S-H···O in all four polymorphs. The energetics for dihedral angle rotation are explored, and the barriers for rotation between the hydrogen bonding motifs have been calculated for each polymorph. Two possible models for the experimental disorder observed in Form I at room temperature are explored using both static and dynamic methods; a domain disorder model, where the disorder is localized, and a dispersed disorder model, where the disorder is randomly distributed throughout the crystal. Molecular dynamics calculations show transitions between the two hydrogen bonding motifs occurring in the dispersed disorder model at 300 and 350 K. In addition, molecular dynamics calculations of Form IV also showed the onset of hydrogen bond disorder at 300 K. Calculations of the predicted infrared and terahertz absorption are performed for both the static and dynamic simulations, and the results are compared with experimental results to understand the influence of disorder on the observed spectra.

Anharmonic Correction to Free Energy Barriers from DFT-Based Molecular Dynamics Using Constrained Thermodynamic Integration

For the calculation of anharmonic contributions to free energy barriers, constrained thermodynamic λ-path integration (λ-TI) from a harmonic reference force field to density functional theory is presented as an alternative to the established Blue Moon ensemble method (ξ-TI), in which free energy gradients along the reaction coordinate ξ are integrated. With good agreement in all cases, the λ-TI method is benchmarked against the ξ-TI method for several reactions, including the internal CH₃ group rotation in ethane, a nucleophilic substitution of CH₃Cl, a retro-Diels-Alder reaction, and a proton transfer in zeolite H-SSZ-13. An advantage of λ-TI is that one can use virtually any reference state to compute anharmonic contributions to reaction free energies or free energy barriers. This is particularly relevant for catalysis, where it is now possible to compute anharmonic corrections to the free energy of a transition state relative to any reference, for example, the most stable state of the active site and the reactants in the gas phase. This is in contrast to ξ-TI, where free energy barriers can only be computed relative to an initial state with all reactants coadsorbed. Finally, the Bennett acceptance ratio method combined with λ-TI is demonstrated to reduce the number of required integration grid points with tolerable accuracy, favoring thus λ-TI over ξ-TI in terms of computational efficiency.

Iron nitride nanoparticles for rapid dechlorination of mixed chlorinated ethene contamination

Sulfidation and, more recently, nitriding have been recognized as promising modifications to enhance the selectivity of nanoscale zero-valent iron (nZVI) particles for trichloroethene (TCE). Herein, we investigated the performance of iron nitride (Fe_xN) nanoparticles in the removal of a broader range of chlorinated ethenes (CEs), including tetrachloroethene (PCE), cis-1,2-dichloroethene (cis-DCE), and their mixture with TCE, and compared it to the performance of sulfidated nZVI (S-nZVI) prepared from the same precursor nZVI. Two distinct types of iron nitride (Fe_xN) nanoparticles, containing γ'-Fe₄N and ε-Fe_2-3N phases, exhibited substantially higher PCE and cis-DCE dechlorination rates compared to S-nZVI. A similar effect was observed with a CE mixture, which was completely dechlorinated by both types of Fe_xN nanoparticles within 10 days, whereas S-nZVI was able to remove only about half of the amount, most of which being TCE. Density functional theory calculations further revealed that the cleavage of the first C-Cl bond was the rate-limiting step for all CEs dechlorinated on the γ'-Fe₄N(001) surface, with the reaction barriers of PCE and cis-DCE being 29.9, and 40.8 kJ mol^-1, respectively. Fe_xN nanoparticles proved to be highly effective in the remediation of PCE, cis-DCE, and mixed CE contamination.

Application of DFT Calculations in Designing Polymer-Based Drug Delivery Systems: An Overview

Drug delivery systems transfer medications to target locations throughout the body. These systems are often made up of biodegradable and bioabsorbable polymers acting as delivery components. The introduction of density functional theory (DFT) has tremendously aided the application of computational material science in the design and development of drug delivery materials. The use of DFT and other computational approaches avoids time-consuming empirical processes. Therefore, this review explored how the DFT computation may be utilized to explain some of the features of polymer-based drug delivery systems. First, we went through the key aspects of DFT and provided some context. Then we looked at the essential characteristics of a polymer-based drug delivery system that DFT simulations could predict. We observed that the Gaussian software had been extensively employed by researchers, particularly with the B3LYP functional and 6-31G(d, p) basic sets for polymer-based drug delivery systems. However, to give researchers a choice of basis set for modelling complicated organic systems, such as polymer–drug complexes, we then offered possible resources and presented the future trend.

Impact of interstitial elements on the stacking fault energy of an equiatomic CoCrNi medium entropy alloy: theory and experiments

We investigated the effects of interstitial N and C on the stacking fault energy (SFE) of an equiatomic CoCrNi medium entropy alloy. Results of computer modeling were compared to tensile deformation and electron microscopy data. Both N and C in solid solution increase the SFE of the face-centered cubic (FCC) alloy matrix at room temperature, with the former having a more significant effect by 240% for 0.5 at % N. Total energy calculations based on density functional theory (DFT) as well as thermodynamic modeling of the Gibbs free energy with the CALPHAD (CALculation of PHAse Diagrams) method reveal a stabilizing effect of N and C interstitials on the FCC lattice with respect to the hexagonal close-packed (HCP) CoCrNi-X (X: N, C) lattice. Scanning transmission electron microscopy (STEM) measurements of the width of dissociated ½<110> dislocations suggest that the SFE of CoCrNi increases from 22 to 42-44 mJ·m^-2 after doping the alloy with 0.5 at. % interstitial N. The higher SFE reduces the nucleation rates of twins, leading to an increase in the critical stress required to trigger deformation twinning, an effect which can be used to design load-dependent strain hardening response.

Anharmonic Lattice Dynamics in Sodium Ion Conductors

We employ terahertz-range temperature-dependent Raman spectroscopy and first-principles lattice dynamical calculations to show that the undoped sodium ion conductors Na₃PS₄ and isostructural Na₃PSe₄ both exhibit anharmonic lattice dynamics. The anharmonic effects in the compounds involve coupled host lattice-Na⁺ ion dynamics that drive the tetragonal-to-cubic phase transition in both cases, but with a qualitative difference in the anharmonic character of the transition. Na₃PSe₄ shows an almost purely displacive character with the soft modes disappearing in the cubic phase as the change in symmetry shifts these modes to the Raman-inactive Brillouin zone boundary. Na₃PS₄ instead shows an order-disorder character in the cubic phase, with the soft modes persisting through the phase transition and remaining Raman active in the cubic phase, violating Raman selection rules for that phase. Our findings highlight the important role of coupled host lattice-mobile ion dynamics in vibrational instabilities that are coincident with the exceptional conductivity of these Na⁺ ion conductors.

Visualizing a SCSC [2 + 2] photodimerization through its lattice dynamics: an experimental and theoretical investigation

In homogeneous solid‐state reactions, the single‐crystal nature of the starting material remains unchanged, and the system evolves seamlessly through a series of solid solutions of reactant and product. Among [2+2] photodimerizations of cinnamic acid derivatives in the solid state, those involving salts of the 4‐aminocinnamic acid have been recognized to proceed homogeneously in a “single‐crystal‐to‐single‐crystal” fashion by X‐ray diffraction techniques. Here the bromide salt of this compound class is taken as a model system in a Raman spectroscopy study at low wavelengths, to understand how such a mechanism defines the trend of the crystal lattice vibrations during the reaction. Vibrational mode calculations, based on dispersion corrected DFT simulations of the crystal lattices involved in the transformation, have assisted the interpretation of the experiments. Such an approach has allowed us to clarify the spectral signatures and to establish a correlation between the dynamics of the monomer and dimer systems in a process where chemical progress and crystal structural changes are demonstrated to occur simultaneously.

Chemically Accurate Vibrational Free Energies of Adsorption from Density Functional Theory Molecular Dynamics: Alkanes in Zeolites

We present a methodology to compute, at reduced computational cost, Gibbs free energies, enthalpies, and entropies of adsorption from molecular dynamics. We calculate vibrational partition functions from vibrational energies, which we obtain from the vibrational density of states by projection on the normal modes. The use of a set of well-chosen reference structures along the trajectories accounts for the anharmonicities of the modes. For the adsorption of methane, ethane, and propane in the H-CHA zeolite, we limit our treatment to a set of vibrational modes localized at the adsorption site (zeolitic OH group) and the alkane molecule interacting with it. Only two short trajectories (1–20 ps) are required to reach convergence (<1 kJ/mol) for the thermodynamic functions. The mean absolute deviations from the experimentally measured values are 2.6, 2.8, and 4.7 kJ/mol for the Gibbs free energy, the enthalpy, and the entropy term (−TΔS), respectively. In particular, the entropy terms show a major improvement compared to the harmonic approximation and almost reach the accuracy of the previous use of anharmonic frequencies obtained with curvilinear distortions of individual modes. The thermodynamic functions so obtained follow the trend of the experimental values for methane, ethane, and propane, and the Gibbs free energy of adsorption at experimental conditions is correctly predicted to change from positive for methane (5.9 kJ/mol) to negative for ethane (−4.8 kJ/mol) and propane (−7.1 kJ/mol).

Understanding the Fundamentals of Microporosity Upgrading in Zeolites: Increasing Diffusion and Catalytic Performances

Hierarchical zeolites are regarded as promising catalysts due to their well-developed porosity, increased accessible surface area, and minimal diffusion constraints. Thus far, the focus has been on the creation of mesopores in zeolites, however, little is known about a microporosity upgrading and its effect on the diffusion and catalytic performance. Here the authors show that the "birth" of mesopore formation in faujasite (FAU) type zeolite starts by removing framework T atoms from the sodalite (SOD) cages followed by propagation throughout the crystals. This is evidenced by following the diffusion of xenon (Xe) in the mesoporous FAU zeolite prepared by unbiased leaching with NH4 F in comparison to the pristine FAU zeolite. A new diffusion pathway for the Xe in the mesoporous zeolite is proposed. Xenon first penetrates through the opened SOD cages and then diffuses to supercages of the mesoporous zeolite. Density functional theory (DFT) calculations indicate that Xe diffusion between SOD cage and supercage occurs only in hierarchical FAU structure with defect-contained six-member-ring separating these two types of cages. The catalytic performance of the mesoporous FAU zeolite further indicates that the upgraded microporosity facilitates the intracrystalline molecular traffic and increases the catalytic performance.

Correlation analysis of materials properties by machine learning: illustrated with stacking fault energy from first-principles calculations in dilute fcc-based alloys

Advances in machine learning (ML), especially in the cooperation between ML predictions, density functional theory (DFT) based first-principles calculations, and experimental verification are emerging as a key part of a new paradigm to understand fundamentals, verify, analyze, and predict data, and design and discover materials. Taking stacking fault energy (γ_SFE) as an example, we perform a correlation analysis ofγ_SFEin dilute Al-, Ni-, and Pt-based alloys by descriptors and ML algorithms. Theseγ_SFEvalues were predicted by DFT-based alias shear deformation approach, and up to 49 elemental descriptors and 21 regression algorithms were examined. The present work indicates that (i) the variation ofγ_SFEaffected by alloying elements can be quantified through 14 elemental attributes based on their statistical significances to decrease the mean absolute error (MAE) in ML predictions, and in particular, the number of p valence electrons, a descriptor second only to the covalent radius in importance to model performance, is unexpected; (ii) the alloys with elements close to Ni and Co in the periodic table possess higherγ_SFEvalues; (iii) the top four outliers of DFT predictions ofγ_SFEare for the alloys of Al₂₃La, Pt₂₃Au, Ni₂₃Co, and Al₂₃Be based on the analyses of statistical differences between DFT and ML predictions; and (iv) the best ML model to predictγ_SFEis produced by Gaussian process regression with an average MAE < 8 mJ m^-2. Beyond detailed analysis of the Al-, Ni-, and Pt-based alloys, we also predict theγ_SFEvalues using the present ML models in other fcc-based dilute alloys (i.e., Cu, Ag, Au, Rh, Pd, and Ir) with the expected MAE < 17 mJ m^-2and observe similar effects of alloying elements onγ_SFEas those in Pt₂₃X or Ni₂₃X.

Perspective on computational reaction prediction using machine learning methods in heterogeneous catalysis

Heterogeneous catalysis plays a significant role in the modern chemical industry. Towards the rational design of novel catalysts, understanding reactions over surfaces is the most essential aspect. Typical industrial catalytic processes such as syngas conversion and methane utilisation can generate a large reaction network comprising thousands of intermediates and reaction pairs. This complexity not only arises from the permutation of transformations between species but also from the extra reaction channels offered by distinct surface sites. Despite the success in investigating surface reactions at the atomic scale, the huge computational expense of ab initio methods hinders the exploration of such complicated reaction networks. With the proliferation of catalysis studies, machine learning as an emerging tool can take advantage of the accumulated reaction data to emulate the output of ab initio methods towards swift reaction prediction. Here, we briefly summarise the conventional workflow of reaction prediction, including reaction network generation, ab initio thermodynamics and microkinetic modelling. An overview of the frequently used regression models in machine learning is presented. As a promising alternative to full ab initio calculations, machine learning interatomic potentials are highlighted. Furthermore, we survey applications assisted by these methods for accelerating reaction prediction, exploring reaction networks, and computational catalyst design. Finally, we envisage future directions in computationally investigating reactions and implementing machine learning algorithms in heterogeneous catalysis.

First-principles calculations of hybrid inorganic-organic interfaces: from state-of-the-art to best practice

The computational characterization of inorganic-organic hybrid interfaces is arguably one of the technically most challenging applications of density functional theory. Due to the fundamentally different electronic properties of the inorganic and the organic components of a hybrid interface, the proper choice of the electronic structure method, of the algorithms to solve these methods, and of the parameters that enter these algorithms is highly non-trivial. In fact, computational choices that work well for one of the components often perform poorly for the other. As a consequence, default settings for one materials class are typically inadequate for the hybrid system, which makes calculations employing such settings inefficient and sometimes even prone to erroneous results. To address this issue, we discuss how to choose appropriate atomistic representations for the system under investigation, we highlight the role of the exchange-correlation functional and the van der Waals correction employed in the calculation and we provide tips and tricks how to efficiently converge the self-consistent field cycle and to obtain accurate geometries. We particularly focus on potentially unexpected pitfalls and the errors they incur. As a summary, we provide a list of best practice rules for interface simulations that should especially serve as a useful starting point for less experienced users and newcomers to the field.

Anharmonic Correction to Adsorption Free Energy from DFT-Based MD Using Thermodynamic Integration

Adsorption processes are often governed by weak interactions for which the estimation of entropy contributions by means of the harmonic approximation is prone to be inaccurate. Thermodynamic integration (TI) from the harmonic to the fully interacting system (λ-path integration) can be used to compute anharmonic corrections. Here, we combine TI with (curvilinear) internal coordinates in periodic systems to make the formalism available in computational studies. Our implementation of ab initio molecular dynamics in VASP is independent of the reaction path and can be thus applied to study adsorption processes relative to the gas phase and does hence provide a useful tool for computational catalysis. We discuss the application of the approach on three model systems for which exact semianalytical solutions exist and illustrate and quantify the importance of anharmonic vibrations, hindered rotations, and hindered translations (dissociation). Eventually, we apply the method to study the adsorption of small adsorbates in a zeolite (H-SSZ-13).

Anharmonic Lattice Vibrations in Small-Molecule Organic Semiconductors

The intermolecular lattice vibrations in small-molecule organic semiconductors have a strong impact on their functional properties. Existing models treat the lattice vibrations within the harmonic approximation. In this work, polarization-orientation (PO) Raman measurements are used to monitor the temperature-evolution of the symmetry of lattice vibrations in anthracene and pentacene single crystals. Combined with first-principles calculations, it is shown that at 10 K, the lattice dynamics of the crystals are indeed harmonic. However, as the temperature is increased, specific lattice modes gradually lose their PO dependence and become more liquid-like. This finding is indicative of a dynamic symmetry breaking of the crystal structure and shows clear evidence of the strongly anharmonic nature of these vibrations. Pentacene also shows an apparent phase transition between 80 and 150 K, indicated by a change in the vibrational symmetry of one of the lattice modes. These findings lay the groundwork for accurate predictions of the electronic properties of high-mobility organic semiconductors at room temperature.

Surface Induced Phenytoin Polymorph. 2. Structure Validation by Comparing Experimental and Density Functional Theory Raman Spectra

A method for structure solution in thin films that combines grazing incidence X-ray diffraction data analysis and crystal structure prediction was presented in a recent work (Braun et al. Cryst. Growth Des.2019, DOI: 10.1021/acs.cgd.9b00857). Applied to phenytoin form II, which is only detected in films, the approach gave a very reasonable, but not fully confirmed, candidate structure with Z = 4 and Z' = 2. In the present work, we demonstrate how, by calculating and measuring the crystal Raman spectrum in the low wavenumber energy region with the aim of validating the candidate structure, this can be further refined. In fact, we find it to correspond to a saddle point of the energy landscape of the system, from which a minimum of lower symmetry may be reached. With the new structure, with Z = 4 and Z' = 2, we finally obtain an excellent agreement between experimental and calculated Raman spectra.

Accuracy and reproducibility in crystal structure prediction: the curious case of ROY

Because of excessive electron delocalization, the polymorphs of ROY constitute a surprisingly challenging system for crystal structure prediction.

Intermediate Bands in Zero-Dimensional Antimony Halide Perovskites

Using density functional theory, the structural and electronic-structure properties of a recently discovered, zero-dimensional antimony halide perovskite are studied. It is found that the herein considered material EtPySbBr₆ exhibits very promising electronic-structure properties: a direct band gap close to the peak of the solar spectrum and effective masses allowing for efficient carrier transport of electrons in particular. These results are rationalized by analysis of the electronic structure, which reveals the formation of intermediate bands due to orbital-hybridization effects of the Sb s-states. This study shows that the formation of intermediate bands can lead to highly favorable electronic-structure properties of zero-dimensional perovskites and discusses the possibility of fabricating lead-free halide perovskites with promising optoelectronic properties by targeted substitution of ions and emergence of intermediate bands. These insights are important when understanding and further enhancing the capabilities of antimony and other promising lead-free compounds.

Exploring the driving forces behind the structural assembly of biphenylthiolates on Au(111)

In this contribution, we use dispersion-corrected density functional theory to study inter- and intramolecular interactions in a prototypical self-assembled monolayer (SAM) consisting of biphenylthiolates bonded to Au(111) via thiolate groups. The goal is to identify the nature of the interactions that drive the monolayer into a specific conformation. Particular focus is laid on sampling realistic structures rather than high symmetry model configurations. This is achieved by studying conceptually different local minimum structures of the SAM that are obtained via exploring the potential energy surface from systematically varied starting geometries. The six obtained packing motifs differ in the relative arrangement of the two molecules in the unit cell (co-planar versus herringbone) and in the intramolecular configuration (twisted versus planar rings). We find that van der Waals interactions within the organic adsorbate and between the adsorbate and substrate are the main reason that these molecular assemblies can form stable structures at all. The van der Waals interactions are, however, very similar for all observed motifs; by analyzing various types of interactions in the course of three notional SAM-formation steps, we find that the main driving force stabilizing the actual global minimum structure originates from electrostatic interactions between the molecules.

Depolymerization of sodium polyphosphates on an iron oxide surface at high temperature

Density functional theory (DFT) and first principles molecular dynamics (FPMD) studies of pyrophosphate cluster Na₄P₂O₇ and triphosphate cluster Na₅P₃O₁₀ absorbed and decomposed on an Fe₂O₃(0001) surface have been conducted. Comparative analyses of the structure properties and adsorption processes during the simulation at elevated temperature have been carried out. The results depict the key interactions including the covalent P-O bonds, pure ionic Na-O or Fe-O interactions. The iron oxide surface plays an important role in the bridging bond decomposition scheme which can both promote and suppress phosphate depolymerization. It is found that the chain length of polyphosphates does not have considerable effects on the decomposition of phosphate clusters. This study provides detailed insights into the interaction of a phosphate cluster on an iron oxide surface at high temperature, and in particular the depolymerization/polymerization of an inorganic phosphate glass lubricant, which has an important behavior under hot metal forming conditions.

Fully Atomistic Understanding of the Electronic and Optical Properties of a Prototypical Doped Charge-Transfer Interface

The current study generates profound atomistic insights into doping-induced changes of the optical and electronic properties of the prototypical PTCDA/Ag(111) interface. For doping K atoms are used, as K_xPTCDA/Ag(111) has the distinct advantage of forming well-defined stoichiometric phases. To arrive at a conclusive, unambiguous, and fully atomistic understanding of the interface properties, we combine state-of-the-art density-functional theory calculations with optical differential reflectance data, photoelectron spectra, and X-ray standing wave measurements. In combination with the full structural characterization of the K_xPTCDA/Ag(111) interface by low-energy electron diffraction and scanning tunneling microscopy experiments (ACS Nano 2016, 10, 2365-2374), the present comprehensive study provides access to a fully characterized reference system for a well-defined metal-organic interface in the presence of dopant atoms, which can serve as an ideal benchmark for future research and applications. The combination of the employed complementary techniques allows us to understand the peculiarities of the optical spectra of K₂PTCDA/Ag(111) and their counterintuitive similarity to those of neutral PTCDA layers. They also clearly describe the transition from a metallic character of the (pristine) adsorbed PTCDA layer on Ag(111) to a semiconducting state upon doping, which is the opposite of the effect (degenerate) doping usually has on semiconducting materials. All experimental and theoretical efforts also unanimously reveal a reduced electronic coupling between the adsorbate and the substrate, which goes hand in hand with an increasing adsorption distance of the PTCDA molecules caused by a bending of their carboxylic oxygens away from the substrate and toward the potassium atoms.

Global structure search for molecules on surfaces: Efficient sampling with curvilinear coordinates

Efficient structure search is a major challenge in computational materials science. We present a modification of the basin hopping global geometry optimization approach that uses a curvilinear coordinate system to describe global trial moves. This approach has recently been shown to be efficient in structure determination of clusters [C. Panosetti et al., Nano Lett. 15, 8044-8048 (2015)] and is here extended for its application to covalent, complex molecules and large adsorbates on surfaces. The employed automatically constructed delocalized internal coordinates are similar to molecular vibrations, which enhances the generation of chemically meaningful trial structures. By introducing flexible constraints and local translation and rotation of independent geometrical subunits, we enable the use of this method for molecules adsorbed on surfaces and interfaces. For two test systems, trans-β-ionylideneacetic acid adsorbed on a Au(111) surface and methane adsorbed on a Ag(111) surface, we obtain superior performance of the method compared to standard optimization moves based on Cartesian coordinates.

Employing X-ray Photoelectron Spectroscopy for Determining Layer Homogeneity in Mixed Polar Self-Assembled Monolayers

Self-assembled monolayers (SAMs) containing embedded dipolar groups offer the particular advantage of changing the electronic properties of a surface without affecting the SAM-ambient interface. Here we show that such systems can also be used for continuously tuning metal work functions by growing mixed monolayers consisting of molecules with different orientations of the embedded dipolar groups. To avoid injection hot-spots when using the SAM-modified electrodes in devices, a homogeneous mixing of the two components is crucial. We show that a combination of high-resolution X-ray photoelectron spectroscopy with state-of-the-art simulations is an ideal tool for probing the electrostatic homogeneity of the layers and thus for determining phase separation processes in polar adsorbate assemblies down to inhomogeneities at the molecular level.

Valence and Conduction Band Densities of States of Metal Halide Perovskites: A Combined Experimental-Theoretical Study

We report valence and conduction band densities of states measured via ultraviolet and inverse photoemission spectroscopies on three metal halide perovskites, specifically methylammonium lead iodide and bromide and cesium lead bromide (MAPbI3, MAPbBr3, CsPbBr3), grown at two different institutions on different substrates. These are compared with theoretical densities of states (DOS) calculated via density functional theory. The qualitative agreement achieved between experiment and theory leads to the identification of valence and conduction band spectral features, and allows a precise determination of the position of the band edges, ionization energy and electron affinity of the materials. The comparison reveals an unusually low DOS at the valence band maximum (VBM) of these compounds, which confirms and generalizes previous predictions of strong band dispersion and low DOS at the MAPbI3 VBM. This low DOS calls for special attention when using electron spectroscopy to determine the frontier electronic states of lead halide perovskites.

High Chloride Doping Levels Stabilize the Perovskite Phase of Cesium Lead Iodide

Cesium lead iodide possesses an excellent combination of band gap and absorption coefficient for photovoltaic applications in its perovskite phase. However, this is not its equilibrium structure under ambient conditions. In air, at ambient temperature it rapidly transforms to a nonfunctional, so-called yellow phase. Here we show that chloride doping, particularly at levels near the solubility limit for chloride in a cesium lead iodide host, provides a new approach to stabilizing the functional perovskite phase. In order to achieve high doping levels, we first co-deposit colloidal nanocrystals of pure cesium lead chloride and cesium lead iodide, thereby ensuring nanometer-scale mixing even at compositions that potentially exceed the bulk miscibility of the two phases. The resulting nanocrystal solid is subsequently fused into a polycrystalline thin film by chemically induced, room-temperature sintering. Spectroscopy and X-ray diffraction indicate that the chloride is further dispersed during sintering and a polycrystalline mixed phase is formed. Using density functional theory (DFT) methods in conjunction with nudged elastic band techniques, low-energy pathways for interstitial chlorine diffusion into a majority-iodide lattice were identified, consistent with the facile diffusion and fast halide exchange reactions observed. By comparison to DFT-calculated values (with the PBE exchange-correlation functional), the relative change in band gap and the lattice contraction are shown to be consistent with a Cl/I ratio of a few percent in the mixed phase. At these incorporation levels, the half-life of the functional perovskite phase in a humid atmosphere increases by more than an order of magnitude.

Adsorption Behavior of Nonplanar Phthalocyanines: Competition of Different Adsorption Conformations

Using density functional theory augmented with state-of-the-art van der Waals corrections, we studied the geometric and electronic properties of nonplanar chlorogallium-phthalocyanine GaClPc molecules adsorbed on Cu(111). Comparing these results with published experimental data for adsorption heights, we found indications for breaking of the metal-halogen bond when the molecule is heated during or after the deposition process. Interestingly, the work-function change induced by this dissociated geometry is the same as that computed for an intact adsorbate layer in the "Cl-down" configuration, with both agreeing well with the experimental photoemission data. This is unexpected, as the chemical natures of the adsorbates and the adsorption distances are markedly different in the two cases. The observation is explained as a consequence of Fermi-level pinning due to fractional charge transfer at the interface. Our results show that rationalizing the adsorption configurations on the basis of electronic interface properties alone can be ambiguous and that additional insight from dispersion-corrected DFT simulations is desirable.

Complex Stoichiometry-Dependent Reordering of 3,4,9,10-Perylenetetracarboxylic Dianhydride on Ag(111) upon K Intercalation

Alkali metal atoms are frequently used for simple yet efficient n-type doping of organic semiconductors and as an ingredient of the recently discovered polycyclic aromatic hydrocarbon superconductors. However, the incorporation of dopants from the gas phase into molecular crystal structures needs to be controlled and well understood in order to optimize the electronic properties (charge carrier density and mobility) of the target material. Here, we report that potassium intercalation into the pristine 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) monolayer domains on a Ag(111) substrate induces distinct stoichiometry-dependent structural reordering processes, resulting in highly ordered and large KxPTCDA domains. The emerging structures are analyzed by low-temperature scanning tunneling microscopy, scanning tunneling hydrogen microscopy (ST[H]M), and low-energy electron diffraction as a function of the stoichiometry. The analysis of the measurements is corroborated by density functional theory calculations. These turn out to be essential for a correct interpretation of the experimental ST[H]M data. The epitaxy types for all intercalated stages are determined as point-on-line. The K atoms adsorb in the vicinity of the oxygen atoms of the PTCDA molecules, and their positions are determined with sub-Ångström precision. This is a crucial prerequisite for the prospective assessment of the electronic properties of such composite films, as they depend rather sensitively on the mutual alignment between donor atoms and acceptor molecules. Our results demonstrate that only the combination of experimental and theoretical approaches allows for an unambiguous explanation of the pronounced reordering of KxPTCDA/Ag(111) upon changing the K content.

Understanding Chemical versus Electrostatic Shifts in X-ray Photoelectron Spectra of Organic Self-Assembled Monolayers

The focus of the present article is on understanding the insight that X-ray photoelectron spectroscopy (XPS) measurements can provide when studying self-assembled monolayers. Comparing density functional theory calculations to experimental data on deliberately chosen model systems, we show that both the chemical environment and electrostatic effects arising from a superposition of molecular dipoles influence the measured core-level binding energies to a significant degree. The crucial role of the often overlooked electrostatic effects in polar self-assembled monolayers (SAMs) is unambiguously demonstrated by changing the dipole density through varying the SAM coverage. As a consequence of this effect, care has to be taken when extracting chemical information from the XP spectra of ordered organic adsorbate layers. Our results, furthermore, imply that XPS is a powerful tool for probing local variations in the electrostatic energy in nanoscopic systems, especially in SAMs.

Role of Dispersive Interactions in Determining Structural Properties of Organic-Inorganic Halide Perovskites: Insights from First-Principles Calculations

A microscopic picture of structure and bonding in organic-inorganic perovskites is imperative to understanding their remarkable semiconducting and photovoltaic properties. On the basis of a density functional theory treatment that includes both spin-orbit coupling and dispersive interactions, we provide detailed insight into the crystal binding of lead-halide perovskites and quantify the effect of different types of interactions on the structural properties. Our analysis reveals that cohesion in these materials is characterized by a variety of interactions that includes important contributions from both van der Waals interactions among the halide atoms and hydrogen bonding. We also assess the role of spin-orbit coupling and show that it causes slight changes in lead-halide bonding that do not significantly affect the lattice parameters. Our results establish that consideration of dispersive effects is essential for understanding the structure and bonding in organic-inorganic perovskites in general and for providing reliable theoretical predictions of structural parameters in particular.

Effect of Anharmonicity on Adsorption Thermodynamics

The effect of anharmonic corrections to the vibrational energies of extended systems is explored. Particular attention is paid to the thermodynamics of adsorption of small molecules on catalytically relevant systems typically affected by anharmonicity. The implemented scheme obtains one-dimensional anharmonic model potentials by distorting the equilibrium structure along the normal modes using both rectilinear (Cartesian) or curvilinear (internal) representations. Only in the latter case, the modes are decoupled also at higher order of the potential and the thermodynamic functions change in the expected directions. The method is applied to calculate ab initio enthalpies, entropies, and Gibbs free energies for the adsorption of methane in acidic chabazite (H-CHA) and on MgO(001) surface. The values obtained for the adsorption of methane in H-CHA (273.15 K, 0.1 MPa, θ = 0.5) are ΔH = -19.3, -TΔS = 11.9, and ΔG = -7.5 kJ/mol. For methane on the MgO(001) (47 K, 1.3 × 10(-14) MPa, θ = 1) ΔH = -14.4, -TΔS = 16.6, and ΔG = 2.1 kJ/mol are obtained. The calculated desorption temperature is 44 K, and the desorption prefactor is 4.26 × 10(12) s(-1). All calculated results agree within chemical accuracy limits with experimental data.

Understanding the adsorption of CuPc and ZnPc on noble metal surfaces by combining quantum-mechanical modelling and photoelectron spectroscopy

Phthalocyanines are an important class of organic semiconductors and, thus, their interfaces with metals are both of fundamental and practical relevance. In the present contribution we provide a combined theoretical and experimental study, in which we show that state-of-the-art quantum-mechanical simulations are nowadays capable of treating most properties of such interfaces in a quantitatively reliable manner. This is shown for Cu-phthalocyanine (CuPc) and Zn-phthalocyanine (ZnPc) on Au(111) and Ag(111) surfaces. Using a recently developed approach for efficiently treating van der Waals (vdW) interactions at metal/organic interfaces, we calculate adsorption geometries in excellent agreement with experiments. With these geometries available, we are then able to accurately describe the interfacial electronic structure arising from molecular adsorption. We find that bonding is dominated by vdW forces for all studied interfaces. Concomitantly, charge rearrangements on Au(111) are exclusively due to Pauli pushback. On Ag(111), we additionally observe charge transfer from the metal to one of the spin-channels associated with the lowest unoccupied π-states of the molecules. Comparing the interfacial density of states with our ultraviolet photoelectron spectroscopy (UPS) experiments, we find that the use of a hybrid functionals is necessary to obtain the correct order of the electronic states.

Anticorrelation between the Evolution of Molecular Dipole Moments and Induced Work Function Modifications

We explore the limits of modifying metal work functions with large molecular dipoles by systematically increasing the dipole moment of archetype donor-acceptor molecules in self-assembled monolayers on gold. Contrary to intuition, we find that enhancing the dipoles leads to a reduction of the adsorption-induced change of the work function. Using atomistic simulations, we show that large dipoles imply electronic localization and level shifts that drive the interface into a thermodynamically unstable situation and trigger compensating charge reorganizations working against the molecular dipoles. Under certain circumstances, these are even found to overcompensate the effect that increasing the dipoles has for the work function.