Density Functional Theory Level Research Articles

A Robust and Efficient Propane Dehydrogenation Catalyst from Unexpectedly Segregated Pt2Mn Nanoparticles

The increasing demand for short chain olefins like propene for plastics production and the availability of shale gas make the development of highly performing propane dehydrogenation (PDH) catalysts, robust toward industrially applied harsh regeneration conditions, a highly important field of research. A combination of surface organometallic chemistry and thermolytic molecular precursor approach was used to prepare a nanometric, bimetallic Pt-Mn material (3 wt % Pt, 1.3 wt % Mn) supported on silica via consecutive grafting of a Mn and Pt precursor on surface OH groups present on the support surface, followed by a treatment under a H2 flow at high temperature. The material exhibits a 70% fraction of the overall Mn as MnII single sites on the support surface; the remaining Mn is incorporated in segregated Pt2Mn nanoparticles. The material shows great performance in PDH reaction with a low deactivation rate. In particular, it shows outstanding robustness during repeated regeneration cycles, with conversion and selectivity stabilizing at ca. 37 and 98%, respectively. Notably, a material with a lower Pt loading of only 0.05 wt % shows an outstanding catalytic performance─initial productivity of 4523 gC3H6/gPt h and an extremely low kd of 0.003 h-1 under a partial pressure of H2, which are among the highest reported productivities. A combined in situ X-ray absorption spectroscopy, scanning transmission electron microscopy, electron paramagnetic resonance, and metadynamics at the density functional theory level study could show that the strong interaction between the MnII-decorated support and the unexpectedly segregated Pt2Mn particles is most likely responsible for the outstanding performance of the investigated materials.

Beryllium incorporation in corundum

AbstractThe structure of corundum is not amenable to accommodating beryllium, yet Be is commonly added to corundum for purposes of colour modification. Where the main sites in corundum are octahedrally coordinated, Be is tetrahedrally coordinated in all known Be minerals. To attempt to explain this discrepancy, the configurations of Be in the Be–Al–O±H system were determined using density functional theory (DFT). In the Be–Al–O system, the most likely Be configuration is in triangular coordination, replacing Al and bonded to three oxygen on the basal plane (large triangle) of the Al-vacant octahedral site. When H is added, OH groups form at the opposite face of the same octahedron, pointing either into or out of the site. Be–H (beryllium hydride) defects are also stable at the DFT level, with Be bonded to three O and one H. As some defects contain O–H or Be–H bonds, the DFT calculations can be corroborated by FTIR spectroscopy. Spectra recorded from 1000 corundum crystals with elevated Be confirm that bands centred at 3062 and 2490 cm–1correspond to Be-associated defects. Polarised spectra show that the band at 2490 cm–1resolves into two, one centred at 2491 cm–1, with a shoulder at 2523 cm–1, one of which is probably associated with a Be–H bond. The 3062 cm–1band resolves into at least three, including a major band at 3058 cm–1, a shoulder at 3140 cm–1and a small, sharp band at 3082 cm–1. Whilst there are caveats relating to curve fitting and baseline subtraction, the 3058 cm–1band can probably be attributed to the defect where H points into the Al-vacant octahedral site, and the 3140 cm–1band to the defect where the H points out. To our knowledge, this is the first occurrence of Be in triangular coordination proposed for a naturally occurring mineral. This substitution mechanism may also explain the high diffusivity of Be, as Be is effectively associated with its own Al vacancy.

Atomistic kinetic Monte Carlo simulation on atomic layer deposition of TiN thin film

The atomic layer deposition (ALD) process of TiN thin films is widely used in microelectronics, but the detailed growth mechanism is still elusive at the atomistic level. In the present computational study, we carry out kinetic Monte Carlo (kMC) simulations on the ALD process using TiCl4 and NH3 precursors. Based on the on-lattice model, we sort out key reactions relevant for the ALD process such as adsorption/desorption of precursors, generation of surface Cl atoms, and evolution of free HCl and Cl2 molecules. The reaction energies considering local environments are calculated at the level of density functional theory (DFT) while the activation barriers are linearly fitted to sampled cases among distinct reaction families. The resulting kMC model produces the temperature-dependent growth rates and the amounts of Cl residues in reasonable agreement with experiments. The detailed growth pathway is discussed based on the simulation results, which underscores the critical role of surface Cl atoms in the ALD process by generating HCl gas molecules. By revealing the atomistic mechanisms in the TiN-ALD process, the present work would help optimize material properties of TiN thin films.

Interaction of 5-fluorouracil anticancer drug with nucleobases: insight from DFT, TD-DFT, and AIM calculations

In this study, the interaction of 5-fluorouracil (5FU) drug with adenine (A), guanine(G), cytosine(C), uracil (U), and thymine (T) nucleobases of DNA and RNA are surveyed at the ωB97XD/LANL2DZ, M06-2X/6-31G (d, p), MPW1PWQ1/6-31G(d, p), PBEPBE/6-31(d, p) and ωB97XD/6-31G(d, p) levels of density functional theory (DFT). The considered complexes of 5FU drug with nucleobases are optimized at the above level of theories. Max Force and RMS of optimization criteria are 0.00035 (Ha), and 0.0003 respectively. From optimized structures, the adsorption energy, thermodynamic parameters in gas and solvent media, quantum theory atom in molecule (QTAIM), electron localized function (ELF), and reduced density gradient (RDG) are calculated at ωB97XD/LANL2DZ and M06-2X/6-31G (d, p) level of DFT theory. The QTAIM, ELF, and RDG results confirm that the nature of bonding between 5FU drug with A, C, G, U, and T nucleobases is electrostatic or hydrogen bond type. The adsorption and thermodynamic energy results demonstrate that the interaction of the 5FU drug with C and G nucleobases is stronger than other nucleobases. The results of this study can be suggested the mechanism of interaction of the 5FU drug with nucleobases of DNA and RNA. Communicated by Ramaswamy H. Sarma

Near-Quantitative Predictions of the First-Shell Coordination Structure of Hydrated First-Row Transition Metal Ions Using K-Edge X-ray Absorption Near-Edge Spectroscopy.

The solvation structure of transition metal ions is important for applications in geochemistry, biochemistry, energy storage, and environmental chemistry. We study the X-ray absorption pre-edge and near-edge spectra at the K-edge of a nearly complete series of hydrated first-row transition metal ions with d orbital occupancy from d2 to d10. We optimize all of the structures at the density functional theory (DFT) level with explicit solvation and then compute the pre-edge X-ray absorption spectra with time-dependent DFT (TDDFT) and restricted active space second-order perturbation theory (RASPT2). TDDFT provides accurate results for spectra that are dominated by single excitations, while RASPT2 correctly distinguishes between singly and doubly excited states with quantitative accuracy compared with experiment. We analyze the pre-edge features for each metal ion to reveal the impact of the variations in d orbital occupancy on the first-shell coordination environment. We also report the lowest-energy ligand field d-d transitions using complete active space second-order perturbation theory.

Top-down formation of ethylene from fragmentation of superhydrogenated polycyclic aromatic hydrocarbons

Context. Fragmentation is an important decay mechanism for polycyclic aromatic hydrocarbons (PAHs) under harsh interstellar conditions and represents a possible formation pathway for small molecules such as H2, C2H2, and C2H4. Aims. Our aim is to investigate the dissociation mechanism of superhydrogenated PAHs that undergo energetic processing and the formation pathway of small hydrocarbons. Methods. We obtain, experimentally, the mass distribution of protonated tetrahydropyrene (C16H15+, [py + 5H]+) and protonated hex-ahydropyrene (C16H17+, [py + 7H]+) upon collision-induced dissociation (CID). The infrared (IR) spectra of their main fragments are recorded by infrared multiple-photon dissociation (IRMPD). Extended tight-binding (GFN2-xTB) based molecular dynamics (MD) simulations were performed in order to provide the missing structure information for this experiment and to identify fragmentation path ways. The pathways for fragmentation were further investigated at a hybrid density functional theory (DFT) and dispersion-corrected level. Results. A strong signal for loss of 28 mass units of [py + 7H]+ is observed both in the CID experiment and the MD simulation, while [py + 5H]+ shows a negligible signal for the product corresponding to a mass loss of 28. The 28 mass loss from [py + 7H]+ is assigned to the loss of ethylene (C2H4) and a good fit between the calculated and experimental IR spectrum of the resulting fragment species is obtained. Further DFT calculations show favorable kinetic pathways for loss of C2H4 from hydrogenated PAH configurations involving three consecutive CH2 molecular entities. Conclusions. This joint experimental and theoretical investigation proposes a chemical pathway of ethylene formation from fragmentation of superhydrogenated PAHs. This pathway is sensitive to hydrogenated edges (e.g., the degree of hydrogenation and the hydrogenated positions). The inclusion of this pathway in astrochemical models may improve the estimated abundance of ethylene.

DFTB Parameters for the Periodic Table: Part III, Spin-Orbit Coupling

Spin-orbit coupling (SOC) is crucially important for the correct description of the electronic structure and transport properties of inorganic semiconductors, and for assessing topological properties as in topological insulators. We present a consistent set of SOC parameters for the density-functional based tight-binding (DFTB) method covering the elements throughout the periodic table. The parameters are based on atomic SOC data calculated at the level of density-functional theory (DFT). We tested these parameters for representative systems with significant SOC, including transition metal dichalcogenide two-dimensional crystals, III-V bulk semiconductors, and topological insulators. Our parameterization opens the door for DFTB-based electronic structure and transport calculations of very large systems, such as twisted van der Waals heterostructures.

Pyridoxal 5′-phosphate 2-methyl-3-furoylhydrazone as a selective sensor for Zn2+ ions in water and drug samples

Present paper reports on the synthesis and characterization of novel chemosensor for zinc(II) ion, a hydrazone derived from pyridoxal 5′-phosphate. The conformational diversity of the free ligand was studied by quantum chemistry methods at the B3LYP/ECP10MWB (Zn)/cc-pVTZ (H, C, N, O, P) level of density functional theory, and the optimal structures of free ligand and zinc(II) complex were chosen. The ligand has a selective ability to detect Zn2+ in the aqueous solution, which also contains Na+, K+, Ca2+, Mg2+, Ba2+, Cd2+, Pb2+, UO22+. The detection is based on the formation of the zinc(II) complex, which has the enhanced fluorescent intensity in comparison with that of free hydrazone. The complex was also characterized comprehensively; the stability constant, quantum yield, and structure peculiarities were determined. Potential practical applications of the developed chemosensor for water and drug analysis, as well as bioimaging, were demonstrated.

Tritopic Bis-Urea Receptors for Anion and Ion-Pair Recognition.

This work reports on the synthesis and characterization of three tritopic receptors and their binding properties toward various anions, as their tetrabutylammonium salts, and three alkali metal–acetate salts by UV–vis, fluorescence, 1H, 7Li, 23Na, and 39K NMR in MeCN/dimethyl sulfoxide (DMSO) 9:1 (v/v). Molecular recognition studies showed that the receptors have good affinity for oxyanions. Furthermore, these compounds are capable of ion-pair recognition of the alkali metal–acetate salts studied through a cooperative mechanism. Additionally, molecular modeling at the density functional theory (DFT) level of some lithium and sodium acetate complexes illustrates the ion-pair binding capacity of receptors. The anion is recognized through strong hydrogen bonds of the NH– groups from the two urea sites, while the cation interacts with the oxygen atoms of the polyether spacer. This work demonstrates that these compounds are good receptors for anions and ion pairs.

PH Dependence of MgO, TiO2, and γ-Al2O3 Surface Chemistry from First Principles

We investigate the pH-dependent surface chemistry of three relevant and widely used oxides, MgO, TiO2, and γ-Al2O3, from ab initio molecular dynamics simulations at the level of density functional theory (DFT). We studied the MgO (001), anatase TiO2 (101), and γ-Al2O3 (001) low-index surfaces and considered solvation effects by explicitly simulating the solid/water interfaces. The analysis of the MgO/H2O, TiO2/H2O, γ-Al2O3/H2O interfaces allowed us to access atomistic details of the structure and the effects induced by water on these surfaces. We also investigated the pH dependence by means of the Grand Canonical formulation of species in solution. This allowed us to evaluate acid–base equilibrium constants and the point-of-zero charge (pHPZC) values. The calculated pHPZC values compare well with available experimental measurements. Based on the above result, we also predicted the fraction of charged species (H+ and OH–) and neutral molecules (H2O) present on the surface as a function of pH, a fundamental aspect if one wants to identify suitable catalysts for water splitting reactions.

Thermodynamics up to the melting point in a TaVCrW high entropy alloy: Systematic ab initio study aided by machine learning potentials

Multi-principal-component alloys have attracted great interest as a novel paradigm in alloy design, with often unique properties and a vast compositional space auspicious for materials discovery. High entropy alloys (HEAs) belong to this class and are being investigated for prospective nuclear applications with reported superior mechanical properties including high-temperature strength and stability compared to conventional alloys. Computational materials design has the potential to play a key role in screening such alloys, yet for high-temperature properties, challenges remain in finding an appropriate balance between accuracy and computational cost. Here we develop an approach based on density-functional theory (DFT) and thermodynamic integration aided by machine learning based interatomic potential models to address this challenge. We systematically evaluate and compare the efficiency of computing the full free energy surface and thermodynamic properties up to the melting point at different stages of the thermodynamic integration scheme. Our new approach provides a $\ifmmode\times\else\texttimes\fi{}4$ speed-up with respect to comparable free energy approaches at the level of DFT, with errors on high-temperature free energy predictions less than 1 meV/atom. Calculations are performed on an equiatomic HEA, TaVCrW---a low-activation composition and therefore of potential interest for next generation fission and fusion reactors.

QMugs, quantum mechanical properties of drug-like molecules

Machine learning approaches in drug discovery, as well as in other areas of the chemical sciences, benefit from curated datasets of physical molecular properties. However, there currently is a lack of data collections featuring large bioactive molecules alongside first-principle quantum chemical information. The open-access QMugs (Quantum-Mechanical Properties of Drug-like Molecules) dataset fills this void. The QMugs collection comprises quantum mechanical properties of more than 665 k biologically and pharmacologically relevant molecules extracted from the ChEMBL database, totaling ~2 M conformers. QMugs contains optimized molecular geometries and thermodynamic data obtained via the semi-empirical method GFN2-xTB. Atomic and molecular properties are provided on both the GFN2-xTB and on the density-functional levels of theory (DFT, ωB97X-D/def2-SVP). QMugs features molecules of significantly larger size than previously-reported collections and comprises their respective quantum mechanical wave functions, including DFT density and orbital matrices. This dataset is intended to facilitate the development of models that learn from molecular data on different levels of theory while also providing insight into the corresponding relationships between molecular structure and biological activity.

Hydrogenation of CO and CO2 Catalyzed by Potassium Chloride F Centers

The role of F centers on the KCl (100) surface in the hydrogenation of carbon monoxide and carbon dioxide was investigated theoretically at density-functional theory level. The surface defect was found to reduce all carbon-containing species involved in the reactions. In all cases, the defect electron occupies the lowest antibonding orbital of the molecules which weakens at least one of the C–O bonds. All reaction barriers of the hydrogenation on the defect are significantly reduced in comparison with the gas-phase reactions. The thermodynamic and kinetic parameters of the reaction pathways were computed, allowing for a comparison with the industrially established Cu/ZnO catalyst for methanol synthesis. It was found that methanol synthesis from CO2 is thermodynamically and kinetically hindered, yielding formate as a product that blocks the F center. The reaction rate for the rate limiting step of the methanol synthesis from CO on the F center is about 10 times higher than that for the conventional catalyst. However, the end product methanol further dissociates into methanolate and free radical hydrogen with only a small activation barrier. Furthermore, it was found that water dissociates into OH– and H• on the defective surface, so that even trace amounts can deactivate the F center.

Spin–Orbit Couplings for Nonadiabatic Molecular Dynamics at the ΔSCF Level

A procedure for the calculation of spin-orbit coupling (SOC) at the delta self-consistent field (ΔSCF) level of theory is presented. Singlet and triplet excited electronic states obtained with the ΔSCF method are expanded into a linear combination of singly excited Slater determinants composed of ground electronic state Kohn-Sham orbitals. This alleviates the nonorthogonality between excited and ground electronic states and introduces a framework, similar to the auxiliary wave function at the time-dependent density functional theory (TD-DFT) level, for the calculation of observables. The ΔSCF observables of the formaldehyde system were compared to reference TD-DFT values. Our procedure gives all components (energies, gradients, nonadiabatic couplings, and SOC terms) at the ΔSCF level of theory for conducting efficient, full-atomistic nonadiabatic molecular dynamics with intersystem crossing, particularly in condensed phase systems.

PH-Responsive switching properties of a water-soluble dinuclear Cu(II) complex containing oximato bridges chelating ligand: Synthesis, crystal structure and computational study

This study presents a combined experimental and computational investigation on a dinuclear Cu(II) complex containing 3-[2-[(ethanol amino)ethyl]imino]-2-butanoneoxime ligand (L). The compound [CuL]2(NO3)2 was studied by IR, UV–Vis spectroscopy, thermogravimetry analysis, and molar conductance measurements. The square-pyramid geometry of the complex was confirmed by both the density functional theory level (DFT) calculation and X-ray crystallography. The complex was halochromic, and its halochromism was studied in an aqueous solution. The original green complex displayed reversible color change to blue in alkaline and colorless in acidic solutions. The pH effect on the visible absorption spectrum of the complex was studied that functions as pH-induced “off–on–off” switches triggered by the protonation and loss of the ligand L in acidic medium and deprotonation of ligand in a basic aqueous solution. Further computational analysis of the electronic structure of the complex was carried out to gain a deeper insight into the properties associated with molecular orbitals. Its electronic spectrum was analyzed, and bands were assigned through the time-dependent density functional theory level (TDDFT) calculation.

Classical Force-Field Parameters for CsPbBr3 Perovskite Nanocrystals.

Understanding the chemico-physical properties of colloidal semiconductor nanocrystals (NCs) requires exploration of the dynamic processes occurring at the NC surfaces, in particular at the ligand–NC interface. Classical molecular dynamics (MD) simulations under realistic conditions are a powerful tool to acquire this knowledge because they have good accuracy and are computationally cheap, provided that a set of force-field (FF) parameters is available. In this work, we employed a stochastic algorithm, the adaptive rate Monte Carlo method, to optimize FF parameters of cesium lead halide perovskite (CsPbBr3) NCs passivated with typical organic molecules used in the synthesis of these materials: oleates, phosphonates, sulfonates, and primary and quaternary ammonium ligands. The optimized FF parameters have been obtained against MD reference trajectories computed at the density functional theory level on small NC model systems. We validated our parameters through a comparison of a wide range of nonfitted properties to experimentally available values. With the exception of the NC–phosphonate case, the transferability of the FF model has been successfully tested on realistically sized systems (>5 nm) comprising thousands of passivating organic ligands and solvent molecules, just as those used in experiments.

Mixtures of Diethyl Sulfoxide and Methanol: Structure and Thermodynamics

Mixtures of sulfoxides with molecular solvents possess interesting physicochemical properties and may have applications in chemical synthesis. Hereby we confirm and rationalize the previously reported excellent miscibility of diethyl sulfoxide (DESO) with methanol (MeOH). By performing a comprehensive potential energy surface investigation we identified a global minimum for each system and a significant number of local minima described at the hybrid density functional level of theory. A strong 0.18 nm long hydrogen bond forming between the oxygen atom of DESO and the polarized hydrogen atom of MeOH was evidenced both via the structural and spectral analyses. Our results robustly explain negative deviations in the DESO–MeOH mixtures from ideal behavior and interpret the experimental observations with microscopic precision.Graphical Abstract

The pKBHX Hydrogen-Bond Basicity Scale: From Molecules to Anions

The pKBHX (logarithm of complexation constant K of 4-fluorophenol with bases) hydrogen-bond basicity scale of neutral hydrogen-bond acceptors (HBAs) is extended to anionic HBAs. The scale is constructed for 26 anions through (i) the infrared measurement of K on NBu4+X- ion pairs in CCl4, (ii) the estimation of K from linear free energy relationships between measured K values and literature K values for various phenols in polar solvents, and (iii) the computation of K at the density functional theory level in CCl4. The scale extends on a 9.4 pK unit range from fluoride to tetraphenylborate. Considering a number of anions as organic functions substituted with unipolar substituents, their pKBHX values can be related to the Hammett-Taft substituent constants σ. Unipolar substituents (O- and S-) obey the same pKBHX versus σ relationships as dipolar ionic (N-N+R3) and dipolar (OH, CF3, NR2, or OR) ones for the nitrile, carbonyl, nitroso, nitro, sulfonyl, and phosphoryl functions. Like dipolar substituents, unipolar substituents at carbon and nitrogen operate by field-inductive and resonance effects, whereas substituents at sulfur and phosphorus operate only by the field-inductive effect.

СПЕЦИФИЧЕСКАЯ РОЛЬ ИОНА ЦИНКА ПРИ ПЕРЕНОСЕ ЭЛЕКТРОНА В МЕДНО-ЦИНКОВОЙ СУПЕРОКСИДДИСМУТАЗЕ

The interaction of the superoxide radical ion O2– with the active center of Cu,Zn-superoxide dismutase was studied by computer simulation using the ORCA software package version 5.0.2. at the level of density functional theory using the PBE functional. The main characteristics for two processes of electron transfer in the catalytic cycle of deactivation of the radical ion are obtained. The variable factor in the modeling was the presence of the Zn2+ ion in the active site of the enzyme. It has been established that the presence of the Zn2+ ion contributes to a large extent only to the second electron transfer from the Cu+ ion to the protonated form of the radical ion, to the hydroperoxide radical HO2

Changes in electronic structure of graphene by adsorption of low melamine coverages

Using first-principles simulations at Density Functional Theory (DFT) level, we concluded a comprehensive study of the molecular doping of graphene by melamine adsorption. We characterized the different possible positions achieved by the molecule on a pristine graphene or a Stone-Wales defect (5-7-7-5) were characterized. We also analyzed adsorption energies, deformations experienced by melamine and charge separation involved in the process. The defective graphene sheet turned out to be more flexible than the pristine one, exhibiting greater deformations. Melamine adsorption on Stone-Wales defect is preferred and it can be used as a useful strategy to carry out the molecular doping of graphene. Due to adsorption, a charge separation is generated between melamine and graphene, giving rise to an organic/organic interface with a net interfacial dipole. This change in the electronic structure of graphene favors the dynamics of the excited electronic state, tuning it an interesting material used in optoelectronic devices.