Plane-wave DFT Research Articles

Determination of stability constants of Cu(II)2-bistren cascade complexes by cellmetry method

Cu(II)2-bistren cascade complexes were studied by cellmetry methodology where by choosing appropriate cell sizes of the box the logK values can be calculated by a plane wave DFT method. Different types of anions were chosen to study the effect of the size, shape, and bite length of the donor atoms on the stability constants. It was found that the ligand strain needs to be taken into account to calculate reasonable logK values. Correction factors were determined regarding the energy of the anions and the length of the bistren ligands which resulted in accurate calculated stability constants for all types of anions.

Probing the Molecular and Macroscopic Structure of Solid Solutions by Dynamic Nuclear Polarization (DNP) Enhanced 13C and 15N Solid-State NMR Spectroscopy.

Crystallization is a widely used purification technique in the manufacture of active pharmaceutical ingredients (APIs) and precursor molecules. However, when impurities and desired compounds have similar molecular structures, separation by crystallization may become challenging. In such cases, some impurities may form crystalline solid solutions with the desired product during recrystallization. Understanding the molecular structure of these recrystallized solid solutions is crucial to devise methods for effective purification. Unfortunately, there are limited analytical techniques that provide insights into the molecular structure or spatial distribution of impurities that are incorporated within recrystallized products. In this study, we investigated model solid solutions formed by recrystallizing salicylic acid (SA) in the presence of anthranilic acid (AA). These two molecules are known to form crystalline solid solutions due to their similar molecular structures. To overcome challenges associated with the long 1H longitudinal relaxation times (T1(1H)) of SA and AA, we employed dynamic nuclear polarization (DNP) and 15N isotope enrichment to enable solid-state NMR experiments. Results of solid-state NMR experiments and DFT calculations revealed that SA and AA are homogeneously alloyed as a solid solution. Heteronuclear correlation (HETCOR) experiments and plane-wave DFT structural models provide further evidence of the molecular-level interactions between SA and AA. This research provides valuable insights into the molecular structure of recrystallized solid solutions, contributing to the development of effective purification strategies and an understanding of the physicochemical properties of solid solutions.

Determination of dissociation constants of cephalosporin antibiotics by cellmetry method

Acid dissociation constants of three cephalosporin antibiotics (cefapirin, ceftiofur, and cefotaxime) were calculated by a newly developed methodology. Plane-wave DFT calculations were performed to determine the pKa values, and by choosing the appropriate cell sizes, accurate values could be calculated. Some characteristic points were found which helped us to find correlations among the structural and physic-chemical parameters, and correlation factors were defined as well. This present study can be a base for further approaches to determining acid dissociation constants of cephalosporin molecules.Graphical

Theoretical study of NH3 , H2 S, and HCN adsorption enhancement on defective graphene-supported Cu19 clusters.

Recent studies have shown that graphene-supported metal clusters can enhance catalytic reactivity compared with corresponding metal clusters. In this study, the adsorptions of NH3 , H2 S, and HCN on Cu19 and defective graphene-supported Cu19 clusters are investigated using plane-wave density functional theory. The results reveal the three gas molecules can be adsorbed on three types of top sites of Cu atoms, respectively. The adsorption energies of the corresponding adsorption sites on the defective graphene-supported Cu19 clusters are all increased compared with those on the Cu19 clusters. The orbital-resolved, crystal orbital Hamilton population analysis demonstrates that the larger the integrated crystal orbital Hamilton population, the stronger the adsorption between the gas molecule and the bonded Cu atom. The center of antibonding states on the defective graphene-supported Cu19 is shifted upward relative to Fermi level compared to the corresponding one on pure Cu19 , which explains the enhanced adsorption energy on defective graphene-supported Cu19. In addition, the closer d-band center to the Fermi level on the defective graphene-supported Cu19 indicates a stronger adsorption capacity than on pure Cu19 .

Single-Crystal X-ray Structure Determination of Tris(pyrazol-1-yl)methane Triphenylphosphine Copper(I) Tetrafluoroborate, Hirshfeld Surface Analysis and DFT Calculations

The tetrafluoroborate salt of the cationic Cu(I) complex [Cu(CHpz3)(PPh3)]+, where CHpz3 is the tridentate N-donor ligand tris(pyrazol-1-yl)methane and PPh3 is triphenylphosphine, was synthesized through a displacement reaction on the acetonitrile complex [Cu(NCCH3)4][BF4]. The compound crystallizes in the monoclinic P21/c space group. The single-crystal X-ray diffraction revealed that the copper(I) centre is tetracoordinated, with a disposition of the donor atoms surrounding the metal centre quite far from the ideal tetrahedral geometry, as confirmed by continuous shape measures and by the τ4 parameter. The intermolecular interactions at the solid state were investigated through the Hirshfeld surface analysis, which highlighted the presence of several non-classical hydrogen bonds involving the tetrafluoroborate anion. The electronic structure of the crystal was modelled using plane-wave DFT methods. The computed band gap is around 2.8 eV and separates a metal-centred valence band from a ligand-centred conduction band. NMR spectroscopy indicated the fluxional behaviour of the complex in CDCl3 solution. The geometry of the compound in the presence of chloroform as implicit solvent was simulated by means of DFT calculations, together with possible mechanisms related to the fluxionality. The reversible dissociation of one of the pyrazole rings from the Cu(I) coordination sphere resulted in an accessible process.

Tailoring surface morphology on anatase TiO2 supported Au nanoclusters: implications for O2 activation.

Strong interaction between the support surface and metal clusters activates the adsorbed molecules at the metal cluster-support interface. Using plane-wave DFT calculations, we precisely model the interface between anatase TiO2 and small Au nanoclusters. Our study focusses on the adsorption and activation of oxygen molecules on anatase TiO2, considering the influence of oxygen vacancies and steps on the surface. We find that the plane (101) and the stepped (103) surfaces do not support O2 activation, but the presence of oxygen vacancies results in strong adsorption and O-O bond length elongation. Modifying the TiO2 surface with supported small Au n nanoclusters (n = 3-5) also significantly enhances O2 adsorption and stretches the O-O bond. We observe that manipulating the cluster orientation through discrete rotations results in improved O2 adsorption and promotes charge transfer from the surface to the molecule. We propose that the orientation of the supported cluster may be manipulated by making the cluster adsorb at the step-edge of (103) TiO2. This results in activated O2 at the cluster-support interface, with a peroxide-range bond length and a low barrier for dissociation. Our modeling demonstrates a straightforward means of exploiting the interface morphology for O2 activation under low precious metal loading, which has important implications for electrocatalytic oxidation reactions and the rational design of supported catalysts.

Experimental and quantum chemical investigation into the nature of jet fuel deposition on surfaces

Chemical analysis of undissolved deposits formed on a simulated jet fuel burner feed arm suggest a higher concentration of oxidized polar fuel species at the wall-deposit interface. To investigate the nature of their adsorption, the adsorption energies of various jet fuel species classes were calculated using plane-wave DFT methods on two oxide surfaces Fe2O3-(0001) and Cr2O3-(0001), which were chosen to represent a stainless steel surface. A mixed termination approach was chosen to encapsulate the heterogeneous nature of stainless steel surfaces. On metal-terminated Fe2O3 and Cr2O3 surfaces, the order of the absolute adsorption energies was RSO3H > RSO2H > RCOOH > RSH > ROH > RCOH > RH. Dissociative chemisorption was observed for all the acid species, with sulfur acids having a higher absolute adsorption energy on Cr2O3 but carboxylic acids having a higher adsorption energy on Fe2O3. On oxygen-terminated Fe2O3, the order of the absolute adsorption energies was RSO2H > RSR > RSO3H > RSH > ROH > RCOH > RCOOH > RH. On the other hand, for oxygen-terminated Cr2O3, the order of the absolute adsorption energies were RSO2H > RSR > RSH > RSO3H > RCOH > ROH > RCOOH > RH. In contrast to the metal terminated surface, acids do not chemisorb on the oxygen terminated surfaces. Instead, the sulfur acids are found to form surface hydroxyl species from the dissociation of the acidic -OH group. The reactivity of the surfaces followed the general pattern: metal terminated-Fe2O3> metal-terminated Cr2O3, oxygen-terminated Fe2O3≈ Cr2O3. Overall, a combination of experimental and quantum chemical techniques confirmed the theory that sulfur acids are the initial species to deposit on stainless steel.

Catalytic Activity of LnCo0.5Ni0.5O3-Δ (Ln = La, Pr, Nd) "Positrodes" on Ceramic Protonic Electrolytes

Proton-conducting solid-oxide electrolyzers and fuel cells represent viable, intermediate-temperature green energy conversion and storage technologies. Interest in this class of materials as electrolytes stems from their high ionic conductivity and inherent advantages in the gas flow configuration over traditional solid oxide cells in which the electrolyte is an oxygen ion conductor. However, their commercial viability has been hindered, in part, by the development of corresponding single-phase electrode components with mixed proton-electron conductivity and effective catalytic activity toward oxygen reduction and evolution reactions (ORR/OER). This paper investigates the origin of catalytic activity in LnCo0.5Ni0.5O3-δ (Ln=La, Pr and Nd) perovskites positrodes (positive electrode) by low energy-ion scattering (LEIS) and DFT studies. LEIS results reveal that La, Pr, and Pr cations dominate the outer atomic layer, with profound implications for catalytic activity. Whereas First principle calculations were performed using the plane-wave DFT method and hybrid HSE06 functional suggest, the catalytic activity and electronic properties depend on the valence shell structure of the Ln-site cation and their redox properties.AcknowledgmentsThe authors gratefully acknowledge financial support through JSPS KAKENHI Grant-in-Aid for Scientific Research (C), No. 19K05672, NEDO (International collaboration work in the field of clean energy) JPNP20005, the International Institute for Carbon-Neutral Energy Research (I2CNER) sponsored by the World Premier International Research Center Initiative (WPI),

Self-Consistent Chemical Pressure Analysis: Resolving Atomic Packing Effects through the Iterative Partitioning of Space and Energy.

While planewave DFT methods offer capabilities to calculate the relative stabilities and many physical properties exhibited by solid state structures, their detailed numerical output does not easily map onto the often empirical concepts and parameters used by synthetic chemists or materials scientists. The DFT-chemical pressure (CP) method is an approach to bridging this divide by explaining or anticipating a variety of structural phenomena in terms of atomic size and packing effects, but its reliance on adjustable parameters has limited the method's predictive potential. In this article, we present the self-consistent (sc)-DFT-CP analysis, in which the criterion of self-consistency is used to automatically solve these parameterization issues. We begin by illustrating the need for this improved method with the results for a series of CaCu5-type/MgCu2-type intergrowth structures, where unphysical trends emerge that have no clear structural origin. To address these challenges, we derive iterative treatments for assigning ionicity and for the partitioning of the EEwald + Eα terms in the DFT total energy into homogeneous and localized terms. In this method, self-consistency is achieved between the input and output charges from a variation of the Hirshfeld charge scheme, while the partitioning of the EEwald + Eα terms is adjusted to create equilibrium between the net atomic pressures calculated within atomic regions and from the interatomic interactions. The behavior of the sc-DFT-CP method is then tested using electronic structure data for several hundred compounds from the Intermetallic Reactivity Database. Finally, we return to the CaCu5-type/MgCu2-type intergrowth series with the sc-DFT-CP approach, showing that trends in the series are now easily traced to changes in the thicknesses of the CaCu5-type domains and lattice mismatch at the interface. Through this analysis and the complete update to the CP schemes in the IRD, the sc-DFT-CP method is demonstrated as a theoretical tool for the investigation of atomic packing issues across intermetallic chemistry.

Different Dynamic Behavior of Methyl Groups in Crystalline Carbimazole as Revealed by a Multitechnique Experimental and Theoretical Approach

Dynamic properties of carbimazole (a drug used in hyperthyroidism treatment) were thoroughly investigated by combining solid-state nuclear magnetic resonance spectroscopy and quasielastic neutron scattering with periodic density functional theory (plane-wave DFT) and molecular dynamics simulations. These complementary methods allowed the full description of internal carbimazole motions. Particularly, in crystalline carbimazole, only the reorientations of the two methyl groups were found to be active in the explored timescale. The combination of different techniques allowed the quantitative characterization of the two methyl reorientations, which differ by almost 2 orders of magnitude in the timescale, in agreement with results previously reported in the literature for methyl groups in similar chemical environments. These results could also assume a particular relevance considering the role of methyl groups in determining the biochemical and biological activities of active pharmaceutical ingredients.

Oxygen Reduction and Hydrogen Evolution Reactions on Zigzag ReS2 Nanoribbons

Two-dimensional (2D) rhenium disulfide (ReS2) has received a lot of attention recently as a potential electrocatalyst. Since monolayer ReS2 is catalytically inactive, surface modifications are required to enhance the activity. Some of the methods adopted for this include single-atom doping, vacancy creation, creation of lower dimensional nanostructures like nanoribbons, quantum dots etc. ReS2 nanoribbons have not been as intensely explored as other transition metal dichalcogenides in electrocatalysis. The oxygen reduction and hydrogen evolution activities of two structurally distinct ReS2 nanoribbons are investigated in this work using plane wave DFT. Both type of nanoribbons investigated demonstrates enhanced catalytic activity compared to monolayer ReS2. One of the nanoribbons modelled in our studies promises good performance as a catalyst for oxygen reduction and hydrogen evolution reactions. Based on our model we conclude that the catalytic activity of ReS2 arises primarily from the edges of finite sized nanostructures. Edge activity combined with stability in acidic media and methanol tolerance make ReS2 nanoribbons a promising material for electrochemical applications.

Experimental and theoretical insights into the structure and molecular dynamics of 2,3,3',4'-tetramethoxy-trans-stilbene - a chemopreventive agent.

The methoxy analogue of a trans-stilbene compound - 2,3,3',4'-tetramethoxy-trans-stilbene - was selected to characterize its crystallographic structure, intermolecular interactions and molecular dynamics. The sample was studied using single-crystal X-ray diffraction (XRD), infrared spectroscopy (FT-IR), liquid and solid-state 1H and 13C nuclear magnetic resonance (NMR) and quasielastic neutron scattering (QENS). The compound crystallized in the orthorhombic Pbca space group. The experimental methods were supported by theoretical calculations, density functional theory (plane-wave DFT) and molecular dynamics simulations (MD) methods. Combining several experimental and simulation techniques allowed the detailed analysis of molecular reorientations and provided a consistent picture of the molecular dynamics. The internal molecular mobility of the studied compound can be associated with the reorientational dynamics of four methyl groups. Interestingly, a large diversity of the energy barriers was observed - one methyl group reoriented across low activation barriers (∼3 kJ mol-1), while three methyl groups exhibited a high activation energy (10-14 kJ mol-1) and they are characterised by very different correlation times differing by almost two orders of magnitude at room temperature. The intramolecular interactions mainly influence the activation barriers.

A combined solid-state NMR and quantum chemical calculation study of hydrogen bonding in two forms of α-d-glucose

Hydrogen bonding plays an important role in the structure and function of a wide range of materials. Solid-state 1H nuclear magnetic resonance (NMR) spectroscopy provides a very sensitive tool to investigate the local structure of hydrogen atoms involved in hydrogen bonding. While there is extensive 1H solid-state NMR data on O–H - - O hydrogen bonding in solid carboxylic acids, there has been no systematic 1H solid-state NMR studies of hydroxyl groups in carbohydrates (and hydroxyl groups in general). With a view to studying the hydrogen bonding in more complex materials such as cellulose polymorphs, we carried out a detailed solid-state 1H NMR investigation of the model compounds α-d-glucose and α-d-glucose monohydrate. Through a combination of fast magic-angle spinning (MAS), combined rotation and multiple pulse spectroscopy (CRAMPS), and two-dimensional (2D) correlation experiments carried out at ultrahigh magnetic fields, it was possible to assign all of the aliphatic (CH), hydroxyl (OH), and water (H2O) 1H chemical shifts in both forms of α-d-glucose. Plane-wave DFT calculations were employed to improve the hydrogen atom positions for α-d-glucose monohydrate and to calculate 1H chemical shifts, providing additional support for the experimentally determined peak assignments. Finally, the relationship between the hydroxyl 1H chemical shifts and their hydrogen bonding geometry was investigated and compared to the well-established relationship for carboxylic acid protons.

Influence of impurity configuration on electronic and optical properties of Ce-doped YVO4: Semi-local & hybrid functionals

We investigate the impact of impurity configuration on electronic and optical properties of YVO4 through application of plane-wave DFT. Since this crystal is a common host material for optical devices and it has been widely used as a phosphor and a laser host material, it is important to identify a correlation between impurity location and the intrinsic properties of the material. To further improve the accuracy of the results several semi-local and a hybrid functional are tested. To find the most stable structure among possible configurations of doping, the electronic structures and formation energies of the available configurations are calculated and compared. We report that while the valence is formed by O-2p orbitals and conduction is made of V-3d orbitals in all configurations, the band width varies with the impurity configuration. Additionally, the formation energy is changing depending on where the dopant is located. Then the absorption coefficient and the refractive index are obtained using a modified HSE functional.

Extremely low barrier activation of methane on spin-polarized ferryl ion [FeO]2+ at the four-membered ring of zeolite

The Panov's α-O center in ZSM-5 zeolite revealing extraordinary activity in the oxidation of methane to methanol has been a subject of intense experimental and theoretical studies. Consensus on the structure and the origin of α-O superactivity seems to be achieved only in that α-O represents the ferryl group [FeO]2+ (bound by four lattice oxo sites) in cation-exchange position at some zeolite ring containing two framework Al atoms. Among rings with various sizes only three ones (four-, five-, and six-membered) can provide the ferryl ion with the necessary four number of oxo ligands (in the “plane” of ring) at reasonable Fe-O distance of about 2.0 Å. The six-membered ring is considered as the most probable one due to the 29Si MAS NMR data on Al pairs distribution on zeolite rings. However, the six-membered model in ZSM-5 has not been checked on behalf of the possibility of axial Fe-O coordination along Fe and terminal oxygen axis. By means of plane-wave DFT modeling, the present work shows that this coordination in fact takes place for six-membered ring unlike the four- and five-membered ones in which the Fe cation appears well above the plane of ring making the axial coupling impossible. Therefore, by known strong negative effect of axial oxo ligand on the ferryl species oxidizing activity, the six-membered model has to be discarded. Instead, a model of [FeO]2+ at four- or five-membered ring is to be put forward. In this work the four-membered model is shown to form the oxyl ground state Fe(III)–O• with the radical-like β-spin polarized oxygen. Calculated barrier of hydrogen abstraction from methane on this center is as low as 1.7 kcal/mol. The obtained prediction opens a way for other reactions to be probed on this center, particularly, the condensation of methane and oxidative dehydrogenation of hydrocarbons at low temperatures.

Advanced DFT–NEGF Transport Techniques for Novel 2-D Material and Device Exploration Including HfS2/WSe2 van der Waals Heterojunction TFET and WTe2/WS2 Metal/Semiconductor Contact

We present, here, advanced DFT-NEGF techniques that we have implemented in our ATOmistic MOdelling Solver, ATOMOS, to explore transport in novel materials and devices and in particular in van-der-Waals heterojunction transistors. We describe our methodologies using plane-wave DFT, followed by a Wannierization step, and linear combination of atomic orbital DFT, that leads to an orthogonal and non-orthogonal NEGF model, respectively. We then describe in detail our non-orthogonal NEGF implementation including the Sancho-Rubio and electron-phonon scattering within a non-orthogonal framework. We also present our methodology to extract electron-phonon coupling from first principle and include them in our transport simulations. Finally, we apply our methods towards the exploration of novel 2D materials and devices. This includes 2D material selection and the Dynamically-Doped FET for ultimately scaled MOSFETS, the exploration of vdW TFETs, in particular the HfS2/WSe2 TFET that could achieve high on-current levels, and the study of Schottky-barrier height and transport through a metal-semiconducting WTe2/WS2 VDW junction transistor.

Adsorption of benzene on defective Pt surfaces: A DFT study

Defects occur naturally on surfaces during formation. The interaction of a benzene molecule with a defective surface of platinum is investigated using plane wave DFT. Adsorption energy, adsorbate geometry and electronic structure of benzene on defective surfaces of platinum is obtained and compared with those on a perfect platinum (111) facet. We observe that the presence of defects in the form of steps and vacancy leads to an increase in the strength of adsorption. It is found that the atop is the most stable site for adsorption on a Pt (111) surface having a vacancy defect, which agrees with the available experimental results. The terrace region, which has a symmetry similar to a perfect Pt(111) surface, gives the 3-fold symmetric fcc hollow site as energetically preferred for adsorption. The step edge has the hcp hollow as the preferred site for adsorption. Analysis of electronic structure and charge transfer at the preferred sites is performed. The presence of defects brings out major changes in adsorption process, as compared to that on perfect surfaces. Reduction in coordination of surface sites due to defects is identified as the main reason for more reactive nature of defective surfaces.

Highly exfoliated NiPS3 nanosheets as efficient electrocatalyst for high yield ammonia production

The development of electrocatalytic nitrogen reduction reaction (NRR) at ambient conditions as an alternative to traditional high-temperature ammonia synthesis is a vibrant research topic due to the potential to significantly reduce the energy consumption required for the production of ammonia. Several noble metal-based materials have already been identified as highly active electrocatalysts for this purpose. However, the development of non-precious metal-based electrocatalysts is necessary for realizing cost-effective ammonia synthesis at large scales. This work has explored the potential of the less exploited transition metal phosphorus trichalcogenide NiPS3 as an NRR electrocatalyst. Excellent NRR activities have been achieved by exfoliating bulk NiPS3 into bi- or tri-layered nanosheets. The NH3 yield attained using exfoliated NiPS3 is 118 μg h−1 mgcat-1 with a Faraday efficiency of > 17 % at an applied potential of −0.4 V vs RHE. The NRR performance of exfoliated NiPS3 in terms of NH3 yield surpasses many non-noble metal-based catalysts reported in the literature. Further, it also exhibited a stable NRR activity of > 90% even after several repetitive cycles. Plane-wave DFT calculations at the GGA + U level have been used to investigate the reaction pathways. It could be shown that the NNR follows an associative mechanism, with the very first hydrogenation step being the potential determining step.

Quantum mechanical investigations of mechanical and thermodynamic properties of SiC and ZrO2 ceramics.

The mechanical and thermodynamic properties of β and α structures of SiC and also monoclinic and cubic structures of ZrO2 have been considered via first-principles investigations based on the ultrasoft pseudopotential plane-wave DFT method. The calculated lattice constants, elastic constants, and mechanical properties of all the structures are in agreement with earlier DFT works and experimental reports, which show that the applied method is applicable. Also, the pressure-dependency performances of thermodynamic and mechanical properties of cubic structures of ZrO2 and SiC, from 0 to 50 Gpa pressure, have been studied. The obtained elastic constants and mechanical properties of both structures increase with the enhancement of pressure. These results show that SiC is more difficult to be compacted as pressure increases. The thermodynamic properties of these structures show that variations of thermodynamic properties with temperature and pressure for ZrO2 are slightly higher than SiC.

Adsorption and spin polarization of pyridine on Fe/W(1 1 0) interface: A DFT study

Organic molecules containing conjugated π electrons acquire a magnetic moment when adsorbed on ferromagnetic surfaces. Plane-wave DFT calculations show that pyridine molecule, which has no magnetism in the gas phase, acquires a magnetic moment of 0.10 μB magnitude after adsorption on the ferromagnetically ordered Fe/W (110) surface. The molecule is strongly chemisorbed onto the surface, and the induced moment anti-aligns with respect to the surface moment. Analysis of the interface electronic structure shows that the spin polarization results from the hybridization of the out-of-plane pz orbitals of carbon and nitrogen in pyridine molecule with the d orbitals of Fe atoms on the ferromagnetic surface. As a result of this interaction, the magnetization of individual atoms in the Fe/W (110) layers directly beneath the molecule change from their clean surface values. The electronegativity of nitrogen results in the induction of a more substantial magnetic moment in pyridine than benzene. Understanding this organic-ferromagnetic interface is important to developing research in the fields of organic spintronics and molecular electronics.