Plane-wave DFT Calculations Research Articles

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

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.

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.

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.

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.

Chlorine-35 Solid-State Nuclear Magnetic Resonance Spectroscopy as an Indirect Probe of the Oxidation Number of Tin in Tin Chlorides

Ultrawideline 35Cl solid-state nuclear magnetic resonance (SSNMR) spectra of a series of 12 tin chlorides were recorded. The magnitude of the 35Cl quadrupolar coupling constant (CQ) was shown to consistently indicate the chemical state (oxidation number) of the bound Sn center. The chemical state of the Sn center was independently verified by tin Mössbauer spectroscopy. CQ(35Cl) values of >30 MHz correspond to Sn(IV), while CQ(35Cl) readings of <30 MHz indicate that Sn(II) is present. Tin-119 SSNMR experiments would seem to be the most direct and effective route to interrogating tin in these systems, yet we show that ambiguous results can emerge from this method, which may lead to an incorrect interpretation of the Sn oxidation number. The accumulated 35Cl NMR data are used as a guide to assign the Sn oxidation number in the mixed-valent metal complex Ph3PPdImSnCl2. The synthesis and crystal structure of the related Ph3PPtImSnCl2 are reported, and 195Pt and 35Cl SSNMR experiments were also used to investigate its Pt-Sn bonding. Plane-wave DFT calculations of 35Cl, 119Sn, and 195Pt NMR parameters are used to model and interpret experimental data, supported by computed 119Sn and 195Pt chemical shift tensor orientations. Given the ubiquity of directly bound Cl centers in organometallic and inorganic systems, there is tremendous potential for widespread usage of 35Cl SSNMR parameters to provide a reliable indication of the chemical state in metal chlorides.

Identifying the Molecular Edge Termination of Exfoliated Hexagonal Boron Nitride Nanosheets with Solid-State NMR Spectroscopy and Plane-Wave DFT Calculations

Hexagonal boron nitride nanosheets (h-BNNS), the isoelectronic analog to graphene, have received interest over the past decade due to their high thermal oxidative resistance, high bandgap, catalyti...

Correction to “Solid Oganesson via a Many-Body Interaction Expansion Based on Relativistic Coupled-Cluster Theory and from Plane-Wave Relativistic Density Functional Theory”

Many-body potentials up to fourth order are constructed using nonrelativistic, scalar-relativistic, and relativistic coupled-cluster theory to accurately describe the interaction between superheavy oganesson atoms. The obtained distance-dependent energy values were fitted to extended two-body Lennard-Jones and three-body Axilrod-Teller-Muto potentials, with the fourth-order term treated through a classical long-range Drude dipole interaction model. From these interaction potentials, spectroscopic constants for the oganesson dimer and solid-state properties were obtained. Furthermore, these high-level results are compared to scalar-relativistic and two-component plane-wave DFT calculations based on a tailor-made projector augmented wave pseudopotential (PAW-PP) and newly derived parameters for Grimme's dispersion correction. It is shown that the functionals PBE-D3(BJ), PBEsol, and in particular SCAN provide excellent agreement with the many-body reference for solid oganesson. Finally, the results for oganesson are compared and related to the lighter rare gas elements, and periodic trends are discussed.

Solid Oganesson via a Many-Body Interaction Expansion Based on Relativistic Coupled-Cluster Theory and from Plane-Wave Relativistic Density Functional Theory.

Many-body potentials up to fourth order are constructed using nonrelativistic, scalar-relativistic, and relativistic coupled-cluster theory to accurately describe the interaction between superheavy oganesson atoms. The obtained distance-dependent energy values were fitted to extended two-body Lennard-Jones and three-body Axilrod-Teller-Muto potentials, with the fourth-order term treated through a classical long-range Drude dipole interaction model. From these interaction potentials, spectroscopic constants for the oganesson dimer and solid-state properties were obtained. Furthermore, these high-level results are compared to scalar-relativistic and two-component plane-wave DFT calculations based on a tailor-made projector augmented wave pseudopotential (PAW-PP) and newly derived parameters for Grimme's dispersion correction. It is shown that the functionals PBE-D3(BJ), PBEsol, and in particular SCAN provide excellent agreement with the many-body reference for solid oganesson. Finally, the results for oganesson are compared and related to the lighter rare gas elements, and periodic trends are discussed.

Atomistic Explanation for Interlayer Charge Transfer in Metal-Semiconductor Nanocomposites: The Case of Silver and Anatase.

A concerted theoretical and experimental investigation of the silver/anatase hybrid nanocomposite, a very promising material for advanced sensing applications, is presented. We measure its exceptional electrochemical virtues in terms of current densities and reproducibility, providing their explanation at the atomic-scale level and demonstrating how and why silver acts as a positive electrode. Using periodic plane-wave DFT calculations, we estimate the overall amount of electron transfer toward the semiconductor side of the interface at equilibrium. Suitably designed (photo)electrochemical experiments strictly agree, both qualitatively and quantitatively, with the theoretical charge transfer estimates. The unique permanent charge separation occurring in the device is possible because of the favorable synergy of Ag and TiO2, which exploits in a favorable band alignment, while the electron–hole recombination rate and carrier mobility decrease when electrons cross the metal–semiconductor interface. Finally, the hybrid material is proven to be extremely robust against aging, showing complete regeneration, even after 1 year.

Ab initio DFT studies of adsorption characteristics of benzene on close-packed surfaces of transition metals

We investigate the adsorption of benzene on close-packed surfaces like the (111) surface of fcc, the (110) surface of bcc and the (0001) surface of hcp transition metals, using plane wave DFT calculations. The bridge site is the most stable adsorption site for all (111) surfaces, except in case of Rh, Ru where the hollow site is found to be most stable and for Mo, W where an intermediate position between bridge and hollow is preferred. Comparing with experimental measurements wherever available shows that van der Waals (vdW) interaction are significant in determining the adsorption energy accurately. Changes in geometry and electronic structure after adsorption are studied. It is found that in case of transition metals having partially filled d bands, a net electron transfer takes place, towards the benzene molecule and for metals having filled or nearly filled d band (Pt, Pd) the net transfer is towards the substrate.

Effects of Dopant Addition on Lattice and Luminescence Intensity Parameters of Eu(III)-Doped Lanthanum Orthovanadate

A series of La1–xEuxVO4 samples with a different Eu3+ content was synthesized via a hydrothermal route. An increase in the dopant content resulted in a decrease in lattice constants of the materials. Plane-wave DFT calculations with PBE functional in CASTEP confirmed this trend. Next, CASTEP calculations were used to obtain force constants of Eu–O bond stretching, using a novel approach which involved displacement of the Eu3+ ion. The force constants were then used to calculate charge donation factors g for each ligand atom. The chemical bond parameters and the geometries from DFT calculations were used to obtain theoretical Judd–Ofelt intensity parameters Ωλ. The effects of geometry changes caused by the dopant addition were analyzed in terms of Ωλ. The effects of distortions in interatomic angles of the Eu3+ coordination geometry on the Ωλ were analyzed. Effects of distortions of atomic positions in the crystal lattice on the Ωλ and photoluminescence intensities of Eu3+ 4f–4f transitions were discussed....

14 N Solid-State NMR Spectroscopy of Amino Acids.

14 N ultra-wideline solid-state NMR (SSNMR) spectra were obtained for 16 naturally occurring amino acids and four related derivatives by using the WURST-CPMG (wideband, uniform rate, and smooth truncation Carr-Purcell-Meiboom-Gill) pulse sequence and frequency-stepped techniques. The 14 N quadrupolar parameters were measured for the sp3 nitrogen moieties (quadrupolar coupling constant, CQ , values ranged from 0.8 to 1.5 MHz). With the aid of plane-wave DFT calculations of the 14 N electric-field gradient tensor parameters and orientations, the moieties were grouped into three categories according to the values of the quadrupolar asymmetry parameter, ηQ : low (≤0.3), intermediate (0.31-0.7), and high (≥0.71). For RNH3+ moieties, greater variation in N-H bond lengths was observed for systems with intermediate ηQ values than for those with low ηQ values (this variation arose from different intermolecular hydrogen-bonding arrangements). Strategies for increasing the efficiency of 14 N SSNMR spectroscopy experiments were discussed, including the use of sample deuteration, high-power 1 H decoupling, processing strategies, high magnetic fields, and broadband cross-polarization (BRAIN-CP). The temperature-dependent rotations of the NH3 groups and their influence on 14 N transverse relaxation rates were examined. Finally, 14 N SSNMR spectroscopy was used to differentiate two polymorphs of l-histidine through their quadrupolar parameters and transverse relaxation time constants. The strategies outlined herein permitted the rapid acquisition of directly detected 14 N SSNMR spectra that to date was not matched by other proposed methods.

Rationalization of the Color Properties of Fluorescein in the Solid State: A Combined Computational and Experimental Study.

Fluorescein is known to exist in three tautomeric forms defined as quinoid, zwitterionic, and lactoid. In the solid state, the quinoid and zwitterionic forms give rise to red and yellow materials, respectively. The lactoid form has not been crystallized pure, although its cocrystal and solvate forms exhibit colors ranging from yellow to green. An explanation for the observed colors of the crystals is found using a combination of UV/Vis spectroscopy and plane‐wave DFT calculations. The role of cocrystal coformers in modifying crystal color is also established. Several new crystal structures are determined using a combination of X‐ray and electron diffraction, solid‐state NMR spectroscopy, and crystal structure prediction (CSP). The protocol presented herein may be used to predict color properties of materials prior to their synthesis.

High-field solid-state 35Cl NMR in selenium(IV) and tellurium(IV) hexachlorides

We report solid-state 35Cl NMR spectra in three hexachlorides, (NH4)2SeCl6, (NH4)2TeCl6 and Rb2TeCl6. The CQ(35Cl) quadrupole coupling constants in the three compounds were found to be 41.4±0.1 MHz, 30.3±0.1 MHz and 30.3±0.1 MHz, respectively, some of the largest CQ(35Cl) quadrupole coupling constants ever measured in polycrystalline powdered solids directly via 35Cl NMR spectroscopy. The 35Cl EFG tensors are axial in all three cases reflecting the C4v point group symmetry of the chlorine sites. 35Cl NMR experiments in these compounds were only made possible by employing the WURST-QCPMG pulse sequence in the ultrahigh magnetic field of 21.1 T. 35Cl NMR results agree with the earlier reported 35Cl NQR values and with the complementary plane-wave DFT calculations. The origin of the very large CQ(35Cl) quadrupole coupling constants in these and other main-group chlorides lies in the covalent-type chlorine bonding. The ionic bonding in the ionic chlorides results in significantly reduced CQ(35Cl) values as illustrated with triphenyltellurium chloride Ph3TeCl. The high sensitivity of 35Cl NMR to the chlorine coordination environment is demonstrated using tetrachlorohydroxotellurate hydrate K[TeCl4(OH)]∙0.5H2O as an example. 125Te MAS NMR experiments were performed for tellurium compounds to support 35Cl NMR findings.

On the electrochemical behavior of formamidine disulfide on gold electrodes in acid media

The adsorption and reactivity of formamidine disulfide (FDS) were studied at gold single crystal and thin film electrodes in perchloric acid solutions and the results of cyclic voltammetry and in situ infrared spectroscopy (SNIFTIR and ATR-SEIRAS) experiments compared with those previously obtained with thiourea (TU). In addition, optimized geometries and theoretical harmonic vibrational frequencies were obtained for adsorbed FDS, TU and thioureate from plane-wave DFT calculations using periodic surface models. These results were compared in the case of TU and thioureate to those previously obtained with a model Au cluster surface with (111) orientation. In the case of FDS, weak adsorption takes place with the S–S bond essentially parallel to the metal surface. No specific bands for adsorbed FDS can be identified in the experimental ATR-SEIRA spectra. These latter spectra suggest that adsorbed thioureate species are spontaneously formed upon dissociative adsorption of FDS when dosing this molecule at open circuit. Some of the adsorbed thioureate species undergo reductive protonation giving rise to a mixed adlayer formed by adsorbed thioureate and thiourea in a surface process which is faster when a controlled potential of 0.70V is applied. In agreement with the observations reported when dosing TU, the ratio between TU and thioureate adsorbates is found to depend on the electrode potential, being higher for potentials close to the hydrogen evolution limit and decreasing for higher potential values.

An Adsorption Study of CH4 on ZSM-5, MOR, and ZSM-12 Zeolites

CH4 adsorption was studied experimentally and theoretically on ZSM-5, MOR, and ZSM-12 zeolites using calorimetric measurements at 195 K and plane wave DFT calculations. Differential heats measured on four different H-ZSM-5 samples were determined to be 22.5 ± 1 kJ/mol, independent of Brønsted site density or defect concentration. However, DFT calculations performed using various functionals and on the most stable Brønsted site indicated that CH4 should bind to this site by an additional 1–7 kJ/mol, a discrepancy that is due to the inability of standard DFT methods to capture hydrogen-bonding effects accurately with CH4. Differential heats for CH4 in MOR were 30 ± 1 kJ/mol at low coverages, falling to 25 kJ/mol for coverages above one molecule per 8-membered-ring side pocket, while differential heats on ZSM-12 were initially 22.5 kJ/mol, decreasing to 21 kJ/mol with coverage. DFT calculations on the siliceous form of the zeolites were able to predict these values within 5 kJ/mol in most cases. The results indicate that CH4 is an excellent probe molecule for characterizing the pore structure of zeolites.

On the “Preconditioning” Function Used in Planewave DFT Calculations and its Generalization

AbstractThe Teter, Payne, and Allan “preconditioning” function plays a significant role in planewave DFT calculations. This function is often called the TPA preconditioner. We present a detailed study of this “preconditioning” function. We develop a general formula that can readily generate a class of “preconditioning” functions. These functions have higher order approximation accuracy and fulfill the two essential “preconditioning” purposes as required in planewave DFT calculations. Our general class of functions are expected to have applications in other areas.

DFT Study of CO Oxidation Catalyzed by Au/TiO&lt;sub&gt;2&lt;/sub&gt;: Activity of Small Clusters

CO oxidation over a rutile TiO2(110) surface supporting a tetrahedral Au10 cluster has been examined by plane-wave DFT calculations. O2 adsorbs sideon to the pentacoordinate Ti site of the oxide support with a large energy gain (∼ 2 eV), activated to a peroxide state. O2 adsorption on the cluster is much weaker. The stability and activation state of sideon O2 depends weakly on distance to the cluster. On a Ti site next to the cluster, a sideon O2 reacts with CO adsorbed on the cluster to yield CO2 with a very small energy barrier of 0.13 eV. On a more remote Ti site, a sideon O2 reacts with a gaseous CO to yield CO2 with a barrier of 0.55 eV. Thus, O2 + CO reaction is much faster at the perimeter even for a small cluster such as Au10. Similar results are obtained for a truncated pyramidal Au9, except that a carbonate is formed at the perimeter. The carbonate formation is inhibited if H2O is adsorbed next to O2. [DOI: 10.1380/ejssnt.2015.129]

Influence of interconfigurational electronic States On Fe, Co, Ni-silicene materials selection for spintronics.

Growth through controlled adsorption of ferromagnetic elements such as Fe, Co and Ni on two-dimensional silicene provides an alternative route for silicon-based spintronics. Plane wave DFT calculations show that Fe, Co and Ni adatoms are strongly chemisorbed via strong sigma bonds, with adsorption energies (1.55 - 2.29 eV) that are two to six times greater compared to adsorption on graphene. All adatoms adsorb more strongly at the hole site than at the atom site, with Ni adsorbing strongest. Of the dimer configurations investigated, the hole – hole, b-atom – hole, vertically stacked at hole, vertically stacked at b-atom and bridge sites were found to be stable. The Co and Ni dimers are most stable when adsorbed in the hole-hole configuration while the Fe dimer is most stable when adsorbed in the atom-hole configuration. Metal-to-silicene and interconfigurational s-to-d electron transfer processes underpin the trends observed in adsorption energies and magnetic moments for both adatoms and dimers. Adsorption of these metals induces a small band gap at the Dirac Cone. In particular Co adatom adsorption at the hole site induces the largest spin-polarized band gaps of 0.70 eV (spin-up) and 0.28 eV (spin-down) making it a potential material candidate for spintronics applications.