PBE Functionals Research Articles

Diastereoselective synthesis and structure-affinity relationships of σ1 receptor ligands with spirocyclic scaffold.

Spirocyclic scaffolds play an increasing role in drug discovery as they define a rigid three-dimensional space to increase specific interactions with protein binding sites. Herein, a spirocyclic center was introduced into the lead compound 1 to rigidify its flexible benzylaminoethyl side chain. The key step of the synthesis was the reaction of different α,β-unsaturated amides 6 and 13-16 with methyl acrylate in the presence of TBDMSOTf. DFT calculations explain the mechanism of this transformation as concerted Diels-Alder reaction (functionals B3LYP and TPSS) or double (aza)-Michael addition (functionals PBE and wB97X-D). After separation of the diastereomeric spirocyclic products 8 and 17-20, LiAlH4 reduction provided the spirocyclic hydroxymethyl piperidines 21a,b-25a,b showing low nanomolar σ1 affinity (Ki < 100 nM). trans-Configured ligands (a-series) showed higher or equal σ1 affinity and higher selectivity over σ2 receptors and GluN2B-NMDA receptors than their cis-configured analogs (b-series). The additional hydroxymethyl moiety brings the log D7.4 value in a promising range. The high σ1 affinity (Ki = 3.6 nM) and the low lipophilicity result in the highest lipophilic ligand efficiency for the dispiro compound 23a (LLE = 6.0). The spirocyclic compounds reported herein and in particular the dispiro compound 23a demonstrate that ligands containing a large number of sp3 C-atoms possess favorable pharmacological (σ1 receptor affinity, receptor selectivity) and physicochemical properties (log D7.4 value) resulting in promising LLE.

Greater transferability and accuracy of norm-conserving pseudopotentials using nonlinear core corrections.

We present an investigation into the transferability of pseudopotentials (PPs) with a nonlinear core correction (NLCC) using the Goedecker, Teter, and Hutter (GTH) protocol across a range of pure GGA, meta-GGA and hybrid functionals, and their impact on thermochemical and non-thermochemical properties. The GTH-NLCC PP for the PBE density functional demonstrates remarkable transferability to the PBE0 and ωB97X-V exchange-correlation functionals, and relative to no NLCC, improves agreement significantly for thermochemical benchmarks compared to all-electron calculations. On the other hand, the B97M-rV meta-GGA functional performs poorly with the PBE-derived GTH-NLCC PP, which is mitigated by reoptimizing the NLCC parameters for this specific functional. The findings reveal that atomization energies exhibit the greatest improvements from use of the NLCC, which thus provides an important correction needed for covalent interactions relevant to applications involving chemical reactivity. Finally we test the NLCC-GTH PPs when combined with medium-size TZV2P molecularly optimized (MOLOPT) basis sets which are typically utilized in condensed phase simulations, and show that they lead to consistently good results when compared to all-electron calculations for atomization energies, ionization potentials, barrier heights, and non-covalent interactions, but lead to somewhat larger errors for electron affinities.

Theoretical investigation of intermolecular interactions between CNT, SiCNT and SiCGeNT nanomaterials with vinyl chloride molecule: A DFT, NBO, NCI, and QTAIM study

Vinyl chloride (VCM) or chloroethylene is reactive in the gaseous state and its adsorption with pristine armchair (5,5) carbon nanotube (CNT) and silicon carbide nanotube (SiCNT) has been studied. Germanium (Ge) element as an impurity has been introduced to silicon carbide structure (i.e. SiCGeNT) so as to increase the reactivity of the surface of SiCNT and thus increase the sensitivity of the adsorbent during the adsorption process. The B3LYP-D3(GD3BJ) hybrid functional has been used to optimize the isolated nanostructures and vinyl chloride as well as their clusters (gas/nanotube). In addition, energy single-point calculations were performed using ωB97XD, PBE0, B3LYP-D3(GD3BJ), and M06-2X functionals. The selected basis function is 6-311G(d), which is a good approximation to cover the integration space with respect to the constituent atoms of the molecules studied in this research. Wave function analysis including non-covalent interaction (NCI), natural bond orbital (NBO), and quantum theory of atoms in molecules (QTAIM), have also been done to reveal the intermolecular interactions nature. The results of these analyses, which are calculated using B3LYP-D3(GD3BJ)/6-311G(d) level of theory, are in agreement with each other and emphasize that among the mentioned nanotubes, silicon carbide nanotube doped with Ge element is more sensitive with respect to gas adsorption. Therefore, it will be a good option to design and build a nanosensor.

Comparison of Hybrid Functionals HSE and PBE0 in Calculating the Defect Properties of CsPbI3

Comparison of Hybrid Functionals HSE and PBE0 in Calculating the Defect Properties of CsPbI₃

2D BN-biphenylene: structure stability and properties tenability from a DFT perspective.

With state-of-the-art density functional theory and ab initio molecular dynamics, we explored the BN-analog of a recently synthesized 2D biphenylene sheet. Its dynamical, thermal, and mechanical stability has been confirmed with phonon spectrum calculations, ab initio molecular dynamics (AIMD), and Born criteria, and its synthesis feasibility has been ascertained in terms of cohesive energy. The phonon spectrum and AIMD results show all positive frequencies and negligible variations in structure (bond length), kinetic and total energy for 5 ps, respectively. Having found this stable BN-BPh, we have analyzed its electronic, mechanical, optical, and vibration properties. Electronic property results (density of states and band structure) show that the BN-equivalent of metallic BPh has a large band gap of 3.12 eV and 4.48 eV with the PBE and HSE06 DFT functionals, respectively, similar to the graphene BN-equivalent (hBN) with a band gap of 6.1 eV. The mechanical strength of BN-BPh is close to that of BPh with a difference of ∼15 N m-1 and ∼10 N m-1 along the x- and y-directions, and its Young's modulus indicates that BN-BPh is stiffer than BN-graphyne. The optical absorption coefficient of BN-BPh shows a first peak at 4.48 eV (3.12 eV) with the HSE06 (PBE) functional. Infrared and Raman spectrum intensity and irreducible representation are computed, and the first IR (Raman) peak is found at 1300 cm-1 (1000 cm-1) for BN-BPh. Finally, substitutions of external atoms such as P, Al, As, C, Li, Mg, S, and Si for B and N atoms in BN-BPh tune its electronic properties to semiconducting, semi-metallic, and even metallic. Considering its mechanical, optical, and band gap tunability, BN-BPh might be useful in electronic, optical, and spintronics devices, even in high-pressure environments.

Hybrid-Density Functional Calculations of Structural, Electronic, Magnetic, and Thermodynamic Properties of α-Cu2P2O7

We present a comparative study (using PBE, PBE0, and HSE functionals) of electronic and atomic structure, magnetism, and phonon dispersion relations of α-Cu2P2O7. Four possible magnetic configurations are considered, FM, AFM-1, AFM-2, and AFM-3. The calculations reveal that α-Cu2P2O7 is mechanically and thermodynamically stable. The elastic moduli indicate a weak resistance of the compound to volume and shear deformations. The electronic structure at the valence band maximum is dominated by O, with a small admixture of Cu-dx2−y2 states. The conduction band results from the hybridization between Cu and O states which, in the case of AFM-2, produces the largest band gap of 3.966 eV and the smallest magnetic moment of ±0.785 μB on Cu. AFM-2 is found to be the lowest-energy structure that may be viewed as consisting of quasi-one-dimensional −Cu1−Cu2−Cu3−Cu4− chains along the b axis; the antiferromagnetism is due to two identical Cu−O−Cu paths with a bond angle of 100.301∘. The phonon spectra exhibit four distinct frequency ranges corresponding to different vibrational modes of ions and ionic groups. Thus, a quantitative description of the structural, electronic, and magnetic properties of α-Cu2P2O7 is possible using the HSE hybrid functional, which enables computational studies of transition metal pyro compounds.

Synthesis, Characterization, and Electronic Properties of ZnO/ZnS Core/Shell Nanostructures Investigated Using a Multidisciplinary Approach

ZnO/ZnS core/shell nanostructures, which are studied for diverse possible applications, ranging from semiconductors, photovoltaics, and light-emitting diodes (LED), to solar cells, infrared detectors, and thermoelectrics, were synthesized and characterized by XRD, HR-(S)TEM, and analytical TEM (EDX and EELS). Moreover, band-gap measurements of the ZnO/ZnS core/shell nanostructures have been performed using UV/Vis DRS. The experimental results were combined with theoretical modeling of ZnO/ZnS (hetero)structures and band structure calculations for ZnO/ZnS systems, yielding more insights into the properties of the nanoparticles. The ab initio calculations were performed using hybrid PBE0 and HSE06 functionals. The synthesized and characterized ZnO/ZnS core/shell materials show a unique three-phase composition, where the ZnO phase is dominant in the core region and, interestingly, the auxiliary ZnS compound occurs in two phases as wurtzite and sphalerite in the shell region. Moreover, theoretical ab initio calculations show advanced semiconducting properties and possible band-gap tuning in such ZnO/ZnS structures.

Lattice dynamical and thermodynamic properties study of ceria using density functional theory and Hubbard correction

In this study, the lattice dynamical and thermodynamic properties of CeO2 were investigated with first principles density functional theories LDA, PBE and DFT + U approximations. The phonon dispersion relation, phonon density of states, Brillion Zone-center phonon frequencies, Born effective charge and polarizability of CeO2 were calculated to investigate the lattice dynamical properties. The value of acoustic phonon frequency TA (Γ) , TO1(Γ) and TO2(Γ) calculated with DFT + U approximation is in better agreement with experimental value as compared to LDA and PBE calculations. The polarizability of CeO2 decreases with increasing frequency and approaches zero with further increase in frequency. Moreover, the temperature dependence of Helmholtz free energy, internal energy, entropy, chemical potential and specific heat capacity at constant volume were analyzed to investigate the thermodynamic properties of CeO2. The lattice dynamical and thermodynamic properties of CeO2 calculated with density functional theories are in agreement with both experimental values and theoretical findings.

SBH17: Benchmark Database of Barrier Heights for Dissociative Chemisorption on Transition Metal Surfaces.

Accurate barriers for rate controlling elementary reactions on metal surfaces are key to understanding, controlling, and predicting the rate of heterogeneously catalyzed processes. While barrier heights for gas phase reactions have been extensively benchmarked, dissociative chemisorption barriers for the reactions of molecules on metal surfaces have received much less attention. The first database called SBH10 and containing 10 entries was recently constructed based on the specific reaction parameter approach to density functional theory (SRP-DFT) and experimental results. We have now constructed a new and improved database (SBH17) containing 17 entries based on SRP-DFT and experiments. For this new SBH17 benchmark study, we have tested three algorithms (high, medium, and light) for calculating barrier heights for dissociative chemisorption on metals, which we have named for the amount of computational effort involved in their use. We test the performance of 14 density functionals at the GGA, GGA+vdW-DF, and meta-GGA rungs. Our results show that, in contrast with the previous SBH10 study where the BEEF-vdW-DF2 functional seemed to be most accurate, the workhorse functional PBE and the MS2 density functional are the most accurate of the GGA and meta-GGA functionals tested. Of the GGA+vdW functionals tested, the SRP32-vdW-DF1 functional is the most accurate. Additionally, we found that the medium algorithm is accurate enough for assessing the performance of the density functionals tested, while it avoids geometry optimizations of minimum barrier geometries for each density functional tested. The medium algorithm does require metal lattice constants and interlayer distances that are optimized separately for each functional. While these are avoided in the light algorithm, this algorithm is found not to give a reliable description of functional performance. The combination of relative ease of use and demonstrated reliability of the medium algorithm will likely pave the way for incorporation of the SBH17 database in larger databases used for testing new density functionals and electronic structure methods.

Schwarz P‐surface via isolated sp2 carbon heptagons: Design and properties

Described are the first two molecular designs of the triply periodic Schwarz P surface using merely the Schläfli t{3,7} pattern of sp2 -hybridized carbon atoms. Each atom is exactly part of one heptagon and two hexagon rings so that two heptagons do not share the same edge or vertex. Such pattern, called hyperbolic soccer ball obeys the isolated-heptagon rule with the minimum possible number of hexagons between heptagons similar to the isolation of pentagons from hexagons in the C60 fullerene. Both of the designed P surfaces are unbalanced, that is, they have two unequal sides, and belong to space groups P432 of the cubic system, and P4/ncc of the tetragonal system, respectively. Unit cells have a multiple of 24 heptagons similar to the only one previously known in literature Schwarzite with the hyperbolic soccer ball pattern-the D surface of Vanderbilt and Tersoff. The geometry of the periodic structures and unit cell parameters were fully optimized by DFT calculations using CASTEP software with PBE and PBESOL functionals under generalized gradient approximation. The effect of P and D surface dilution by hexagons on the calculated density, elastic and electronic properties is discussed.

Computational and experimental investigation of photoresponsive behavior of 4,4′-dihydroxyazobenzene diglycidyl ether

The photochromic properties of 4,4′-dihydroxyazobenzene diglycidyl ether have been investigated to gain further insight into the photoisomerization pathways. The light induced trans–cis isomerization, thermal cis–trans recovery and light induced cis–trans isomerization were monitored using electronic absorption spectroscopy. The pohotoisomerization and thermal relaxation kinetics of azobenzene chromophores were investigated in solution. It was found that the trans–cis isomerization process occurs very fast and a high content of cis isomer was obtained (94 %). The optimization of the ground and transition state geometries as well as the electronic structure of the azo epoxy derivative was performed by the density functional theory (DFT) and time-dependent DFT with PBE0 and CAM-B3LYP functionals, using 6-31 + G(d,p) as basis set. Also, the theoretical UV–vis absorption spectra were calculated. The mechanism of isomerization along the S2, S1 and S0 energy levels has been described. It was shown how each internal coordinate contributes to the isomerization mechanism. TD-DFT and DFT methods revealed that modification of the NN bond length was the internal coordinate responsible for the trans to cis as well as cis to trans conversion.

An evaluation for geometries, formation enthalpies, and dissociation energies of diatomic and triatomic (C, H, N, O), NO3, and HNO3 molecules from the PAW DFT method with PBE and optB88-vdW functionals

The structural geometries, formation enthalpies, and dissociation energies of all diatomic and triatomic molecules consisting of the four basic elements C, H, N, and/or O are calculated using the projector augmented wave density functional theory (DFT) method with the Perdew–Burke–Ernzerhof and optB88-vdW exchange-correlation functionals. The calculations are also extended to two larger molecules NO3 and HNO3, which consist of four and five atoms, respectively. In total, 82 molecules or isomers are considered in the calculations. The geometric parameters including 42 bond lengths and 15 bond angles of these molecules calculated using the planewave DFT method are highly satisfactory, relative to the available experimental data. The error analysis is also performed for 49 formation enthalpies and 138 dissociation energies (including 51 atomization energies as well as the corresponding bond dissociation energies). The results are also compared with the previous data from various atomic-orbital-based methods for molecules and from similar or different planewave DFT methods for various solids and other molecules. This provides an informative and instructive evaluation especially for calculating the large-size material systems containing these small molecules as well as for developing the DFT methods further.

Atom-to-Device Simulation of MoO3/Si Heterojunction Solar Cell

Metal oxides are commonly used in optoelectronic devices due to their transparency and excellent electrical conductivity. Based on its physical properties, each metal oxide serves as the foundation for a unique device. In this study, we opt to determine and assess the physical properties of MoO3 metal oxide. Accordingly, the optical and electronic parameters of MoO3 are evaluated using DFT (Density Functional Theory), and PBE and HSE06 functionals were mainly used in the calculation. It was found that the band structure of MoO3 calculated using PBE and HSE06 exhibited indirect semiconductor properties with the same line quality. Its band gap was 3.027 eV in HSE06 and 2.12 eV in PBE. Electrons and holes had effective masses and mobilities of 0.06673, -0.10084, 3811.11 cm2V-1s-1 and 1630.39 cm2V-1s-1, respectively. In addition, the simulation determined the dependence of the real and imaginary components of the complex refractive index and permittivity of MoO3 on the wavelength of light, and a value of 58 corresponds to the relative permittivity. MoO3 has a refractive index of between 1.5 and 3 in the visible spectrum, which can therefore be used as an anti-reflection layer for solar cells made from silicon. In addition, based on the semiconducting properties of MoO3, it was estimated that it could serve as an emitter layer for a solar cell containing silicon. In this work, we calculated the photoelectric parameters of the MoO3/Si heterojunction solar cell using Sentaurus TCAD (Technology Computing Aided Design). According to the obtained results, the efficiency of the MoO3/Si solar cell with a MoO3 layer thickness of 100 nm and a Si layer thickness of 9 nm is 8.8%, which is 1.24% greater than the efficiency of a homojunction silicon-based solar cell of the same size. The greatest short-circuit current for a MoO3/Si heterojunction solar cell was observed at a MoO3 layer thickness of 60 nm, which was determined by studying the dependency of the heterojunction short-circuit current on the thickness of the MoO3 layer.

The Halogen Effect on the Magnetic Behaviour of Dimethylformamide Solvates in [Fe(halide-salEen)2]BPh4

Complexes [Fe(X-salEen)2]BPh4·DMF, with X = Br (1), Cl (2), and F (3), were crystallised from N,N′-dimethylformamide with the aim of understanding the role of a high boiling point N,N′-dimethylformamide solvate in the spin crossover phenomenon. The counter ion was chosen for only being able to participate in weak intermolecular interactions. The compounds were structurally characterised by single crystal X-ray diffraction. Complex 1 crystallised in the orthorhombic space group P212121, and complexes 2 and 3 in the monoclinic space group P21/n. Even at room temperature, low spin was the predominant form, although complex 2 exhibited the largest proportion of the high-spin species according to both the magnetisation measurements and the Mössbauer spectra. Density Functional Theory calculations were performed both on the periodic solids and on molecular models for complexes 1–3 and the iodide analogue 4. While all approaches reproduced the experimental structures very well, the energy balance between the high-spin and low-spin forms was harder to reproduce, though some calculations pointed to the easier spin crossover of complex 2, as observed. Periodic calculations with the functional PBE led to very similar ΔEHS-LS values for all complexes but showed a preference for the low-spin form. However, the single-point calculations with B3LYP* showed, for the model without solvate, that the Cl complex should undergo spin crossover more easily. The molecular calculations also reflected this fact, which was more clearly defined when the cation–anion–solvate model was used. In the other models there was not much difference between the Cl, Br, and I complexes.

Ab initio construction of full phase diagram of MgO-CaO eutectic system using neural network interatomic potentials

While several studies confirmed that machine-learned potentials (MLPs) can provide accurate free energies for determining phase stabilities, the abilities of MLPs for efficiently constructing a full phase diagram of multicomponent systems are yet to be established. In this work, by employing neural network interatomic potentials (NNPs), we demonstrate construction of the MgO-CaO eutectic phase diagram with temperatures up to 3400 K, which includes liquid phases. The NNP is trained over trajectories of various solid and liquid phases at several compositions that are calculated within the density functional theory (DFT). For the exchange-correlation energy among electrons, we compare the PBE and SCAN functionals. The phase boundaries such as solidus, solvus, and liquidus are determined by free energy calculations based on the thermodynamic integration or semigrand ensemble methods, and salient features in the phase diagram such as solubility limit and eutectic points are well reproduced. In particular, the phase diagram produced by the SCAN-NNP closely follows the experimental data, exhibiting both eutectic composition and temperature within the measurements. On a rough estimate, the whole procedure is more than 1000 times faster than pure-DFT based approaches. We believe that this work paves the way to fully ab initio calculation of phase diagrams.

Molecular Structure, Vibrational Spectrum and Conformational Properties of 4-(4-Tritylphenoxy)phthalonitrile-Precursor for Synthesis of Phthalocyanines with Bulky Substituent.

By DFT method with B3LYP, PBE, CAM-B3LYP, and B97D functionals, it was found that the molecule 4-(4-tritylphenoxy)phthalonitrile (TPPN) has four conformers. The geometric structure, vibrational frequencies, electronic characteristics, and thermodynamic functions of conformers, as well as the structure and energy of transition states, were determined. IR spectrum of TPPN film contains vibrational bands belonging to different conformers. The assignment of bands was performed basing the distribution of normal vibration energy on internal coordinates. A synchronous electron diffraction/mass spectrometric experiment was performed to determine the structure of conformers in a saturated TPPN vapor. The elemental composition of the ions recorded in the mass spectrum indicates the thermal stability of TPPN at least up to T = 200 °C. The difference in the structure of tetrasubstituted metal phthalocyanines, which can be synthesized from different TPPN conformers, has been shown.

The structural, mechanical, and optoelectronic properties of Cu2-II-Sn-VI4 (II = Mg, Zn, Cd; VI = S, Se): A DFT study

Quaternary compound Cu2ZnSnX4 (X = S, Se) is of great interest to many researchers for photovoltaic applications in recent years. In the present study, the first-principles calculations are performed to investigate the influence of cation substitution on the different physical properties of Cu2ZnSnS4 (CZTS) and Cu2ZnSnSe4 (CZTSe). The difference in stability between two Kesterite and Stannite structures is examined for each compound. The results show that the pristine Kesterite structure will be transformed into the Stannite structure when the Zn atoms are replaced by the Mg or Cd atoms. Our results are consistent well with the available literature. The mechanical stability of six compounds are proved and they are ductile materials. The allowed direct electronic transition is found for all compounds at the Γ point. The band gap variation is analyzed in detail. The band gaps calculated from hybrid functional PBE0 of the studied compounds can agree well with the experimental data. The suitable band gap values of 1.12 and 1.28 eV are obtained for Cu2MgSnSe4 (CMTSe) and Cu2CdSnS4 (CCTS) in single-junction solar cells, whereas the band gaps of Cu2MgSnS4 (CMTS, 1.70 eV) and Cu2CdSnSe4 (CCTSe, 0.77 eV) are too large or small. The band gap energy difference between two tetragonal structures is shown to be negligible for CMTS, CMTSe, CCTS, and CCTSe. Furthermore, the optical properties are compared, and CMTSe and CCTS show strong light absorption capacity from 300 to 800 nm. Our study indicates that both CMTSe and CCTS are the promising materials for solar cell applications.

Pressure-dependent electronic properties in the rocksalt structure of lithium fluoride: A DFT Study

Density functional theory (DFT) calculation are carried out for the cubic structure of lithium fluoride (LiF). Variation of applied pressure is considered, ranging from 0 to 120 GPa with an increment of 30 GPa based on PBE and SCAN functional scheme. In zero pressure and energy-cut off 100 Ry, best result on lattice parameter is obtained by using PBE functional with the value of 4.06 Å, while SCAN functional overestimates the lattice parameter at 4.15 Å. The insulating gap of both results is significantly underestimated with 8.82 eV and 9.26 eV for PBE and SCAN functionals respectively. With the applied hydrostatic pressure, the lattice parameter are reduced exponentially, while still retaining the insulating behaviour with an increased value of gap energy.

Exploring 129Xe NMR parameters for structural investigation of biomolecules: relativistic, solvent, and thermal effects.

In recent years, the study of new probes has aroused great interest in the scientific community around the world. Therefore, in the present work, we present a potential candidate for a new spectroscopic probe, the Xe(CO)3(NNO) conjugated to 2-(4'-aminophenyl) benzothiazole complex, XeABT. For this proposal, chemical shift calculations at the DFT level were performed; thus, a factorial design was carried out in order to choose the best computational method. The best combination was the base function ZORA-def2-TZVP, with the functional PBE0 and considering the relativistic effects with the ZORA implementation. Our findings reveal that the 129Xe chemical shifts are affected by thermal and solvent effects, and considering an enzymatic environment, a significant decrease in δ(129Xe) values is observed, suggesting with the XeABT complex it may be a promising spectroscopic probe.

Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation.

Accurate calculation of relative tautomer energies in different environments is a prerequisite to many parameters of relevance in drug discovery. This work provides a thorough benchmark of the semiempirical methods AM1, PM3 and GFN2-xTB, the force-field OPLS4, Hartree-Fock and HF-3c, the density functionals PBEh-3c, B97-3c, r2SCAN-3c, PBE, PBE0, TPSS, r2SCAN, ω-B97X-V, M06-2X, B3LYP, B2PLYP, and second-order perturbation theory MP2 versus the gold-standard coupled-cluster DLPNO-CCSD(T) using the def2-QZVPP basis set. The outperforming method identified is M06-2X, whereas r2SCAN-3c is the best-perfoming one in the set of cost-optimized methods. Application of the two methods on a challenging subset from the SAMPL2 challenge provides evidence that deviations from experiment are caused by deficiencies of current continuum solvation methods.