Density Functional Theory Formalism Research Articles

Valence skipping, internal doping, and site-selective Mott transition in PbCoO3 under pressure

We present a computational study of PbCoO$_3$ at ambient and elevated pressure. We employ the static and dynamic treatment of local correlation in form of density functional theory + $U$ (DFT+$U$) and + dynamical mean-field theory (DFT+DMFT). Our results capture the experimentally observed crystal structures and identify the unsaturated Pb $6s$ - O $2p$ bonds as the driving force beyond the complex physics of PbCoO$_3$. We provide a geometrical analysis of the structural distortions and we discuss their implications, in particular, the internal doping, which triggers transition between phases with and without local moments and a site selective Mott transition in the low-pressure phase.

Readdressing molecular dissociation within the Kohn–Sham formalism of density-functional theory: simple models and a different point of view

Within the Kohn–Sham (KS) formalism of density-functional theory (DFT), most available exchange-correlation (XC) density-functionals are known to yield incorrect molecular dissociation even when dealing with simple molecules as H. It is known that the KS potential must develop a peak and a step in the region between the isolated atoms, in order to prevent electrons to hop from one atom to another, and hence avoiding fractionally charged dissociated atoms. Considering one-dimensional models of two-electron homo and heteronuclear molecules, we here (i) readdress the limit of dissociated molecules, with a different point of view on the formation of the peaks and steps in the KS potential and (ii) investigate a simple approach to treat not necessarily dissociated molecules, by employing single-particle orbitals (not KS orbitals). Our results indicate that an accurate description of dissociation can be achieved.

Quantum Biochemical Investigation of Lys49-PLA2 from Bothrops moojeni.

Envenomation via snakebites occurs largely in areas where it is harder to access the hospital. Its mortality rate and sequelae acquired by the survivors symbolize a big challenge for antivenom therapy. In particular, the homologous phospholipase A2 (Lys49-PLA2) proteins can induce myonecrosis and are not effectively neutralized by current treatments. Thus, by taking advantage of crystallographic structures of Bothrops moojeni Lys49-PLA2 complexed with VRD (varespladib) and AIN (aspirin), a quantum biochemistry study based on the molecular fractionation with conjugate cap scheme within the density functional theory formalism is performed to unveil these complexes' detailed interaction energies. The calculations revealed that important interactions between ligands and the Lys49-PLA2 pocket could occur up to a pocket radius of r = 6.5 (5.0 Å) for VRD (AIN), with the total interaction energy of the VRD ligand being higher than that of the AIN ligand, which is well-correlated with the experimental binding affinity. Furthermore, we have identified the role played by the amino acids LYS0069, LYS0049, LEU0005, ILE0009, CYS0029, GLY0030, HIS0048, PRO0018, ALA0019, CYS0045, TYR0052, TYR0022, PRO0125*, and PHE0126* (LYS0069, LYS0049, GLY0032, LEU0002, and LEU0005) in the VRD↔Lys49-PLA2 (AIN↔Lys49-PLA2) complex. Our simulations are a valuable tool to support the big challenge for neutralizing the damages in victims of snakebites.

Computational Investigation of Li-Ion Adsorption on Charged Graphene

Two-dimensional (2D) materials with very high specific surface areas are considered as promising electrode materials for lithium-ion batteries (LIBs). Graphene, in particular, is a good candidate for anode material for LIBs due primarily to its tunable electronic properties, and high mobility. However, this allotrope of carbon has low storage capacity due to its inert characteristic that leads to a poor adsorption of lithium-ion. Recently, there has been several suggestions made to enhance the capacity of graphene by doping the structure with the same group elements that result in improvement of the lithium-ion adsorption.1 In this study, electronic structure investigations of the lithium-ion adsorption on charged graphene single layers doped with germanium have been made by employing a modified first principles technique in the density functional theory (DFT) formalism. The effective screening medium (ESM) extension of the DFT method involves building a non-repeated slab model placed in between semi-infinite domain of media as macroscopic description of surfaces in contact with vacuum/conductor/solution with a prescribed permittivity.2 With this approach, it becomes possible to flexibly model the adsorption characteristics of charged graphene surfaces under potential bias. As a test case, the electrical charge (+0.026e) is applied to the graphene slab to simulate the negative electrode of LIBs, where Li-ion is placed on the hallow site above the carbon ring. In Figure 1a, the local accumulation and depletion of charges are shown in yellow and blue isosurfaces respectively. Charge density difference plot, shown in Figure 1b, depicts the variation of planar averages of electron density along the z-coordinate of the surface slab. Additionally, in Figure 1c, electrostatic potential energy difference between charged and neutral slabs is shown with the Li atom existence on the hollow site. The result confirms the accumulation of induced charge on the adsorbed Li-ion on the hallow site of the graphene layer. Furthermore, the results of electronic structure calculations for charged graphene single layers doped with germanium will be presented and the results will be compared with the neutral slab models.

Asymptotics of the metal-surface Kohn-Sham exact exchange potential revisited

The asymptotics of the Kohn-Sham (KS) exact exchange potential $V_x(z)$ of a jelliumlike semi-infinite metal is investigated, in the framework of the optimized-effective-potential formalism of density-functional theory. Our numerical calculations clearly show that deep into the vacuum side of the surface $V_x(z) \propto e^2 \ln(az) / z$, with $a$ being a system-dependent constant, thus confirming the analytical calculations reported in Phys. Rev. B {\bf 81}, 121106(R) (2010). A criticism of this work published in Phys. Rev. B {\bf 85}, 115124 (2012) is shown to be incorrect. Our rigorous exchange-only results provide strong constraints both for the building of approximate exchange functionals and for the determination of the still unknown KS correlation potential.

Internal Conversion between Bright (11Bu+) and Dark (21Ag-) States in s-trans-Butadiene and s-trans-Hexatriene.

Internal conversion (IC) between the two lowest singlet excited states, 11Bu+ and 21Ag-, of s-trans-butadiene and s-trans-hexatriene is investigated using a series of single- and multi- reference wave function and density functional theory (DFT) methodologies. Three independent types of the equation-of-motion coupled-cluster (EOMCC) theory capable of providing an accurate and balanced description of one- as well as two-electron transitions, abbreviated as δ-CR-EOMCC(2,3), DIP-EOMCC(4h2p){No}, and DEA-EOMCC(4p2h){Nu} or DEA-EOMCC(3p1h,4p2h){Nu}, consistently predict that the 11Bu+/21Ag- crossing in both molecules occurs along the bond length alternation coordinate. However, the analogous 11Bu+ and 21Ag- potentials obtained with some multireference approaches, such as CASSCF and MRCIS(D), as well as with the linear-response formulation of time-dependent DFT (TDDFT), do not cross. Hence, caution needs to be exercised when studying the low-lying singlet excited states of polyenes with conventional multiconfigurational methods and TDDFT. The multistate many-body perturbation theory methods, such as XMCQDPT2, do correctly reproduce the curve crossing. Among the simplest and least expensive computational methodologies, the DFT approaches that incorporate the contributions of doubly excited configurations, abbreviated as MRSF (mixed reference spin-flip) TDDFT and SSR(4,4), accurately reproduce our best EOMCC results. This is highly promising for nonadiabatic molecular dynamics simulations in larger systems.

MCD and MCPL Characterization of Luminescent Si(IV) and P(V) Tritolylcorroles: The Role of Coordination Number.

Two triarylcorrole complexes, (hydroxy)[5,10,15-tritolylcorrolato]silicon-(TTC)Si(OH) and (dihydroxy)[5,10,15-tritolylcorrolato]phosphorous-(TTC)P(OH)2, have been investigated by magnetic circular dichroism (MCD) and magnetic circularly polarized luminescence (MCPL). The spectroscopic investigations have been combined with explicit calculation of MCD response through time-dependent density functional theory (TD-DFT) formalism. This has allowed us to better define the role of molecular orbitals in the transitions associated with the Soret and Q bands. Besides and more importantly, MCD has made it possible to follow the titration process of (TTC)Si(OH) in dimethyl sulfoxide (DMSO) solution with NaF and of (TTC)P(OH)2 in dichloromethane solution with alcohols in a complementary and, we dare say, more sensitive way with respect to absorption and fluorescence data. Finally, the MCPL spectra and the ancillary TD-DFT calculations have allowed us to characterize the excited state of (TTC)Si(OH).

Considering Density Functional Approaches for Actinide Species: The An66 Molecule Set.

The importance of spin-orbit effects on the predictions of energetic properties of actinide compounds has been considered for 18 different density functionals, comparing the spin-orbit and non-spin-orbit ("standard") forms of density functional theory (DFT). A set of enthalpies of formation for 66 small actinide (Th-Am) compounds-the An66 set, for which experimental data are available-have been investigated. The set includes actinide halides, oxides, and oxohalides in the general form AnOmXn, where n = 0-6, m = 0-3, and X = F, Cl, Br, or I. The impact of basis set choice was investigated, and to help account for the impact of relativity, the Stuttgart general and segmented contracted atomic natural orbital (ANO) basis sets paired with small core relativistic effective core potentials (RECP) as well as all-electron calculations utilizing the third-order Douglas-Kroll-Hess were considered.

Thermodynamic evidence of the ferroelectric Berry phase in europium-based ferrobismuthite Eu2Bi2Fe4O12

The possible low temperature biferroic feature of Eu2Bi2Fe4O12 complex perovskites was recently reported. The aim of this work is to present a theoretical study of the structural, magnetic, electronic and ferroelectric properties of this material. Several energy minimization processes were performed for three types of cationic distributions, different angles of rotation, octahedral inclination, and some kinds of magnetic ordering. The results reveal that the most stable crystallographic arrangement corresponds to an intercalated distribution of the Eu3+ and Bi3+ cations between the FeO6 octahedra. Similarly, energy is minimized for rotations and octahedral inclinations corresponding to angles θe = 12.86° and ϕe= 13.32°, respectively. With respect to the distribution of magnetic moments, the results reveal that a G-type antiferromagnetic configuration is the most energetically favorable. The electronic structure is studied from ab initio calculations following the formalism of density functional theory and the pseudopotential plane wave method. In this formalism, the exchange and correlation mechanisms are described by means of the generalized gradient approach (GGA + U), considering spin polarization. The ferroelectric characteristic is analysed by determining ferroelectric polarization based on the calculation of the Berry phase. The theoretical results obtained are consistent with the experimental reports, which is why the Eu2Bi2Fe4O12 material is expected to exhibit biferroic behavior at low temperatures, because the Berry phase introduces hybridizations between the 3d-Fe and 2p-O states that favor the occurrence of Dzyaloshinskii-Moriya interactions, which facilitate the occurrence of ferroelectricity coexisting with weak ferromagnetism. An extensive study of the thermodynamic properties in the presence and absence of the Berry phase is undertaken by means of the Debye quasi harmonic model. The specific heat difference with and without the Berry phase reveals the occurrence of a ferroelectric transition at T = 113 K without the application of external pressure. When the applied pressure is incremented, a systematic increase in the transition temperature is observed due to the reduction of overlap between the 3d-Fe orbitals and the 2p-O orbitals in the compressed octahedra of perovskite.

Electronic density of states and optical spectra of zigzag SiC nanoribbons from first principles

The electronic and optical behavior of zigzag silicon carbide nanoribbons (ZSiCNRs) have been simulated exploiting density functional theory (DFT) formalism. Our results show that zigzag silicon nanoribbons (w = 14 to 20) have metallic behavior. The optical graphs confirm that ε1x(ω), ε1y(ω), nx(ω), and ny(ω) are less than that of the z polarization at energies below 2.5 eV. The static refractive index of ZSiCNRs is almost close to that of the other nanoribbons, except for the GNRs, which have a considerably larger static refractive index. Last but not least, the optical susceptibility shows that ZSiCNRs with larger width have a weaker polarization field which eventuates in lower optical susceptibility for the ZSiCNRs (w = 20).

Spectroscopic, Structural, Aromaticity and Electronic Properties of Isatoic Anhydride - Experimental and Theoretical Investigations

The paper compares the experimental FT-IR, 1 H- and 13 C-NMR spectra of isatoic anhydride (ISA) with the Hartree-Fock (HF) and Density Functional Theory (DFT) calculations using three different basis sets (6-31+G(d,p), 6-311+G(d,p), cc-pVTZ). The best compatibility between the experimental and theoretical FT-IR spectrum was observed with the use of B3LYP/6-31+G(d,p) method for ISA. Furthermore, the theoretical 1 H- and 13 C-NMR spectra interpreted by GIAO method depict that the DFT formalism, particularly the B3LYP/6-311+G(d,p) theory of level, gives an accurate description of the ISA experimental chemical shifts. The calculated structural data were also compared with experimental findings. The statistical regression analyses show that the B3LYP/6-31+G(d,p) method results in a correct description of the ISA crystallographic data. Moreover, the frontier molecular orbitals (FMOs), molecular electrostatic potential (MEP) map, and NBO atomic charges of the ISA have been discussed at B3LYP/6-31+G(d,p) theory of level. The FMO analysis were used to determine the charge transfer within ISA and some chemical descriptors such as ionization potential, electron affinity, chemical hardness, softness, chemical potential and electro negativity. The Nucleus-Independent Chemical Shifts (NICS) were also computed for ISA derivatives, 2 - 10 . In the X: O and Y: S derivative, 4 , sulphur substitution increases slightly the aromaticity of ISA skeleton

Magnetically induced currents and aromaticity in ligand-stabilized Au and AuPt superatoms

Understanding magnetically induced currents (MICs) in aromatic or metallic nanostructures is crucial for interpreting local magnetic shielding and NMR data. Direct measurements of the induced currents have been successful only in a few planar molecules but their indirect effects are seen in NMR shifts of probe nuclei. Here, we have implemented a numerically efficient method to calculate gauge-including MICs in the formalism of auxiliary density functional theory. We analyze the currents in two experimentally synthesized gold-based, hydrogen-containing ligand-stabilized nanoclusters [HAu9(PPh3)8]2+ and [PtHAu8(PPh3)8]+. Both clusters have a similar octet configuration of Au(6s)-derived delocalized “superatomic” electrons. Surprisingly, Pt-doping in gold increases the diatropic response of the superatomic electrons to an external magnetic field and enhances the aromaticity of [PtHAu8(PPh3)8]+. This is manifested by a stronger shielding of the hydrogen proton in the metal core of the cluster as compared to [HAu9(PPh3)8]2+, causing a significant upfield shift in agreement with experimental proton NMR data measured for these two clusters. Our method allows the determination of local magnetic shielding properties for any component in large 3D nanostructures, opening the door for detailed interpretation of complex NMR spectra.

Fission Fragment Intrinsic Spins and Their Correlations.

The intrinsic spins and their correlations are the least understood characteristics of fission fragments from both theoretical and experimental points of view. In many nuclear reactions, the emerging fragments are typically excited and acquire an intrinsic excitation energy and an intrinsic spin depending on the type of the reactions and interaction mechanism. Both the intrinsic excitation energies and the fragments' intrinsic spins and parities are controlled by the interaction mechanism and conservations laws, which lead to their correlations and determines the character of their deexcitation mechanism. We outline here a framework for the theoretical extraction of the intrinsic spin distributions of the fragments and their correlations within the fully microscopic real-time density-functional theory formalism and illustrate it on the example of induced fission of ^{236}U and ^{240}Pu, using two nuclear energy density functionals. These fission fragment intrinsic spin distributions display new qualitative features previously not discussed in literature. Within this fully microscopic framework, we extract for the first time the intrinsic spin distributions of fission fragments of ^{236}U and ^{240}Pu as well as the correlations of their intrinsic spins, which have been debated in literature for more than six decades with no definite conclusions so far.

Benchmarking density functional theory methods for modelling cationic metal–argon complexes

Noble gas chemistry is fascinating because noble gases can make formal chemical bonds with metal ions, despite their closed electronic configuration. Argon–metal ion complexes are particularly interesting since their bonding is halfway between dispersion and covalent interactions. Although many metal ion–noble gas complexes have been synthesized, there are still disagreeing theoretical descriptions about their bonding, which is not yet fully understood. Accurate experimental data are important as solid reference for theoretical methodologies, but such data are currently scarce for complexes of a metal ion with noble gas atoms. We measured infrared spectra of MArn+ (n = 3–5; M = Au, Ag, Pd) complexes and used these spectra as benchmark data for different theory levels within the density functional theory formalism. Several basis sets, exchange–correlation functionals, and the inclusion of dispersion corrections were considered. The agreement between the measured spectra and the calculations strongly depends on the applied level of theory. Functionals of a higher level of complexity do not consistently provide a better agreement with the experiment; this is particularly the case for the B3LYP hybrid functional that performs worse than the PBE GGA functional. On the other hand, the inclusion of dispersion corrections and the use of a large basis sets are crucial for a good description of the interaction between M+ and argon atoms.

Identification of promiscuous T cell epitopes on Mayaro virus structural proteins using immunoinformatics, molecular modeling, and QM:MM approaches.

The Mayaro virus (MAYV) belongs to genus Alphavirus (family Togaviridae) and has been reported in several countries, especially in tropical regions of America. Due to its outbreaks and potential lack of medication, an effective vaccine formulation is strongly required. This study aimed to predict promiscuous T cell epitopes from structural polyproteins of MAYV using an immunoinformatics approach. For this purpose, consensus sequences were used to identify short protein sequences capable of binding to MHC class I and class II alleles. Our analysis pointed out 4 MHC-I/TCD8+ and 21 MHC-II/TCD4+ epitopes on capside (1;3), E1 (2;5), E2 (1;10), E3 (0;2), and 6K (0;1) proteins. These predicted epitopes were characterized by high antigenicity, immunogenicity, conservancy, non-allergenic, non-toxic, and good population coverage rate values for North and South American geographical areas. Afterwards, we used the crystal structure of human toll-like receptor 3 (TLR3) ectodomain as a template to predict, through docking essays, the placement of a vaccine prototype at the TLR3 receptor binding site. Finally, classical and quantum mechanics/molecular mechanics (QM:MM) computations were employed to improve the quality of docking calculations, with the QM part of the simulations being accomplished by using the density functional theory (DFT) formalism. These results provide important insights into the advancement of diagnostic platforms, the development of vaccines, and immunotherapeutic interventions.

Investigation of magnetic properties of FeMnP1-xAx (A = In, Se and Sn, where x = 0.33) by use of GGA functionals

Magnetic properties of stable iron-based compounds (FeMnP1-xAx (A = Si, In, Se and Sn) were investigated by use of Quantum Espresso (QE) within the Density Functional Theory (DFT) formalism as a viable magnetic refrigerant. In this research work, DFT technique was the first principle theoretical approach that was employed along with the planewave pseudopotentials (ultrasoft), and the projected augmented wave (PAW) within the generalized gradient approximation (GGA) to describe the electronic structure and investigation of magnetic properties. Magnetic stability is described as the repeated magnetic performance of a material under specific conditions over the life of a magnet. In this case our reference compound, FeMnP0.67 Si0.33 was optimized and its properties were examined in both ferromagnetic (FM) and antiferromagnetic (AFM) states. Two Si atoms were later substituted with atoms of post-transitional metals in period four and five which has shown first-order magnetic transition at near room temperatures. In, Se and Sn were chosen to replace silicon since they would easily mimic the bond, their availability and nontoxic nature. The results showed that only ferromagnetic states of both host and doped compounds gave promising magnetic properties that can be applied in magnetocaloric effect phenomenon. Their band structure results indicated that they were all metals. Antiferromagnetic states showed no magnetic properties as the spin-polarized graph resulted in perfect symmetry of spin up projected density of states (PDOS) and spin down PDOS. From the thermo_pw calculations, it was realized that FeMnP0.67 In0.33 is the best candidate for near room temperature magnetic refrigeration among the studied compounds.

Machine-learning free-energy functionals using density profiles from simulations

The formally exact framework of equilibrium Density Functional Theory (DFT) is capable of simultaneously and consistently describing thermodynamic and structural properties of interacting many-body systems in arbitrary external potentials. In practice, however, DFT hinges on approximate (free-)energy functionals from which density profiles (and hence the thermodynamic potential) follow via an Euler–Lagrange equation. Here, we explore a relatively simple Machine-Learning (ML) approach to improve the standard mean-field approximation of the excess Helmholtz free-energy functional of a 3D Lennard-Jones system at a supercritical temperature. The learning set consists of density profiles from grand-canonical Monte Carlo simulations of this system at varying chemical potentials and external potentials in a planar geometry only. Using the DFT formalism, we nevertheless can extract not only very accurate 3D bulk equations of state but also radial distribution functions using the Percus test-particle method. Unfortunately, our ML approach did not provide very reliable Ornstein–Zernike direct correlation functions for small distances.

From Intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis

Quantum chemistry in the form of density functional theory (DFT) calculations is a powerful numerical experiment for predicting intermolecular interaction energies. However, no chemical insight is gained in this way beyond predictions of observables. Energy decomposition analysis (EDA) can quantitatively bridge this gap by providing values for the chemical drivers of the interactions, such as permanent electrostatics, Pauli repulsion, dispersion, and charge transfer. These energetic contributions are identified by performing DFT calculations with constraints that disable components of the interaction. This review describes the second-generation version of the absolutely localized molecular orbital EDA (ALMO-EDA-II). The effects of different physical contributions on changes in observables such as structure and vibrational frequencies upon complex formation are characterized via the adiabatic EDA. Example applications include red- versus blue-shifting hydrogen bonds; the bonding and frequency shifts of CO, N2, and BF bound to a [Ru(II)(NH3)5]2 + moiety; and the nature of the strongly bound complexes between pyridine and the benzene and naphthalene radical cations. Additionally, the use of ALMO-EDA-II to benchmark and guide the development of advanced force fields for molecular simulation is illustrated with the recent, very promising, MB-UCB potential. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 72 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Charge transport in polythiophene molecular device: DFT analysis.

We report the charge transport phenomenon in polythiophene molecular device and the ways of controlling the nature of charge transport through the device. By using density functional theory (DFT) and non-equilibrium Green's function (NEGF) formalisms, two ways of controlling the nature of charge transport have successfully been demonstrated by introducing conformational changes in the channel and applying external gate potential. Functional groups with negative mesomeric effect such as nitrous and carboxyl and positive mesomeric effect such as amino have been used as substituents as part of introducing conformational changes in the channel. The results indicate that the nature of charge transport in polythiophene molecular device can be changed from hole dominant to electron dominant and vice versa just by introducing minor conformational changes in the channel and by changing the polarity of external gate potential. Moreover, the negative differential resistance (NDR) behavior has been observed in amino-substituted thiophene device. These findings will be very useful in understanding the design of both p and n-type transistors out of same molecule for the next-generation molecular electronics.

Low field electron transport in α−Ga2O3: An ab initio approach

Trigonal α−Ga2O3 is an ultrawideband semiconductor with potential applications in power electronics and ultraviolet opto-electronic devices. In this Letter, we calculate the low field electron mobility in α−Ga2O3 from first principles calculations. The effect of all the 30 phonon modes is taken into account for the transport calculation. The phonon dispersion and the Raman and Infrared spectra are calculated under the density functional perturbation theory formalism and compared with experiments. The electron–phonon interaction (EPI) elements on a dense reciprocal space grid are obtained using the Wannier function interpolation. The full energy dispersion of the phonons is included in both the polar and nonpolar EPI calculations. The electron mobility is then evaluated incorporating the effects of the polar, nonpolar, and ionized impurity scattering using Rode's iterative method. At room temperature, the low field isotropic average electron mobility is estimated to be ∼220 cm2/V s predominantly limited by the polar optical phonon scattering at a doping density of 1.0×1015 cm−3. The anisotropy in the mobility arising from the phonon scattering is also evaluated. Temperature and dopant concentration variation of mobility is also studied, which can help in optimization of the growth for transport measurements.