Calculation of the electronic and optical properties of indium tin oxide by density functional theory

Density functional theory (DFT) was used to calculate the bulk electronic and optical properties of indium tin oxide (ITO). The ITO model was constructed replacing indium atoms with tin atoms in the cubic unit cell of indium oxide. To allow more possibilities for tin atom substitution than afforded by the forty-atom primitive cell of indium oxide all eighty atoms of the unit cell were included in the stoichiometry (In_32−xSn_xO₄₈) using periodic boundary conditions. A number of properties of ITO were calculated including the optical band gap, charge carrier density and plasma frequency. The dependence of the electronic and optical properties of ITO on a variety of parameters such as the tin content, cubic lattice parameter and the distance between adjacent tin atoms was investigated. The electronic and optical properties agreed well with experimental data and allowed insight into the origin of the electronic and optical properties of ITO.     

Electronic properties of liquid water by sequential molecular dynamics/density functional theory

Electronic properties of liquid water were analysed by a sequential molecular dynamics (MD)/density functional theory approach. MD simulations are based on a polarisable model for water. Emphasis was placed on the prediction of the water dipole moment, liquid state polarisability, ionisation potential (IP), and vertical electron affinity. The dipole moment of the water molecule in liquid water is not dependent on the number of molecules included in the quantum mechanical calculations. The polarisability of the water molecule in liquid water is 4% lower than its gas phase value. The IP of liquid water (9.7 ± 0.06 eV) is in good agreement with recent experimental data.     

Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals.

The generalized hybrid orbital (GHO) method has previously been formulated for combining molecular mechanics with various levels of quantum mechanics, in particular semiempirical neglect of diatomic differential overlap theory, ab initio Hartree-Fock theory, and self-consistent charge density functional tight-binding theory. To include electron-correlation effects accurately and efficiently in GHO calculations, we extend the GHO method to density functional theory in the generalized-gradient approximation and hybrid density functional theory (denoted by GHO-DFT and GHO-HDFT, respectively) using Gaussian-type orbitals as basis functions. In the proposed GHO-(H)DFT formalism, charge densities in auxiliary hybrid orbitals are included to calculate the total electron density. The orthonormality constraints involving the auxiliary Kohn-Sham orbitals are satisfied by carrying out the hybridization in terms of a set of L?wdin symmetrically orthogonalized atomic basis functions. Analytical gradients are formulated for GHO-(H)DFT by incorporating additional forces associated with GHO basis transformations. Scaling parameters are introduced for some of the one-electron integrals and are optimized to obtain the correct charges and geometry near the QM/MM boundary region. The GHO-(H)DFT method based on the generalized gradient approach (GGA) (BLYP and mPWPW91) and HDFT methods (B3 LYP, mPW1PW91, and MPW1 K) is tested-for geometries and atomic charges-against a set of small molecules. The following quantities are tested: 1) the C--C stretch potential in ethane, 2) the torsional barrier for internal rotation around the central C--C bond in n-butane, 3) proton affinities for a set of alcohols, amines, thiols, and acids, 4) the conformational energies of alanine dipeptide, and 5) the barrier height of the hydrogen-atom transfer between n-C4H10 and n-C4H9, where the reaction center is described at the MPW1 K/6-31G(d) level of theory.     

Ferric complexes of 3-hydroxy-4-pyridinones characterized by density functional theory and Raman and UV-vis spectroscopies

Deferiprone and other 3-hydroxy-4-pyridinones are used in metal chelation therapy of iron overload. To investigate the structure and stability of these compounds in the natural aqueous environment, ferric complexes of deferiprone and amino acid maltol conjugates were synthesized and studied by computational and optical spectroscopic methods. The complexation caused characteristic intensity changes, a 300× overall enhancement of the Raman spectrum, and minor changes in UV-vis absorption. The spectra were interpreted on the basis of density functional theory (DFT) calculations. The CAM-B3LYP and ωB97XD functionals with CPCM solvent model were found to be the most suitable for simulations of the UV-vis spectra, whereas B3LYP, B3LYPD, B3PW91, M05-2X, M06, LC-BLYP, ωB97XD, and CAM-B3LYP functionals were all useful for simulation of the Raman scattering. Characteristic Raman band frequencies for 3-hydroxy-4-pyridinones were assigned to molecular vibrations. The computed conformer energies consistently suggest the presence of another isomer of the deferiprone-ferric complex in solution, in addition to that found previously by X-ray crystallography. However, the UV-vis and Raman spectra of the two species are similar and could not be resolved. In comparison to UV-vis, the Raman spectra and their combination with calculations appear more promising for future studies of iron sequestrating drugs and artificial metalloproteins as they are more sensitive to structural details.     

Theoretical investigation of the molecular structure,vibrational spectra,and molecular docking of tramadol using density functional theory

The optimized molecular structures, harmonic vibrational wavenumbers, and the corresponding vibrational assignments of (1S,2S)-tramadol and (1R,2R)-tramadol are computationally examined using the B3LYP density functional theory method together with the standard 6–311++G(d,p) and def2-TVZP basis sets. The optimized structures show that phenolic rings of both 1R,2R and 1S,2S tramadol adopt planar geometry, which are slightly distorted due to the substitution at the meta-position; and the six-membered cyclohexane adopts a slightly distorted chair conformation. The 1S,2S enantiomer is energetically more favorable than 1R,2R with the energy differences of 1.32 and 1.03 kcal/mol obtained at B3LYP/6–311++G(d,p) and B3LYP/Def2-TVZP levels, respectively. The analysis of the binding pocket in the silico molecular docking with the m-opioid receptor shows that it originated two clusters with the 1S,2S enantiomer and one cluster with the 1R,2R enantiomer of tramadol. The results point to a more stable complex of the m-opioid receptor with the 1R,2R enantiomer of tramadol.     

The Green's function density functional tight-binding (gDFTB) method for molecular electronic conduction

A review is presented of the nonequilibrium Green's function (NEGF) method "gDFTB" for evaluating elastic and inelastic conduction through single molecules employing the density functional tight-binding (DFTB) electronic structure method. This focuses on the possible advantages that DFTB implementations of NEGF have over conventional methods based on density functional theory, including not only the ability to treat large irregular metal-molecule junctions with high nonequilibrium thermal distributions but perhaps also the ability to treat dispersive forces, bond breakage, and open-shell systems and to avoid large band lineup errors. New results are presented indicating that DFTB provides a useful depiction of simple gold-thiol interactions. Symmetry is implemented in DFTB, and the advantages it brings in terms of large savings of computational resources with significant increase in numerical stability are described. The power of DFTB is then harnessed to allow the use of gDFTB as a real-time tool to discover the nature of the forces that control inelastic charge transport through molecules and the role of molecular symmetry in determining both elastic and inelastic transport. Future directions for the development of the method are discussed.     

Double-hybrid density functional theory for excited electronic states of molecules

Double-hybrid density functionals are based on a mixing of standard generalized gradient approximations (GGAs) for exchange and correlation with Hartree-Fock (HF) exchange and a perturbative second-order correlation part (PT2) that is obtained from the Kohn-Sham (GGA) orbitals and eigenvalues. This virtual orbital-dependent functional (dubbed B2PLYP) contains only two empirical parameters that describe the mixture of HF and GGA exchange (ax) and of the PT2 and GGA correlation (ac), respectively. Extensive testing has recently demonstrated the outstanding accuracy of this approach for various ground state problems in general chemistry applications. The method is extended here without any further empirical adjustments to electronically excited states in the framework of time-dependent density functional theory (TD-DFT) or the closely related Tamm-Dancoff approximation (TDA-DFT). In complete analogy to the ground state treatment, a scaled second-order perturbation correction to configuration interaction with singles (CIS(D)) wave functions developed some years ago by Head-Gordon et al. [Chem. Phys. Lett. 219, 21 (1994)] is computed on the basis of density functional data and added to the TD(A)-DFTGGA excitation energy. The method is implemented by applying the resolution of the identity approximation and the efficiency of the code is discussed. Extensive tests for a wide variety of molecules and excited states (of singlet, triplet, and doublet multiplicities) including electronic spectra are presented. In general, rather accurate excitation energies (deviations from reference data typically <0.2 eV) are obtained that are mostly better than those from standard functionals. Still, systematic errors are obtained for Rydberg (too low on average by about 0.3 eV) and charge-transfer transitions but due to the relatively large ax parameter (0.53), B2PLYP outperforms most other functionals in this respect. Compared to conventional HF-based CIS(D), the method is more robust in electronically complex situations due to the implicit account of static correlation effects by the GGA parts. The (D) correction often works in the right direction and compensates for the overestimation of the transition energy at the TD level due to the elevated fraction of HF exchange in the hybrid GGA part. Finally, the limitations of the method are discussed for challenging systems such as transition metal complexes, cyanine dyes, and multireference cases.     

Ab initio Hartree-Fock and density functional theory study on molecular structures, energies, and vibrational frequencies of conformations of 2-hydroxy-3-nitropyridine and 3-hydroxy-2-nitropyridine

The optimized molecular structures, vibrational frequencies and corresponding vibrational assignments of conformations of 2-hydroxy-3-nitropyridine and 3-hydroxy-2-nitropyridine molecules have been investigated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-311++G(d,p) basis set. The comparison of the experimental and calculated spectra of the molecules have shown that they exist in two conformations with the two OH bond angles (110 degrees and 250 degrees ) respective to the CO bond in the ground state and their energy curves having two minimums have been drawn.     

Improved anti-inflammatory and anticancer properties of celecoxib loaded zinc oxide and magnesium oxide nanoclusters: A molecular docking and density functional theory simulation

Present study offers great prospects for the adsorption of anti-inflammatory celecoxib molecule (CXB) over the surface of zinc oxide (Zn₁₂O₁₂) and magnesium oxide (Mg₁₂O₁₂) nanoclusters in several environments by performing robust theoretical calculations. Density functional theory (DFT), time-dependent density functional theory (TDDFT) and molecular docking calculations have been extensively carried out to predict the foremost optimum site of CXB adsorption. It has been observed that the CXB molecule prefers to be adsorbed by its SO₂ site on the Zn-O and Mg-O bonds of the Zn₁₂O₁₂ and Mg₁₂O₁₂ nanoclusters instead of NH₂ and NH sites, where electrostatic interactions dominate over the bonding characteristics of the conjugate complexes. Furthermore, the presence of interactions between the CXB molecule and nanoclusters has also been evidenced by the UV–Vis absorption spectra and IR spectra. Molecular docking analysis has revealed that both adsorption states including CXB/Zn₁₂O₁₂ and CXB/Mg₁₂O₁₂ have good inhibitory potential against protein tumor necrosis factor alpha (TNF-α) and Interleukin-1 (IL-1), and human epidermal growth factor receptor 2 (HER2). Hence they might be explored as efficient TNF-α, IL-1, and HER2 inhibitors. Hence from the study, it can be anticipated that these nanoclusters can behave as an appropriate biomedical carrier for the CXB drug delivery.     

The determination of intrinsic reaction coordinates by density functional theory

The first implementation of the intrinsic reaction coordinate (IRC ) method within the density functional theory (DFT ) framework is presented. The implementation has been applied to four different types of chemical reactions represented by the isomerization process, HCN ? HNC (A); the S_N2 process, H^? + CH₄ ? CH₄ + H^? (B); the exchange process, H˙ + HX ? HX + H˙ (X ? F,Cl) (C); and the elimination process, C₂H₅Cl ? C₂H₄ + HCl (D). The present study presents for each process optimized structures and calculated harmonic vibrational frequencies for the reactant(s), the transition state, and the product(s) along with the IRC path connecting the stationary points. The calculations were carried out within the local density approximation (LDA ) as well as the LDA/NL scheme where the LDA energy expression is augmented by Perdew's and Becke's nonlocal (NL ) corrections. The LDA and LDA/NL results are compared with each other as well as the best available ab initio calculations and experimental data. For reaction (D), ab initio calculations based on MP 2 geometries and MP 4SDTQ energies have been added due to the lack of accurate published post-HF calculations on this process. A detailed discussion is provided on the efficiency of the IRC algorithms, the relative accuracy of the DFT and ab initio schemes, as well as the reaction mechanisms of the four reactions. It is concluded that the LDA/NL scheme affords the same accuracy as does the MP 4 method. The post-HF methods seem to overestimate activation energies, whereas the corresponding LDA/NL estimates are too low. The LDA activation energies are even lower than the LDA/NL counterparts. The incorporation of the IRC method into the DFT framework provides a promising and reliable tool for probing the chemical reaction path on the potential energy surfaces, even for large-size systems. IRC calculations by ab initio methods of an accuracy similar to the LDA/NL scheme, such as the MP 4 scheme, are not feasible. © John Wiley & Sons, Inc.     

Differential functional theory and molecular docking studies of newly synthesized carbamates

Four new carbamates (RZ1–RZ4) were synthesized from different amine moieties through reported methods. The reaction was monitored using thin layer chromatography and characterization was done using m.p., fourier‐transform infrared spectroscopy (FTIR), and X‐ray diffraction (XRD) techniques. Density functional theory (DFT) studies were carried out using Gaussian 09 software to compare the theoretical and practical parameters of the synthesized compounds. Highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) were also drawn to calculate the energy difference between orbitals. In‐vitro enzyme inhibition potential against acetylcholine esterase (AChE), butyrylcholine esterase (BChE), and protease was checked through standard protocols that suggested moderate inhibition against selected enzymes. Docking studies were also carried out, which depicted that these compounds have ability to bind on the active site of AChE and BChE.     

Some properties of the Lagrange multiplier μ in density functional theory

Some new properties of the Lagrange multiplier μ introduced through the normalization constraint on ρ in the variations of energy density functionals are determined. Through arguments concerning the homogeneity properties of these functionals with respect to μ, it is demonstrated that at the point of variation μ = μ₀ = E₀/N, where E₀ is the ground state energy and N is the total particle number. It is also shown that the value of μ₀ is independent of the normalization imposed on ρ. The interpretation of μ₀ as a chemical potential is discussed in the light of these findings.     

Sterically driven electronic properties of naphthalene- and anthracene-end-capped 2,2′-bipyridine luminophores: synthesis and density functional theory

Two naphthalene- and one anthracene-end-capped 4,4′-π-conjugated-2,2′-bipyridine chromophores have been synthesized via the Horner-Wordsworth-Emmons reaction protocol and their electronic absorption and emission properties have been examined. DFT and TD-DFT computational studies have been carried out in order to comprehend the role of steric factor over the electronic factor.     

Time-dependent density functional theory study on electronic and spectroscopic properties for Ph<Subscript>2</Subscript>Bq and its complexes

The molecular structures of the ground state and the first singlet excited state for diphenylboron analogs of Alq₃ [Ph₂Bq where q is 8-hydroxyquinoline (QH)] and its three derivatives were optimized with the Density Functional Theory and ab initio “configuration interaction with single excitations” method, respectively. The frontier molecular orbital characteristics of Ph₂Bq were analyzed systematically in order to study the electronic transition mechanism. Electronic and spectroscopic properties of complexes have been investigated with Time-Dependent Density Functional Theory, which indicates that the emissions of Ph₂Bq and its derivatives originate from the electronic π → π* transitions within the QH ligands. That means that one might tune the emission wavelengths and improve charge transfer properties through the effect of substituent on the 8-hydroxyquinoline ligand. Similar calculations were carried out for isolated QH and its three derivatives for comparison. We found that the highest occupied molecular orbital and the lowest unoccupied molecular orbital of Ph₂Bq are similar to those of QH and their spectroscopic properties change similarly when they are substituted by the same group, which suggests that one can search possibility of a red or blue emission from Ph₂Bq derivatives by analyzing QH and its derivatives.     

Molecular properties via a subsystem density functional theory formulation: a common framework for electronic embedding

In this article, we present a consistent derivation of a density functional theory (DFT) based embedding method which encompasses wave-function theory-in-DFT (WFT-in-DFT) and the DFT-based subsystem formulation of response theory (DFT-in-DFT) by Neugebauer [J. Neugebauer, J. Chem. Phys. 131, 084104 (2009)] as special cases. This formulation, which is based on the time-averaged quasi-energy formalism, makes use of the variation Lagrangian techniques to allow the use of non-variational (in particular: coupled cluster) wave-function-based methods. We show how, in the time-independent limit, we naturally obtain expressions for the ground-state DFT-in-DFT and WFT-in-DFT embedding via a local potential. We furthermore provide working equations for the special case in which coupled cluster theory is used to obtain the density and excitation energies of the active subsystem. A sample application is given to demonstrate the method.     

Spectroscopic properties of trichlorofluoromethane CCl(3)F calculated by density functional theory

Density functional theory is used to generate local potential energy surfaces in normal coordinates for several chlorine isotopomers of trichlorofluoromethane (CCl(3)F, CFC11). An examination of predicted structures suggested that the PBE0 functional would be suitable. Anharmonic surfaces around the equilibrium geometries are reported, as determined by energies, gradients, and second derivatives. Vibrational levels for fundamentals, overtones and combination bands are reported, as well as harmonic frequencies, anharmonic constants, rotational constants, isotope shifts, and infrared intensities. These are compared with experimental information.     

Characterization and optical properties of mechanochemically synthesized molybdenum-doped rutile nanoparticles and their electronic structure studies by density functional theory

The optical and electronic properties of molybdenum (Mo) doped rutile TiO₂ prepared by the mechanochemical method were studied both experimentally and using density functional theory (DFT). The synthesized nanoparticles were characterized by XRD, TEM, EDS-MAP, and XPS. The XRD results showed the successful incorporation of Mo in the rutile crystal lattice. High-resolution TEM images illustrated a decreasing trend in the (110) d-spacing for samples doped up to 3 at%. The shift toward higher binding energies in the XPS spectra was due to the higher oxidization tendencies of Mo⁵⁺ and Mo⁶⁺ substituted in Ti⁴⁺ sites. The optical behavior of samples was examined by UV–Vis and photoluminescence spectroscopy. The bandgap energy value of rutile was reduced from 3.0 eV to 2.4 eV by 2 at% Mo doping. The DFT calculations showed a reduction of bandgap energy value of rutile to 2.35 eV with 2 at% Mo, which is in harmony with the experimental results. The creation of energy states below the conduction band because of Mo doping was identified as the reason for reducing the bandgap energy and photoluminescence emission of rutile.     

Structural, electronic, and vibrational characterization of Fe-HNO porphyrinates by density functional theory

A recent report of the structural and vibrational properties of heme-bound HNO in myoglobin, MbHNO, revealed a long Fe-N(HNO) bond with the hydrogen atom bonded to the coordinated N atom. The Fe-N(H)-O moiety was reported to exhibit an unusually high Fe-N(HNO) stretching frequency relative to those of the corresponding [FeNO]6 and [FeNO]7 porphyrinates, despite the Fe-N(HNO) bond being longer than either of its Fe-N(NO) counterparts. Herein, we present results from density functional theory calculations of an active site model of MbHNO that support the previous assignment and clarify this seemingly contradictory result. The results are consistent with the experimental evidence for a ground-state Fe-N(H)-O structure having a long Fe-N(HNO) bond and a uniquely high nu(Fe)(-)(N(HNO)) frequency. This high frequency is the result of the correspondingly low reduced mass of the normal mode, which is largely attributable to significant motion of the N-bound hydrogen atom. Additionally, the calculations show the Fe-N(H)O bonding in this complex to be remarkably insensitive to whether the HNO and ImH ligand planes are parallel or perpendicular. This is attributed to insensitivities of the Fe-L(axial) characters of molecular orbitals to the relative HNO and ImH orientation in both the parallel and perpendicular conformers.