Corrected Density Functional Method Research Articles

Stacking effect on the orbital characters and transition probability of bilayer MoS2

In this paper, employing the van der Waals (vdW) corrected density functional method, the electronic and optical properties of bilayer MoS2 are calculated for five different stacking patterns ( and ). In this regard, the structural stability and the van der Waals interlayer distance are investigated. The minimum formation energy has indicated the overall trend of relative stability to be as This means and have the most and and have the least stable structures. The band structure and probability distribution for finding electrons in atomic orbitals have also been calculated in the Brillouin zone. The results obtained from band structures and orbital characters show the same trend in the three most stable and a different but the same trend for the two least stable orders. In addition, the oscillator strength has been derived from the calculation of the momentum operator matrix elements using first-principles methods. The calculation of transition probabilities from matrix elements indicates that and have higher transition probabilities than that of and The study of transition probability also shows the y-polarized light is stronger than the x-polarized light for all stacking patterns.

Unravelling the Origin of the Linear Structures Distortions of the Acetylene Isoelectronic Compounds (Disilyne, Digermyne, and Distannyne)

The role and contributions of the effective factors on the structural properties of acetylene (1), disilyne (2), digermyne (3), and distannyne (4) were examined by means of LC-ωPBE long-range corrected density functional method with TZP basis set on all atoms. Although the ground state structure of acetylene (1) is linear (D∞h-symmetry), the trans-bent (C2h, as a local minimum) and di-bridged structures (C2v, as a global minimum) were found for compounds 2–4. Plotted electronic energies of the ground and excited states versus the nuclear displacement (by considering the symmetries of the normal modes) revealed that the negative curvatures of the ground state electronic configurations and the positive curvatures of the excited states of the adiabatic potential energy surfaces (APESs) result from mixing of the ground $$^{1}\Sigma _{{\text{g}}}^{ + }$$ and excited 1Πg states, revealing the presence of the strong pseudo Jahn–Teller effect (i.e., PJT ( $$^{1}\Sigma _{{\text{g}}}^{ + }$$ + 1Πg) ⊗ πg problem). The weak PJTE in acetylene (1) does not distort its linear configurations. The distortions of the linear (D∞h) configurations of compounds 2–4 to their corresponding trans-bent structures (C2h) are due to the PJTE associated with the mixing of the ground $$^{1}\Sigma _{{\text{g}}}^{ + }$$ state and third excited Πg states through the mixing of their HOMOs(πu) with their corresponding LUMOs+2(σu) ([HOMO(πu)] + [LUMO+1(σu)]) in compound 2, the mixing of the ground $$^{1}\Sigma _{{\text{g}}}^{ + }$$ state and second excited Πg states ([HOMO(πu)] + [LUMO(σu)]) in compound 3 and the ground $$^{1}\Sigma _{{\text{g}}}^{ + }$$ state and second excited Πg states ([HOMO(πu)] – [LUMO+1(σu)]) in compound 4. The higher- and lower-lying $$^{1}\Sigma _{{\text{u}}}^{ - }$$ , $$^{1}\Sigma _{{\text{u}}}^{ - }$$ , 1Δu, and 1Πu states are not involved in the PJT interactions. The trans-bent local minimum structures could be converted to their corresponding global minimum structures (di-bridge, C2v) by passing from axial symmetrical (C2) transition state geometries. The energy gaps between reference states (∆) in the linear (D∞h) configurations decrease from disilyne (2) to distannyne (4) while the energy difference between the linear (D∞h) and trans-bent (C2h) configurations increases from compound 2 to 3 but decreases from compound to compound 4, revealing the determining impacts of their corresponding vibronic coupling constants (F) which may control their corresponding D∞h → C2h distortion PJT stabilization energies. Importantly, the variations of the M–M-bond length differences in the linear (D∞h) and trans-bent (C2h) structures of compounds 2–4, Δ(rM–M) D∞h–C2h, correlate well with their corresponding PJT-stabilization energies.

Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain.

A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine Nδ atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the Nδ(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to be a single elementary step process in all the methods we applied.

Revisiting the structural pattern and the stability of (H2O)20 clusters using the dispersion corrected density functional method

The structure and relative stability of the most stable isomers of different families of (H2O)20 clusters viz. edge-sharing pentagonal prism, face-sharing pentagonal prism, fused cube, dodecahedron and irregular-dodecahedron are studied using dispersion corrected density functional Becke97-D in conjunction with cc-pVTZ basis set. The relative stability of water clusters followed the order ESPP>FSPP>FC>DD>IDD. It is found that the relative stability depends mainly on degree of fusion, number of AADD water molecules and four-membered rings present. For a given family, the energy of isomers increases with decrease in the number of t1d hydrogen bonds.

Density functional studies of fused dodecahedral and irregular-dodecahedral water cages

The fused cages of dodecahedral and irregular-dodecahedral water cages with the maximum number of t1d hydrogen bonds were studied using the dispersion corrected density functional method.

Can two T-shaped isomers of OCS–C2H2 van der Waals complex exist?

Molecular properties of the OCS–C2H2 van der Waals complex are studied in detail in order to explore the possibility of formation of three isomers of the complex and to verify the experimental findings. Both dispersion-corrected and -uncorrected double hybrid density functional theories with correlation consistent triple zeta basis set are used to investigate the complex. The results obtained by the dispersion corrected density functional method, mPW2PLYP-D, agree very well with the experimental values. The Symmetry Adapted Perturbation Theory (SAPT) is applied to study the interaction.

Dual nature of acceptors in GaN and ZnO: The curious case of the shallow MgGa deep state

Employing a Koopmans corrected density functional method, we find that the metal-site acceptors Mg, Be, and Zn in GaN and Li in ZnO bind holes in deep levels that are largely localized at single anion ligand atoms. In addition to this deep ground state (DGS), we observe an effective-masslike delocalized state that can exist as a short lived shallow transient state (STS). The Mg dopant in GaN represents the unique case where the ionization energy of the localized deep level exceeds only slightly that of the shallow effective-mass acceptor, which explains why Mg works so exceptionally well as an acceptor dopant.

An experimental and computational study of the valence photoelectron spectra of halogenated pyrimidines

The electronic structures of pyrimidine and a selection of its halogen-substituted derivatives have been investigated using ultraviolet photoelectron spectroscopy and ab initio quantum chemical methods. Assignments are proposed for all of the features in the PES spectra by comparison with the vertical ionization energies of the molecular orbitals calculated using the partial third-order quasiparticle approximation as applied to electron propagator theory and a corrected density functional method based on the B3LYP functional. The shifts of the outermost five molecular orbitals of the pyrimidine ring structure in the halogen-substituted derivatives with respect to the binding energies of the equivalent orbitals in the parent pyrimidine molecule are discussed as a function of the identity and ring position of the halogen atom.

Ab initiostudy of ferromagnetism inGa1−xCrxNthin films

Electronic structure and magnetic properties of ${\mathrm{Ga}}_{1\ensuremath{-}x}{\mathrm{Cr}}_{x}\mathrm{N}$ thin films are studied using the gradient corrected density functional method and a supercell slab model. Calculations are carried out by varying the concentration of doped Cr atoms and the sites they occupy. Cr atoms are found to prefer to reside on the surface sites and cluster around N as Mn atoms do. However, unlike Mn-doped GaN, Cr-doped GaN is found to be ferromagnetic for all concentrations studied. The calculated ferromagnetism is in agreement with recent experimental observations.

Assignment of surface IR absorption spectra observed in the oxidation reactions: 2H + H 2O/Si(1 0 0) and H 2O + H/Si(1 0 0)

Infrared reflection absorption spectroscopy that used buried metal layer substrates (BML-IRRAS) and density functional cluster calculations were employed to investigate the water related oxidation reactions of 2H + H 2O/Si(1 0 0)-(2 × 1), 2D + H 2O/Si(1 0 0)-(2 × 1), and H 2O + H/Si(1 0 0)-(2 × 1). In addition to the oxygen inserted coupled monohydrides, which were previously reported in the former reaction system, we report several other oxidized Si hydride species in our BML-IRRAS experiments. Three new pairs of vibrational bands are identified between 900 and 1000 cm −1. These vibrational frequencies were calculated using Si9 and Si10 cluster models that included all possible structures from zero to five oxygen insertions into the top layer silicon atoms using a B3LYP gradient corrected density functional method with a polarized 6-31G** basis set for all atoms. The three pairs of vibrational modes are assigned to the scissoring modes of adjacent and isolated SiH 2 with zero, one, and two oxygen atoms inserted into the Si back bonds. All the other newly observed vibrational peaks related to Si oxidation are also assigned in this study. The Si–O stretching bands observed in the reaction 2D + H 2O/Si(1 0 0)-(2 × 1) show an isotope effect, which suggests that in the system 2H + H 2O/Si(1 0 0)-(2 × 1) also, hydrogen atom tunneling plays an important role for the insertion of oxygen atoms into Si back bonds that form oxidized adjacent dihydrides.

Theoretical analysis of the triplet excited states of difluorosilylene. A density functional study

We calculated the geometry and vibrational frequencies of the ground 1A 1 and first excited 3B 1 states of SiF 2 by local and gradient corrected density functional methods. Further, we have determined the geometry, adiabatic and vertical excitation energies of SiF 2 in 3A 2 and 3B 2 states. We have also simulated the vibrational fine structure of the emission and absorption spectrum based on Frank Condon principles between the ground and first triplet and singlet excited states. The results of the calculations is compared to the available experimental and theoretical data.

N2 and CO molecules as probes of zeolite acidity: an infrared spectroscopy and density functional investigation

The interaction of N2 with Bronsted acid centers of H-ZSM-5 zeolite has been investigated employing Fourier transform infrared spectroscopy and cluster model calculations based on a gradient corrected density functional method. A comparison is made with CO, which is widely used as a probe for surface acidity. It is shown that the computational approach is capable of almost quantitatively reproducing a number of sensitive parameters of the H-bonded dinitrogen and carbonyl complexes, like adsorption energy, adsorption-induced changes of the vibrational frequencies and of their intensities. According to a constraint space orbital variation analysis, the carbonyl and dinitrogen complexes mainly differ by the somewhat stronger σ donation ability of CO as compared to N2. It is concluded that dinitrogen may serve as a convenient probe for the acidity of zeolites.

On the accuracy of gradient corrected density functional methods for transition metal complexes

Density functional theory with gradient corrections (DFTG) is applied to a series of second-row transition metal compounds. The mean absolute deviations from experiment for the atomic excitation energies and ionization potential are in the range 0.2–0.4 eV. In comparison with accurate multireference configuration interaction (MR-CI) and parametrized CI with parameter 80 (PCI-80) results for the binding energies of the MCH+2 cations, the mean absolute deviation is 6.7 kcal/mol to be compared with 17.8 kcal/mol at the modified coupled pair functional (MCPF) level. The DFTG result is more sensitive to the choice of asymptote with a mean deviation of 14 kcal/mol if the bonding atomic state is not used as asymptote. Product energies and transition states for the addition of methane to RhXL (X=H, Cl, L=H2O, NH3, PH3, and CO) also show the same trends as the PCI-80 comparison and represent an improvement over the MCPF results.

Calculation of some atomic properties by gradient corrected density functional method

Using thePerdew andPerdew-Wang Yue gradient expansion functionals the total electronic binding energies, the ionization potentials and the KL transitin energies are calculated for the atoms of elements from Be to Cu, and the 3d–4s transition energies are determined for the third row elements. There is a general improvement with respect to the results found without gradient corrections. However the asymptotic behavior of the potential does not changes.