Orbital Density Functional Theory Research Articles

13C GIAO DFT calculation as a tool for configuration prediction of N–O group in saturated heterocyclic N‐oxides

Tropane, tropinone, pseudopelletierine and cocaine were oxidized in situ in a nuclear magnetic resonance (NMR) tube providing mixtures of exo/endo N-oxides. Observed (13)C chemical shifts were correlated with values calculated by gauge-including atomic orbitals density functional theory (DFT) OPBE/6-31G* method using DFT B3LYP/6-31G* optimized geometries. The same method of (13)C chemical shift calculation was applied on series of methyl-substituted 1-methylpiperidines and their epimeric N-oxides described in literature. The results show that using this undemanding calculation method enables assignment of configuration of N-O group in N-epimeric saturated heterocyclic N-oxides. The approach enables assigning of the configuration with high degree of certainty even if NMR data of only one isomer are available. An improved method of in situ oxidation of starting amines in an NMR tube is also described.

Localization of molecular orbitals on fragments

A non-iterative algorithm for the localization of molecular orbitals (MOs) from complete active space self consistent field (CASSCF) and for single-determinantal wave functions on predefined moieties is given. The localized fragment orbitals can be used to analyze chemical reactions between fragments and also the binding of fragments in the product molecule with a fragments-in-molecules approach by using a valence bond expansion of the CASSCF wave function. The algorithm is an example of the orthogonal Procrustes problem, which is a matrix optimization problem using the singular value decomposition. It is based on the similarity of the set of MOs for the moieties to the localized MOs of the molecule; the similarity is expressed by overlap matrices between the original fragment MOs and the localized MOs. For CASSCF wave functions, localization is done independently in the space of occupied orbitals and active orbitals, whereas, the space of virtual orbitals is mostly uninteresting. Localization of Hartree-Fock or Kohn-Sham density functional theory orbitals is not straightforward; rather, it needs careful consideration, because in this case some virtual orbitals are needed but the space of virtual orbitals depends on the basis sets used and causes considerable problems due to the diffuse character of most virtual orbitals.

Architectures, electronic structures, and stabilities of Cu-doped Ge n clusters: density functional modeling

The present study reports the geometries, electronic structures, growth behavior, and stabilities of neutral and ionized copper-doped germanium clusters containing 1-20 Ge atoms within the framework of linear combination of atomic orbitals density functional theory (DFT) under the spin-polarized generalized gradient approximation. It was found that Cu-capped Ge(n) (or Cu-substituted Ge( n+1)) and Cu-encapsulated Ge(n) clusters mostly occur in the ground state at a particular cluster size (n). In order to explain the relative stabilities of the ground-state clusters, parameters such as the average binding energy per atom (BE), the embedding energy (EE), and the fragmentation energy (FE) of the clusters were calculated, and the resulting values are discussed. To explain the chemical stabilities of the clusters, parameters such as the energy gap between the highest occupied and the lowest unoccupied molecular orbitals (the HOMO-LUMO gap), the ionization energy (IP), the electron affinity (EA), the chemical potential (μ), the chemical hardness (η), and the polarizability were calculated, and the resulting values are also discussed. Natural atomic orbital (NAO) and natural bond orbital (NBO) analyses were also used to determine the electron-counting rule that should be applied to the most stable Ge(10)Cu cluster. Finally, the relevance of the calculated results to the design of Ge-based superatoms is discussed.

Mechanism and regioselectivity of the 1,3‐dipolar cycloaddition of thiocarbonyl S‐imide with cyclopent‐3‐ene‐1,2‐dione and methoxyethene: a density functional theory approach

A theoretical study on the regioselectivity of 1,3‐dipolar cycloaddition reaction between an uncommon dipole (thiocarbonyl S‐imide) with cyclopent‐3‐ene‐1,2‐dione (DPh1) and methoxyethene (DPh2) has been carried out by means of several theoretical approaches, namely, activation energy, Houk's rule based on the frontier molecular orbital theory and density functional theory (DFT) reactivity indices. The calculations were performed at the DFT‐B3LYP/6‐31G(d) level of theory using GAUSSIAN 09. The present analysis shows that the 1,3‐dipolar cycloaddition of thiocarbonyl S‐imide with DPh1 and DPh2 has normal‐electron demand and inverse‐electron demand character, respectively. Moreover, the results obtained from energetic point view are in agreement with electronic approaches, and the Houk's rule is capable to predict true regioselectivity. Copyright © 2012 John Wiley & Sons, Ltd.

Simple Approximate Physical Orbitals forGWQuasiparticle Calculations

Generating unoccupied orbitals within density functional theory (DFT) for use in GW calculations of quasiparticle energies becomes prohibitive for large systems. We show that, without any loss of accuracy, the unoccupied orbitals may be replaced by a set of simple approximate physical orbitals made from appropriately prepared plane waves and localized basis DFT orbitals that represent the continuum and resonant states of the system, respectively. This approach allows for accurate quasiparticle calculations using only a very small number of unoccupied DFT orbitals, resulting in an order of magnitude gain in speed.

Synthesis, Crystal Structure and ab Initio Studies of 5-Phenylamino-3-phenylimino-3H[1, 2]dithiole-4-carboxylic acid ethyl ester

Phenylamino-3-phenylimino-3H(1, 2)dithiole- 4-carboxylic acid ethyl ester, C18H16N2O2S2, (I), has been synthesized and the structure has been solved by X-ray diffraction. The crystals are triclinic, space group P 1, with a = 5.7127(2) A u , b = 12.1757(5) A u , c = 14.0734(5) A u , a =112.1217(16), b = 97.786(2), c = 100.694(2), Mr = 356.45, V = 868.11(6) A u 3 , Z = 2 and R = 0.0373. In the title compound there is an intramolecular N-HO hydrogen bond. The crystal structure is stabilized only by weak C-Hp and pp interactions as well as by van der Waals forces. The geometry of the isolated molecule was optimized by ab initio quantum mechanical calculations, employing both molecular orbital Hartree-Fock (HF) and density functional theory (DFT) methods. In the DFT cal- culation the minimum energy was achieved for a confor- mation very similar to that of the solid-state molecule.

Quantitative Structure-Activity Relationship (QSAR) on New Benzothiazoles Derived Substituted Piperazine Derivatives

Several derivatives of N-(2-(4-(benzothiazol-2-yl)piperazin-1-yl)-2-oxoethyl)benzamides 2a-l and three analogues of thioureas 3a-c have been theoretically investigated by applying semiempirical molecular orbital theory and density functional theory (B3LYP/6-31G ∗∗ ) to obtain approximate minimum energy structures, as well as the DZVP basis set. A quantitative structure–activity relationship (QSAR) of the same series has been studied. The amide substituents are: R = 4-Ph, 4-Cl-2-nitro-Ph, ClCH2, 2-OEt, benzo[1,3]dioxole; 2-thiophene; 2-furane, 2-pyrrolidine, N-piperidine, N-methyl-piperazine, and -(1-benzyl-2-ethyl-4-nitro-1H-imidazol-5-ylthio) group.

Architecture, electronic structure and stability of TM@Ge(n) (TM = Ti, Zr and Hf; n = 1-20) clusters: a density functional modeling

The present study reports the geometry, electronic structure and properties of neutral and anionic transition metal (TM = Ti, Zr and Hf)) doped germanium clusters containing 1 to 20 germanium atoms within the framework of linear combination of atomic orbitals density functional theory under spin polarized generalized gradient approximation. Different parameters, like, binding energy (BE), embedding energy (EE), energy gap between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO), ionization energy (IP), electron affinity (EA), chemical potential etc. of the energetically stable clusters (ground state cluster) in each size are calculated. From the variation of these parameters with the size of the clusters the most stable cluster within the range of calculation is identified. It is found that the clusters having 20 valence electrons turn out to be relatively more stable in both the neutral and the anionic series. The sharp drop in IP as the valence electron count increases from 20 to 21 in neutral cluster is in agreement with predictions of shell models. To study the vibrational nature of the clusters, IR and Raman spectrum of some selected TM@Ge(n) (n = 15,16,17) clusters are also calculated and compared. In the end, relevance of calculated results to the design of Ge-based super-atoms is discussed.

Structures, Frequencies, and Energy Properties of Small Neutral, Cationic, and Anionic Niobium Clusters

A density functional study of small neutral, cationic, and anionic niobium clusters ranging from two to six atoms using the linear combination of Gaussian-type orbitals density functional theory (LCGTO-DFT) approach was performed. The calculations employed a gradient-corrected exchange-correlation functional and a newly developed niobium scalar-relativistic model core potential optimized for gradient-corrected density functional calculations. For neutral and charged systems, several isomers and different multiplicities were studied with the aim to determine the lowest energy structures. A vibrational analysis was performed to characterize these isomers. Structural parameters, harmonic frequencies, ionization potentials, and electron affinities are reported. The obtained results are compared with available data from the literature. Based on this comparison new assignments for the ground state structures of the pentamer and hexamer niobium clusters are proposed.

Band gap of InxGa1−xN: A first principles analysis

We report first principles analysis of the band gap Eg of ternary group-III nitride InxGa1−xN in both the wurtzite and zincblende form, within the linear muffin-tin orbital (LMTO) density functional theory method. We have implemented the semilocal modified Becke–Johnson (MBJ) exchange potential to accurately determine the band gap. The doping of In atoms into the GaN crystal is handled by the InxGa1−xN alloy model within the coherent potential approximation (CPA). The LMTO-CPA-MBJ approach allows us to predict Eg as a function of arbitrary In concentration x. Quantitative comparison to the experimental data is made.

Chemisorptions effect of oxygen on the geometries, electronic and magnetic properties of small size Nin (n = 1-6) clusters

The present study reports the effect of oxygen addition on small size Ni(n) (n = 1-6) clusters in different spin states within the framework of linear combination of atomic orbital (LCAO) density functional theory (DFT) under spin polarized generalized gradient approximation (GGA) functional. Relative stabilities of the optimized clusters are discussed on the basis of the calculated parameters, such as, binding energy (BE), embedding energy (EE) and fragmentation energy (FE). Other parameters, like ionization potential (IP), electron affinity (EA), etc. show that though the additions of oxygen can affect the chemical properties of Ni(n) clusters with an additional stability to Ni(n)O. In most of the cases the magnetic moment of the stable isomers are geometry dependent for a particular size both in pure and oxidized clusters. Calculated magnetic moments of Ni(n)O (n = 1-6) clusters reveal that the magnetic moment of ground state Ni(4)O isomers in different geometries is same as in pure Ni(4) isomers. Present study also explains the cause of stable magnetic moment in Ni(4)O cluster through the distribution of electrons in different orbitals.

Correcting Systematic Errors in DFT Spin-Splitting Energetics for Transition Metal Complexes.

Spin-splittings of 57 octahedral first-row transition metal complexes calculated with B3LYP are compared with a database of experimental spectra collected from the literature. A variety of transition metal centers in various oxidation states and multiplicities along with a number of different coordinating ligands are considered. Environmental effects have been included to enable reasonable quantitative comparison with experiment. The manifold of states is studied using initial guesses constructed from ligand field theory. A localized orbital correction (LOC) model, referred to as DBLOC-DFT (d-block localized orbital corrected density functional theory), systematically corrects B3LYP calculations using five parameters. The final results are a considerable improvement over conventional DFT, bringing the mean unsigned error (MUE) from 10.14 kcal/mol with a standard deviation of 4.56 to 1.98 kcal/mol with a standard deviation of 1.62. Depending on the relative multiplicities of the ground and excited states, it is shown that B3LYP*, which has 15% exact nonlocal exchange, can lead to larger errors with respect to experiment than B3LYP. Application to 7 complexes from Swart et al. [ J. Phys. Chem. A 2004 , 108 , 5479. ] and 14 small-gap spin-crossover complexes, from the literature, shows the DBLOC model provides good agreement with a variety of experimental data.

X-ray Crystal Structure, Raman Spectroscopy, and Ab Initio Density Functional Theory Calculations on 1,1,3,3-Tetramethylguanidinium Bromide

The salt 1,1,3,3-tetramethylguanidinium bromide, [((CH(3))(2)N)(2)C═NH(2)](+)Br(-) or [tmgH]Br, was found to melt at 135(5) °C, forming what may be referred to as a moderate temperature ionic liquid. The chemistry was studied and compared with the corresponding chloride compound. We present X-ray diffraction and Raman evidence to show that also the bromide salt contains dimeric ion pair "molecules" in the crystalline state and probably also in the liquid state. The structure of [tmgH]Br determined at 120(2) K was found to be monoclinic, space group P2(1)/n, with a = 7.2072(14), b = 13.335(3), c = 9.378(2) Å, β =104.31(3)°, Z = 2, based on 11769 reflections, measured from θ = 2.71-28.00° on a small colorless needle crystal. Raman and IR spectra are presented and assigned. When heated, both the chloride and the bromide salts form vapor phases. The Raman spectra of the vapors are surprisingly alike, showing, for example, a characteristic strong band at 2229 cm(-1). This band was interpreted by some of us to show that the [tmgH]Cl gas phase should consist of monomeric ion pair "molecules" held together by a single N-H(+)···Cl(-) hydrogen bond, the stretching vibration of which should be causing the band, based on ab initio molecular orbital density functional theory type calculations. It is not likely that both the bromide and chloride should have identical spectra. As explanation, the formation of 1,1-dimethylcyanamide gas is proposed, by decomposition of [tmgH]X leaving dimethylammonium halogenide (X = Cl, Br). The Raman spectra of all gas phases were quite identical and fitted the calculated spectrum of dimethylcyanamide. It is concluded that monomeric ion pair "molecules" held together by single N-H(+)···X(-) hydrogen bonds probably do not exist in the vapor phase over the solids at about 200-230 °C.

GIAO DFT 13C/15N chemical shifts in regioisomeric structure determination of fused pyrazoles

The combined use of two-dimensional NMR correlation experiments and gauge including atomic orbital density functional theory in (13)C NMR chemical shift (CS) calculations allowed reliable and simple structural determination of regioisomeric heterocyclic systems that originate from the reactions of acylquinolinones with substituted hydrazines. Moreover, the results of differential analysis between the calculated (15)N NMR CSs for hypothetical structures and the experimental data of the title azaheterocyclic systems were even more advantageous with respect to (13)C because there was no need for correlational analysis: structures of the regioisomeric compounds could be determined just by direct comparison.

Synthetic and Computational Studies on Factors Controlling Structures of Molecular Triangles and Squares and Their Equilibrium in Solutions

Reactions of (en*)Pd(NO(3))(2) (en* = N,N,N',N'-tetramethylethylenediamine)with a series of organic bridging ligands of pyrazine, 1,2-bis(4-pyridyl)ethylene, 1,2-bis(4-pyridyl)acetylene, and 1,4-bis(4-pyridyl)benzene are carried out to investigate factors controlling the supramolecular structures and the equilibrium between the molecular triangles and the squares in solutions. The molecular structures of solid triangular [(en*)Pd(L(n))](3)(NO(3))(6) with 1,2-bis(4-pyridyl)ethylene and 1,2-bis(4-pyridyl)acetylene bridging ligands are determined by X-ray crystallography: [(en*)Pd(1,2-bis(4-pyridyl)ethylene)](3)(NO(3))(6), monoclinic Pn (No. 7), a = 17.3242(3) A, b = 15.0804(3) A, c = 17.3223(3) A, beta = 103.5100(10) degrees , V = 4400.33(14) A(3), Z = 2; [(en*)Pd(1,2-bis(4-pyridyl)acetylene)](3)(NO(3))(6), orthorhombic Aba2 (No. 41), a = 14.6642(3) A, b = 27.8763(5) A, c = 21.4233(4) A, V = 8757.5(3) A(3), Z = 4. In contrast, an infinite chain structure of {[(en*)Pd(pyrazine)](NO(3))}(infinity) (monoclinic P2(1)/m (No. 11), a = 14.4740(7) A, b = 8.9209(3) A, c = 28.9705(13) A, beta = 89.974(2) degrees , V = 3740.7(3) A(3), Z = 2) is observed with the shortest pyrazine. The steric hindrance between the supporting and the bridging ligands or the neighboring supporting ligands would contribute to the formation of the infinite chain complex 1. The N(Py)-Pd-N(Py) angles in the solid molecular triangles monotonically increased closely to 90 degrees with the increase in the lengths of the bridging ligands, indicating the relaxation of the steric hindrance between the supporting and the bridging ligands. The structures of the molecular triangles and squares in solutions are optimized with density functional theory (DFT) calculations using the conductor-like polarizable continuum model (C-PCM), and the resulting structures are almost the same as those in the solid state. The (1)H NMR spectra indicate that (i) the equilibrium between the molecular triangles and the squares is attained upon the introduction of the methyl substituents into the en supporting ligands (en*), (ii) the DeltaG degrees values decreased with the increase in the lengths of the straight bridging ligands, and (iii) the equilibrium constants depend on the kinds of solvents. The (1)H NMR spectra estimated with the gauge invariant atomic orbital DFT (GIAO-DFT) calculations well reproduce the experimental data, and the single-point energy DFT calculations with C-PCM in the presence of the solvents approximately reproduce the facts (i)-(iii).

Density Functional Investigation of Structure and Stability of Gen and GenNi (n = 1−20) Clusters: Validity of the Electron Counting Rule

Structure and electronic properties of neutral and cationic pure and Ni-doped Ge clusters containing 1-20 Ge atoms are calculated within the framework of linear combination of atomic orbitals density functional theory. It is found that in clusters containing more than 8 Ge atoms the Ni atom is absorbed endohedrally in the Ge cage. Relative stability of Ni-doped clusters at different sizes is studied by calculating their binding energy, embedding energy of a Ni atom in a Ge cluster, highest-occupied molecular orbital to lowest-unoccupied molecular orbital gap, and the second-order energy difference. Clusters having 20 valence electrons turn out to be relatively more stable in both the neutral and the cationic series. There is, infact, a sharp drop in IP as the valence electron count increases from 20 to 21, in agreement with predictions of shell models. Relevance of these results to the designing of Ge-based superatoms is discussed.

Orbital Control of the Conductance Photoswitching in Diarylethene

Diarylethenes are photosensitive π-conjugated molecules whose application to various molecular devices is expected. The molecular and electronic structures of diarylethenes are switchable upon photoirradiation with their reversible structural isomerization. Site-specific electron transport phenomena through a diarylethene molecule, 1,2-di(2-methyl-1-naphthyl) perfluorocyclopentene, are studied by using the nonequilibrium Green’s function method combined with the Huckel molecular orbital method (NEGF−HMO) and density functional theory (NEGF−DFT). On the basis of the orbital symmetry rule, the conductance of the diarylethene is predicted to be efficiently switchable when the C3 and C10 atoms are appropriately connected with electrodes. Transmission spectra, spatial distribution of the MPSH (molecular projected self-consistent Hamiltonian) states, and I−V curves are obtained from DFT calculations. These results obtained from the higher-level DFT calculations are consistent with the prediction based on the qu...

Theoretical and experimental 1H, 13C and 15N NMR studies of N‐alkylation of substituted tetrazolo[1,5‐a]pyridines

The (15)N as well as (1)H and (13)C chemical shifts of nine substituted tetrazolopyridines and their corresponding tetrazolopyridinium salts have been determined by using NMR spectroscopy at the natural abundance level of all nuclei in CD(3)CN. In this paper, we report, for the first time, the N-alkylation reaction of electron deficient tetrazolopyridines. The treatment of tetrazolopyridines 5-13 with one equivalent of trialkyloxonium tetrafluoroborate leads to a mixture of two isomers, i.e. N3- and N2-alkyl tetrazolo[1,5-a]pyridinium salts. It has been observed that the N3-isomer is always the major isomer, except in the case of the CF(3) substituent, where the two isomers are obtained in the same amount. The quaternary tetrazolopyridinium nitrogen N3 is shielded by around 100 ppm (parts per million) with respect to the parent tetrazolopyridine. Experimental data are interpreted by means of density functional theory (DFT) calculations, including solvent-induced effects, within the conductor-like polarizable continuum model (CPCM). Good agreements between theoretical and experimental (1)H, (13)C and (15)N NMR were found. The combination of multinuclear magnetic resonance spectroscopy with gauge including atomic orbital (GIAO) DFT calculations is a powerful tool in the structural elucidation for both neutral and cationic heterocycles and in the determination of the orientation of N-alkylation of tetrazolopyridines.

Metal coordination converts the tub-shaped cyclo-octatetraene into an aromatic molecule: Electronic states and half-sandwich structures of group III metal-cyclo-octatetraene complexes

Group III (Sc, Y, and La) metal-(1,3,5,7-cyclo-octatetraene) (COT) complexes were produced in a laser-vaporization molecular beam source and studied by pulsed-field-ionization zero-electron-kinetic-energy (ZEKE) spectroscopy. Adiabatic ionization energies and metal-ligand stretching frequencies were measured from the ZEKE spectra. Metal-ligand bonding and low-lying electronic states of the neutral and ionized complexes were analyzed by combining the spectroscopic measurements with the molecular orbital treatment and density functional theory calculations. The ionization energies and metal-ligand stretching frequencies of these complexes are in the order of Sc>Y>La. The ground electronic state of the neutral complexes is A21, whereas the ground state of the ions is A11. The molecular symmetry is C8v in both neutral and ionic ground states. Although free COT is a nonaromatic molecule with a tublike structure, coordination of the group III metal atoms converts the tub-shaped molecule into a planar, aromatic structure. This conversion is induced by a two-electron transfer from the metal atoms to the ligand upon the formation of the complexes.

Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree-Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.