Structure of the ammonia dimer studied by density functional theory

Self-consistent Kohn–Sham density functional calculations have been carried out to study the structure of the ammonia dimer. The local-density approximation yields unusually large binding energy and short internitrogen distance compared with the experimental and more accurate theoretical data. The results from the Becke–Perdew gradient-corrected functionals are generally in good agreement with those at the SCF MP 2 level when the geometry is fully optimized with various large basis sets. With our best estimation, the staggered quasi-linear structure (C_s) is 0.6 kcal/mol lower in energy than the symmetric cyclic one (C_2h). The hydrogen-bonded N—H bond in the staggered quasi-linear structure is found to be 0.008 Å longer than the N—H bond in ammonia. In our calculations, we could not find the minima on the energy surface corresponding to the two asymmetric cyclic structures suggested by microwave spectra and coupled pair functional calculations. © 1994 John Wiley & Sons, Inc.     

Geometries, thermodynamic properties and reactions of methylzinc alkoxide clusters studied by density functional theory calculations

Methylzinc alkoxide complexes are precursors for the preparation of nanosized zinc oxide particles, which in turn are catalysts or reagents in important industrial processes such as methanol synthesis and rubber vulcanization. We report for the first time the structures, energies, atomic charges, dipole moments, and vibrational spectra of more than 20 species of the type [(MeZnOR')n] with R' = H, Me, tBu and n = 1-6, calculated by density functional theory methods, mostly at the B3LYP/6-31+G* level of theory. For R' = Me, the global minimum structure of the tetramer (n = 4) is a highly symmetrical heterocubane but a ladder-type isomer is by only 70.9 kJ mol(-1) less stable. The corresponding trimer is most stable as a rooflike structure; a planar six-membered ring of relative energy 13.5 kJ mol(-1) corresponds to a saddle point connecting two equivalent rooflike trimer structures. All dimers form planar four-membered Zn2O2 rings whereas the monomer has a planar CZnOC backbone. A hexameric drumlike structure represents the global minimum on the potential energy hypersurface of [(MeZnOMe)6]. The enthalpies and Gibbs energies of the related dissociation reactions hexamer --> tetramer --> trimer --> dimer --> monomer as well as of a number of isomerization reactions have been calculated. The complexes [(MeZnOMe)n] (n = 1-3) form adducts with Lewis bases such as tetrahydrofuran (thf) and pyridine (py). The binding energy of py to the zinc atoms is about 65% larger than that of thf but is not large enough to break up the larger clusters. The bimolecular disproportionation of [(MeZnOMe)4] with formation of the dicubane [Zn{(MeZn)3(OMe)4}2] and Me2Zn is less endothermic than any isomerization or dissociation reaction of the heterocubane, but for steric reasons this reaction is not possible if R' = tBu. A novel reaction mechanism for the reported interconversion, disproportionation and ligand exchange reactions of zinc alkoxide complexes is proposed.     

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.     

Water cluster anions studied by the long-range corrected density functional theory

Long-range corrected density functional theory (LC-DFT) is applied to a series of small water cluster anions(n= 2-6) to compute their vertical detachment energies (VDEs). The LC scheme is shown to eliminate an unphysical overestimation of the electron-water attraction in the hybrid functional by properly accounting for the long-range exchange repulsions. It is shown that a correct correlation energy behavior for a rapidly varying density is also important for describing a spatially extent, excess electron. The one-parameter progressive (OP) correlation functional, which satisfies this condition, leads to a remarkable improvement in the calculated VDE over the conventional one. The LC-BOP method produces highly accurate VDEs with a mean absolute deviation of 13.8 meV from the reference CCSD(T) results, reducing the error of B3LYP by more than 15 times. LC-BOP is found to be more accurate than MP2 which yields an excess electron underbound by 43.6 meV. The effect of basis sets on the calculated VDE is also examined. The aug-cc-pVDZ basis set with an extra diffuse function is found to be more accurate and reliable than the extended Pople-type basis sets used in the previous works. The extrapolation of the calculated VDE of different electron binding motifs is compared with the VDEs of experimentally observed three isomers (Verlet, J. R. R.; Bragg,A. E.; Kammrath, A.; Cheshnovsky, O.; Neumark, D. M. Science 2005, 307, 93).     

Topological analysis of electron densities from Kohn-Sham and subsystem density functional theory

In this study, we compare the electron densities for a set of hydrogen-bonded complexes obtained with either conventional Kohn-Sham density functional theory (DFT) calculations or with the frozen-density embedding (FDE) method, which is a subsystem approach to DFT. For a detailed analysis of the differences between these two methods, we compare the topology of the electron densities obtained from Kohn-Sham DFT and FDE in terms of deformation densities, bond critical points, and the negative Laplacian of the electron density. Different kinetic-energy functionals as needed for the frozen-density embedding method are tested and compared to a purely electrostatic embedding. It is shown that FDE is able to reproduce the characteristics of the density in the bonding region even in systems such as the F-H-F(-) molecule, which contains one of the strongest hydrogen bonds. Basis functions on the frozen system are usually required to accurately reproduce the electron densities of supermolecular calculations. However, it is shown here that it is in general sufficient to provide just a few basis functions in the boundary region between the two subsystems so that the use of the full supermolecular basis set can be avoided. It also turns out that electron-density deformations upon bonding predicted by FDE lack directionality with currently available functionals for the nonadditive kinetic-energy contribution.     

Couplings between electronic transitions in a subsystem formulation of time-dependent density functional theory

A subsystem formulation of time-dependent density functional theory (TDDFT) within the frozen-density embedding (FDE) framework and its practical implementation are presented, based on the formal TDDFT generalization of the FDE approach by Casida and Wesolowski [Int. J. Quantum Chem. 96, 577 (2004)]. It is shown how couplings between electronic transitions on different subsystems can be seamlessly incorporated into the formalism to overcome some of the shortcomings of the approximate TDDFT-FDE approach in use so far, which was only applicable for local subsystem excitations. In contrast to that, the approach presented here allows to include couplings between excitations on different subsystems, which become very important in aggregates composed of several similar chromophores, e.g., in biological or biomimetic light-harvesting systems. A connection to Forster- and Dexter-type excitation energy coupling expressions is established. A hybrid approach is presented and tested, in which excitation energy couplings are selectively included between different chromophore fragments, but neglected for inactive parts of the environment. It is furthermore demonstrated that the coupled TDDFT-FDE approach can cure the inability of the uncoupled FDE approach to describe induced circular dichroism in dimeric chromophores, a feature known as a "couplet," which is also related to couplings between (nearly) degenerate electronic transitions.     

Electronic structure and optical properties of charged oligofluorenes studied by VIS/NIR spectroscopy and time-dependent density functional theory

The electronic structure and optical properties of charged oligofluorenes were studied experimentally and theoretically. Measurements of the optical absorption spectra of charged oligofluorenes in dilute solutions have been performed by using the pulse radiolysis technique. In addition, optical absorption spectra of radical cations and anions in a solid matrix were measured after gamma-irradiation at 77 K. The optical absorption spectra were measured in the range of 440-2100 nm (0.6-2.8 eV) and compared with results from time-dependent density functional theory (TDDFT) calculations. The calculated charge induced deformations and charge distribution do not indicate the occurrence of polaronic effects. The potential energy profiles for rotation around the inter-unit bond show that oligofluorenes are nonplanar in their neutral state, while they tend to more planar structures in their charged state. The optical absorption spectra of charged oligofluorenes are dependent on the angle between neighboring units. TDDFT absorption energies shift to lower values with increasing chain length, which suggests that the charge delocalizes along the oligomer chain.     

Analytical gradients for subsystem density functional theory within the slater‐function‐based amsterdam density functional program

We present a new implementation of analytical gradients for subsystem density‐functional theory (sDFT) and frozen‐density embedding (FDE) into the Amsterdam Density Functional program (ADF). The underlying theory and necessary expressions for the implementation are derived and discussed in detail for various FDE and sDFT setups. The parallel implementation is numerically verified and geometry optimizations with different functional combinations (LDA/TF and PW91/PW91K) are conducted and compared to reference data. Our results confirm that sDFT‐LDA/TF yields good equilibrium distances for the systems studied here (mean absolute deviation: 0.09 Å) compared to reference wave‐function theory results. However, sDFT‐PW91/PW91k quite consistently yields smaller equilibrium distances (mean absolute deviation: 0.23 Å). The flexibility of our new implementation is demonstrated for an HCN‐trimer test system, for which several different setups are applied. © 2016 Wiley Periodicals, Inc.     

Voltammetric determination of chlorothalonil and its respective reduction mechanism studied by density functional theory

Journal of Solid State Electrochemistry - A simple, fast, and direct electroanalytical method has been developed for the pesticide chlorothalonil determination using a boron-doped diamond electrode...     

Excited state property of hardly photodissociable heme-CO adduct studied by time-dependent density functional theory

While most of CO-bound hemes are easily photodissociated with a quantum yield of nearly unity, we occasionally encounter a CO-heme which appears hardly photodissociable under the ordinary measurement conditions of resonance Raman spectra using CW laser excitation and a spinning cell. This study aims to understand such hemes theoretically, that is, the excited-state properties of the five-coordinate heme-CO adduct (5cH) as well as the 6c heme-CO adduct (6cH) with a weak axial ligand. Using a hybrid density functional theory, we scrutinized the properties of the ground and excited spin states of the computational models of a 5cH and a water-ligated 6cH (6cH-H(2)O) and compared these properties with those of a photodissociable imidazole-ligated 6cH (6cH-Im). Jahn-Teller softening for the Fe-C-O bending potential in the a(1)-e excited state was suggested. The excited-state properties of 6cH-Im and 5cH were further studied with time-dependent DFT theory. The reaction products of 6cH-Im and 5cH were assumed to be quintet and triplet states, respectively. According to the time-dependent DFT calculations, the Q excited state of 6cH-Im, which is initially a pure pi-pi state, crosses the Fe-CO dissociative state (2A') without large elongation of the Fe-CO bond. In contrast, the Q state of the 5cH does not cross the Fe-CO dissociative state but results in the formation of the excited spin state with a bent Fe-C-O. Consequently, photoisomerization from linear to bent Fe-C-O in the 5cH is a likely mechanism for apparent nonphotodissociation.     

Solvation and crystal effects in bilirubin studied by NMR spectroscopy and density functional theory

The open-chain tetrapyrrole compound bilirubin was investigated in chloroform and dimethyl sulfoxide solutions by liquid-state NMR and as solid by (1)H, (13)C, and (15)N magic-angle spinning (MAS) solid-state NMR spectroscopy. Density functional theory (DFT) calculations were performed to interpret the data, using the B3LYP exchange-correlation functional to optimize geometries and to compute NMR chemical shieldings by the gauge-including atomic orbital method. The dependence of geometries and chemical shieldings on the size of the basis sets was investigated for the reference molecules tetramethylsilane, NH(3), and H(2)O, and for bilirubin as a monomer and in clusters consisting of up to six molecules. In order to assess the intrinsic errors of the B3LYP approximation in calculating NMR shieldings, complete basis set estimates were obtained for the nuclear shielding values of the reference molecules. The experimental liquid-state NMR data of bilirubin are well reproduced by a monomeric bilirubin molecule using the 6-311+G(2d,p) basis set for geometry optimization and for calculating chemical shieldings. To simulate the bilirubin crystal, a hexameric model was required. It was constructed from geometry-optimized monomers using information from the X-ray structure of bilirubin to fix the monomeric entities in space and refined by partial optimization. Combining experimental (1)H-(13)C and (1)H-(15)N NMR correlation spectroscopy and density functional theory, almost complete sets of (1)H, (13)C, and (15)N chemical shift assignments were obtained for both liquid and solid states. It is shown that monomeric bilirubin in chloroform solution is formed by 3-vinyl anti conformers, while bilirubin crystals are formed by 3-vinyl syn conformers. This conformational change leads to characteristic differences between the liquid- and solid-state NMR resonances.     

Valence electronic structure of benzo-2,1,3-chalcogenadiazoles studied by photoelectron spectroscopy and density functional theory

The He I photoelectron spectra of benzo-2,1,3-thia-, selena-, and telluradiazole were measured, and the observed ionization bands were assigned by comparison with the results of DFT calculations. Whereas the B3LYP exchange-correlation functional provided orbital energies that permitted a preliminary assignment by application of Koopman's theorem, a more-accurate interpretation was established by calculation of the vertical ionization energies with the PW91 functional and analysis of the correlation of energy levels along the homologous series. This strategy clarified earlier disagreements in the assignment of the spectrum of benzo-2,1,3-thiadiazole.     

Chemical shifts in nucleic acids studied by density functional theory calculations and comparison with experiment

NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the (1) H and (13) C?NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when (13) C and (1) H chemical shift data are combined. The approximate linear dependence of the C1' shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects.     

Structure and ionization energies of some analogues of iron-only hydrogenases studied by density functional theory methods

Density functional theory calculations using both the B3LYP and BP86 functional in conjunction with a medium and large size basis set have been used to predict the structures and ionization energies of 12 models of iron-only hydrogenases. Although the structural predictions do not allow a clear discrimination between the different computational models, these models do yield significantly different adiabatic and vertical ionization energies. The closest agreement with experiment is given by the BP86 functional and the large all-electron basis. At this level of theory the adiabatic ionization energies are very close to experiment, but the vertical values are uniformly too small, leading to an underestimation of the reorganization energies. The calculations also suggest that measured ionization energies may help in identifying both the bridge-head group and whether CO bridging takes place upon ionization.     

Accurate description of van der Waals complexes by density functional theory including empirical corrections

An empirical method to account for van der Waals interactions in practical calculations with the density functional theory (termed DFT-D) is tested for a wide variety of molecular complexes. As in previous schemes, the dispersive energy is described by damped interatomic potentials of the form C6R(-6). The use of pure, gradient-corrected density functionals (BLYP and PBE), together with the resolution-of-the-identity (RI) approximation for the Coulomb operator, allows very efficient computations for large systems. Opposed to previous work, extended AO basis sets of polarized TZV or QZV quality are employed, which reduces the basis set superposition error to a negligible extend. By using a global scaling factor for the atomic C6 coefficients, the functional dependence of the results could be strongly reduced. The "double counting" of correlation effects for strongly bound complexes is found to be insignificant if steep damping functions are employed. The method is applied to a total of 29 complexes of atoms and small molecules (Ne, CH4, NH3, H2O, CH3F, N2, F2, formic acid, ethene, and ethine) with each other and with benzene, to benzene, naphthalene, pyrene, and coronene dimers, the naphthalene trimer, coronene. H2O and four H-bonded and stacked DNA base pairs (AT and GC). In almost all cases, very good agreement with reliable theoretical or experimental results for binding energies and intermolecular distances is obtained. For stacked aromatic systems and the important base pairs, the DFT-D-BLYP model seems to be even superior to standard MP2 treatments that systematically overbind. The good results obtained suggest the approach as a practical tool to describe the properties of many important van der Waals systems in chemistry. Furthermore, the DFT-D data may either be used to calibrate much simpler (e.g., force-field) potentials or the optimized structures can be used as input for more accurate ab initio calculations of the interaction energies.     

A computational and conceptual density functional theory study of the properties of Re and Tc tricarbonyl complexes

A computational and conceptual density functional study has been performed on metal tricarbonyl complexes (MTC) of both Re(I) and Tc(I). The fully optimized complexes of fac-[Tc(OH(2))(CO(3))](+) and mer-[Tc(OH(2))(CO(3))](+) show geometries that compare favorably with the X-ray data. These structures were used as a starting point to investigate the relative stability of MTC complexes with various ligands containing combinations of N, O, and S as chelating atoms and to evaluate the stabilizing/destabilizing influence of these ligands. Both for Tc and for Re complexes the nitrogen content turns out to be decisive in the stability of the metaltricarbonyl complexes, the finer details being determined by the hardness sequence N > O > S. As the core of the complexes, [(M(CO)(3)(+)], is hard, the main ordering parameter is changed as compared to our previous studies on Tc(V) [3+1] complexes where the number of sulfur atoms was decisive in accordance with the much softer character of the MOCl core. All results are successfully interpreted in terms of the hard and soft acids and bases principle (HSAB) at the local level.     

Reactions of ·OH with thymine studied using density functional theory

We studied three possible reactions of a free ·OH radical with thymine by using density functional theory calculations. The results indicate that there is no energy barrier in the reactions of a free ·OH radical adding to the C₆ position of thymine, while the reactions of a free ·OH radical adding to the C₅ position of thymine and the reaction of an ·OH abstracting a hydrogen from the C₅ methyl group should overcome the energy barriers of ～0.70 kcal/mol and ～1.88 kcal/mol, respectively. The C₆‐hydroxylated radical formed is energetically more favorable than the C₅‐hydroxylated radical. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Stability of Zn(II) cations in chabazite studied by periodical density functional theory.

The location of the Zn(2+) cation in Zn-exchanged chabazite has been studied by the periodical density functional method. Chabazite was chosen as a zeolite model, because it contains three different types of rings commonly found in the zeolite structures: four-, six-, and eight-membered rings. Two aluminum atoms have been employed to substitute the silicon atoms in the same D6R unit cell of the zeolite framework. This leads to different arrangements for the Br?nsted site pair and the Zn(II) cation. The two Br?nsted sites are found to be more stable when placed in the small ring (4T ring) than in the other rings. This suggests that the most reactive Br?nsted sites are located in the large rings. Two Br?nsted sites are most stable when the O(H)-Al-O-Si-O(H)-Al sequence is followed in the same ring instead of being located in two different rings. This resembles the aluminum distribution in the small four-membered ring and agrees with bond order conservation rules. The cation stability is markedly influenced by the distortions of the framework. Other factors that also contribute to the stabilization are the aluminum content near the cation and the stability of the original Br?nsted sites. The Zn(2+) cation is more stable in the large rings than in the small ones, the six-membered one being the most stable configuration. In the small rings, the cation is, therefore, more reactive. Two different probe molecules have been used to study the interaction with the Zn(II) cation: water and methane. These probe molecules can extract the active center from its original position. For the water molecule, this effect is large and leads to a high framework relaxation. The value of the binding energy of this molecule to the active sites is influenced by these framework relaxations as well as by the cationic position environment. For weakly interacting methane, these effects are significantly less.     

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.