C?H Bond dissociation of acetylene: Local density functional calculations

The C? H bond dissociation energy of acetylene was computed by both ab initio approaches and density functional theory in a local density approximation (DFT–LDA ). Structures and energies for acetylene and its dissociation products (the ethynyl and hydrogen radicals) are presented and compared. Using directly computed HCCH and HCC· energies and the exact H· value, the DFT–LDA calculations are found to yield C? H dissociation energies ranging from 129 to 131 kcal/mol, in good agreement with recent experimental and the highest level theoretical results. The DFT–LDA results show little dependence upon the computational procedure used to obtain geometries.     

An analysis of molecular electrostatic potentials obtained by a local density functional approach

Local density functional theory (DFT –LDA ) has been explored as a tool for obtaining the molecular electrostatic potential V(r), using the code DMol. We have presented and discussed DFT –LDA electrostatic potentials for a representative series of molecules: ethylene, benzene, formamide, cytosine, and 2,3,7,8–tetrachlorodibenzo–p–dioxin. V(r) results obtained with a double numerical plus polarization (DNP ) basis set show the key features that are characteristic of the ab initio potentials of these compounds and suggest that this is a useful approach, especially for large molecules that are difficult to study by ab initio methods.     

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.     

Electronic structures and hydrogen bond network of high-density and very high-density amorphous ices

Electronic structures of hexagonal ice (ice Ih), high-density amorphous ice (HDA), and very high-density amorphous ice (VHDA) are investigated using ab initio density functional theory (DFT) at 77 K under a pressure of 0.1 MPa, focusing on band structure, density of states (DOS), partial density of states (PDOS), and electron density. It is found that the integration intensity of the O-2p bonding band in HDA is 1.53 eV wider than that in the VHDA. Because more 2p electrons in HDA participate the 2p-1s hybridization of O-H. The classical molecular dynamics (MD) method has further been carried out to analyze the hydrogen bond network of HDA and VHDA with larger numbers of water molecules under the same temperature, pressure, and boundary conditions used as those during the DFT calculation. MD results show that there exists some water molecules with five hydrogen bonds in both HDA (4.1 +/- 0.1%) and VHDA (2.8 +/- 0.1%), as compared with the LDA, being consistent with the integration intensity results of PDOS. This result can be used to interpret the physical nature of the similar transition temperature of HDA and VHDA to LDA with different heating rates.     

Polarizability of small carbon cluster anions from first principles

We examine the applicability of density functional theory (DFT) to the polarizability of Cn- (n = 3-9) cluster anions. This was achieved by comparing DFT calculations using two different exchange-correlation functionals (the non-empirical local density approximation, LDA, and the semiempirical hybrid functional B97-1) to quantum chemical calculations using the coupled cluster method in the CCSD(T) "gold standard" approximation. We find that, unless the extra electron is not bound at all by DFT, both LDA and B97-1 agree with the CCSD(T) calculation to within 5-10%, allowing for a meaningful qualitative and semiquantitative analysis. Furthermore, the polarizability is found to increase monotonically with chain size, consistent with the trend inferred from electron detachment experiments.     

Theoretical study of the red‐ and blue‐shifted hydrogen bonds of nitroxyl and acetylene dimers

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the C? H…O red‐shifted and N? H…π blue‐shifted hydrogen bonds in HNO? C₂H₂ dimers. The geometric structures, vibrational frequencies and interaction energies were calculated by both standard and counterpoise (CP)‐corrected methods. In addition, the G3B3 method was employed to calculate the interaction energies. The topological and natural bond orbital (NBO) analysis were investigated the origin of N? H…π blue‐shifted hydrogen bond. From the NBO analysis, the electron density decrease in the σ* (N? H) is due to the significant electron density redistribution effect. The blue shifts of the N? H stretching frequency are attributed to a cooperative effect between the rehybridization and electron density redistribution. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Computational assessment of electron density in metallo‐organic nickel pincer complexes for formation of PC bonds

Hydrophosphination is an atomically efficient method for introducing new carbon‐phosphorous bonds in organic synthesis. New late‐transition metal catalytic complexes are proposed to facilitate this process. These nickel‐based complexes are analyzed using semiempirical (SE), Hartree–Fock (H–F), and density functional theory (DFT) models. H–F proves to be ineffective, while the SE approach has limited, qualitative use. DFT shows electron density at the metal center suitable for catalyzing bond formation in the proposed, reductive hydrophosphination mechanism. It also shows that the pincer complexes under investigation are relatively insensitive to solvent dielectric constant and to the chemical character of the monodentate ligand, both in terms of electron distribution and in terms of molecular orbital energies. © 2015 Wiley Periodicals, Inc.     

Calculation of quasiparticle energy of molecular systems by the GW method

The quasiparticle energy of the H₂ molecule is calculated by using the GW method, in which the self‐energy operator fully depends on the frequency. The initial Green function G₀ is constructed from the wave function obtained by the Hartree–Fock approximation (HFA) and local density approximation (LDA) in the framework of the density functional theory (DFT). From the results obtained we have shown that the wave function from the DFT–LDA is more effective than that from the HFA for G₀. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem 84: 348–353, 2001     

Interaction of the important species HNO and HFSO2 in the atmosphere: Theoretical study of the N?H and S?H blue‐shifted hydrogen bonds

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the N? H…O and S? H…O blue‐shifted H‐bonds in the HNO…HFSO₂ complex. The geometric structures, vibrational frequencies, and interaction energies were calculated by both standard and CP‐corrected methods. Natural bond orbital (NBO) analysis was used to investigate the origin of blue‐shifted H‐bonds, showing that the decrease in the σ*(N? H) and σ*(S? H) is due to the electron density redistribution effect. The structure reorganization effect on the blue‐shifted hydrogen bonds was discussed in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Producing DFT/MM enzyme reaction trajectories from SCC‐DFTB/MM driving forces to probe the underlying electronics of a glycosyltransferase reaction

The SCC‐DFTB/MIO/CHARMM free energy surface for a glycosyltransferase, TcTS, is benchmarked against a DFT/MM reaction trajectory using the same CHARMM MM force field ported to the NWChem package. The popular B3LYP functional, against which the MIO parameter set was parameterized is used to optimize TS structures and run DFT reaction dynamics. A novel approach was used to generate reaction forces from a SCC‐DFTB/MIO/CHARMM reaction surface to drive B3LYP/6‐31G/MM and B3LYP/6‐31G(d)/MM reaction trajectories. Although TS structures compare favorably, differences stemming primarily from a minimal basis set approximation prevented a successful 6‐31G(d) FEARCF reaction dynamics trajectory. None the less, the dynamic evolution of the B3LYP/6‐31G/MM‐computed electron density provided an opportunity to perform NBO analysis along the reaction trajectory. Here, we illustrate that a successful ab initio reaction trajectory is computationally accessible when the underlying potential energy function of the semi‐empirical method used to produce driving forces is sufficiently close to the ab initio potential. © 2017 Wiley Periodicals, Inc.     

Interaction energies in hydrogen-bonded systems: a testing ground for subsystem formulation of density-functional theory

The formalism based on the total energy bifunctional (E[rhoI,rhoII]) is used to derive interaction energies for several hydrogen-bonded complexes (water dimer, HCN-HF, H2CO-H2O, and MeOH-H2O). Benchmark ab initio data taken from the literature were used as a reference in the assessment of the performance of gradient-free [local density approximation (LDA)] and gradient-dependent [generalized gradient approximation (GGA)] approximations to the exchange-correlation and nonadditive kinetic-energy components of E[rhoI,rhoII]. On average, LDA performs better than GGA. The average absolute error of calculated LDA interaction energies amounts to 1.0 kJ/mol. For H2CO-H2O and H2O-H2O complexes, the potential-energy curves corresponding to the stretching of the intermolecular distance are also calculated. The positions of the minima are in a good agreement (less than 0.2 A) with the reference ab initio data. Both variational and nonvariational calculations are performed to assess the energetic effects associated with complexation-induced deformations of molecular electron densities.     

Gradient corrections in density functional theory calculations for surfaces: Co on Pd{110}

Ab initio total energy calculations have been performed for CO chemisorption on Pd{110}. Local density approximation (LDA) calculations yield chemisorption energies which are significantly higher than experimental values but inclusion of the generalised gradient approximation (GGA) gives better agreement. In general, sites with higher coordination of the adsorbate to surface atoms lead to a larger degree of overbinding with LDA, and give larger corrections with GGA. The reason is discussed using a first-order perturbation approximation. It is concluded that this may be a general failure of LDA for chemisorption energy calculations. This conclusion may be extended to many surface calculations, such as potential energy surfaces for diffusion.     

Role of the electronic properties of azurin active site in the electron‐transfer process

Electron transfer proteins, such as azurin (a blue copper protein), are promising candidates for the implementation of biomolecular nanoelectronic devices. To understand the details of electron transfer in redox active azurin molecules, we performed plane‐wave pseudo‐potential density functional theory (DFT) calculations of the protein active site in the two possible oxidation states Cu(I) and Cu(II). The ab initio results are used to discuss how the electronic spectrum and wavefunctions may mediate the shuttling of electrons through the copper ion. We find that the Cu‐ligand hybridization is very similar in the two charge states of the metal center, but the energy spectrum changes substantially. This result might indicate important effects of electronic correlations in the redox activity and consequent electron transfer through the Cu site. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Magnetic Properties and Electronic Structure of Neptunyl(VI) Complexes: Wavefunctions,Orbitals, and Crystal‐Field Models

The electronic structure and magnetic properties of neptunyl(VI), NpO₂²⁺, and two neptunyl complexes, [NpO₂(NO₃)₃]^? and [NpO₂Cl₄]^2?, were studied with a combination of theoretical methods: ab initio relativistic wavefunction methods and density functional theory (DFT), as well as crystal‐field (CF) models with parameters extracted from the ab initio calculations. Natural orbitals for electron density and spin magnetization from wavefunctions including spin–orbit coupling were employed to analyze the connection between the electronic structure and magnetic properties, and to link the results from CF models to the ab initio data. Free complex ions and systems embedded in a crystal environment were studied. Of prime interest were the electron paramagnetic resonance g‐factors and their relation to the complex geometry, ligand coordination, and nature of the nonbonding 5f orbitals. The g‐factors were calculated for the ground and excited states. For [NpO₂Cl₄]^2?, a strong influence of the environment of the complex on its magnetic behavior was demonstrated. Kohn–Sham DFT with standard functionals can produce reasonable g‐factors as long as the calculation converges to a solution resembling the electronic state of interest. However, this is not always straightforward.     

Ab initio electron propagators in molecules with strong electron-phonon interaction. I. Phonon averages

Ab initio electron propagators in molecular systems with strong electron-electron and electron-phonon interactions are considered to study molecular electronic properties. This research is important in electron transfer reactions where the electron transition is not considered any longer as a single electron transfer process or in temperature dependences of current-voltage characteristics in molecular wires or aggregates. To calculate electron Green's functions, the authors apply a small polaron canonical transformation that intrinsically contains strong electron-phonon effects. According to this transformation, the excitation energies of the noninteracting Hamiltonian are shifted down by the relaxation (solvation) energy for each state. The electron-electron interaction is also renormalized by the electron-phonon coupling. For some values of the electron-phonon coupling constants, the renormalized Coulomb integrals can be negative resulting in the attraction between two electrons. Within this transformation, they develop a diagrammatic expansion for electron Green's function in which the electron-phonon interaction is included into the multiple phonon correlation functions. The multiple phonon correlation functions are exactly found. It is pointed out that Wick's theorem for such correlation functions is invalid. Consequently, there is no Dyson equation for electron Green's functions. The proposed approach can be considered for future method developments for quantum chemical calculations that include strong nonadiabatic (non-Born-Oppenheimer) effects.