Density functional theory (DFT) and ab initio investigations of the electronic and molecular structures of the monomer and the dimer of trimethylaluminium

The electronic and molecular structures of the monomer and dimer of trimethylalu-minium have been studied using density functional theory and ab initio MP2 method. The optimized geometry of the monomer Al(CH3)3 is of C3h symmetry, whereas that of the dimer [A1(CH3)3]2 contains a carbon-bridged four-membered ring structure with C2h symmetry. The hydrogen-bridged six-membered ring structure is found to be unstable. The calculated dimerization energy for the four-membered ring structure is 78 kJ/mol, in close proximity to the experimental value of 85.27 kJ/mol.     

Optoelectronic properties of benzotrithiophene isomers: A density functional theory study

Benzotrithiophene (BTT) isomers were investigated using density functional theory (DFT) and time‐dependent DFT (TD‐DFT) with the aim to explore their structures, linear optical properties, vertical and adiabatic ionization potentials (IP_v and IP_a), electron affinities (EA_v and EA_a), and reorganization energies (λ). The computed bond lengths and bond angles at the B3LYP/6–311+G (d, p) level of theory are in good agreement with experimental crystal structures of the known BTTs. These molecules are planar with zero dihedral angle, making them an ideal backbone for high charge mobility. The UV–visible spectra of BTT isomers are in the range 280–360 nm. All BTT isomers have low hole/electron reorganization energies, which is the main characteristic of good hole/electron transporting materials, and these isomers in turn have potential applications in the field of organic materials.     

Unimolecular isomerization/decomposition of cyclopentadienyl and related bimolecular reverse process: ab initio MO/statistical theory study

The cyclopentadienyl radical decomposition has been studied in detail by high‐level correlation MO methods combined with multichannel RRKM rate constant calculations. The product channels of the reaction were examined by calculating their pressure‐dependent branching rate constants. The overall reaction rate has been shown to be controlled by the first transition state corresponding to 1,2‐hydrogen atom migration. Also, the reverse bimolecular reactions (C₃H₃ + C₂H₂ → products) have been included in the study. We provide a summary of pressure dependent rate constant expressions for the 1000–3000 K temperature range that may be useful for kinetic modeling of relevant combustion systems. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 415–425, 2000     

Density functional theory and CCSD(T) evaluation of ionization potentials,redox potentials,and bond energies related to zirconocene polymerization catalysts

Quantum-mechanical-based computational design of molecular catalysts requires accurate and fast electronic structure calculations to determine and predict properties of transition-metal complexes. For Zr-based molecular complexes related to polyethylene catalysis, previous evaluation of density functional theory (DFT) and wavefunction methods only examined oxides and halides or select reaction barrier heights. In this work, we evaluate the performance of DFT against experimental redox potentials and bond dissociation enthalpies (BDEs) for zirconocene complexes directly relevant to ethylene polymerization catalysis. We also examined the ability of DFT to compute the fourth atomic ionization potential of zirconium and the effect the basis set selection has on the ionization potential computed with CCSD(T). Generally, the atomic ionization potential and redox potentials are very well reproduced by DFT, but we discovered relatively large deviations of DFT-calculated BDEs compared to experiment. However, evaluation of BDEs with CCSD(T) suggests that experimental values should be revisited, and our CCSD(T) values should be taken as most accurate.     

Molecular design of specific metal-binding peptide sequences from protein fragments: theory and experiment

A novel strategy is presented for designing peptides with specific metal-ion chelation sites, based on linking computationally predicted ion-specific combinations of amino acid side chains coordinated at the vertices of the desired coordination polyhedron into a single polypeptide chain. With this aim, a series of computer programs have been written that 1) creates a structural combinatorial library containing Z(i)-(X)(n)-Z(j) sequences (n=0-14; Z: amino acid that binds the metal through the side chain; X: any amino acid) from the existing protein structures in the non-redundant Protein Data Bank; 2) merges these fragments into a single Z(1)-(X)(n(1) )-Z(2)-(X)(n(2) )-Z(3)-(X)(n(3) )--Z(j) polypeptide chain; and 3) automatically performs two simple molecular mechanics calculations that make it possible to estimate the internal strain in the newly designed peptide. The application of this procedure for the most M(2+)-specific combinations of amino acid side chains (M: metal; see L. Rulísek, Z. Havlas J. Phys. Chem. B 2003, 107, 2376-2385) yielded several peptide sequences (with lengths of 6-20 amino acids) with the potential for specific binding with six metal ions (Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+) and Hg(2+)). The gas-phase association constants of the studied metal ions with these de novo designed peptides were experimentally determined by MALDI mass spectrometry by using 3,4,5-trihydroxyacetophenone as a matrix, whereas the thermodynamic parameters of the metal-ion coordination in the condensed phase were measured by isothermal titration calorimetry (ITC), chelatometry and NMR spectroscopy methods. The data indicate that some of the computationally predicted peptides are potential M(2+)-specific metal-ion chelators.     

Density functional theory for molecular and periodic systems using density fitting and continuous fast multipole method: Stress tensor

A full implementation of the analytical stress tensor for periodic systems is reported in the TURBOMOLE program package within the framework of Kohn–Sham density functional theory using Gaussian-type orbitals as basis functions. It is the extension of the implementation of analytical energy gradients (Lazarski et al., Journal of Computational Chemistry 2016, 37, 2518–2526) to the stress tensor for the purpose of optimization of lattice vectors. Its key component is the efficient calculation of the Coulomb contribution by combining density fitting approximation and continuous fast multipole method. For the exchange-correlation (XC) part the hierarchical numerical integration scheme (Burow and Sierka, Journal of Chemical Theory and Computation 2011, 7, 3097–3104) is extended to XC weight derivatives and stress tensor. The computational efficiency and favorable scaling behavior of the stress tensor implementation are demonstrated for various model systems. The overall computational effort for energy gradient and stress tensor for the largest systems investigated is shown to be at most two and a half times the computational effort for the Kohn–Sham matrix formation. © 2019 Wiley Periodicals, Inc.     

From rare gas atoms to fullerenes: spherical aromaticity studied from the point of view of atomic structure theory

The characteristic features of molecules like polyhedra and fullerenes, which follow the 2(N+1)(2) rule of spherical aromaticity, can be related to energetically stable closed-shell configurations of (pseudo-)atoms. This unifying view relies on a thought experiment, which produces a polyhedron in a two-step process and which can, in turn, relate the electronic configuration of any spherical polyhedron to the one of a corresponding closed-shell atom. In the first step, the electronic ground-state configuration is identified. In the second step, a group theoretical analysis can be carried out; this relates the spherically symmetric atomic orbitals to the molecular orbitals classified according to the irreducible representations of the point group of the polyhedron under consideration. This procedure explains and justifies the pseudo-l classification of molecular orbitals, which is the basis of the 2(N+1)(2) rule. For the transition from the electronic configuration of the rare gas Eka-Rn (Uuo) to the icosahedral fullerene C(20) (2+), we show how a change in the ground-state configuration leads to the phenomenologically found 2(N+1)(2) rule for spherically aromatic fullerenes.     

Density functional theory for molecular and periodic systems using density fitting and continuous fast multipole method: Analytical gradients

A full implementation of analytical energy gradients for molecular and periodic systems is reported in the TURBOMOLE program package within the framework of Kohn–Sham density functional theory using Gaussian‐type orbitals as basis functions. Its key component is a combination of density fitting (DF) approximation and continuous fast multipole method (CFMM) that allows for an efficient calculation of the Coulomb energy gradient. For exchange‐correlation part the hierarchical numerical integration scheme (Burow and Sierka, Journal of Chemical Theory and Computation 2011, 7, 3097) is extended to energy gradients. Computational efficiency and asymptotic O(N) scaling behavior of the implementation is demonstrated for various molecular and periodic model systems, with the largest unit cell of hematite containing 640 atoms and 19,072 basis functions. The overall computational effort of energy gradient is comparable to that of the Kohn–Sham matrix formation. © 2016 Wiley Periodicals, Inc.     

High level of ab initio and density functional theory computational study of structural and energetic properties of tetrafluorhydrazine rotamers

The HF, MP2, MP3, MP4, and QCISD ab initio methods were compared with local, hybrid, and gradient-corrected density functional theory (DFT) methods for computing structures and energies of N2F4 rotamers. In all DFT calculations 6-311 + G(2d) basis set was used. The generated structures energies of trans- and gauche-N₂F₄ rotamers, and their dissociation energies to nitrogen difluoride were compared with experimental data. Suitable hybrid and gradient-corrected DFT methods for determining structures and energies for these and similar molecular systems were discussed.     

Hydrogen bonding in acetylacetaldehyde: Theoretical insights from the theory of atoms in molecules

All the possible conformations of tautomeric structures (keto and enol) of acetylacetaldehyde (AAD) were fully optimized at HF, B3LYP, and MP2 levels with 6‐31G(d,p) and 6‐311++G(d,p) basis sets to determine the conformational equilibrium. Theoretical results show that two chelated enol forms have extra stability with respect to the other conformers, but identification of global minimum is very difficult. The high level ab initio calculations G2(MP2) and CBS‐QB3) also support the HF conclusion. It seems that the chelated enol forms have equal stability, and the energy gap between them is probably lies in the computational error range. Finally, the analysis of hydrogen bond in these molecules by quantum theory of atoms in molecules (AIM) and natural bond orbital (NBO) methods fairly support the ab initio results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Influence of Defects on the Stability and Hydrogen-Sorption Behavior of Mg-Based Hydrides

This review deals with the destabilization methods for improvement of storage properties of metal hydrides. Both theoretical and experimental approaches were used to point out the influence of various types of defects on structure and stability of hydrides. As a case study, Mg, and Ni based hydrides has been investigated. Theoretical studies, mainly carried out within various implementations of DFT, are a powerful tool to study mostly MgH₂ based materials. By providing an insight on metal-hydrogen bonding that governs both thermodynamics and hydrogen kinetics, they allow us to describe phenomena to which experimental methods have a limited access or do not have it at all: to follow the hydrogen sorption reaction on a specific metal surface and hydrogen induced phase transformations, to describe structure of phase boundaries or to explain the impact of defects or various additives on MgH₂ stability and hydrogen sorption kinetics. In several cases theoretical calculations reveal themselves as being able to predict new properties of materials, including the ways to modify Mg or MgH₂ that would lead to better characteristics in terms of hydrogen storage. The influence of ion irradiation and mechanical milling with and without additives has been discussed. Ion irradiation is the way to introduce a well-defined concentration of defects (Frankel pairs) at the surface and sub-surface layers of a material. Defects at the surface play the main role in sorption reaction since they enhance the dissociation of hydrogen. On the other hand, ball-milling introduce defects through the entire sample volume, refine the structure and thus decrease the path for hydrogen diffusion. Two Severe Plastic Deformation techniques were used to better understand the hydrogenation/dehydrogenation kinetics of Mg- and Mg₂Ni-based alloys: Equal-Angular-Channel-Pressing and Fast-Forging. Successive ECAP passes leads to refinement of the microstructure of AZ31 ingots and to instalment therein of high densities of defects. Depending on mode, number and temperature of ECAP passes, the H-sorption kinetics have been improved satisfactorily without any additive for mass H-storage applications considering the relative speed of the shaping procedure. A qualitative understanding of the kinetic advanced principles has been built. Fast-Forging was used for a “quasi-instantaneous” synthesis of Mg/Mg₂Ni-based composites. Hydrogenation of the as-received almost bi-phased materials remains rather slow as generally observed elsewhere, whatever are multiple and different techniques used to deliver the composite alloys. However, our preliminary results suggest that a synergic hydrogenation / dehydrogenation process should assist hydrogen transfers from Mg/Mg₂Ni on one side to MgH₂/Mg₂NiH₄ on the other side via the rather stable a-Mg₂NiH_0.3, acting as in-situ catalyser.     

Ionic dissociations of chlorosulfonic acid in microsolvated clusters: A density functional theory and ab initio MO study

Ionic dissociation of chlorosulfonic acid (HSO3Cl) in the molecular clusters HSO3Cl-(H2O)n (n = 1-4) and HSO3Cl-NH3-(H2O)n (n = 0-3) was investigated by density functional theory and ab initio molecular orbital theory. The equilibrium structures, binding energies, and thermodynamic properties, such as relative enthalpy and relative Gibbs free energy, and were calculated using the hybrid density func- tional (B3LYP) method and the second order M?ller-Plesset approximation (MP2) method with the 6-311 G** basis set. Chlorosulfonic acid was found to require a minimum of three water molecules for ionization to occur and at least one water molecule to protonate ammonia. The corresponding clusters with fewer water molecules were found to be strongly hydrogen-bonded. The related properties and acid strength of chlorosulfonic acid were discussed and compared to the acid strengths of perchloric acid and sulfuric acid in the context of clusters with ammonia and water. The relative stabilities of these clusters were also investigated.     

Complete basis set model chemistry applied to molecules of increasing molecular complexity: Thermochemical properties of organic sulfur derivatives

To estimate the thermochemical properties, bond dissociation energies and atomization energies of sulfur organic derivatives, the complete basis set (CBS) method was employed at the lower computational level (CBS‐4) owing to the large molecular size of a number of the molecules chosen. By comparison with experimental values, calculated values of thermochemical properties are subject to error, which increases in line with the increase in molecular complexity. The main source of error affecting the calculated enthalpy of formation stems from the difference between the energy of the molecule and that of the single atoms: the greater the size of the molecule, the greater the accumulation of error. By acting on the empirical correction to the CBS energy and minimizing the error due to the contribution of the single atoms to the dissociation energy a parameter d_i for each atom i is obtained. Application of these corrections does not greatly affect the heats of formation of the small molecules included in test sets employed for previous comparisons of calculated and experimental values, while there is a great improvement in the case of large molecules, for example, diphenyl disulfide. The mean absolute deviation turns out to be 2.52, which is greater than that obtained in recent reexaminations of model chemistry methods including the G3 and G3(MP3) approaches. The improvement in the results calculated for large molecules, whose heats of formation are calculated with large errors at the CBS‐4 level, in comparison also with the CBS‐4M version, justify our approach. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1405–1418, 2000     

Study of chemical bonding in H2 and HF molecules: Wave function and density functional theory (DFT) parameters approach

Balint Kurti's Fourier grid Hamiltonian method is employed to obtain the molecular wave function and equilibrium bond length for H₂ and HF molecules. The density functional theory parameter, namely, the chemical hardness (η) value, was determined for some diatomic hydride molecules using this wave function and the results are found to be in good agreement with the values obtained from the ab initio HF–SCF method. A new formula for chemical hardness (η=1/2Dr, where D is the proportionality constant and r is the internuclear distance) is introduced in binding energy and change of hardness equations to determine the chemical hardness and chemical potential values for different bond lengths. The binding energy and change of hardness values are calculated for H₂, H, H, HF, HF⁺, and HF⁻ molecules and the bond stability is discussed. Finally, the concept of an atom in a molecule is examined in the context of DFT parameters and comparison is made between an atom in a molecule and the isolated atom. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 662–669, 2000     

Comparative studies on the structures,infrared spectrum,and thermodynamic properties of phthalocyanine using ab initio Hartree–Fock and density functional theory methods

The molecular structure, vibrational spectrum, standard thermodynamic functions, and enthalpy of formation of free base phthalocyanine (Pc) have been studied using the density functional theory B3LYP procedure, as well as the ab initio Hartree–Fock method. Various basis sets 3‐21G, 6‐31G*, and LANL2DZ have been employed. The results obtained at various levels are discussed and compared with each other and with the available experimental data. It is shown that calculations performed at the Hartree–Fock level cannot produce a reliable geometry and related properties such as the dipole moment of Pc and similar porphyrin‐based systems. Electron correlation must be included in the calculations. The basis set has comparatively less effect on the calculated results. The results derived at the B3LYP level using the smaller 3‐21G and LANL2DZ basis sets are very close to those produced using the medium 6‐31G* basis set. The geometry of Pc obtained at the B3LYP level has D_2h symmetry and the diameter of the central macrocycle is about 4 Å. The enthalpy of formation of Pc in the gas phase has been predicted to be 1518.50 kJ/mol at the B3LYP/6‐311G(2d,2p)//B3LYP/6‐31G* level via an isodesmic reaction. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

CIO自由基与CN自由基反应的密度泛函理论研究

应用量子化学从头算和密度泛函理论（DFT）对CIO与CN的双自由基反应进行了研究．结果表明,CIO自由基的O原子进攻CN自由基的C原子是主要的进攻方式,并形成了中间体1 CIOCN．随后,中间体1发生异构化和分解反应得到热力学上可行的3种产物P4（CINCO）,P1（CO＋CIN）和P3（NO＋CCl）．其中P4是主要产物,P1和P3是次要产物．与单态势能面上相比,三态势能面对整个反应的贡献可以忽略．     

Complete basis set ab initio and hybrid density functional theory exploration of the potential energy surface in the reaction between an amino radical and nitrogen oxide

The potential energy surface for the reaction involving NH₂ plus NO was explored with a quadratic complete basis set ab initio approach and three hybrid density functional theory methods, the target being to accurately estimate activation barriers and the relative stability of the nitrogen–oxygen isomers. The computational results were compared with previously performed ab initio calculations and new, more accredited values for the NH₂NO rearrangement to HNNOH and for the HNNOH decomposition reaction were suggested. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 409–414, 1998     

An alternative approach to the g-matrix: theory and applications.

Starting from the formula proposed by Gerloch and McMeeking in 1975, the electronic g-matrix is expressed as a sum of two matrices called Lambda and Sigma describing the orbital and spin contributions respectively. This approach is applied on benchmark diatomic and triatomic molecules, and on TiF3 and Cu(NH3)4(2+) using either CASPT2 or CCSD(T) methods to calculate the spin-free states and SO-RASSI to calculate spin-orbit coupling. Results compare very well to experimental data and to previous theoretical work; and, for each molecule, the anisotropy of the g-matrix is modeled by the mean of a few parameters.