Fourier space for accurate ab initio RHF band structure calculations on chainlike systems

Minimal basis-set (STO-3G) direct and Fourier space restricted Hartree-Fock (RHF) calculations on the infinite regular (metallic) and alternating chains of lithium molecules, (-Li₂-)_x, are reported to illustrate two advantages of the Fourier representation method: accurate calculation of all lattice summations and faithful reproduction of the genuine features of the RHF approach for metallic cases. © 1996 John Wiley & Sons, Inc.     

Molecular structure and vibrational spectra of phenobaraitone by density functional theory and ab initio hartree-Fock calculations

Quantum chemistry calculations have been performed using Gaussian03 program to compute optimized geometry, harmonic vibrational frequency along with intensities in IR and Raman spectra at RHF/6-31++G** and B3LYP/6-31++G** levels for phenobarbitone (C₁₂H₁₂N₂O₃) in the ground state. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR and FT-Raman spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions (PEDs) using MOLVIB program. A detailed interpretation of the infrared spectra of the title compound is reported. On the basis of the agreement between the calculated and observed results, the assignments of fundamental vibrational modes of phenobarbitone were examined and some assignments were proposed. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title compound have been constructed.     

Potentials of an alternative scheme for ab initio polymer band structure calculations. Illustration on the chain of hydrogen atoms

An alternative scheme for ab initio polymer band structure calculations based on a Filon-type quadrature is proposed. This scheme avoids the explicit calculation and the storage of the “troublesome” Fourier transforms of the LCAO density matrix elements and is a first step towards a better control of the convergence of the different lattice sums appearing in the configuration space LCAO-SCF-CO method. The potential of the proposed technique is illustrated by a minimal basis set calculations on an infinite chain of H atoms.     

Local-orbital-based correlated ab initio band structure calculations in insulating solids: LiF

 A local-orbital-based ab initio approach to calculate correlation effects on quasi-particle energies in insulating solids is presented. The use of localized Wannier-type Hartree–Fock orbitals allows correlation effects to be efficiently assessed. First a Green's function approach based on exact diagonalization is introduced and this is combined with an incremental scheme, while subsequently different levels of perturbative approximations are derived from the general procedure. With these methods the band structure of LiF is calculated and good agreement with experiment is found. By comparing the different approximations proposed, including the exact diagonalization procedure, their relative quality is established. Received: 25 June 2001 / Accepted: 31 August 2001 / Published online: 19 December 2001     

Valence basis sets for lanthanide 4f-in-core pseudopotentials adapted for crystal orbital ab initio calculations

Crystal orbital adapted Gaussian (4s4p3d), (5s5p4d) and (6s6p5d) valence primitive basis sets have been derived for calculating periodic bulk materials containing trivalent lanthanide ions modeled with relativistic energy-consistent 4f-in-core lanthanide pseudopotentials of the Stuttgart-Koeln variety. The calibration calculations of crystalline A-type Pm₂O₃ using different segmented contraction schemes (4s4p3d)/[2s2p2d], (4s4p3d)/[3s3p2d], (5s5p4d)/[2s2p2d], (5s5p4d)/[3s3p3d], (5s5p4d)/[4s4p3d], (6s6p5d)/[2s2p2d], (6s6p5d)/[3s3p3d] and (6s6p5d)/[4s4p4d] are discussed at both Hartree–Fock (HF) and density functional theory (DFT) levels for the investigation of basis set size effects. Applications to the geometry optimization of A-type Ln₂O₃ (Ln = La-Pm) show a satisfactory agreement with experimental data using the lanthanide valence basis sets (6s6p5d)/[4s4p4d] and the standard set 6-311G* for oxygen. The corresponding augmented sets (8s7p6d)/[6s5p5d] with additional diffuse functions for describing neutral lanthanide atoms were applied to calculate atomic energies of free lanthanide atoms for the evaluation of cohesive energies for A-Ln₂O₃ within both conventional Kohn-Sham DFT and the a posteriori-HF correlation DFT schemes.     

Syntheses, crystal structure and ab initio calculations of two new phosphoric triamides

The reaction of N-benzoylphosphoramidic dichloride with piperidine and 4-methylpiperidine lead to PhC(O)N(H)P(O)R₂ with R=piperidine (1) and R=4-methylpiperidine (2) as N-benzoyl-N′,N″-bis(piperidine) phosphoric triamide and N-benzoyl-N′,N″-bis(4-methylpiperidine) phosphoric triamide, respectively. The products have been characterized by ¹H, ¹³C, ³¹P NMR spectra, and by elemental analysis. The crystalline solid for (1) and (2) consists surprisingly of four and two independent molecules, respectively. There is a disorder in one amine group due to ring inversion in each conformer in compound 1. In the solid state, comparable magnitudes for the stabilization of the stable conformers for the more or less discrete molecules, the polarization effects, hydrogen bonding and the packing effects could be anticipated.

The geometry of compound (1) optimized by density functional calculations at the B3LYP/6-31++G* (d,p) level, is in good agreement with data obtained from X-ray crystallography.     

Ab initio band structure calculations on polymers (C5H3X)n (X=CH,N,P,As)

The ab initio crystal orbital calculations on conjugated aromatic six-membered rings polymers,namely,poly(p-phenylene) (PPP),poly(2,5-pyridinediyl) (PPD),poly(2,5-phosphabenzene) (PPB) and ploy(2,5-arsabenzene) (PAB) are reported.The comparison of the important electronic properties of these polymers,such as band gap,bandwidth,ionization potential and electron affinity,indicates that PPP is the best intrinsic semiconductor,and PPD has the best prospects for forming n-doped conducting materials.     

New insights into oxidation properties and band structure of fluorescein dyes from ab initio calculations

During recent years, several publications have investigated the electrical bistability of spin cast films of halogenated fluorescein dyes. In the present contribution, we simulate the excited states of single fluorescein dyes with time-dependent density functional theory (TD-DFT) and we analyzed the band structure of the corresponding molecular crystals with DFT. More precisely, the molecules examined are fluorescein, erythrosine B, and rose bengal. We consider the molecular crystals of fluorescein in salt and lactone forms as well as erythrosine B. Rose bengal showed high quantum yield of the triplet state and high electronic affinity. Therefore, the rose bengal has very strong oxidation properties and it is able to form electrically bistable thin oxide layer. The poor crystal order and small bandwidths of fluorescein in salt form and erythrosine B indicated high resistivity for both crystals.     

Study on the behavior of energy convergence in ab initio crystal orbital calculations

Summary This article studies the dependence on the cutoff scheme of ab initio crystal orbital calculations with no long-range correction. We have thoroughly studied the Namur cutoff and cell-wise cutoff schemes through calculations of polyethylene and LiH chains. The Namur cutoff gives the fastest energy convergence with respect to the number of neighbors (N ₀). The energy convergence behavior with respect to N ₀ depends on the basis set. The Namur cutoff shows the fastest convergence with the STO-3G basis set, intermediate convergence with the MINI basis set, and the slowest convergence with the (7s4p/3s) basis set. The cell-wise cutoff shows exactly the reverse order of the Namur cutoff. The Namur cutoff destroys the translational symmetry. Both the Namur cutoff and cell-wise cutoff schemes introduce slight asymmetry on the two equivalent C-C bonds of polyethylene when calculating with a C₂H₄ unit cell. The asymmetry with the Namur cutoff can be made to disappear by increasing N ₀ a little. The calculations on two different unit-cell structures of trans-polyacetylene show the effect of the cutoff scheme on the total energy. Only the symmetric cutoff energies are the same. Disagreement related to the Namur cutoff disappears at N ₀ = 20, however, that related to the cell-wise and modified symmetric cutoff schemes remains at N ₀ 20. The optimized geometry and vibrational frequency are not as sensitive to the cutoff method except with the symmetric cutoff. A compilation of all results shows that the Namur cutoff is the superior cutoff scheme when calculating the insulator using the minimal basis set, especially the STO-3G basis set.     

IMiCMO: a new integrated ab initio multicenter molecular orbitals method for molecular dynamics calculations in solvent cluster systems

A new computational scheme integrating ab initio multicenter molecular orbitals for determining forces of individual atoms in large cluster systems is presented. This method can be used to treat systems of many molecules, such as solvents by quantum mechanics. The geometry parameters obtained for three models of water clusters by the present method are compared with those obtained by the full ab initio MO method. The results agree very well. The scheme proposed in this article also intended for use in modeling cluster systems using parallel algorithms. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1107–1112, 2001     

Molecular structure, vibrational spectra and HOMO, LUMO analysis of yohimbine hydrochloride by density functional theory and ab initio Hartree-Fock calculations

Yohimbine hydrochloride (YHCl) is an aphrodisiac and promoted for erectile dysfunction, weight loss and depression. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of yohimbine hydrochloride have been determined using ab initio, Hartree–Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and IR spectra of YHCl. The UV absorption spectrum was examined in ethanol solvent and compared with the calculated one in gas phase as well as in solvent environment (polarizable continuum model, PCM) using TD-DFT/6-31G basis set. These methods are proposed as a tool to be applied in the structural characterization of YHCl. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap are presented.     

Molecular structure, IR spectra of 2-mercaptobenzothiazole and 2-mercaptobenzoxazole by density functional theory and ab initio Hartree–Fock calculations

Quantum chemistry calculations have been performed using Gaussian03 program to compute optimized geometry, harmonic vibrational frequency along with intensities in IR and Raman spectra and atomic charges at RHF/6-31+G*, B3LYP/6-31+G* and B3LYP/6-31++G* levels for 2-mercaptobenzothiazole (MBT, C₇H₅NS₂) and 2-mercaptobenzoxazole (MBO, C₇H₅NOS) in the ground state. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR and FT-Raman spectra. The results show that the scaled theoretical vibrational frequencies is very good agreement with the experimental values. A detailed interpretation of the infrared and Raman spectra of 2-mercaptobenzothiazole and 2-mercaptobenzoxazole was reported. Comparison of calculated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes.     

Linear and non-linear optical properties of some donor–acceptor oxadiazoles by ab initio Hartree-Fock calculations

The molecular hyperpolarizability of some donor–acceptor oxadiazoles was investigated using ab initio methods. Ab initio optimizations were performed at the Hartree-Fock level using different basis sets, starting with the minimal basis set, and then split valence sets. The first hyperpolarizabilities were calculated at the Hartree-Fock level employing the corresponding basis sets using Gaussian 98W. In general, the first hyperpolarizability is dependent on the choice of method and basis set. In order to understand this phenomenon in the context of molecular orbital picture, we examined the molecular HOMOs and molecular LUMOs generated via HF/6-31G level. It has also been calculated the polarizability, anisotropy of polarizability and ground state dipole moment of all the molecules. Several of these oxadiazoles display significant second-order molecular nonlinearity, β(8.57–195.05 × 10⁻³⁰ esu) and provide the basis for future design of efficient nonlinear optical materials having the oxadiazole core.     

A numerical integration scheme for iterative calculations on atomic systems

A recursive numerical integration scheme based on the method of Clenshaw and Curtis is proposed for the efficient implementation of the variation–iteration procedure for the computation of approximate energies and wave functions for atomic systems. Extensive numerical tests are carried out to assess the accuracy and efficiency of the method and inaccuracies in some earlier calculations are pointed out.     

Roles of K151 and D180 in L‐2‐haloacid dehalogenase from Pseudomonas sp. YL: Analysis by molecular dynamics and ab initio fragment molecular orbital calculations

L ‐2‐haloacid dehalogenase (L ‐DEX) catalyzes the hydrolytic dehalogenation of L ‐2‐haloalkanoic acids to produce the corresponding D ‐2‐hydroxyalkanoic acids. This enzyme is expected to be applicable to the bioremediation of environments contaminated with halogenated organic compounds. We analyzed the reaction mechanism of L ‐DEX from Pseudomonas sp. YL (L ‐DEX YL) by using molecular modeling. The complexes of wild‐type L ‐DEX YL and its K151A and D180A mutants with its typical substrate, L ‐2‐chloropropionate, were constructed by docking simulation. Subsequently, molecular dynamics (MD) and ab initio fragment molecular orbital (FMO) calculations of the complexes were performed. The ab initio FMO method was applied at the MP2/6‐31G level to estimate interfragment interaction energies. K151 and D180, which are experimentally shown to be important for enzyme activity, interact particularly strongly with L ‐2‐chloropropionate, catalytic water, nucleophile (D10), and with each other. Our calculations suggest that K151 stabilizes substrate orientation and balances the charge around the active site, while D180 stabilizes the rotation of the nucleophile D10, fixes catalytic water around D10, and prevents K151 from approaching D10. Further, D180 may activate catalytic water on its own or with K151, S175, and N177. These roles are consistent with the previous results. Thus, MD and ab initio FMO calculations are powerful tools for the elucidation of the mechanism of enzymatic reaction at the molecular level and can be applied to other catalytically important residues. The results obtained here will play an important role in elucidating the reaction mechanism and rational design of L ‐DEX YL with improved enzymatic activity or substrate specificity. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Excited-state structure and vibrations of p-diaminobenzene studied by ab initio calculations

The structures and vibrations of p-diaminobenzene (PDAB) in the S₀ and S₁ states have been studied by ab initio quantum-chemical calculations. Results from geometry optimization show that the two stable cis and trans conformers of PDAB are non-planar in the S₀ state. Upon electronic excitation to the S₁ state, enhanced interaction between the ring and the amino substituent causes the molecule to become planar and contract along the long in-plane axis. A detailed analysis of the normal vibrations of PDAB in both states has been done on the basis of the motions of individual atoms as well as reduced masses, force constants and frequencies. The computed frequencies are in reasonably good agreement with the available experimental data.     

Extrapolation of the linear and nonlinear polarizabilities from ab initio finite oligomer calculations

Different definitions of property per unit cell and different fitting functions are employed to obtain the asymptotic limit values per unit cell of the polarizability (α), the first (β), and the second (γ) hyperpolarizabilities of an infinite oligomer. A 1/n power series function is found to be suitable for the average value and logarithmic average value per unit cell definition, and an exponentially decreasing function is found to be suitable for the difference value per unit cell definition. These conclusions are derived based on an equation expressing the total energy per unit cell of a finite linear oligomer as a power series of 1/n, presented from a perturbation treatment. Several calculations of long chain systems have been carried out to reach our conclusions. An equation of p(n)/n = a + b/n + c/n² is strongly recommended for a least‐squares fitting of the properties per unit cell to achieve a stabilization behavior when the chain length is increased. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006