Density functional theory for efficient ab initio molecular dynamics simulations in solution

We present a density functional for first-principles molecular dynamics simulations that includes the electrostatic effects of a continuous dielectric medium. It allows for numerical simulations of molecules in solution in a model polar solvent. We propose a smooth dielectric model function to model solvation into water and demonstrate its good numerical properties for total energy calculations and constant energy molecular dynamics.     

An ab initio Study of the Rotamers and Rotations of Propane-1,3-dial by DFT and SCF Calculations

Summary.  Eight planar rotamers of the enol form of malonaldehyde were considered at the HF (Hartree-Fock) and DFT (density functional theory) levels with 6-311G^** and D95^** (Dunning/Huzinaga full double-ζ) basis sets with the aim to establish the most stable of them and to find the energy barriers of their conversions. The results show that the rotamer with an intramolecular hydrogen bond is the most stable one. High energy barriers were ascertained for the conversions including rotations around a CC double bond. Most of the reactions connected with breaking of the hydrogen bond display strongly asymmetric energy barriers. Their transition states were determined as first-order saddle points because of one imaginary frequency in the IR spectrum related with a negative energy gradient. Received July 6, 2000. Accepted (revised) September 7, 2000     

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.     

Ab initio and DFT investigation of the structures and properties of chloromethyl and chlorofluoromethyl peroxyl radicals

Ab initio and Density Functional Theory (DFT) calculations were performed to determine the equilibrium geometries, charge distributions, spin density distributions, dipole moments, electron affinities (EAs), and C–O bond dissociation energies (BDEs) of CH₂ClO₂^? CHCl₂O₂^?, CCl₃O₂^?, CF₂ClO₂^?, CFCl₂O₂^?, and CHFClO₂^? peroxyl radicals. The C–H BDEs of the parent methanes were calculated using the same levels of theories. Both MP2(full) and B3LYP methods, using the 6‐31G(d,p) basis set, were found to be capable of accurately predicting the geometries of peroxyl radicals. The B3LYP/6‐31G(d,p) method was found to be comparable to high ab initio levels in predicting C–O BDEs of studied peroxyl radicals and C–H BDEs of the parent alkanes. The progressive chlorine substitution of hydrogen atoms in methyl peroxyl radicals results in an increase (decrease) of the spin density on the terminal (inner) oxygen, a decrease in dipole moments, and an increase in electron affinities. The substitution of fluorine by chlorine in the series CF₃O₂^? – CCl₃O₂^? was found to lengthen (destabilize) the C–O bonds. Both C–O BDEs and EAs of peroxyl radicals (RO₂^?) were found to correlate well with Taft σ* substituent constants for the R groups. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Molecular conformations and harmonic force field of 1,3,5-benzenetriol molecule from ab initio and density functional theory investigations

The molecular conformers of the molecule 1,3,5-benzenetriol have been studied by ab initio and density functional methods to determine optimized equilibrium geometries, harmonic vibrational frequencies and relative stability. The results of the quantum-chemical calculations have been used to investigate the functional theory-infrared (FT-IR) spectrum of the 1,3,5-benzenetriol vapors trapped in Ar matrix at 12 K.     

Theoretical study for the HNSi–HSiN isomerization: ab initio and DFT calculations

Ab initio and density functional theory (DFT) calculations using the GAUSSIAN 94 program have been performed to investigate the molecular structures of HNSi and HSiN in the ground state as well as the transition state for the HNSi–HSiN isomerization reaction at the 6-311G(d,p), 6-311+G(2d,p) and 6-311+G(2df,p) basis sets. The results show that DFT calculations at higher levels of theory reproduce experimental vibrational frequencies of both HNSi and HSiN better than ab initio methods including electron correlation effects. Those calculated geometries are accurate enough to predict the rotational constant of HNSi. The barrier height for the isomerization reaction is found to be about 10 kcal/mol.     

Interaction of angelicin with DNA‐bases (III) DFT and ab initio second‐order Moeller–Plesset study

Angelicin geometry was optimized at MP2/6‐31+G(d,p) level and compared with X‐ray experimental data. The highest π‐electron density was found to be localized on C1? C2 and on C13? C14 as confirmed by the calculated bond length and bond order values. Spectrophptometric properties of angelicin were measured and compared with the computed within the TD‐DFT. Quantum chemical methods were used to study the interaction of angelicin, as a nonlinear furocoumarin, with DNA bases and base pairs. The interactions with DNA bases and base pairs were studied to shade more light on the nature of the intercalation binding forces between angelicin and DNA. Comparing computed electronic properties of angelicin with that of linear psoralens show that the former is a weaker intercalator. The geometry of complexes of angelicin with adenine, thymine, adenine–thymine base pair, cytocine, guanine as well as cytocine–guanine base pair have been optimized in two main orientations, planar and stacked, at the levels of B3LYP/cc‐pVDZ, MP2/6‐31G(d,p) and MP2/cc‐pVDZ. Effect of vertical distance and rotational angle between the stacked molecules on the interaction energy were investigated by the aforementioned methods in gas phase and water media. It was found that ab initio methods which account for the electron correlation effects are the minimum level for studying the noncovalent interactions. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

In cation interactions with some organics: ab initio molecular orbital and density functional theory

Ab initio molecular orbital and density functional theory studies were undertaken to investigate the structural and energetic characteristics of complexes of In⁺ with several different organic molecules for the first time. HF, MP2, QCISD, and CCD levels of theory in ab initio MO as well as B3LYP, B3PW91 hybrid functionals in density functional theory were used. A valence TZ+P basis set with relativistic effective core potentials was used for the In atom while the 6-311++G(3d, 2p) basis set was utilized for all other atoms. Both closed-shell (H₂O, CH₄, CH₃OH, and C₆H₆) and open-shell (CH₃ and C₂H₃) molecules were considered for complexation with In⁺. In⁺ affinities of 21.5, 24.8, 28.6, 18.4, and 23.0 kcal/mol were obtained with the B3PW91 hybrid functional for H₂O, CH₃OH, C₆H₆, CH₃, and C₂H₃, respectively. The large values for the calculated affinities indicate the validity of our recent experimental detection of In⁺ ion attachment to some organic molecules.     

Ab initio and DFT study of the electronic structures and spectroscopic properties of pyrene ligands and their cyclometalated complexes

Two ligands 1‐diphenylphosphinopyrene (1‐PyP) ( L ₁ ), 1,6‐bis(diphenylphosphino)‐pyrene (1,6‐PyP) ( L ₂ ) and their cyclometalated complexes [Pt(dppm)(1‐PyP‐H)]⁺ ( 1 ), [Pt₂(dppm)₂(1,6‐PyP‐H₂)]²⁺ (dppm = bis(diphenylphosphino)methane ( 2 ), and [Pd(dppe)(1‐PyP‐H)⁺ (dppe = bis(diphenylphosphino)ethane) ( 3 ) are investigated theoretically to explore their electronic structures and spectroscopic properties. The ground‐ and excited‐state structures are optimized by the density functional theory (DFT) and single‐excitation configuration interaction method, respectively. At the time‐dependent DFT (TDDFT) and B3LYP level, the absorption and emission spectra in solution are obtained. As revealed from the calculations, the lowest‐energy absorptions of 1 and 3 are attributed to the mixing ligand‐to‐metal charge transfer (CT)/intraligand (IL)/ligand‐to‐ligand CT transitions, while that of 2 is attributed to the IL transition. The lowest‐energy phosphorescent emissions of the cyclometalated complexes are attributed to coming from the ³ILCT transitions. With the increase of the spin‐orbit coupling effect, the phosphorescence intensities and the emissions wavelength are correspondingly increased. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Energy bands and bond alternation potential in poly(para-phenylene vinylene): a comparative ab initio quantum chemical and density functional theory study

We present calculations of the total energy per unit cell for different bond alternations of the C-C bonds bridging the distance between two aromatic rings in poly(para-phenylene vinylene) (PPV), using two different parametrizations of the energy functional in the local density approximation (LDA) and the ab initio Hartree-Fock (HF) method. For the application of correlation corrections to the HF results the system is already too large. We find that even simple LDA methods are reliable alternatives to the ab initio HF method for the calculation of potential surfaces in polymers with large unit cells. The results in turn can be used to determine parameters for model Hamiltonians necessary for theoretical studies of the dynamics of nonlinear quasiparticles in the polymers. We further present the LDA band structures of PPV together with their HF and correlation (many body perturbation theory of 2^nd order in Møller-Plesset partitioning, MP2) corrected counterparts. We find that the fundamental gap obtained is too large both with HF and with the correlation corrected band structure compared to experiment. However, we use only a modest correlation method and a small basis set, which already brings us to the limits of the computers available to us. The LDA gaps on the other hand are too small which, however, could be corrected with the help of self interaction corrections. None of the latter methods would lead to exceedingly large computation times.     

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.     

A comparative study of DFT and traditional ab initio methodologies on the OsO4 molecule

The performance of different conventional ab initio methodologies and density functional procedures is compared through its application to the theoretical calculation of the bond distance and harmonic vibrational frequencies of the OsO₄ molecule. The problem of the basis set is first considered, with up to nine different basis sets being tested in calculations using the hybrid Becke3LYP density functional, and the most appropriate basis set is used in the comparison of Hartree–Fock, post‐Hartree–Fock, and density functional methods. The post‐Hartree–Fock methods analyzed are MP2, CISD, and CCSD(T), and the density functionals tested are SVWN, BLYP, BPW91, and Becke3LYP. The results show that for this particular system density functional methods perform better than do HF‐based methods with the exception of CCSD(T), which gives the best overall results. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 77: 544–551, 2000     

Some recent applications of ab initio electronic structure methods to metal,semimetal, and molecular clusters

Recent experimental and theoretical cluster studies are reviewed. Areas of current and developing interest in theoretical and computational chemistry are identified. Some promising methods applied to metal clusters, main group clusters, molecular clusters, spectroscopy, and models of cluster-molecule reactions are indicated. Results of calculations on small hydrogenated lithium clusters and hydrated sodium clusters are discussed in some detail.     

Structural and electronic properties of boron-doped lithium clusters: ab initio and DFT studies

The lowest-energy structures and electronic properties of the BLi(n) (n = 1-7) clusters are reported using the B3LYP, MP2, and CCSD(T) methods with the aug-cc-pVDZ basis set. Though the results at the B3LYP level agree well with those at the CCSD(T) level, the MP2 method is rather unsatisfactory. The first three-dimensional ground state in the BLi(n) clusters occurs for BLi(4), and the impurity B atom is seen to be trapped in a Li cage from the BLi(6) cluster onwards. The evolution of the binding energies, vertical ionization potentials, and polarizability with size of cluster shows the BLi(5) cluster to be most stable among the BLi(n) clusters. Besides, the BLi(5) cluster is also found to have the largest reaction enthalpy (49.8 kcal/mol) upon losing a Li atom, which is different from the previous prediction. The unique stability of the 8-valence electron BLi(5) can be understood from the cluster electronic shell model (CSM). However, in contradiction to the prediction of the CSM, the 2s level is filled prior to the 1d level in the BLi(n) clusters.     

Vibrational spectroscopy investigation using ab initio and density functional theory analysis on the structure of 2-amino-4,6-dimethoxypyrimidine

The FTIR and FT-Raman spectra of 2-amino-4,6-dimethoxypyrimidine (2A46DMP) has been recorded in the region 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of 2A46DMP were obtained by the ab initio and DFT levels of theory with complete relaxation in the potential energy surface using 6-31G(d,p) and 6-311G(d,p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.     

FTIR, FT-Raman spectra and ab initio DFT vibrational analysis of 2,4-dichloro-6-nitrophenol

The FTIR and FT-Raman spectra of 2,4-dichloro-6-nitrophenol (2,4-DC6NP) has been recorded in the region 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of (2,4-DC6NP) were obtained by the ab initio and DFT levels of theory with complete relaxation in the potential energy surface using 6-31G(d,p) and 6-311+G(d,p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.     

Theoretical study of the adsorption of isobutane over H-mordenite zeolite by ab initio and DFT methods

Values of relative interaction energy between an isobutane molecule and the surface of the H-mordenite zeolite were obtained. Sixteen tetrahedral sites were taken into account for the surface. Results showed that the adsorption energies were 4 and 8 kJ/mol, for ab initio restricted Hartree–Fock (RHF) method and density functional Becke–Lee–Yang Parr (B3-LYP) approaches, respectively, when C₂---H₂ bond is located in front of H⁺ atom of H-mordenite surface. The minimum value for the interaction in the adsorption was around 2.25 and 2.50 Å distance from the DFT and ab initio method, respectively. The interaction of isobutane by methyl groups side over the catalytic surface caused a repulsive interaction. Therefore, adsorption of isobutane is a selective process by the H₂ side of the molecule. Calculations were done by employing the 6-31G^** basis set.     

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