Initio Density Functional Theory Study Research Articles

An ab Initio Molecular Dynamics and Density Functional Theory Study of the Formation of Phosphate Chains from Metathiophosphates

The reactions that occur between metathiophosphate (MTP) molecules are identified and examined through ab initio molecular dynamics simulations and static quantum chemical calculations at the density functional level of theory. The simulations show that certain types of MTPs can react to yield phosphate chains, while others only dimerize. These differences are rationalized in terms of reaction energies and the electronic structures of these molecules. In the reaction leading to the formation of phosphate chains, the reactive center, a tri-coordinate phosphorus atom, is continually regenerated. A polymerization mechanism linking MTPs to phosphate chains is developed on the basis of these results. This information sheds light on the underlying processes that may be responsible for the formation of phosphates under high-temperature conditions and may prove useful in the development of protocols for the rational synthesis of complex phosphate structures.

Managing the supercell approximation for charged defects in semiconductors: Finite-size scaling, charge correction factors, the band-gap problem, and theab initiodielectric constant

The errors arising in ab initio density functional theory studies of semiconductor point defects using the supercell approximation are analyzed. It is demonstrated that a) the leading finite size errors are inverse linear and inverse cubic in the supercell size, and b) finite size scaling over a series of supercells gives reliable isolated charged defect formation energies to around +-0.05 eV. The scaled results are used to test three correction methods. The Makov-Payne method is insufficient, but combined with the scaling parameters yields an ab initio dielectric constant of 11.6+-4.1 for InP. Gamma point corrections for defect level dispersion are completely incorrect, even for shallow levels, but re-aligning the total potential in real-space between defect and bulk cells actually corrects the electrostatic defect-defect interaction errors as well. Isolated defect energies to +-0.1 eV are then obtained using a 64 atom supercell, though this does not improve for larger cells. Finally, finite size scaling of known dopant levels shows how to treat the band gap problem: in less than about 200 atom supercells with no corrections, continuing to consider levels into the theoretical conduction band (extended gap) comes closest to experiment. However, for larger cells or when supercell approximation errors are removed, a scissors scheme stretching the theoretical band gap onto the experimental one is in fact correct.

Adsorption and hydrogenation of pyridine and pyrrole on NiMoS: an ab initio density-functional theory study

The adsorption and first-step hydrogenation of pyridine and pyrrole on the Ni-promoted ( 10 1 ¯ 0 ) edge of MoS 2 are studied with the use of periodic density-functional theory calculations under generalized gradient approximation. This study represents the first systematic theoretical investigation of the energetics and reaction pathways of possible reaction mechanisms (Langmuir–Hinshelwood, Eley–Rideal) for the hydrogenation of pyridine and pyrrole on the NiMoS catalyst edge plane. The most stable configuration for adsorbed pyridine on the Ni-edge surface is with the molecular plane perpendicular to the surface through N Ni bonding. Pyrrole preferably interacts with the surface through the bonding of an α-carbon to a nickel site with the molecular plane flat on the surface. For the hydrogenation of pyridine via a Langmuir–Hinshelwood mechanism, the lowest-activation-energy reaction pathway involves hydrogen from adsorbed H 2S; for pyrrole the lowest-activation-energy reaction pathway involves hydrogen from the SH groups at the edge of the MoS 2 (0001) basal plane. Eley–Rideal reaction pathways involving gas-phase pyridine or pyrrole and surface hydrogen species require very low activation energy, and thus the dissociation of hydrogen on the catalyst surface would be the rate-determining step under these reaction conditions.

Correlating the electronic properties and HDN reactivities of organonitrogen compounds: an ab initio DFT study

The electronic structures and properties of representative organonitrogen compounds present in crude oil have been calculated using density-functional theory (DFT) under generalized gradient approximation (GGA). These basic and non-basic organonitrogen compounds have distinct electronic structures and properties that determine their HDN reactivities on hydrotreating catalyst surfaces. The HDN reactivities of cyclohexylamines and piperidines can be correlated to the Mulliken charges on the nitrogen atoms of the organonitrogen molecules, and the hydrogenation activities of aromatic molecules can be correlated to the highest occupied π-orbitals or lowest unoccupied π-orbitals depending on the electronic structure of the catalyst surface. Adjusting electronic structures of hydrotreating catalysts by insightful incorporation of select promoters will change catalyst HDN selectivity for the hydrotreatment of basic and non-basic nitrogen compounds.

Ab initio density functional theory studies on oxygen stabilization at the V 2O 3(0 0 0 1) surface

Geometric and electronic details of the V ′OV and VV ′O terminated V 2O 3(0 0 0 1) surface after oxygen chemisorption are studied theoretically by density-functional theory using large cluster models. Adsorption of oxygen above vanadium centers of the V ′OV terminated surface (O tV ′O termination) results in very strongly bound vanadyl groups removing part of the relaxation of the initial adsorbate-free surface. In addition, it affects the oxygen 2p dominated valence band region of V 2O 3(0 0 0 1) which increases its width by 1.5 eV due to the adsorbate, as shown in partial densities-of-states curves. Oxygen adsorption between vanadium centers of the VV ′O terminated surface is considered for coverages Θ(O b)=1/3 and Θ(O b)=2/3 yielding terminations O bVV ′ and O b 2VV ′. For both coverages the adsorbate stabilizes above the surface and forms V ′–O b–V bridges. As before, the adsorption removes part of the perpendicular relaxation of the topmost layers at the initial VV ′O terminated surface. In addition, the V–O b–V ′ bridges lead to decreased lateral distances between the corresponding V/V ′ centers. As a result, the lateral honeycomb geometry of the combined V/V ′ layers of the VV ′O termination is distorted by adsorbed oxygen where the distortion leads to different surface patterns for the O bVV ′ and O b 2VV ′ termination. The theoretical analysis suggests that only the O b 2VV ′ termination, corresponding to an oxygen coverage Θ(O b)=2/3, is compatible with the geometry obtained from STM images of V 2O 3(0 0 0 1) films on Cu 3Au(0 0 1).

Where do the H atoms reside in PdH x systems?

We present an ab initio density-functional theory study of PdH x systems. We evaluated the total energy of PdH x systems with the H atoms occupying interstitial (octahedral and tetrahedral) sites of a Pd supercell, allowing for the relaxation of the coordinates and supercell dimensions. The majority of our calculations were based on supercells consisting of four Pd atoms, and up to four H atoms, covering the range from x = 0.25 to x = 1. In addition some larger calculations are reported. In order to compare the relative stability of systems at different values of x (at fixed pressure and temperature T = P = 0), we computed the enthalpy of formation ΔH f (x) of the (non)stoichiometric systems. In the regime x = 0 → 1, the ΔH f (x) decrease in a manner indicative of the existence of attractive interactions between the dissolved H atoms. Ideal-solution theory cannot be applied to this system. Furthermore, we find that tetrahedral occupation is favoured over octahedral occupation at high x, leading to the formation of a zincblende structure at x = 1. A preliminary vibrational analysis of normal modes has been performed. Inclusion of vibrational zero-point energies in a harmonic approximation leads us to conclude, tentatively, that the observed stability of octahedral site occupation is due to more favourable zero-point energies of the H atoms in those sites. The results indicate that a proper understanding of this system must take into account the quantum nature of the dissolved hydrogen.

Ab initio modeling of B and N in C29 and C29H24 nanodiamond

An ab initio density functional theory study of the structure and stability of a select group of dopants in a diamond nanocrystal is presented. The dopants studied here are boron and nitrogen. These atoms have been included substitutionally in the center of a 29 atom nanodiamond crystal, and the entire structure relaxed using the Vienna Ab Initio Simulation Package. The relaxed structures are then described by the relaxation energy, the structural (total) energy and a qualitative examination of the overall change in structure and bonding, considered via examination of the electron charge density. It is anticipated that these results will provide a better understanding of the crystal stability of doped nanodiamonds for use in diamondoid nanodevices.

Ab Initio MP2 and DFT Study of the Thermal Syn Elimination Reaction in Ethyl Formate

The thermal elimination reaction that appears in some polycarbonates has been studied by density functional theory (DFT) and ab initio methods of different levels. This work has been focused in the elimination process of ethyl formate, as a good model of this kind of reaction. Different minima and the transition state have been found to characterize the thermal elimination reaction, and the activation energy has been obtained. In this study, we have used different methods to calculate the contribution of the correlation energy; different basis sets were also employed. This will allow us to perform an analysis of the influence of the applied method in the obtained results to study the thermal elimination. The lengthening of the bonds has also been analyzed to shown how concerted the thermal elimination is in the ethyl formate. Three minima have been found for the ethyl formate, two of them are very close and the third is higher in energy. In general, the DFT method with a B3LYP functional gives a less concerted reaction. A nonplanar transition state is predicted by most of the methods used.

Ab initio and hybrid DFT study on the electronic states of fluorenone–Na complexes

Structures and electronic states of a molecular complex formed between fluorenone and sodium atom (denoted by FL–Na) have been investigated by means of ab initio density functional theory (DFT). The most stable structure of FL–Na has a Cs symmetry where the sodium atom is located on the Cs plane perpendicular to the molecular plane of FL where all atoms are located. The sodium atom binds to the carbonyl oxygen of FL and the angle of Na–O–C is calculated to be 157° at the B3LYP/6-311+G(d) level. The charge on the Na atom shows a positive value (∼+0.80), and unpaired electron is delocalized over the FL molecule, indicating that the FL–Na complex exists as an ion-pair state expressed by (CO)δ−(Na)δ+ at the ground state (δ∼+0.80). The proton hyperfine coupling constants and excitation energies calculated at the B3LYP/6-311+G(d) and B3LYP/6-31++G(d,p) levels are in good agreement with previous experiments. The electronic states at the ground and first excited states were discussed.

An Ab Initio Molecular Orbital Theory and Density Functional Theory (DFT) Study of Conformers and Rotamers of 4-Substituted (Methyl, Hydroxymethyl, Methanoyl, Ethanoyl, Cyano, Fluoro, Chloro, Bromo, Acetoxy) Tetrahydro-2H-thiopyran-1,1-dioxides

The structures and energies of axial and equatorial conformers and rotamers of 4-substituted tetrahydro-2H-thiopyran-1,1-dioxides (tetrahydrothiopyran-1,1-dioxides, thiacyclohexane-1,1-dioxides, thiane-1,1-dioxides, and 1,1-dioxothianes; CH3, CH2OH, CHO, COCH3, CN, F, Cl, Br, and OCOCH3) were calculated using the hybrid density functionals B3LYP, B3P86, and B3PW91, as well as MP2 and the 6-31G(d), 6-31G(2d), 6-31G(3d), 6-31G(d,p), and 6-31+G(d) basis sets. MP2/6-31+G(d)/ /HF/6-31+G(d) [−ΔG° = 1.73 kcal/mol], B3P86/6-31G(d) [−ΔG° = 1.75 kcal/mol], and B3PW91/6-31G(d) [−ΔG° = 1.85 kcal/mol] gave conformational free energy (ΔG°) values at 180 K for 4-methyltetrahydro-2H-thiopyran-1,1-dioxide which were similar to the reported experimental values for methylcyclohexane (−ΔG° = 1.80 kcal/mol), 4-methyltetrahydro-2H-thiopyran (−ΔG° = 1.80 kcal/mol), and other 4-methyl-substituted heterocycles. All levels of theory showed that the conformational preferences of the 4-methanoyl (4-formyl), 4-ethanoyl (4-acetyl), and 4-cyano substituents were small. The HF calculations gave conformational free energy (ΔG°) values for 4-chlorotetrahydro-2H-thiopyran-1,1dioxide which were closer to the experimental value than the MP2 and density functional methods. The best agreement with available experimental data for 4-bromotetrahydro-2H-thiopyran-1,1-dioxide was obtained from the HF/6-31G(2d), HF/6-31G(3d), and B3LYP/6-31G(2d) calculations, and, for 4-acetoxytetrahydro-2H-thiopyran-1,1-dioxide, from the HF/6–31G(3d) calculations. The conformational free energies (ΔG°) and relative energies (ΔE) of the conformers and rotamers have been compared with the correspondingly substituted cyclohexanes and tetrahydro-2H-thiopyrans and are discussed in terms of dipole–dipole (electrostatic) interactions and repulsive nonbonded interactions (steric) in the most stable axial and equatorial conformers. The axial S=O bond lengths are shorter than the equatorial S=O bond lengths and the C2–C3 bond lengths in the substituents with carbon-bonded to the ring are shorter than the C3–C4 and C4–C-5 bond lengths. In contrast, the C2–C3 bond lengths in the 4-halogen and 4-acetoxy substituents are longer than the C3–C4 and C4–C-5 bond lengths.

Alpha- and 3(10)-helix interconversion: a quantum-chemical study on polyalanine systems in the gas phase and in aqueous solvent.

Helices are among the predominant secondary structures in globular proteins. About 90% of the residues in them are found to be in the alpha-helical conformation, and another 10% in the 3(10) conformation. There is a standing controversy between experimental and some theoretical results, and controversy among theoretical results concerning the predominance of each conformation, in particular, helices. We address this controversy by ab initio Hartree-Fock and density functional theory studies of helices with different lengths in a vacuum and in the aqueous phase. Our results show that (1) in a vacuum, all oligo(Ala) helices of 4-10 residues adopt the 3(10) - conformation; (2) in aqueous solution, the 6-10 residue peptides adopt the alpha-helical conformation; (3) there might be two intermediates between these helical conformers allowing for their interconversion. The relevance of these results to the structure and folding of proteins is discussed.

Highlevel ab initio and hybrid density functional theory study of the energy profile for the 1CO+2CO+ reaction

Two complete basis set and three hybrid density functional computational studies were applied in the exploration of the 1CO+2CO+ reaction potential energy surface. One molecular carbon monoxide–carbon monoxide cation molecular associate was elucidated as the structure with the lowest energy on the potential energy surface. Ionization energies, bond dissociation energies, and enthalpies of formation for every di and tri-atomic molecule on the potential energy surface were estimated with the two complete basis sets and the three hybrid density functional theory methods. Six different endothermic channels for the 1CO+2CO+ reaction were evaluated with ab initio and DFT methods. The computed energies and structural parameters are compared with experimental values where available. Some new energies for this reaction system were suggested.

Density Functional Studies of Molecular Polarizabilities. 10. Fulvenes and Fulvalenes

We report accurate Ab Initio Hartree Fock (HF) and Density Functional Theory (DFT) studies of the static dipole polarizabilities and first hyperpolarizabilities of the [n] fulvene and the [n,m] fulvalene series of molecules (with n, m = 3,5,7). Calculations are also reported for the parent cycloalkenes: cyclopropene, cyclopentadiene and cycloheptatriene (1-3 respectively). Geometries were optimized at the HF/6-311G(3d,2p) level of theory. All the fulvenes (4-6) and the smaller fulvalenes (7, 9 and 10) are found to be planar. Pentaheptafulvalene (11) is slightly non-planar whilst heptafulvalene (12) has a folded C2h structure. Calculated C-C bond lengths are consistently smaller than the experimental values. Dipole polarizabilities and non-zero hyperpolarizabilities were calculated at the HF/6-311++G(3d,2p) and BLYP/6-311++G(3d,2p) levels of theory, using HF/6-311G(3d,2p) geometries. Dipole polarizabilities correlate well with those given on the basis of atom additivity. Molecules (8), (9) and (11) show very large dipole hyperpolarizabilities.

An ab initio molecular orbital theory and density functional theory study of the conformational free energies of methyltetrahydro-2H-thiopyrans

Ab initio Hartree–Fock calculations using the 6-31G(d), 6-31G(2d), 6-31G(d,p), 6-311G(d,p), 6-31+G(d), and 6-311+G(d,p) basis sets, second-order Møller–Plesset perturbation theory (MP2) using the same basis sets, and density functional theory [SVWN/DN ∗, SVWN/DN ∗∗, pBP/DN ∗, pBP/DN ∗∗, BLYP/6–31G(d), B3BLYP/6–31G(d)] were used to calculate the geometry optimized structure of tetrahydro-2 H-thiopyran (tetrahydrothiopyran, thiacyclohexane, thiane) and the conformational enthalpy (Δ H°), entropy (Δ S°), and free energy (Δ G°) of the chair conformers of methylcyclohexane and 2-methyl-, 3-methyl-, and 4-methyltetrahydro-2 H-thiopyran. The DFT methods generally overestimate the conformational free energies (−Δ G°) while some of the MP2 methods give values closer to the experimental results. The MP2/6-311G(d,p) calculated value (− ΔG°=1.46 kcal/mol) for 2-methyltetrahydro-2 H-thiopyran is in excellent agreement with the experimentally reported value and the MP2/6-21G(2d) calculated value (− ΔG°=1.46 kcal/mol) for 3-methyltetrahydro-2 H-thiopyran is also in excellent agreement with the experimentally reported value. The equatorial preference of the methyl group is discussed in terms of the repulsive nonbonded interactions in the equatorial conformer, gauche butane (torsional) interactions in the axial conformer, and repulsive nonbonded interactions of the axial methyl group with the ring carbons and hydrogens.

Theoretical study of structural properties, infrared spectra, and energetic properties of C 4H 4 isomers

A high level of ab initio and several density functional theory studies were performed with the target being to elucidate structural, spectroscopic, and energetic properties of triafulvene, cyclobutadiene, and tetrahedrane as three C 4H 4 isomers. For triafulvene all of the experimental values are available, but for cyclobutadiene only the IR spectra is known, while for tetrahedrane none of these physical values have been estimated experimentally. An excellent agreement between the computed and the experimental values were obtained where data are available, which makes it confident that the computed data should be very accurate. New structural data, IR spectra, and enthalpies of formation for both cyclobutadiene and tetrahedrane are offered.

Ab Initio Study of Magnetic Structure and Chemical Reactivity of Cr2O3 and Its (0001) Surface

We present the first ab initio density functional theory study of the oxygen-terminated Cr2O3 (0001) surface within the local spin-density approximation (LSDA). We find that spin plays a critical role for even the most basic properties of Cr2O3, such as the structure and mechanical response of the bulk material. The surface exhibits strong relaxations and changes in electronic and magnetic structure with important implications for the chemical reactivity and unusual spin-dependent catalytic activity of the surface. Unlike the bulk, the outermost chromium bilayer is ferromagnetically ordered, and the surface oxygen layer exhibits appreciable net spin polarization in the opposite sense. Surprisingly, despite this ferrimagnetic order, the chemically important states near the Fermi level exhibit ferromagnetic order and thus favor electronic spin alignment of species interacting with the surface. Finally, we also find a high density of unoccupied electronic surface states available to participate in the chemic...

Ab Initio MO and Density Functional Theory Study of Substituent Effects on Electron Attachment to Benzyl Chlorides

Reductive cleavage of para-substituted benzyl chlorides 4-Y−C6H4CH2Cl (Y = NH2, MeO, Me, H, F, Cl, CF3, NO2) (1) and of C6F5CH2Cl (2) has been studied by MP2 and DFT methods. In contrast to the MP2 calculations, DFT calculations reveal the formation of radical anions from benzyl chlorides including those bearing donor substituents. The calculations also show the possibility of the formation of complexes of benzyl radicals with the chloride anion along the path of the reductive cleavage.

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 (H 2O, CH 4, CH 3OH, and C 6H 6) and open-shell (CH 3 and C 2H 3) 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 H 2O, CH 3OH, C 6H 6, CH 3, and C 2H 3, 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 Density Functional Theory Study of the Structure and Vibrational Spectra of Cyclohexanone and its Isotopomers

We report ab initio density functional theory (DFT) calculations of the structure of cyclohexanone (1) in its chair conformation and of the unpolarized vibrational absorption (IR) spectra of four isotopomers of 1 (d0, d4, d6, and d10). DFT calculations use hybrid functionals, B3PW91 and B3LYP, and the TZ2P basis set. The results are compared to the electron diffraction (ED) structure of Dillen and Geise and liquid-phase IR spectra. Calculated and experimental structures are in reasonable agreement; however, the constraints imposed on the ED structure determination limit its accuracy. In the mid-IR (<2000 cm-1), predicted vibrational spectra are in excellent agreement with experiment, permitting an essentially unambiguous assignment of all fundamentals; in the C−H and C−D stretching regions, agreement is worse due to anharmonicity/Fermi resonance and the spectra cannot be unambiguously assigned. Our assignments differ substantially from earlier assignments of Fuhrer et al., based on a constrained valence force field. Vibrational circular dichroism (VCD) spectra of d1 and d2 isotopomers have been reported for C−H and C−D stretching regions. Predicted spectra are in poor agreement with experiment, a result again attributable to anharmonicity.

Computational studies of interstellar silicon–nitrogen molecular species

Ab initio and hybrid density functional theory (DFT) studies were performed in order to determine the stability of small silicon–nitrogen compounds. Results obtained with the highest level of ab initio studies currently available (the quadratic complete basis set, CBSQ) were used as a reference to compare results generated with other ab initio and DFT computational studies. The isomerization barriers, ionization potentials, electron affinities, and proton affinities for some of these molecular systems were computed. The values computed with CBSQ and hybrid DFT methods were in good agreement with each other. This suggests that these molecular species are more stable when hydrogen is attached to nitrogen which is contrary to carbon analogs which prefer hydrogen bound to the carbon atom. A comparison between DFT and high level ab initio values was used to determine the accuracy of DFT methods to evaluate silicon–nitrogen compounds.