A density functional theory study on pelargonidin

A complete conformational analysis on the isolated and polarizable continuum model (PCM) modeled aqueous solution cation, quinonoidal, and anion forms of pelargonidin, comprising the diverse tautomers of the latter forms, was carried out at the B3LYP/6-31++G(d,p) level. The results indicate that the most stable conformer of cationic and quinonoidal forms of pelargonidin are completely planar in the gas phase, whereas that of the anionic form is not planar. In contrast, PCM calculations show that the plane of the B ring is slightly rotated with regard to the AC bicycle in the most stable conformer of the cation and quinonoidal form. The most stable conformers of the cation, both in gas phase and aqueous solution, display anti and syn orientations for, respectively, C2-C3-O-H and C6-C5-O-H dihedral angles, whereas syn and anti orientation of hydroxyls at 7 and 4' positions are nearly isoenergetic. The most stable tautomer of quinonoidal pelargonidin is obtained by deprotonating hydroxyl at C5 in gas phase but at C7 according to PCM. Also, the most stable tautomer of the anion is different in gas phase (hydrogens are abstracted from hydroxyls at C5 and C4') and PCM simulation (C3 and C5). Tautomeric equilibria affect substantially the geometries of the AC-B backbone providing bond length variations that basically agree with the predictions of the resonance model. Most of the conformers obtained display an intramolecular hydrogen bond between O3 and H6'. Nevertheless, this interaction is not present in the most stable anions. Ionization potentials and O-H bond dissociation energies computed for the most stable conformers of cation, quinonoidal, and anion forms are consistent with an important antioxidant activity.     

Characterization of the high-pressure structures and phase transformations in SnO2. A density functional theory study

Theoretical investigations concerning the high-pressure polymorphs, the equations of state, and the phase transitions of SnO2 have been performed using density functional theory at the B3LYP level. Total energy calculations and geometry optimizations have been carried out for all phases involved, and the following sequence of structural transitions from the rutile-type (P42/mnm) driven by pressure has been obtained (the transition pressure is in parentheses): --> CaCl2-type, Pnnm (12 GPa) --> alpha-PbO2-type, Pbcn (17 GPa) --> pyrite-type, Pa (17 GPa) --> ZrO2-type orthorhombic phase I, Pbca (18 GPa) --> fluorite-type, Fmm (24 GPa) --> cotunnite-type orthorhombic phase II, Pnam (33 GPa). The highest bulk modulus values, calculated by fitting pressure-volume data to the second-order Birch-Murnaghan equation of state, correspond to the cubic pyrite and the fluorite-type phases with values of 293 and 322 GPa, respectively.     

Silabutadienes. Internal rotations and pi-conjugation. A density functional theory study

The potential energy surfaces (PESs) for internal rotation around the central single bond of nine silabutadienes, which include all possible mono-, di-, tri-, and tetrasilabutadienes, are investigated computationally by using DFT with the B3LYP functional and the 6-311+G(d,p) basis set. For 1-silabutadiene (3), 2-silabutadiene (4), 1,4-disilabutadiene (5), 2,3-disilabutadiene (6), and 1,3-disilabutadiene (7), the s-trans rotamer is the most stable. For 1,2-disilabutadiene (8), 1,2,3-trisilabutadiene (9), and 1,2,4-trisilabutadiene (10), all having a trans-bent SiSi double bond, the most stable conformers are those having an antiperiplanar (ap) structure. For tetrasilabutadiene (11), the global minimum is the gauche rotamer. The internal rotation barriers (RB) (relative to the global minimum) follow the order (kcal/mol) 5 (10.0) > 3 (7.4) > 1,3-butadiene (12, (6.6)) > 10 (4.9) > or = 7 (4.4) > or = 4 (4.0) approximately = 8 (3.9) > 9 (2.7) approximately = 6 (2.6) > 11 (2.4). The barriers are slightly smaller at CCSD(T)/cc-PVTZ, but the trend remains the same. The size of the rotation barrier is mainly dictated by the length of the central single bond; that is, it is the largest for dienes with the shorter C-C central bond (5, 3, and 12), and it is smaller for dienes with the longer Si-C and Si-Si central bonds. The strength of pi-conjugation in the s-trans conformers of silabutadienes was estimated by resonance stabilization energies (RE) calculated by using the Natural Bond Orbital (NBO) and Block Localized Wave function (BLW) methods and bond separation equations. A linear correlation is found between the barrier heights for internal rotation and pi-conjugation energies. The calculated RBs are significantly smaller than the corresponding REs, indicating that pi-resonance energies are not the only factor that dictate the RB, and therefore, RBs, although suitable for estimating trends in pi-conjugation in a series of compounds, cannot be used for estimating absolute resonance energies.     

Gas-phase acidity of D-glucose. A density functional theory study

The gas-phase acidity of D-glucopyranose was studied by means of B3LYP calculations combined with 6-31G(d,p) or 6-31+G(d,p) standard basis sets. For each anomer, deprotonation of the various primary and secondary hydroxyl groups was considered. As in solution, the anomeric hydroxyl is found to be the most acidic for both anomers, but only when the 6-31+G(d,p) basis set is used for geometry optimization. Deprotonation of the anomeric hydroxyl induces an important C(1)--O endocyclic bond elongation and subsequently promotes an energetically favored ring-opening process as attested by the very small calculated activation barriers. The results also suggest that interconversion between the various deprotonated alpha- and beta-anomers may easily occur under slightly energetic conditions. B3LYP/6-311+G(2df,2p) calculations led to the an absolute gas-phase acidity of deltaacidGo(298)(alpha-D-glucose) = 1398 kJ mol(-1). This estimate matches well the only experimental value available to date. Finally, this study again confirms that the use of diffuse functions on heavy atoms is necessary to describe anionic systems properly and to achieve good relative and absolute gas-phase acidities.     

A density functional theory study of sulfur poisoning

Density functional theory calculations have been used to investigate the chemisorption of H, S, SH, and H(2)S as well as the hydrogenation reactions S+H and SH+H on a Rh surface with steps, Rh(211), aiming to explain sulfur poisoning effect. In the S hydrogenation from S to H(2)S, the transition state of the first step S+H-->SH is reached when the S moves to the step-bridge and H is on the off-top site. In the second step, SH+H-->H(2)S, the transition state is reached when SH moves to the top site and H is close to another top site nearby. Our results show that it is difficult to hydrogenate S and they poison defects such as steps. In order to address why S is poisoning, hydrogenation of C, N, and O on Rh(211) has also been calculated and has been found that the reverse and forward reactions possess similar barriers in contrast to the S hydrogenation. The physical origin of these differences has been analyzed and discussed.     

Raman spectroscopic investigations of pressure-induced phase transitions in n-hexane

We report high-pressure Raman studies on n-hexane up to 16 GPa. n-Hexane undergoes solid-solid transition around 9.1 GPa along with an already reported liquid-solid transition around 1.4 GPa. The intensity ratio of the Raman modes relating the all-trans conformation (1147 and 2872 cm-1) to that of the gauche conformation (1074 and 2923 cm-1) shows a sudden change across 9.1 GPa, suggesting an increase in the all-trans population conformers above 9.1 GPa. The disappearance of the torsional modes suggests a steric hindrance to the methyl end group, similar to the n-heptane case, suggesting that the high-pressure phase (above 9.1 GPa) is an orientationally disordered phase. In general, the transition pressure for the solid-solid transition is inversely proportional to the length of the carbon backbone in the medium chain length n-alkanes.     

The cluster Ir4 and its interaction with a hydrogen impurity. A density functional study

To contribute to the understanding of how iridium particles act as catalysts for hydrogenation and dehydrogenation of hydrocarbons, we have determined structures and binding energies of various isomers of Ir(4) as well as HIr(4) on the basis of relativistic density functional theory. The most stable isomer of Ir(4) showed a square planar structure with eight unpaired electrons. The tetrahedral structure, experimentally suggested for supported species, was calculated 49 kJ mol(-1) less stable. Hydrogen coordinates preferentially to a single Ir center of the planar cluster with a binding energy of up to 88 kJ mol(-1) with respect to the atom in the H(2) molecule. Terminal interaction of hydrogen with an Ir(4) tetrahedron causes the cluster to open to a butterfly structure. We calculated terminal binding of hydrogen at different Ir(4) isomers to be more stable than bridge coordination, at variance with earlier studies.     

Density functional theory study of the brookite surfaces and phase transitions between natural titania polymorphs

The present study is concerned with the structural and electronic properties of the low-index surfaces of the brookite form of titanium dioxide. A theoretical investigation is carried out using the density functional formalism under the nonlocal B3LYP approximation to calculate surface energies, band energy values, and to interpret the response to hydrostatic pressure of the bulk and surfaces of the brookite structure. In addition, phase transformations with pressure are predicted from the anatase and the rutile to the brookite polymorph at about 3.8 and 6.2 GPa, respectively. The orthorhombic structure and the fractional coordinates of brookite vary isotropically with the rise in pressure. The calculated band gap energy is 3.78 eV for the bulk brookite. The brookite surface stabilities follow the sequence (010) < (110) < (100), and the minimum gap energy value is found for the (110) surface.     

A density functional theory study of the benzene-water complex

The intermolecular interaction of the benzene-water complex is calculated using real-space pseudopotential density functional theory utilizing a van der Waals density functional. Our results for the intermolecular potential energy surface clearly show a stable configuration with the water molecule standing above or below the benzene with one or both of the H atoms pointing toward the benzene plane, as predicted by previous studies. However, when the water molecule is pulled outside the perimeter of the ring, the configuration of the complex becomes unstable, with the water molecule attaching in a saddle point configuration to the rim of the benzene with its O atom adjacent to a benzene H. We find that this structural change is connected to a change in interaction from H (water)/pi cloud (benzene) to O (water)/H (benzene). We compare our results for the ground-state structure with results from experiments and quantum-chemical calculations.     

A density functional theory study on acetylene-functionalized BN nanotubes

Covalent functionalization of a zigzag boron nitride nanotube (BNNT) with acetylene has been investigated by density functional theory in terms of energetic, geometric, and electronic properties. It has been found that the most stable functionalized BNNT is the one in which the acetylene is diffused into the tube wall so that two heptagonal and two pentagonal rings are formed, releasing energy of 1.54 eV. In addition, the effect of substituting the hydrogen atoms of C₂H₂ by different functional groups including –F, –CH₂F, –CN, and –OCH₃ on the geometric and electronic properties of the BNNT has been investigated. The reaction energies are found to be in the range of ?1.03 to ?3.13 eV so that their relative magnitude order is as follows: C₂F₂ > (OCH₃)₂C₂ > C₂H₂ > (CH₂F)₂C₂ > (CN)₂C₂, suggesting that the functionalization energy is increased by increasing the electron donating character of the functional groups. Overall, chemical modification of BNNT by the studied groups results in little changes in electronic properties of the tube and may be an effective way for the purification of BNNTs.     

Charge-transfer transitions in triarylamine mixed-valence systems: a joint density functional theory and vibronic coupling study

A theoretical model is developed to describe the intramolecular transfer in organic mixed-valence systems. It is applied to rationalize the intervalence charge-transfer transitions in triarylamine mixed-valence compounds. The electronic coupling parameter is evaluated at the density functional theory (DFT) and time-dependent density functional theory (TD-DFT) levels. The shapes of the charge-transfer absorption bands are analyzed in the framework of a dynamic vibronic model. The influence on the optical properties of diagonal and nondiagonal vibronic couplings is discussed. Our results are compared to recent experimental data.     

A characterization study on 2,6-dimethyl-4-nitropyridine N-oxide by density functional theory calculations

This study deals with the identification of a title compound, 2,6-dimethyl-4-nitropyridine N-oxide by means of theoretical calculations. The optimized molecular structures, vibrational frequencies, corresponding vibrational assignments, thermodynamic properties and atomic charges of the title compound in the ground state were evaluated using density functional theory (DFT) with the standard B3LYP/6-311G(d,p) method and basis set combination for the first time. Theoretical vibrational spectra were interpreted with the aid of normal coordinate analysis based on scaled density functional force field. The results show that the optimized geometric parameters (bond lengths and bond angles) and vibrational frequencies were observed to be in good agreement with the available experimental results. Based on the results of comparison between experimental results and theoretical data, the chosen calculation level is powerful approach for understanding the molecular structures and vibrational spectra of the 2,6-dimethyl-4-nitropyridine N-oxide. Moreover, we not only simulated frontier molecular orbitals (FMO) and molecular electrostatic potential (MEP) but also determined the transition state and energy band gap. Based on the investigations, the title compound is found to be useful to bond metallically and interact intermolecularly. Infrared intensities and Raman activities were also reported.     

Pressure-driven phase transitions in NaBH4: theory and experiments

We have investigated pressure-induced structural transitions in NaBH4 through density-functional theory calculations combined with X-ray and neutron diffraction experiments. Our calculations confirm that the cubic phase is stable up to 5.4 GPa and an orthorhombic phase occurs above 8.9 GPa, as observed in X-ray diffraction experiments. Both the calculations and X-ray diffraction measurements identify an intermediate tetragonal phase that appears between 6 and 8 GPa; that is, between the cubic and orthorhombic phases. This result is also confirmed by high-pressure neutron diffraction experiments performed on NaBD4. Our calculations and X-ray diffraction measurements show that the space group of the orthorhombic phase above 8.9 GPa is Pnma and the orthorhombic phase remains stable up to 30 GPa. The calculated equations of state are in excellent agreement with experiments.     

Methane activation on Pt and Pt4: a density functional theory study

The activation mechanisms of a methane molecule on a Pt atom (CH4-Pt) and on a Pt tetramer (CH4-Pt4) were investigated using density functional theory (B3LYP and PW91) calculations. The results from these two functionals are different mostly in predicting the reaction barrier, in particular for the CH4-Pt system. A new lower energy pathway was identified for the CH4 dehydrogenation on a Pt atom. In the new pathway, the PtCH2 + H2 products were formed via a transition state, in which the Pt atom forms a complex with carbene and both dissociated hydrogen atoms. We report here the first theoretical study of methane activation on a Pt4 cluster. Among the five single steps toward dehydrogenation, our results show that the rate-limiting step is the third step, that is, breaking the second C-H bond, which requires overcoming an energy barrier of 28 kcal/mol. On the other hand, the cleavage of the first C-H bond, that is, the first reaction step, requires overcoming an energy barrier of 4 kcal/mol.     

A density functional theory study of interaction between formamide and guanine

Hydrogen bonding in complexes formed between formamide and guanine molecules was completely investigated using density functional theory (DFT) at the 6-311++G(d, p) level. For comparison, the HF and MP2 methods were also used. Nine stable cyclic structures stabilized by two hydrogen bonds were found. One of these was a six-membered ring, five were seven-membered rings, and the others were eight-membered rings. The eight-membered ring is preferable to the seven-and six-membered ones as follows from H-bond lengths and interaction energies. The FG4 structure was calculated to be the most stable, and another cyclic structure, FG5, was least stable because of the six-membered ring and the weakest interaction. The infrared spectrum frequencies, intensities, and vibrational frequency shifts are also reported. The text was submitted by the authors in English.     

A density functional study of a twisted nematic cell and its relation to the Frank-Oseen theory

The numerical results for the twist angle profile xi(z) across a slab-shaped nematic cell obtained from a density functional theory (DFT) are compared to the predictions of the macroscopic Frank-Oseen theory. The latter theory predicts that xi"(z)=0, and this is also seen to be the case for the DFT results. These do, however, verify the Frank-Oseen relation, lambda+/-W+/-=K2, between the de Gennes extrapolation length (lambda+/-), the anchoring energy per unit area of the (+/-) cell wall (W+/-), and the elastic constant of the nematic for twist deformations (K2), only if W+/- is nonlinearly related to the amplitude of the anchoring term of the DFT.     

Photosensitization mechanisms of triplet excited state beta-lapachone. A density functional theory study

Beta-Lapachone is a natural product with multiple pharmacological activities and mechanistic studies indicated that reactive oxygen species (ROS) generated by beta-lapachone play significant roles in its pharmacological actions. As photosensitization is an important ROS-generating pathway, in the present work, the photosensitization mechanisms of beta-lapachone are explored on the basis of density functional theory estimated triplet excited state characters. Starting from triplet excited state beta-lapachone, the possible generating pathways of 1O2 and O2*- are elucidated and the solvent effects on the photosensitizing reactions are also discussed.     

A density functional theory study of copper-catalyzed aziridination of olefins

Density functional theory calculations are reported for the reaction mechanism of selected XCuNHX(X = Cl, Br, I) with olefins to form three-membered ring products. The copper reagents react with olefins via an asynchronous attack on one CH₂ group of ethylene with a relatively low barrier (<78 kJ/mol). These computational results are in good agreement with experimental results, and this suggests that the nitrene transfer process is favored. The BrCuNHBr is found to be the most reactive reagent in the XCuNHX (X = Cl, Br, I) series of reagents. These results are qualitatively consistent with the agreement between copper-catalyzed species character and experimental conditions needed for efficient reaction.     

Electronic transitions involved in the absorption spectrum and dual luminescence of tetranuclear cubane [Cu4I4(pyridine)4] cluster: a density functional theory/time-dependent density functional theory investigation

We present a combined density functional theory (DFT)/time-dependent density functional theory (TDDFT) study of the geometry, electronic structure, and absorption and emission properties of the tetranuclear "cubane" Cu4I4py4 (py = pyridine) system. The geometry of the singlet ground state and of the two lowest triplet states of the title complex were optimized, followed by TDDFT excited-state calculations. This procedure allowed us to characterize the nature of the excited states involved in the absorption spectrum and those responsible for the dual emission bands observed for this complex. In agreement with earlier experimental proposals, we find that while in absorption the halide-to-pyridine charge-transfer excited state (XLCT*) has a lower energy than the cluster-centered excited state (CC*), a strong geometrical relaxation on the triplet cluster-centered state surface leads to a reverse order of the excited states in emission.     

A density functional theory (DFT) and time-dependent density functional theory (TDDFT) study on optical transitions in oligo(p-phenylenevinylene)-fullerene dyads and the applicability to resonant energy transfer

The optical transitions of three different size oligo(p-phenylenevinylene)-fullerene dyads (OPV(n)-MPC(60); n = 2-4) and of the corresponding separate molecules are studied using density functional theory (DFT) and time-dependent density functional theory. The DFT is used to determine the geometries and the electronic structures of the ground states. Transition energies and excited-state structures are obtained from the TDDFT calculations. Resonant energy transfer from OPV(n) to MPC(60) is also studied and the Fermi golden rule is used, along with two simple models to describe the electronic coupling to calculate the energy transfer rates. The hybrid-type PBE0 functional is used with a split-valence basis set augmented with a polarization function (SV(P)) in calculations and the calculated results are compared to the corresponding experimental results. The calculated PBE0 spectra of the OPV(n)-MPC(60) dyads correspond to the experimental spectra very well and are approximately sums of the absorption spectra of the separate OPV(n) and MPC(60) molecules. Also, the absorption energies of OPV(n) and MPC(60) and the emission energies of OPV(n) are predicted well with the PBE0 functional. The PBE0 calculated resonant energy transfer rates are in a good agreement with the experimental rates and show the existence of many possible pathways for energy transfer from the first excited singlet states of the OPV(n) molecules to the MPC(60) molecule.