Infrared characterization of hydroxyl groups on MgO: a periodic and cluster density functional theory study

The infrared OH stretching frequencies of the various types of hydroxyl groups on MgO surfaces have been calculated by periodic (VASP) and cluster (Gaussian) DFT simulations. Surface irregularities (mono and diatomic steps, corners, step divacancies, and kinks) have been considered to model the IR spectra of hydroxylated MgO powders. A good correspondence between calculated and experimental frequencies is obtained with the B3LYP functional. Hydrogen-bonding is the parameter which influences most the IR frequency of OH groups, followed by location of OH groups in concave or convex areas of the surface and then oxygen coordination. The evolution of experimental IR spectra upon evacuation at increasing temperature can be rationalized on the basis of calculated thermal stabilities of each kind of OH groups. A new model is finally proposed to help assign the experimental bands, in terms of hydrogen-bonding, local topology of the hydroxylated sites, and coordination of oxygen.     

Conformational studies of Zn-Ligand-Hexose diastereomers using ion mobility measurements and density functional theory calculations

Ion mobility studies and density functional theory calculations were used to study the structures of [Zn/diethylenetriamine/Hexose/Cl]+ complexes in an effort to probe differences in the three-dimensional conformations. This information allows us to gain insight into the structure of these complexes before collisional activation, which is the first step in understanding the stereoselective dissociations observed under collisionally activated conditions. The collision cross sections obtained from the ion mobility measurements showed that the mannose structure is more compact than the galactose and glucose complexes, respectively. Using density functional theory, candidate structures for each of the experimentally observed complexes were generated. Two criteria were used to determine the most likely structures of these complexes before activation: (1) The allowed relative energies of the molecules (between 0-90 kJ/mol) and (2) collision cross section agreement (within 2%) between the theoretically determined structures and the experimentally determined cross section. It was found that the identity of the monosaccharide made a difference in the overall conformation of the metal-ligand-monosaccharide complex. For glucose and galactose, metal coordination to O(6) was found to be favorable, with the monosaccharide occupying the 4C1 chair conformation, while for mannose, O(2) metal coordination was found with the monosaccharide in a B3,0 conformation. Coordination numbers varied between four and six for the Zn(II) metal centers. Given these results, it appears that the stereochemistry of the monosaccharide influences the conformation and metal coordination sites of the Zn(II)/monosaccharide/dien complex. These differences may influence the dissociation products observed under collisionally activated conditions.     

Spectral analysis of acetylcholine halides by density functional theory calculations

The optimized molecular structures, vibrational frequencies and ¹H and ¹³C NMR chemical shifts of acetylcholine halides (F, Cl, and Br) have been investigated using density functional theory (B3LYP) method with 6-311G(d) basis set. The comparison of their experimental and calculated IR, R and NMR spectra of the compounds has indicated that the spectra of three optimized minimum energy conformers can simultaneously exist in one experimental spectrum. Thus, it was concluded that the compounds simultaneously exist in three conformations in the ground state. The calculated optimized geometric parameters (bond lengths and bond angles), vibrational frequencies and NMR chemical shifts for the minimum energy conformers were seen to be in a good agreement with the corresponding experimental data. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program.     

Doping of polyaniline by acid-base chemistry: density functional calculations with periodic boundary conditions

Calculations with Gaussian orbitals and periodic boundary conditions using several density functionals are carried out to study the proton-doping of polyaniline. We explore previously proposed mechanisms to explain the spectacular increase of the electrical conductivity of polyaniline upon protonation. The structural and spectroscopic theoretical predictions for both polaron and bipolaron lattices agree quite well with the experimental data, and we find that the bipolaron structure is lower in energy.     

Adsorption and dissociation of methanol on Au(1 1 1) surface: A first-principles periodic density functional study

The adsorption and dissociation of methanol on Au(111) surface were studied using the first-principles calculations based on density functional theory (DFT) with the generalized gradient approximation (GGA). Adsorption energies, geometric structures, Mulliken charges population, and vibrational frequencies of the various intermediates were computed from full-geometry optimization with a three-layer slab model. The most stable adsorption modes of the species, i.e. CH₃OH, CH₃O, and HCHO were considered in calculation. The possible decomposition pathways were investigated with transition state search methods. The results indicate that methoxyl radical is likely the decomposition intermediate.     

Nonlocal density functional calculations of the jellium metal surface

The Becke exchange functional is used for calculation of properties of the jellium model using the slab geometry inside a box with the infinite potential barriers at the boundaries. We simplify semianalytical representation of matrix elements. We calculate the surface energies and work functions with self-consistent electron densities. For all densities (here, we give results in erg/cm² for r_s = 2.07 bohr, in comparison with the LSD approximation (?602)) and the uncorrected Pw GGA -II (?730), the Becke-II exchange only (?1212), and the Becke-II exchange with Perdew86 correlation (?830) [always close to Pw GGA -I (?814)] give smaller surface energies. The most important factor determining values of surface energies from different GGAS seems to be a form of a correlation potential. We also calculate the effect of finite slab thickness and the vacuum region thickness on the surface energy at the LSD level and indicate its importance in various jellium model calculations. © 1995 John Wiley & Sons, Inc.     

Dissociation of sulfur oxoacids by two water molecules studied using ab initio and density functional theory calculations

Using ab initio [SCS‐MP2 and CCSD(T)] and density functional theory (M062X) calculations, we have studied the geometries and energies of sulfur oxoacids H₂S_mO₆ (m = 2–4) and their monohydrated and dihydrated clusters. When including the results from previously reported disulfuric acid (H₂S₂O₇) cases, the gas phase acidity is ordered as H₂S₂O₆ < H₂S₃O₆ < H₂S₂O₇ < H₂S₄O₆. The intramolecular H‐bonding, which may indicate the degree of structural flexibility in this molecular series, is an important factor for the order of the gas phase acidity. All these sulfur oxoacids show dissociated (or deprotonated) geometries with only two water molecules, although the energies of the dissociated conformers are ranked differently. All of the dissociated conformers form a unique H‐bonding network structure in which the protonated first water (H₃O⁺) is triply H‐bonded to each oxygen atom of two SO₃ moieties as well as the second water, which in turn is H‐bonded to a SO₃ moiety. H₂S₃O₆ has the best molecular flexibility for adopting such an H‐bonding network structure, and thereby all the low‐lying conformers of H₂S₃O₆(H₂O)₂ are dissociated. In contrast, the least flexible H₂S₂O₆ forms such a structure with a high strain, and dissociation of H₂S₂O₆(H₂O)₂ is found from the third lowest conformer. Although the gas phase acidity of H₂S₄O₆ is the highest in this series, the lowest dissociated conformer and the lowest undissociated conformer of H₂S₄O₆(H₂O)₂ are very close in energy. This is because forming the H‐bonding network structure is somewhat difficult due to the large distance between the two SO₃ moieties.     

Theoretical investigations of the equol molecule: semi-empirical and density functional theory calculations

The structural and electronic properties of the equol molecule, an estrogenic isoflavone, have been investigated theoretically by performing semi-empirical self-consistent field molecular orbital and density functional theory calculations. The geometry of the system has been optimized at the level of AM1 method and the electronic properties have been calculated at the level of B3LYP functional.     

Infrared spectroscopic and density functional theory studies on the CO dissociation by scandium and yttrium dimers

Reactions of laser-ablated scandium and yttrium atoms with dilute carbon monoxide molecules in solid argon have been investigated using matrix-isolation infrared spectroscopy. On the basis of the results of the isotopic substitution, the change of laser power and CO concentration and the comparison with density functional theory (DFT) calculations, the absorption at 1193.4 cm(-1) is assigned to the C-O stretching vibration of the Sc(2)[eta(2)(mu(2)-C,O)] molecule, which has a single bridging CO that is tilted to the side. This CO-activated molecule undergoes ultraviolet-visible photoinduced rearrangement to the CO-dissociated molecule, c-Sc(2)(mu-C)(mu-O). The cyclic c-Sc(2)(mu-C)(mu-O) molecule has a bridging carbon on one side of the Sc(2) unit and a bridging oxygen on the other. The analogous Y(2)[eta(2)(mu(2)-C,O)] molecule has not been observed, but the CO-dissociated c-Y(2)(mu-C)(muO) molecule has been observed in the Y + CO experiments. DFT calculations of the geometry structures, vibrational frequencies, and IR intensities strongly support the assignments. The CO activation mechanism has also been discussed. Our experimental and theoretical results schematically depict an activation process to CO dissociation.     

H2S splitting on Cu(110): Insight from combined periodic density functional theory calculations and microkinetic simulation

Practical copper (Cu)‐based catalysts for the water–gas shift (WGS) reaction was long believed to expose a large proportion of Cu(110) planes. In this work, as an important first step toward addressing sulfur poisoning of these catalysts, the detailed mechanism for the splitting of hydrogen sulfide (H₂S) on the open Cu(110) facet has been investigated in the framework of periodic, self‐consistent density functional theory (DFT‐GGA). The microkinetic model based on the first‐principles calculations has also been developed to quantitatively evaluate the two considered decomposition routes for yielding surface atomic sulfur (S*): (1) H₂S → H₂S* → SH* → S* and (2) 2H₂S → 2H₂S* → 2SH* → S* + H₂S* → S* + H₂S. The first pathway proceeding through unimolecular SH* dissociation was identified to be feasible, whereas the second pathway involving bimolecular SH* disproportionation made no contribution to S* formation. The molecular adsorption of H₂S is the slowest elementary step of its full decomposition, being related with the large entropy term of the gas‐phase reactant under realistic reaction conditions. A comparison of thermodynamic and kinetic reactivity between the substrate and the close‐packed Cu(111) surface further shows that a loosely packed facet can promote the S* formation from H₂S on Cu, thus revealing that the reaction process is structure sensitive. The present DFT and microkinetic modeling results provide a reasonably complete picture for the chemistry of H₂S on the Cu(110) surface, which is a necessary basis for the design of new sulfur‐tolerant WGS catalysts. © 2013 Wiley Periodicals, Inc.     

Exploring odd-even effects of simple oligomer-like DRCNnT series: a study based on density functional theory/time-dependent density functional theory calculations

Odd-even effects of short-circuit current density and power conversion efficiency (PCE) are an interesting phenomenon in some organic solar cells. Although some explanations have been given, why they behave in such a way is still an open question. In the present work, we investigate a set of acceptor-donor-acceptor simple oligomer-like small molecules, named the DRCNnT (n = 5-9) series, to give an insight into this phenomenon because the solar cells based on them have high PCE (up to 10.08%) and show strong odd-even effects in experiments. By modeling the DRCNnT series and using density functional theory, we have studied the ground-state electronic structures of the DRCNnT (n = 5-9) series in condensed phase. The calculated results reproduce the experimental trends well. Furthermore, we find that the exciton-binding energies of the DRCNnT series may be one of the key parameters to explain this phenomenon because they also show odd-even effects. In addition, by studying the effects of alkyl branch and terminal group on odd-even effects of dipole moment, we find that eliminating one or two alkyl branches does not break the odd-even effects of dipole moments, but eliminating one or two terminal groups does. Finally, we conclude that removing one alkyl branch close to the terminal group of DRCN5T can decrease highest occupied molecular orbital (HOMO) energy (thus increasing open circuit voltage) and increase dipole moment (thus enhancing charge separation and short-circuit current). This could be a new and simple method to increase the PCE of DRCN5T-based solar cells.     

Spin quenching of transition metals deposited on MgO insulator and CdO semiconductor density functional calculations

We have analyzed spin quenching of first row transition metals deposited on (001) defect‐free and defect‐containing surfaces of MgO insulator and CdO semiconductor by means of density functional calculations and embedded cluster model. Clusters of moderate sizes were embedded in the simulated Coulomb fields that closely approximate the Madelung fields of the host surfaces, and relaxation of ions that surround the defect sites was taken into account. Spin states of metals deposited on the defect free surfaces were maintained as in the isolated metals except for Ti, V, and Co on MgO, and Ti, V, and Cr on CdO. On the defect containing surfaces, spin states were maintained too except for Fe on MgO, and V and Cr on CdO. The metal‐support interactions stabilize the low spin state of the adsorbed metal with respect to the isolated metal, but the effect was not in general enough to quench the spin. Spin polarization effects tend to preserve the spin states of the adsorbed metals relative to those of the isolated metals. Although charge transfer took place from the adsorbed metal to the insulator surface, it took place the other way round from the semiconductor surface to the adsorbed metal. The encountered variations in magnetic properties were attributed to the smaller band gap of the semiconductor, and the behavior of a single metal atom adsorbed on a particular surface was a result of a competition between Hund's rule for the adsorbed metal and the formation of a chemical bond at the interface. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Hydroxyl radical and hydroxide ion in liquid water: a comparative electron density functional theory study

Ab initio density functional theory molecular dynamics simulations of the solvated states of the hydroxyl radical and hydroxide ion are performed using the Becke-Lee-Yang-Parr (BLYP) exchange-correlation functional (Becke, A. D. Phys. Rev. A 1988, 38, 3098. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785). The structures of the solvation shells of the two species are examined. It is found that the OH radical forms a relatively well-defined solvation complex with four neighboring water molecules. Three of these molecules are hydrogen bonded to the OH, while the fourth is hemibonded via a three-electron two-centered bond between the oxygen atoms of the OH and water. The activity and the diffusion mechanism of the OH radical in water is discussed in comparison with the OH- ion. Although the results are partially influenced by the tendency of the BLYP density functional to overestimate hemibonded structure, the present simulations suggest that the widely accepted picture of rapid diffusion of OH radical in water through hydrogen exchange reaction may need to be reconsidered.     

Gadolinium ion bonding on the surface of carboxylated detonation nanodiamond in terms of magnetochemistry and density functional theory

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Sulfur K-edge X-ray absorption spectroscopy and density functional theory calculations on superoxide reductase: role of the axial thiolate in reactivity

Superoxide reductase (SOR) is a non-heme iron enzyme that reduces superoxide to peroxide at a diffusion-controlled rate. Sulfur K-edge X-ray absorption spectroscopy (XAS) is used to investigate the ground-state electronic structure of the resting high-spin and CN- bound low-spin FeIII forms of the 1Fe SOR from Pyrococcus furiosus. A computational model with constrained imidazole rings (necessary for reproducing spin states), H-bonding interaction to the thiolate (necessary for reproducing Fe-S bond covalency of the high-spin and low-spin forms), and H-bonding to the exchangeable axial ligand (necessary to reproduce the ground state of the low-spin form) was developed and then used to investigate the enzymatic reaction mechanism. Reaction of the resting ferrous site with superoxide and protonation leading to a high-spin FeIII-OOH species and its subsequent protonation resulting in H2O2 release is calculated to be the most energetically favorable reaction pathway. Our results suggest that the thiolate acts as a covalent anionic ligand. Replacing the thiolate with a neutral noncovalent ligand makes protonation very endothermic and greatly raises the reduction potential. The covalent nature of the thiolate weakens the FeIII bond to the proximal oxygen of this hydroperoxo species, which raises its pKa by an additional 5 log units relative to the pKa of a primarily anionic ligand, facilitating its protonation. A comparison with cytochrome P450 indicates that the stronger equatorial ligand field from the porphyrin results in a low-spin FeIII-OOH species that would not be capable of efficient H2O2 release due to a spin-crossing barrier associated with formation of a high-spin 5C FeIII product. Additionally, the presence of the dianionic porphyrin pi ring in cytochrome P450 allows O-O heterolysis, forming an FeIV-oxo porphyrin radical species, which is calculated to be extremely unfavorable for the non-heme SOR ligand environment. Finally, the 5C FeIII site that results from the product release at the end of the O2- reduction cycle is calculated to be capable of reacting with a second O2-, resulting in superoxide dismutase (SOD) activity. However, in contrast to FeSOD, the 5C FeIII site of SOR, which is more positively charged, is calculated to have a high affinity for binding a sixth anionic ligand, which would inhibit its SOD activity.     

水在Au1/CeO2单原子催化剂上吸附与解离的理论研究

自Haruta和Hutchings发现负载的纳米金催化剂的催化活性后,负载型金催化剂一直是非均相催化的研究重点之一.近年来,单原子催化剂因其优异的活性、选择性,超高的原子利用效率,引起了科学家们的广泛关注.越来越多的单原子金催化剂被成功制备,并被证实具有很好的催化活性.水,作为环境中最常见的物质,在实际的催化体系中往往难以避免,即使在超高真空环境中也会有痕量的水气存在.水的解离不仅是水煤气反应的重要步骤之一,而且对别的反应也有一定的促进作用.尽管水和纳米团簇催化剂之间的研究已经颇有成效,但水和单原子金催化剂之间的作用还不是非常清晰.因此,我们采用密度泛函理论从原子尺度研究了水和Au1/CeO2单原子催化剂的相互作用.我们首先研究了水在完美CeO2表面和含有一个氧空位的CeO2–x表面上的解离过程,研究发现分子态的水和解离态的水在完美CeO2表面可以共存,而一旦在表面形成氧空位后,由于较低的能垒和极大的放热,解离态的水将占据绝对优势.接下来探索了水在完美Au1/CeO2表面和含有一个氧空位的Au1/CeO2–x表面上的解离过程,发现结论恰好和CeO2表面相反.水的解离过程在完美的Au1/CeO2表面几乎是一个无能垒的过程,并且解离会放出大量的热量.而一旦在表面形成氧空位后,单原子Au的轨道处于满占状态,无法提供水的吸附位点.水的解离过程在Ce位点进行,分子吸附能与解离吸附能相当,分子态与解离态共存.为了进一步理解单原子金在水的解离过程中起到的作用,我们分析了水和Au1/CeO2之间的电子相互作用.研究结果表明,单原子金不仅为水的吸附提供了位点,金的5d轨道和水的2p轨道之间的相互作用还有效减弱了水中氧氢键的强度,使水的解离更容易进行.由此可见,在涉及到水解离的反应中,以Au1/CeO2为代表的单原子催化剂有望带来新的突破.最后,我们还测试了范德华力对研究体系的影响.研究发现尽管范德华力会使吸附能的绝对值增加,但是并不影响我们得到的结论.     

Study on electronic density topology of various cluster models of Mg/Al hydrotalcite by density functional theory

The geometry and electronic topology properties of Mg/Al hydrotalcite cluster models were comparatively investigated by means of density functional theory at GGA/DND levels. The results suggested that cluster model containing seven octahedral cations was the smallest size to be employed to simulate other properties. The fact that the n+ charge of cluster models containing n aluminum atoms can reflect electronic properties of anionic clay layer sheet. The bond lengths of clusters can be modified by terminating with or without OH~-/H_2O groups in terms of principle of bond order conservation.