Modelling/DFT calculations

Efforts have been made to determine the approach of monomer onto the catalysts by theoretical modelling. DFT calculations on the ion pair [(1,2-... 

To obtain realistic tip models, DFT calculations of the electronic structure of fully relaxed tungsten films with one or two surface layers of either tungsten atoms or adsorbates have proven to be the most suitable choice [22,23], The adsorbates so far considered include most transition metals. In single cases, where the (STM) tip was covered by 10-20 layers of Fe, the tip has been modeled by a Fe(100) film covered by one atom or a layer plus one atom of sample surface atoms [24]. 

The SM1-SM3 methods model solvation in water with various degrees of sophistication. The SM4 method models solvation in alkane solvents. The SM5 method is generalized to model any solvent. The SM5.42R method is designed to work with HF, DFT or hybrid HF/DFT calculations, as well as with AMI or PM3. SM5.42R is implemented using a SCRF algorithm as described below. A description of the differences between these methods can be found in the manual accompanying the AMSOL program and in the reviews listed at the end of this chapter. Available Hamiltonians and solvents are summarized in Table 24.1. 

The substituent effects on the H-bonding in an adenine-uracil (A-U) base pair were studied for a series of common functional groups [99JPC(A)8516]. Substitutions in the 5 position of uracil are of particular importance because they are located toward the major groove and can easily be introduced by several chemical methods. Based on DFT calculation with a basis set including diffuse functions, variations of about 1 kcal/mol were found for the two H-bonds. The solvent effects on three different Watson-Crick A-U base pairs (Scheme 100) have been modeled by seven water molecules creating the first solvation shell [98JPC(A)6167]. 

The ultrahigh vacuum STM was used to investigate the addition of the 2,2,6,6-tetramethyI-l-piperidinyloxy (TEMPO) radical to the dangling bond of Si(l 0 0)-2 X 1 surface. ° ° The TEMPO can bond with a single dangling bond to form stable Si-O coupling products, in contrast to the thermal decomposition of TEMPO-silicon compounds. Semiempiiical and DFT calculations of TEMPO bound to a three-dimer silicon cluster model yielded... 

Radical IV can be considered as a unique phosphorus radical species. Reduction of the parent macrocycle with sodium naphtalenide in THF at room temperature gave a purple solution. The FPR spectrum displayed a signal in a 1 2 1 pattern, with flp(2P)=0.38 mT. DFT calculations on radical IV models indicated a P-P distance of 2.763 A (P - P is3.256 A in the crystal structure of the parent compound and the average value of a single P-P bond is 2.2 A). According to the authors, the small coupling constant arises from the facts that the principal values of the hyperfine tensor are of opposite sign and that the a P P one electron bond results from overlap of two 3p orbitals [88]. 

The proposed mechanism of H2 evolution by a model of [FeFeJ-hydrogenases based upon DFT calculations [204-206] and a hybrid quanmm mechanical and molecular mechanical (QM/MM) investigation is summarized in Scheme 63 [207]. Complex I is converted into II by both protonation and reduction. Migration of the proton on the N atom to the Fe center in II produces the hydride complex III, and then protonation affords IV. In the next step, two pathways are conceivable. One is that the molecular hydrogen complex VI is synthesized by proton transfer and subsequent reduction (Path a). The other proposed by De Gioia, Ryde, and coworkers [207] is that the reduction of IV affords VI via the terminal hydride complex V (Path b). Dehydrogenation from VI regenerates I. 

The complexes [Cu(NHC)(MeCN)][BF ], NHC = IPr, SIPr, IMes, catalyse the diboration of styrene with (Bcat) in high conversions (5 mol%, THF, rt or reflux). The (BcaO /styrene ratio has also an important effect on chemoselectivity (mono-versus di-substituted borylated species). Use of equimolecular ratios or excess of BCcat) results in the diborylated product, while higher alkene B(cat)j ratios lead selectively to mono-borylated species. Alkynes (phenylacetylene, diphenylacety-lene) are converted selectively (90-95%) to the c/x-di-borylated products under the same conditions. The mechanism of the reaction possibly involves a-bond metathetical reactions, but no oxidative addition at the copper. This mechanistic model was supported by DFT calculations [68]. 

Specific aspects examined here include insights and conclusions derived from the most recently performed density functional theory (DFT) calculations, which have been based on a comprehensive model of the electrochemical interface, and the strong disagreements (which seem to defy all recent theoretical efforts) that remain regarding proper interpretation of experimental ORR results and proper identihcation of the ORR mechanism in a PEFC cathode employing Pt catalysts. 

DFT calculations showed that a reaction between surface-bonded CO and OH on Au(l 10) has a low activation barrier (approximately 0.2 eV) whereas the same reaction on Pt(ll l)has amuch higher barrier [Shubina et al., 2004]. Both on Au and on Pt, the resulting COOH is relatively strongly bonded. This is evidence in favor of Weaver s model for CO oxidation on Au, in which adsorbed CO reacts directly with nearby water to form adsorbed COOH. 

In this chapter, we have summarized (recent) progress in the mechanistic understanding of the oxidation of carbon monoxide, formic acid, methanol, and ethanol on transition metal (primarily Pt) electrodes. We have emphasized the surface science approach employing well-defined electrode surfaces, i.e., single crystals, in combination with surface-sensitive techniques (FTIR and online OEMS), kinetic modeling and first-principles DFT calculations. 

To shed hght on the origin of the enhanced ORR activity, Xu and co-workers performed extensive DFT calculations to investigate the reactivity of the Pt skin [Xu et al., 2004], in particular how oxygen interacts in vacuum with the ordered PtsCo alloy and with a monolayer of Pt formed on the alloy as a model for Pt skin. Figure 9.10 identifies the various adsorption sites for O and O2. Experiments have shown that up to four layers of Pt could sustain a 2.5% compressive strain without creating any surface... 

In molecular DFT calculations, it is natural to include all electrons in the calculations and hence no further subtleties than the ones described arise in the calculation of the isomer shift. However, there are situations where other approaches are advantageous. The most prominent situation is met in the case of solids. Here, it is difficult to capture the effects of an infinite system with a finite size cluster model and one should resort to dedicated solid state techniques. It appears that very efficient solid state DFT implementations are possible on the basis of plane wave basis sets. However, it is difficult to describe the core region with plane wave basis sets. Hence, the core electrons need to be replaced by pseudopotentials, which precludes a direct calculation of the electron density at the Mossbauer absorber atom. However, there are workarounds and the subtleties involved in this subject are discussed in a complementary chapter by Blaha (see CD-ROM, Part HI). 

In a crystal-field picture, the electronic structure of iron in the five-coordinate compounds is usually best represented by a (d yf idyz, 4cz) ( zO configuration [66, 70], as convincingly borne out by spin-unrestricted DFT calculations on the Jager compound 20 [68]. The intermediate spin configuration with an empty d 2 yi orbital in the CF model, however, has a vanishing valence contribution to the... 

Both Fe(ll)(TPP) and Fe(II)(OEP) have positive electric quadrupole splitting without significant temperature dependence which, however, cannot be satisfactorily explained within the crystal field model [117]. Spin-restricted and spin-unrestricted Xoi multiple scattering calculations revealed large asymmetry in the population of the valence orbitals and appreciable 4p contributions to the EFG [153] which then was further specified by ab initio and DFT calculations [154,155]. 

---