Density functional theory reactions

J Li, MR Nelson, CY Peng, D Bashford, L Noodleman. Incorporating protein environments in density functional theory A self-consistent reaction field calculation of redox potentials of [2Ee2S] clusters in feiTedoxm and phthalate dioxygenase reductase. J Phys Chem A 102 6311-6324, 1998. 

Because of the complexity of the pathway, the sensitivity of the reagents involved, the heterogeneous nature of the reaction, and the limitations of modern experimental techniques and instrumentation, it is not surprising that a compelling picture of the mechanism of the Simmons-Smith reaction has yet to emerge. In recent years, the application of computational techniques to the study of the mechanism has become important. Enabling theoretical advances, namely the implementation of density functional theory, have finally made this complex system amenable to calculation. These studies not only provide support for earlier conclusions regarding the reaction mechanism, but they have also opened new mechanistic possibilities to view. 

Orlova et al. (2003) theoretically studied the mechanism of the firefly bioluminescence reaction on the basis of the hybrid density functional theory. According to their conclusion, changes in the color of light emission by rotating the two rings on the 2-2 axis is unlikely, whereas the participation of the enol-forms of oxyluciferin in bioluminescence is plausible but not essential to explain the multicolor emission. They predicted that the color of the bioluminescence depends on the polarization of the oxyluciferin molecule (at its OH and O-termini) in the microenvironment of the luciferase active site the... 

There have, however, been attempts to correlate Q-e values and hence reactivity ratios to, for example, c NMR chemical shifts 50 or the results of MO calculations 51153 and to provide a better theoretical basis for the parameters. Most recently, Zhan and Dixon153 applied density functional theory to demonstrate that Q values could be correlated to calculated values of the relative free energy for the radical monomer reaction (PA + Mn — PA ). The e values were correlated to values of the electronegativities of monomer and radical. 

Fischer-type carbene complexes, generally characterized by the formula (CO)5M=C(X)R (M=Cr, Mo, W X=7r-donor substitutent, R=alkyl, aryl or unsaturated alkenyl and alkynyl), have been known now for about 40 years. They have been widely used in synthetic reactions [37,51-58] and show a very good reactivity especially in cycloaddition reactions [59-64]. As described above, Fischer-type carbene complexes are characterized by a formal metal-carbon double bond to a low-valent transition metal which is usually stabilized by 7r-acceptor substituents such as CO, PPh3 or Cp. The electronic structure of the metal-carbene bond is of great interest because it determines the reactivity of the complex [65-68]. Several theoretical studies have addressed this problem by means of semiempirical [69-73], Hartree-Fock (HF) [74-79] and post-HF [80-83] calculations and lately also by density functional theory (DFT) calculations [67, 84-94]. Often these studies also compared Fischer-type and... 

D. L. Phillips, W.H. Fang, and X. Zheng, Isodiiodomethane is the methylene transfer agent in cyclopropanation reactions with olefins using ultraviolet photolysis of diiodomethane in solutions a density functional theory investigation of the reactions of isodiiodomethane, iodomethyl radical, and iodomethyl cation with ethylene. J. Am. Chem. Soc. 123(18), 4197-4203 (2001). 

The authors carried out theoretical calculations on this system as well as on the [ (PMej) ] system to compare their reactivity with hexafluorobenzene. They found that the barrier for [ (liPr) ] is approximately 10 kJ/mol lower in energy than the corresponding barrier for the phosphine-bearing system. This value was in agreement with the different reactivity of both complexes but could not fully explain the large difference in reaction times. Density functional Theory (DFT) calculations also showed that the trans product is more stable than the cis product (total energies are respectively -130.9 and 91.1 kJ/mol), which was in agreement with the experimental values. 

The exact nature of the catalytically active Ni species in these reactions is yet to be conclusively established. Hydrodechlorination proves optimal with a NHC Ni ratio of 2 1 suggesting that 14-electron Ni(NHC)2 is involved, whereas the 1 1 NHC Ni ratio necessary for hydrodefluorination implies that it is the 12-electron mono-carbene adduct Ni(NHC) which is catalytically active [10]. Smdies by Matsubara et al. revealed that treatment of NKacac) with either one or two equivalents of IMes HCl 1 or SlMes HCl 2 in the presence of NaOHu formed the mono-NHC complex Ni(NHC)(acac)j which, upon reduction with NaH in the presence or absence of carbene, formed Ni(NHC)2 [11]. Density functional theory (DFT) calculations suggest that the strength of the Ni-NHC bond (ca. 50 kcal/mol) makes... 

Density Functional Theory (DFT) has shown that low-coordinated sites on the gold nanoparticles can adsorb small inorganic molecules such as O2 and CO, and the presence of these sites is the key factor for the catal5dic properties of supported gold nanoclusters. Other contributions, induced by the presence of the support, can provide parallel channels for the reaction and modulate the final efficiency of Au-based catalysts. Also these calculations extended for the adsorption of O and CO on flat and... 

Karlberg GS, Rossmeisl J, Nprskov JK. 2007b. Estimations of electric field effects on the oxygen reduction reaction based on the density functional theory. Phys Chem Chem Phys 37 5158-5161. 

Skulason E, Karlberg GS, Rossmeisl J, Bligaard T, Greeley J, Jonsson H, Nprskov JK. 2007. Density functional theory calculations for the hydrogen evolution reaction in an electrochemical double layer on the Pt(lll) electrode. Phys Chem Chem Phys 9 3241-3250. 

Vassilev P, Koper MTM. 2007. Electrochemical reduction of oxygen on gold surfaces A density functional theory study of intermediates reaction paths. J Phys Chem C 111 2607-2613. 

Further studies were carried out with halocarbene amides 34 and 357 Although again no direct spectroscopic signatures for specifically solvated carbenes were found, compelling evidence for such solvation was obtained with a combination of laser flash photolysis (LFP) with UV-VIS detection via pyridine ylides, TRIR spectroscopy, density functional theory (DFT) calculations, and kinetic simulations. Carbenes 34 and 35 were generated by photolysis of indan-based precursors (Scheme 4.7) and were directly observed by TRIR spectroscopy in Freon-113 at 1635 and 1650 cm , respectively. The addition of small amounts of dioxane or THF significantly retarded the rate of biomolecular reaction with both pyridine and TME in Freon-113. Also, the addition of dioxane increased the observed lifetime of carbene 34 in Freon-113. These are both unprecedented observations. 

However, even the best experimental technique typically does not provide a detailed mechanistic picture of a chemical reaction. Computational quantum chemical methods such as the ab initio molecular orbital and density functional theory (DFT) " methods allow chemists to obtain a detailed picture of reaction potential energy surfaces and to elucidate important reaction-driving forces. Moreover, these methods can provide valuable kinetic and thermodynamic information (i.e., heats of formation, enthalpies, and free energies) for reactions and species for which reactivity and conditions make experiments difficult, thereby providing a powerful means to complement experimental data. 

Detection of the dA N1 and dC N3 adducts may not in one sense be particularly important for DNA based on their central position within the helical conformation and hydrogen bonding network.37,38 Still, the deoxynucleoside studies helped to focus attention on the reversibility of alkylation by QM and provided insight into the reactions of duplex DNA described below in Section 9.3. Reaction at the deoxynucleoside level also provided an essential system for developing a theoretical treatment of QM reaction.50-52 Computations based on density functional theory well rationalized the published results on d A and correctly anticipated the results on dG and dC reviewed above and described in more detail in Chapter 2 (Freccero). 

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