DFT computational study of the mechanism of allyl halides carbonylation catalyzed by nickel tetracarbonyl

A theoretical investigation at the DFT(B3LYP) level on the carbonylation reaction of allyl bromide catalyzed by nickel tetra-carbonyl Ni(CO)(4) is discussed. The computational results show the following: (i) Three main steps characterize the catalytic cycle: (a) an oxidative addition step, (b) a carbonylation step, and (c) a reductive elimination step where the acyl product is obtained and the catalyst is regenerated. (ii) Both Ni(CO)(3) and Ni(CO)(4) complexes can behave as "active" catalytic species. (iii) The oxidative addition leads to the formation of either eta(3) or eta(1)-allyl nickel complexes, which are involved in a fast equilibrium. (iv) The carbonylation occurs much more easily on the eta(1) than on the eta(3) intermediates.     

A comparative analysis of various gradient methods for geometry optimization at the ab initio SCF-MO level

Various techniques, already suggested for improving the computational efficiency of the force relaxation method, have been applied here in conjunction with the variable metric algorithms suggested by Murtagh and Sargent and by Fletcher. Various tests have been performed to assess the computational efficiency of the resulting minimization procedures. In addition, procedures where the steps are defined in terms of a parabolic fitting of the forces in approximated normal coordinates have been tested. In all cases the forces are computed analytically.     

Migratory aptitudes of simple alkyl groups in the anionotropic rearrangement of quaternary chloromethyl borate species: a combined experimental and theoretical investigation

A combined experimental and theoretical investigation at the DFT and MP2 levels on the boron-to-carbon 1,2-shift in "ate species", coming from the quaternization of boranes (A) and boronate (B), is reported. To discuss the different migratory aptitudes of various alkyl groups, we have examined the migration of primary (R = Me, Et), secondary (R = i-Pr), and tertiary (R = t-Bu) alkyl groups. The effect of the counterion Li(+) and of the solvent (polarized continuous model (PCM) method) has been considered. The following results are relevant: (a) in all cases, the reaction proceeds via a concerted-type mechanism which explains the retention of configuration at the migrating group and the inversion at the migration terminus experimentally observed. (b) The trend of the migration barriers along the direction primary --> secondary --> tertiary alkyl group observed in "ate" species A is reversed in boronate species B, in agreement with the experimental evidences. (c) A simple theoretical model is proposed where the barrier trend is the result of a delicate interplay between two opposite factors: (1) a "steric effect", which favors the most sterically demanding migrating groups, and (2) a "charge effect" associated with the partial carbanionic nature of the migrating carbon atom and which favors the less substituted migrating carbons.     

On the fragmentation modes in PMO analyses

The molecular species 1,1- and 1,2-disubstituted alkenes have been used as model systems for a comparative discussion of the results obtained with quantitative orbital analyses using different fragmentation modes. It is shown that when indices of the overall energy effects are used, the results of a quantitative orbital analysis are independent of the chosen fragmentation mode. On the other hand, the results of such analysis can depend on the fragmentation mode when indices of partial energy effects are used.     

A dichotomy in the enantioselective oxidation of aryl benzyl sulfides: A combined experimental and computational work

Pentafluorobenzyl pentafluorophenyl sulfide is oxidised with moderate e.e. value and a low yield by the usually highly successful oxidation protocol based upon tert-butyl hydroperoxide (TBHP) in the presence of a titanium/hydrobenzoin complex. This disappointing result resisted until the present work, in which the switch of the oxidation agent (from TBHP to cumene hydroperoxide), suggested by our previous computations, yielded the enantiopure sulfoxide. This valuable chiral compound was obtained in good yields (76%) without resorting to a chromatographic separation. DFT computations uncovered that this favourable reactivity was originated by a stabilizing π?π?stacking between the phenyl group of the oxidant and the pentafluorophenyl moiety of the substrate.     

Structure and stability of short beta-peptide nanotubes: a non-natural representative of collagen?

Since secondary structure elements are known to play a key role in stabilizing the 3D-fold of proteins for the design of non-natural proteins composed of beta-amino acid residues, the construction of suitable secondary structural elements is mandatory. Folding analogues of alpha-helices and beta-strands of beta-polypeptides were already described (Chem. Biodiversity 2004, 1, 1111 (1)). Here, we present several collagen-like folds composed exclusively of beta-Ala(s). Unlike their natural counterpart, these tubular nanostructures can be composed of more than three polypeptide chains aligned parallel and/or antiparallel. By using ab initio and DFT calculations we have optimized a large number of versatile collagen-like antiparallel nanostructures. In these tubular systems, oligopeptide strands are interconnected by i --> (i) type H-bonds, except for the "closing" set. This latter is called "the H-bond zipper" and is either (i) --> i, ( i + 1) --> i, or ( i + 2) --> i type. Antiparallel, tubular foldamers composed of l number of strands, each of k number of beta-amino acid residues (e.g., apbeta-T(l) i+l ) k , ap(beta-T(l) i+1 ) k , or ap(beta-T(l) i+2 ) k ), are unexpectedly stable supramolecular complexes. Independent of k and l, the local backbone fold of the amino acid residues is usually spiral, abbreviated as "S(P)" or "S*(P)". Nevertheless, in contrast to parallel, in antiparallel nanotubes the backbone fold can occasionally twist out from S(P) or S*(P) type into an alternative local structure. However, the more the local geometry of the strands resembles to S(P) or S*(P), the higher the stability is. Besides the backbone twisting, the overall stability is determined by the type and the geometrical properties of the constituent H-bonds. Interestingly, higher number of total H-bonds can provide a lower overall stability, when H-bond parameters are inferior. In general, the increase of both the number of strands and their length stabilize the supramolecular complex. Now that, for beta-peptides, collagen-like overall folds with their stability were determined, their POG- or PPG-like sequence specificity has to be revealed.     

Computational clues for a new mechanism in the glycosylase activity of the human DNA repair protein hOGG1. A generalized paradigm for purine-repairing systems?

A theoretical density functional theory (DFT, B3LYP) investigation has been carried out on the catalytic cycle responsible for the glycosylase activity of the human DNA repair protein hOGG1: enzyme activation, cleavage of the glycosidic bond, and expulsion of the damaged base. An unprecedented large quantum mechanics (QM) model system has been used, which includes a complete oxoG molecule, the deoxyribose ring bonded to the phosphate groups, and most of the surrounding residues that simulate the protein binding pocket. It has been found that Asp268 does not play any role in Lys249 activation and that the oxoG basis acts as a coenzyme, triggering nucleophile activation by Lys249 deprotonation. An SN2 nucleophilic attack by Lys249 on the anomeric carbon then follows. This is the rate-determining step of the process with an activation barrier of 16.7 kcal mol(-1) in good agreement with the experimental value of 17.1 kcal mol(-1). The expelled oxoG plays again as an enzyme cofactor at the end of the process by activating (via proton transfer) ribose ring opening and Schiff base formation. This study suggests a recurring catalytic strategy in the enzymatic cleavage of purine nucleoside where the activation of the leaving group by protonation of the nucleoside base (via an enzymatic general acid) triggers the cleavage of the glycosidic bond.