The efficiency of proton transfer in Kirby’s enzyme model, a computational approach

DFT and ab initio calculation results for proton transfer reactions in Kirby’s acetals reveal that the mechanism proceeds via efficient intramolecular general acid catalysis (IGAC) and not through a ‘classical’ general acid catalysis mechanism (GAC). Further, they show that the driving force for the proton transfer efficiency is the proximity of the two reactive centers (r) and the attack angle (α), and the rate of the reaction is linearly correlated with r² and sin (180° − α). Acetals with short r values and with α values close to 180° (forming a linear H-bond) are more reactive due to the development of strong hydrogen bonds in their global minimum, transition state, and product structures.     

Cleavage of Menger’s aliphatic amide: A model for peptidase enzyme solely explained by proximity orientation in intramolecular proton transfer

Ab initio HF/6-31G and DFT B3LYP/6-31G (d,p) calculations for the cleavage of Menger’s aliphatic amide 3 (a peptidase model) under physiological conditions, indicate that the rate limiting step in the cleavage process is a proton transfer from one of the carboxyl groups onto the amidic carbonyl oxygen. The acceleration in rates is mainly due to proximity orientation, and the effect of pseudoallylic strain relief on the rates is negligible. Moreover, the calculations reveal that the mode and the mechanism of the amide cleavage are largely dependent on the pH of the reaction. These results explain the findings that peptidase enzymes are reactive around neutral pH while their activities vanish under basic medium.     

Theoretical study of one‐carbon unit transfer between methyl‐AICA and N1‐methyl‐N1‐acryloyl‐formamide

The mechanism of one‐carbon unit transfer between 1‐methyl‐5‐amino‐4‐carboxamide imidazole (M‐AICA) and N¹‐methyl‐N¹‐acryloyl‐formamide (the model molecule of 10‐f‐H4F) is investigated by the Hartree–Fock and DFT methods, respectively, at the 6‐31G* basis level. There are two different channels for the proton transfer, resulting in two reaction pathways with different properties. The results indicate that both channels can complete the reaction, but path a is slightly favored due to its lower active energy barrier. Furthermore, the influence of 4‐carboxamindde in M‐AICA is also discussed. This group can stabilize the reactant and intermediates, and reduce the active energy barrier through the intermolecular hydrogen bond. The intermolecular hydrogen bond results in an enlarged conjugation system and makes the transition states more stable. Our results are in agreement with experiments. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Intramolecular proton transfer in the cyclization of geranylgeranyl diphosphate to the taxadiene precursor of taxol catalyzed by recombinant taxadiene synthase

BACKGROUND: The committed step in the biosynthesis of the anticancer drug taxol in yew (Taxus) species is the cyclization of geranylgeranyl diphosphate to taxa-4(5),11(12)-diene. The enzyme taxadiene synthase catalyzes this complex olefin cation cyclization cascade involving the formation of three rings and three stereogenic centers. RESULTS: Recombinant taxadiene synthase was incubated with specifically deuterated substrates, and the mechanism of cyclization was probed using MS and NMR analyses of the products to define the crucial hydrogen migration and terminating deprotonation steps. The electrophilic cyclization involves the ionization of the diphosphate with closure of the A-ring, followed by a unique intramolecular transfer of the C11 proton to the re-face of C7 to promote closure of the B/C-ring juncture, and cascade termination by proton elimination from the beta-face of C5. CONCLUSIONS: These findings provide insight into the molecular architecture of the first dedicated step of taxol biosynthesis that creates the taxane carbon skeleton, and they have broad implications for the general mechanistic capability of the large family of terpenoid cyclization enzymes.     

Inversion of states in two conformers of 1,8-bis(dimethylamino) naphthalene—the proton sponge

The S₁↔S₀ transitions of two conformers of 1,8-bis(dimethylamino) naphthalene, the “proton sponge”, have been studied by semiempirical AM1 calculations. They reveal that “inversion of states” occurs in the asymmetric conformer DMAN-2, which in the gas phase may be emitted from the ¹L_a state in comparison to the ¹L_b state in symmetric DMAN-1. It was also concluded that because of the mixed character of the HOMO-1 orbital in both conformers, a certain CT contribution to the S₀↔S₁ transition has to be taken into account. The calculated maxima of absorption and emission have been compared to those experimentally obtained in supersonic expansion.     

A DFT study of proton transfers for the reaction of phenol and hydroxyl radical leading to dihydroxybenzene and H2O in the water cluster

Reactions of phenol and hydroxyl radical were studied under the aqueous environment to investigate the antioxidant characters of phenolic compounds. M06‐2X/6‐311 + G(d,p) calculations were carried out, where proton transfers via water molecules were examined carefully. Stepwise paths from phenol + OH^• + (H₂O)_n (n = 3, 7, and 12) to the phenoxyl radical (Ph O^•) via dihydroxycyclohexadienyl radicals (ipso, ortho, meta, and para OH‐adducts) were obtained. In those paths, the water dimer was computed to participate in the bond interchange along hydrogen bonds. The concerted path corresponding to the hydrogen atom transfer (HAT, apparently Ph OH + OH^• → Ph O^• + H₂O) was found. In the path, the hydroxyl radical located on the ipso carbon undergoes the charge transfer to prompt the proton (not hydrogen) transfer. While the present new mechanism is similar to the sequential proton loss electron transfer (SPLET) one, the former is of the concerted character. Tautomerization reactions of ortho or para (OH)C₆H₅=O + (H₂O)_n → C₆H₄(OH)₂(H₂O)_n were traced with n = 2, 3, 4, and 14. The n = 3 (and n = 14) model of ortho and para was calculated to be most likely by the strain‐less hydrogen‐bond circuit.     

Leading coordinate analysis of reaction pathways in proton chain transfer: Application to a two-proton transfer model for the green fluorescent protein

The ‘leading coordinate’ approach to computing an approximate reaction pathway, with subsequent determination of the true minimum energy profile, is applied to a two-proton chain transfer model based on the chromophore and its surrounding moieties within the green fluorescent protein (GFP). Using an ab initio quantum chemical method, a number of different relaxed energy profiles are found for several plausible guesses at leading coordinates. The results obtained for different trial leading coordinates are rationalized through the calculation of a two-dimensional relaxed potential energy surface (PES) for the system. Analysis of the 2-D relaxed PES reveals that two of the trial pathways are entirely spurious, while two others contain useful information and can be used to furnish starting points for successful saddle-point searches. Implications for selection of trial leading coordinates in this class of proton chain transfer reactions are discussed, and a simple diagnostic function is proposed for revealing whether or not a relaxed pathway based on a trial leading coordinate is likely to furnish useful information.     

Ionization-induced proton transfer in model DNA base pairs: a theoretical study of the radical ions of the 7-azaindole dimer.

Proton-transfer reactions of the radical anion and cation of the 7-Azaindole (7AI) dimer were investigated by means of density functional theory (DFT). The calculated results for the dimer anion and cation were very similar. Three equilibrium structures, which correspond to the non-proton-transferred (normal), the single-proton-transferred (SPT) and the double-proton-transferred (tautomeric) forms, were found. The transition states for proton-transfer reactions were also located. The calculations showed that the first proton-transfer reaction (normal-->SPT) is exothermic and almost barrier-free; therefore, it should occur spontaneously in the period of a vibration. In contrast, the second proton-transfer reaction (SPT-->tautomer) was found to be far less-probable in terms of reaction energy and barrier. Hence, it was concluded that both (7Al)2*- and (7Al)2*+ exist in the SPT form. The conclusion was further confirmed by the calculated electron vertical detachment energy (VDE) of the SPT form of (7Al)2*-, 1.33 eV, which is very close to the experimental measurement of 1.35 eV. The calculated VDEs of the normal and tautomeric (7Al)2*- forms were too small compared to the experimental value. The proton transfer process was found to be multidimensional in nature involving not only proton motion but also intermolecular rocking motion. In addition, IR spectra were calculated and reported. The spectra of the three structures showed very different features and, therefore, can be considered as fingerprints for future experimental identifications. The implications of these results to biology and spectroscopy are also briefly discussed.     

Attachment of a Hydrogen‐Bonding Carboxylate Side Chain to an [FeFe]‐Hydrogenase Model Complex: Influence on the Catalytic Mechanism

Azapropanedithiolate (adt)‐bridged model complexes of [FeFe]‐hydrogenase bearing a carboxylic acid functionality have been designed with the aim of decreasing the potential for reduction of protons to hydrogen. Protonation of the bisphosphine complexes 4 – 6 has been studied by in situ IR and NMR spectroscopy, which revealed that protonation with triflic acid most likely takes place first at the N‐bridge for complex 4 but at the Fe? Fe bond for complexes 5 and 6 . Using an excess of acid, the diprotonated species could also be observed, but none of the protonated species was sufficiently stable to be isolated in a pure state. Electrochemical studies have provided an insight into the catalytic mechanisms under strongly acidic conditions, and have also shown that complexes 3 and 6 are electro‐active in aqueous solution even in the absence of acid, presumably due to hydrogen bonding. Hydrogen evolution, driven by visible light, has been observed for three‐component systems consisting of [Ru(bpy)₃]²⁺, complex 1 , 2 , or 3 , and ascorbic acid in CH₃CN/D₂O solution by on‐line mass spectrometry.     

Nanocomposites derived from in situ grafting of linear and hyperbranched poly(ether‐ketone)s containing flexible oxyethylene spacers onto the surface of multiwalled carbon nanotubes

Linear and hyperbranched poly(ether‐ketone)s (PEKs) containing flexible oxyethylene spacers grafted multiwalled carbon nanotube (PEK‐g‐MWNT) nanocomposites were prepared by direct Friedel‐Crafts acylation as the polymer forming and grafting reaction. To achieve the composites, in situ polycondensations of AB monomers 3‐(2‐phenoxyethoxy)benzoic acid (3‐PEBA) and 4‐(2‐phenoxyethoxy)benzoic acid (4‐PEBA), and AB₂ monomer 3,5‐bis(2‐phenoxyethoxy)benzoic acid (3,5‐BPEBA) were carried out in the presence of multiwalled carbon nanotubes (MWNTs). The reaction conditions, polyphosphoric acid (PPA) with additional phosphorous phentoxide (P₂O₅) in the temperature range of 110–120 °C, were previously optimized. The conditions were used as the polymerization and grafting medium that were indeed benign not to damage MWNTs but strong enough to promote the covalent attachment of PEKs onto the surface of the electron‐deficient MWNTs. From scanning electron microscopy (SEM) and transmission electron microscopy studies, the polymers were uniformly grafted onto the MWNTs. The resultant nanocomposites are soluble in most strong acids such as trifluoroacetic acid, methanesulfonic acid, and sulfuric acid. Both isothermal and dynamic TGA studies in air showed that nanocomposites displayed improved thermo‐oxidative stability when compared with those of corresponding PEK homopolymers. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 3471–3481, 2008     

Synthesis of polystyrene brush on multiwalled carbon nanotubes treated with KMnO4 in the presence of a phase‐transfer catalyst

Multiwalled carbon nanotubes (MWNTs) were effectively functionalized with KMnO₄ in the presence of a phase‐transfer catalyst at room temperature. The hydroxyl functionalized MWNTs were reacted with a vinyl‐group carrying silane‐coupling agent and the terminal vinyl groups were used to fabricate polystyrene (PS) brushes by solution polymerization. Finally, PS‐encapsulated MWNTs were obtained. The synthesis results were verified from FT‐Raman, thermal gravimetric analysis, energy dispersive X‐ray analysis, and transmission electron microscope. PS‐encapsulated MWNTs had much improved dispersion stability in hydrophobic medium, toluene since grafted hydrophobic PS interacts with media and has improved compatibility. This functionalization technique would provide a facile route to prepare various polymer brushes on the surface of MWNTs to improve the dispersion of MWNTs for potential applications. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4413–4420, 2007