Tuning the Aluminum Distribution in Zeolites to Increase their Performance in Acid-Catalyzed Reactions.

The organization of Al atoms in the framework of Si-rich zeolites is very important and includes two classes: (i) the Al siting that determines which individual, crystallographically distinguishable framework T sites are occupied by Al atoms and (ii) the Al distribution, which describes the relation of two or more Al atoms in the framework, their distances, and the possibility of neighboring Al atoms to cooperate in the formation of active sites. The organization of Al significantly affects the catalytic properties of Si-rich, zeolite-based catalysts in acid and redox catalysis. Herein, what is known about the organization of Al in the framework of industrially very important pentasil-ring Si-rich zeolites (ZSM-5, beta zeolite, mordenite, ferrierite, MCM-22, and TNU-9), as well as the very promising SSZ-13 Si-rich zeolite with the CHA structure, is summarized.

TNU-9 Zeolite: Aluminum Distribution and Extra-Framework Sites of Divalent Cations.

The TNU-9 zeolite (TUN framework) is one of the most complex zeolites known. It represents a highly promising matrix for both acid and redox catalytic reactions. We present here a newly developed approach involving the use of 29 Si and 27 Al (3Q) MAS NMR spectroscopy, CoII as probes monitored by UV/Vis and FTIR spectroscopy, and extensive periodic DFT calculations, including molecular dynamics, to investigating the aluminum distribution in the TUN framework and the location of aluminum pairs and divalent cations in extra-framework cationic positions. Our study reveals that 40 and 60 % of aluminum atoms in the TNU-9 zeolite are isolated single aluminum atoms and aluminum pairs, respectively. The aluminum pairs are present in two types of six-membered rings forming the corresponding α and ß (15 and 85 %, respectively, of aluminum pairs) sites of bare divalent cations. The α site is located on the TUN straight channel wall and it connects two channel intersections. The suggested near-planar ß site is present at the channel intersection.

Structure of framework aluminum Lewis sites and perturbed aluminum atoms in zeolites as determined by 27Al{1H} REDOR (3Q) MAS NMR spectroscopy and DFT/molecular mechanics.

Zeolites are highly important heterogeneous catalysts. Besides Brønsted SiOHAl acid sites, also framework AlFR Lewis acid sites are often found in their H-forms. The formation of AlFR Lewis sites in zeolites is a key issue regarding their selectivity in acid-catalyzed reactions. The local structures of AlFR Lewis sites in dehydrated zeolites and their precursors--"perturbed" AlFR atoms in hydrated zeolites--were studied by high-resolution MAS NMR and FTIR spectroscopy and DFT/MM calculations. Perturbed framework Al atoms correspond to (SiO)3AlOH groups and are characterized by a broad (27)Al NMR resonance (δi = 59-62 ppm, CQ = 5 MHz, and η = 0.3-0.4) with a shoulder at 40 ppm in the (27)Al MAS NMR spectrum. Dehydroxylation of (SiO)3AlOH occurs at mild temperatures and leads to the formation of AlFR Lewis sites tricoordinated to the zeolite framework. Al atoms of these (SiO)3Al Lewis sites exhibit an extremely broad (27)Al NMR resonance (δi ≈ 67 ppm, CQ ≈ 20 MHz, and η ≈ 0.1).

Role of glutamate 64 in the activation of the prodrug 5-fluorocytosine by yeast cytosine deaminase.

Yeast cytosine deaminase (yCD) catalyzes the hydrolytic deamination of cytosine to uracil as well as the deamination of the prodrug 5-fluorocytosine (5FC) to the anticancer drug 5-fluorouracil. In this study, the role of Glu64 in the activation of the prodrug 5FC was investigated by site-directed mutagenesis, biochemical, nuclear magnetic resonance (NMR), and computational studies. Steady-state kinetics studies showed that the mutation of Glu64 causes a dramatic decrease in k(cat) and a dramatic increase in K(m), indicating Glu64 is important for both binding and catalysis in the activation of 5FC. (19)F NMR experiments showed that binding of the inhibitor 5-fluoro-1H-pyrimidin-2-one (5FPy) to the wild-type yCD causes an upfield shift, indicating that the bound inhibitor is in the hydrated form, mimicking the transition state or the tetrahedral intermediate in the activation of 5FC. However, binding of 5FPy to the E64A mutant enzyme causes a downfield shift, indicating that the bound 5FPy remains in an unhydrated form in the complex with the mutant enzyme. (1)H and (15)N NMR analysis revealed trans-hydrogen bond D/H isotope effects on the hydrogen of the amide of Glu64, indicating that the carboxylate of Glu64 forms two hydrogen bonds with the hydrated 5FPy. ONIOM calculations showed that the wild-type yCD complex with the hydrated form of the inhibitor 1H-pyrimidin-2-one is more stable than the initial binding complex, and in contrast, with the E64A mutant enzyme, the hydrated inhibitor is no longer favored and the conversion has a higher activation energy, as well. The hydrated inhibitor is stabilized in the wild-type yCD by two hydrogen bonds between it and the carboxylate of Glu64 as revealed by (1)H and (15)N NMR analysis. To explore the functional role of Glu64 in catalysis, we investigated the deamination of cytosine catalyzed by the E64A mutant by ONIOM calculations. The results showed that without the assistance of Glu64, both proton transfers before and after the formation of the tetrahedral reaction intermediate become partially rate-limiting steps. The results of the experimental and computational studies together indicate that Glu64 plays a critical role in both the binding and the chemical transformation in the conversion of the prodrug 5FC to the anticancer drug 5-fluorouracil.

A molecular dynamics exploration of the catalytic mechanism of yeast cytosine deaminase.

Yeast cytosine deaminase (yCD), a zinc metalloenzyme of significant biomedical interest, is investigated by a series of molecular dynamics simulations in its free form and complexed with its reactant (cytosine), product (uracil), several reaction intermediates, and an intermediate analogue. Quantum chemical calculations, used to construct a model for the catalytic Zn ion with its ligands (two cysteines, a histidine, and one water) show, by comparison with crystal structure data, that the cysteines are deprotonated and the histidine is monoprotonated. The simulations suggest that Glu64 plays a critical role in the catalysis by yCD. The rotation of the Glu64 side-chain carboxyl group that can be protonated or deprotonated permits it to act as a proton shuttle between the Zn-bound water and cytosine and subsequent reaction intermediates. Free energy methods are used to obtain the barriers for these rotations, and they are sufficiently small to permit rotation on a nanosecond time scale. In the course of the reaction, cytosine reorients to a geometry to favor nucleophilic attack by a Zn-bound hydroxide. A stable position for a reaction product, ammonia, was located in the active site, and the free energy of exchange with a water molecule was evaluated. The simulations also reveal small motions of the C-terminus and the loop that contains Phe114 that may be important for reactant binding and product release.