Formation and local structure of framework Al Lewis sites in beta zeolites.

Framework AlFR Lewis sites represent a substantial portion of active sites in H-BEA zeolite catalysts activated at low temperatures. We studied their nature by 27Al WURST-QCPMG nuclear magnetic resonance (NMR) and proposed a plausible mechanism of their formation based on periodic density functional theory calculations constrained by 1H MAS, 27Al WURST-QCPMG, and 29Si MAS NMR experiments and FTIR measurements. Our results show that the electron-pair acceptor of AlFR Lewis sites corresponds to an AlTRI atom tricoordinated to the zeolite framework, which adsorbs a water molecule. This AlTRI-OH2 complex is reflected in 27Al NMR resonance with δiso = 70 ± 5 ppm and CQ = 13 ± 2 MHz. In addition, the AlTRI atom with adsorbed acetonitrile-d3 (the probe of AlFR Lewis sites in FTIR spectroscopy) exhibits a similar 27Al NMR resonance. We suggest that these AlFR Lewis sites are formed from Al-OH-Si-O-Si-O-Si-OH-Al sequences located in 12-rings (i.e., close unpaired Al atoms).

Dioxygen splitting at room temperature over distant binuclear transition metal centers in zeolites for direct oxidation of methane to methanol.

Here we demonstrate for the first time the splitting of dioxygen at RT over distant binuclear transition metal (M = Ni, Mn, and Co) centers stabilized in ferrierite zeolite. Cleaved dioxygen directly oxidized methane to methanol, which can be released without the aid of an effluent to the gas phase at RT.

Dioxygen dissociation over man-made system at room temperature to form the active α-oxygen for methane oxidation.

Activation of dioxygen attracts enormous attention due to its potential for utilization of methane and applications in other selective oxidation reactions. We report a cleavage of dioxygen at room temperature over distant binuclear Fe(II) species stabilized in an aluminosilicate matrix. A pair of formed distant α-oxygen species [i.e., (Fe(IV)═O)2+] exhibits unique oxidation properties reflected in an outstanding activity in the oxidation of methane to methanol at room temperature. Designing a man-made system that mimicks the enzyme functionality in the dioxygen activation using both a different mechanism and structure of the active site represents a breakthrough in catalysis. Our system has an enormous practical importance as a potential industrial catalyst for methane utilization because (i) the Fe(II)/Fe(IV) cycle is reversible, (ii) the active Fe centers are stable under the reaction conditions, and (iii) methanol can be released to gas phase without the necessity of water or water-organic medium extraction.

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.

Location of Framework Al Atoms in the Channels of ZSM-5: Effect of the (Hydrothermal) Synthesis.

(27) Al 3Q MAS NMR and UV/Vis spectroscopy with bare Co(II) ions as probes of Al pairs in the zeolite framework were employed to analyze the location of framework Al atoms in the channel system of zeolite ZSM-5. Furthermore, the effect of Na(+) ions together with tetrapropylammonium cation (TPA(+)) in the ZSM-5 synthesis gel on the location of Al in the channel system was investigated. Zeolites prepared using exclusively TPA(+) as a structure-directing agent (i.e., in the absence of Na(+) ions) led to 55-90% of Al atoms located at the channel intersection, regardless the presence or absence of Al pairs [Al-O-(Si-O)2 -Al sequences in one ring] in the zeolite framework. The presence of Na(+) ions in the synthesis gel did not modify the Al location at the channel intersection (55-95% of Al atoms) and led only to changes in i) the distribution of framework Al atoms between Al pairs (decrease) and single isolated Al atoms (increase), and ii) the siting of Al in distinguishable framework tetrahedral sites.

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).

Mechanism of framework oxygen exchange in Fe-zeolites: a combined DFT and mass spectrometry study.

The role of framework oxygen atoms in N(2)O decomposition [N(2)O(g)→N(2)(g) and 1/2O(2)(g)] over Fe-ferrierite is investigated employing a combined experimental (N(2)(18)O decomposition in batch experiments followed by mass spectroscopy measurements) and theoretical (density functional theory calculations) approach. The occurrence of the isotope exchange indicates that framework oxygen atoms are involved in the N(2)O decomposition catalyzed by Fe-ferrierite. Our study, using an Fe-ferrierite sample with iron exclusively present as Fe(II) cations accommodated in the cationic sites, shows that the mobility of framework oxygen atoms in the temperature range: 553 to 593 K is limited to the four framework oxygen atoms of the two AlO(4)(-) tetrahedra forming cationic sites that accomodate Fe(II). They exchange with the Fe extra-framework (18)O atom originating from the decomposed N(2)(18)O. We found, using DFT calculations, that O(2) molecules facilitate the oxygen exchange. However, the corresponding calculated energy barrier of 87 kcal mol(-1) is still very high and it is higher than the assumed experimental value based on the occurrence of the sluggish oxygen exchange at 553 K.

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.

Aluminium siting in the ZSM-5 framework by combination of high resolution 27Al NMR and DFT/MM calculations.

The Al siting in the ZSM-5 zeolite was investigated by (27)Al 3Q MAS NMR spectroscopy and QM/MM calculations. It was found that the occupation of the framework T-sites by Al and the concentration of Al in these T-sites are neither random nor controlled by a simple rule. They both depend on the conditions of the zeolite synthesis. At least 12 out of the 24 distinguishable framework T-sites of ZSM-5 are occupied by Al in the set of the investigated zeolite samples. A partial identification of the Al sites is possible. The calculated (27)Al NMR shielding values were converted to (27)Al isotropic chemical shifts using the experimental isotropic chemical shift of 60.0 ppm referenced to the aqueous solution of Al(NO(3))(3) and the corresponding calculated NMR shielding of 490.0 ppm of a silicon rich (Si/Al 38) chabazite structure zeolite as a secondary internal standard. The observed (27)Al isotropic chemical shifts of 50.0 and 54.7 ppm correspond to Al atoms in the T20 and T6 sites, respectively. The pair of measured isotropic chemical shifts of 52.9 and 53.7 ppm can be assigned to the T4, T8 pair. At the low-shielding end, two assignments are plausible. The smallest deviations between the calculated and observed isotropic chemical shifts are reached for the assignment as follows: T24 (64.8 ppm) is not occupied in the samples and that the observed isotropic chemical shifts 63.6, 62.8, and 60.0 ppm belong to T1, T17, and T7, respectively. It follows then that T-sites T12 (60.8 ppm), T3 (61.7 ppm), and T18 (62.0 ppm) are most likely not occupied by Al in our ZSM-5 samples. If we assume that the calculated isotropic chemical shifts are systematically larger than the observed ones then we can assign the largest observed isotropic chemical shifts of 63.6 and 62.8 ppm to the least shielded T24 and T1 sites, respectively, and 60.0 ppm to T12. Then the sites T3 (61.7 ppm), T18 (62.0 ppm), and T17 (62.5 ppm) would be unoccupied by Al in our ZSM-5 samples. It was further shown that there is no simple linear relationship between the observed (27)Al isotropic chemical shifts and the average Al-O-Si angles.

Permanganate oxidation of alkenes. Substituent and solvent effects. Difficulties with MP2 calculations.

The permanganate oxidation of alkenes has been studied both experimentally and computationally. Transition state structures were located for the reaction of permanganate ion with a variety of monosubstituted alkenes at the B3LYP/6-311++G** level. Although the calculated activation energy for the reaction with ethene was reasonable, the calculated effect of substituents, based on the energies of the reactants, was much larger than that experimentally found. This was shown to be due to the formation of an intermediate charge-dipole complex which led to the transition state. Reaction field calculations found the complex to disappear in a high dielectric constant medium, and the range of activation energies for the reaction in solution became quite small. MP2 calculations were carried out in order to have a comparison with the DFT results. MP2-MP4 gave unusual results for calculations on permanganate ion as well as chromate ion and iron tetraoxide. They also gave markedly unreasonable results for the activation energy of the reaction of permanganate with ethane. CCSD/6-311++G** calculations gave satisfactory results for permanganate ion and chromate ion. At this level of theory, the reaction of permanganate with ethene was found to have a very early transition state, when the bond lengths of the reactants just began to change. The reaction was calculated to be very exothermic (-69 kcal/mol), and this was confirmed via calorimetry. The rates of permanganate oxidation of allyl alcohol and acrylonitrile were determined, and they had similar reactivities. The kinetics and the products of the reaction of permanganate with crotonate ion were examined in some detail.

CuNO2 and Cu(+)NO2 Revisited: A Comparative ab Initio and DFT Study.

We have reinvestigated CuNO2 and Cu(+)NO2 at ab initio as well as at pure and hybrid DFT levels of approximation employing large ANO basis sets. The systems were fully optimized using the CCSD(T), QCISD(T), BPW91, PBE, PBE0, and B3LYP methods. Several stationary points (minima and transition structures) were found on the related potential energy surfaces (PES). The C2v bidentate η(2)-O,O isomer is calculated to be the most stable species on the CuNO2 PES, followed by two monodentate isomers [Formula: see text] the Cs η(1)-O and C2v η(1)-N species which are higher in energy by 12 and 14 kcal/mol, respectively, at CCSD(T)/Basis-II (where Basis-II is 21s15p10d6f4g/8s7p5d3f2g for Cu; 14s9p4d3f/5s4p3d2f for O and N). On the Cu(+)NO2 PES, the Cs monodentate η(1)-O trans (0 kcal/mol) and cis (+3 kcal/mol at CCSD(T)/Basis-II) isomers are found, followed by the C2v monodentate η(1)-N isomer (+14 kcal/mol at CCSD/Basis-II). In contrast to the pure DFT, the hybrid DFT methods perform reasonably well for predicting the relative stabilities (except for η(1)-N of CuNO2) and structures; however, their predictions of the bond dissociation energies are less reliable (for CuNO2 the difference is as much as 10 kcal/mol compared to the CCSD(T) values). The performance of the QCISD(T) method was analyzed, and, furthermore, the issue of symmetry breaking was investigated.

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.

Catalytic mechanism of yeast cytosine deaminase: an ONIOM computational study.

The complete path for the deamination reaction catalyzed by yeast cytosine deaminase (yCD), a zinc metalloenzyme of significant biomedical interest, has been investigated using the ONIOM method. Cytosine deamination proceeds via a sequential mechanism involving the protonation of N(3), the nucleophilic attack of C(4) by the zinc-coordinated hydroxide, and the cleavage of the C(4)-N(4) bond. The last step is the rate determining step for the generation of the zinc bound uracil. Uracil is liberated from the Zn atom by an oxygen exchange mechanism that involves the formation of a gem-diol intermediate from the Zn bound uracil and a water molecule, the C(4)-O(Zn) cleavage, and the regeneration of the Zn-coordinated water. The rate determining step in the oxygen exchange is the formation of the gem-diol intermediate, which is also the rate determining step for the overall yCD-catalyzed deamination reaction.

A comprehensive investigation of the chemistry and basicity of a parent amidoruthenium complex.

trans-(DMPE)(2)Ru(H)(NH(2)) (1) dehydrogenates cyclohexadiene and 9,10-dihydroanthracene to yield benzene (or anthracene), (DMPE)(2)Ru(H)(2), and ammonia. Addition of fluorene to 1 results in the formation of the ion pair [trans-(DMPE)(2)Ru(H)(NH(3))(+)][A(-)] (A(-) = fluorenide, 4a). Complex 1 also reacts with weak acids A-H (A-H = phenylacetylene, 1,2-propadiene, phenylacetonitrile, 4-(alpha,alpha,alpha-trifluoromethyl)phenylacetonitrile, cyclobutanone, phenol, p-cresol, aniline) to form ammonia and trans-(DMPE)(2)Ru(H)(A) (7, 8, 9a, 9b, 10, 11b, 11c, 12, respectively). In the cases where A-H = phenylacetylene, cyclobutanone, aniline, phenol, and p-cresol, the reaction was observed to proceed via ion pairs analogous to 4a. Compound 1 is reactive toward even weaker acids such as toluene, propylene, ammonia, cycloheptatriene, and dihydrogen, but in these cases deuterium labeling studies revealed that only H/D exchange between A-H and the ND(2) group is observed, rather than detectable formation of ion pairs or displacement products. Addition of triphenylmethane to 1 results in the formation of an equilibrium mixture of 1, triphenylmethane, and the ruthenium/triphenylmethide ion pair 4h. If the energetics of ion-pair association are ignored, this result indicates that the basicity of 1 is similar to that of triphenylmethide. All these observations support the conclusion that the NH(2) group in amido complex 1 is exceptionally basic and as a result prefers to abstract a proton rather than a hydrogen atom from a reactive C-H bond. The energetics and mechanism of these proton-transfer and -exchange reactions are analyzed with the help of DFT calculations.