Three-dimensional structure of ribonuclease T-1 complexed with an isosteric phosphonate substrate analogue of GpU: Alternate substrate binding modes and catalysis

The X-ray crystal structure of a complex between ribonuclease T-1 and guanylyl(3'-6')-6'-deoxyhomouridine (GpcU) has been determined at 2.0 Angstrom resolution. This Ligand is an isosteric analogue of the minimal RNA substrate, guanylyl(3'-5')uridine (GpU), where a methylene is substituted for the uridine 5'-oxygen atom. Two protein molecules are part of the asymmetric unit and both have a GpcU bound at the active site in the same manner. The protein-protein interface reveals an extended aromatic stack involving both guanines and three enzyme phenolic groups. A third GpcU has its guanine moiety stacked on His92 at the active site on enzyme molecule A and interacts with GpcU on molecule B in a neighboring unit via hydrogen bonding between uridine ribose 2'- and 3'-OH groups. None of the uridine moieties of the three GpcU molecules in the asymmetric unit interacts directly with the protein. GpcU-active-site interactions involve extensive hydrogen bonding of the guanine moiety at the primary recognition site and of the guanosine 2'-hydroxyl group with His40 and Glu58. on the other hand, the phosphonate group is weakly bound only by a single hydrogen bond with Tyr38, unlike ligand phosphate groups of other substrate analogues and 3'-GMP, which hydrogen-bonded with three additional active-site residues. Hydrogen bonding of the guanylyl 2'-OH group and the phosphonate moiety is essentially the same as that recently observed for a novel structure of a RNase T-1-3'-GMP complex obtained immediately after in situ hydrolysis of exo-(S-p)-guanosine 2',3'-cyclophosphorothioate [Zegers et al. (1998) Nature Struct. Biol. 5, 280-283]. It is likely that GpcU at the active site represents a nonproductive binding mode for GpU [:Steyaert, J., and Engleborghs (1995) fur. J. Biochem. 233, 140-144]. The results suggest that the active site of ribonuclease T-1 is adapted for optimal tight binding of both the guanylyl 2'-OH and phosphate groups (of GpU) only in the transition state for catalytic transesterification, which is stabilized by adjacent binding of the leaving nucleoside (U) group.

The Fabrication and Characterization of a Nickel Nanoparticle Modified Boron Doped Diamond Electrode for Electrocatalysis of Primary Alcohol Oxidation

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Adsorption of heavy metal ions and epoxidation catalysis using a new polyhedral oligomeric silsesquioxane

The objective of this research was the preparation of a silsesquioxane functionalized with eight chloropropyl chains (T8-PrCl) and of a new derivative functionalized with a pendant linear chain (2-amino-1,3,4-thiadiazole - ATD; T8-Pr-ATD). The two nanostructured materials were characterized by 13C and 29Si NMR, FTIR and elemental analysis. The new nanostructured material, octakis[3-(2-amino-1,3,4-thiadiazole)propyl] octasilsesquioxane (T8-Pr-ATD), was tested as a ligand for transition-metal ions with a special attention to adsorption isotherms. The adsorption was performed using a batchwise process and the organofunctionalized surface showed the ability to adsorb the metal ions Cu (II), Co (II), and Ni (II) from water and ethanol. The adsorption isotherms were fitted by Langmuir, Freundlich, Temkin and Dubinin-Radushkevich (D-R) model. The kinetics of adsorption of metals were performed using three models such as pseudo-first order, pseudo-second order and Elovich. The Langmuir and Elovich models were the most appropriate to describe the adsorption and kinetic data, respectively. Furthermore, the T8-Pr-ATD was successfully applied to the analysis of environmental samples (river and sea water). Subsequently, a new nanomaterial was prepared by functionalization of the T8-Pr-ATD with a Mo (II) organometallic complex (T8-Pr-ATD-Mo). Only a few works in the literature have reported this type of substitution, and none dealt with ATD and Mo (II) complexes. The new Mo-silsesquioxane organometallic nanomaterial was tested as precursor in the epoxidation of cyclooctene and styrene. © 2012 Elsevier B.V.

Hydrogen oxidation on ordered intermetallic phases of platinum and tin - A combined experimental and theoretical study

Hydrogen oxidation on the surfaces of the intermetallic compounds Pt 3Sn, PtSn and PtSn2 has been studied by the rotating disc electrode technique. Pt3Sn and PtSn were found to be good catalysts, about as good as Pt, while PtSn2 was inactive over the investigated range of potentials. Underpotential deposition of hydrogen is observed only on Pt3Sn. These results are explained by theoretical calculations based on a theory developed within our own group, and by density functional theory. © 2012 Elsevier B.V.

Heterogeneous catalysis afford biodiesel of babassu, castor oil and blends

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Synthesis and characterization of 3-[(thiourea)-propyl]-functionalized silica gel and its application in adsorption and catalysis

The objective of this research was the preparation of a silica gel functionalized successively with 3-chloropropyltrimethoxysilane (SG-PrCl) and thiourea (SG-Pr-THIO), and its application in adsorption and catalysis. The materials were characterized by 13C and 29Si NMR, FTIR, scanning electron micrographs (SEM), analysis of nitrogen and elemental analysis. Aiming at its application in adsorption, the [3-(thiourea)-propyl] silica gel (SG-Pr-THIO) was tested as an adsorbent for transition-metal ions using a batchwise process. The organofunctionalized surface showed the ability to adsorb the metal ions Cd(ii), Cu(ii), Ni(ii), Pb(ii) and Co(ii) from water, ethanol and acetone. The adsorption isotherms were fitted by Langmuir, Freundlich, Temkin and Dubinin-Radushkevich (D-R) models. The kinetics of adsorption of metals were performed using three models such as pseudo-first order, pseudo-second order and Elovich. The Langmuir and pseudo-first order models were the most appropriate to describe the adsorption and kinetic data, respectively. With the purpose of application in catalysis, the SG-Pr-THIO was reacted with a Mo(ii) organometallic complex, forming the new material SG-Pr-THIO-Mo. Only a few works in the literature have reported this type of reaction, and none dealt with thiourea and Mo(ii) complexes. The new Mo-silica gel organometallic material was tested as catalyst in the epoxidation of cyclooctene and styrene. © 2013 The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.

Some properties of intermetallic compounds of Sn with noble metals relevant for hydrogen electrocatalysis

Using density functional theory and a model developed in our own group, we have investigated the suitability of three intermetallic compounds - AuSn, PdSn, and PtSn - as electrode materials for hydrogen oxidation in fuel cells, focusing on their CO tolerance and their catalytic properties. All three metals were found to have lower susceptibility to be poisoned by CO compared to platinum, but only PtSn promises to be a good catalyst for hydrogen oxidation. (C) 2013 Elsevier Ltd. All rights reserved.

The oxidation of hydroxylamine on Pt-, and Pd-modified Au electrodes in aqueous electrolytes: Electrochemical and in situ spectroscopic studies

The electrooxidation of hydroxylamine, NH2OH, in 0.1 M phosphate buffer (PB, pH = 7) on Pt-, and Pd-modified Au electrodes prepared by galvanic displacement of underpotential deposited Cu, was investigated by electrochemical techniques and three and in situ vibrational probes, substrate-induced surface enhanced Raman scattering, SI-SERS, surface enhanced infrared absorption, SEIRAS, and Fourier transform infrared reflection-absorption, IRAS, spectroscopies. Analyses of the results obtained made it possible to identify at low overpotentials, solution phase (sol) and adsorbed (ads) nitric oxide, NO, as well as solution phase nitrous oxide, N2O. As the potential was increased, the peak(s) ascribed to NO(ads) gained in intensity and new features associated with NO2−(ads) and NO2−(sol) were clearly discerned. Further excursion toward higher potentials yielded an additional peak assigned to NO2(ads). This behavior is analogous to that found for bare Au electrodes in a potential region in which the metal is at least partially oxidized under otherwise the same experimental conditions.

Oxidation of amino acids by chlorpromazine cation radical and co-catalysis by chlorpromazine

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structural and textural studies of NiO impregnation in mesoporous ZrO2-CeO2 for catalysis applications.

The synthesis of zirconia-based ordered mesoporous structures for catalytic applications is a research area under development. These systems are also potential candidates as anodes in intermediate temperature solid oxide fuel cells (it-SOFC) due to an enhancement on their surface area [1-4]. The structural features of mesoporous zirconia-ceria materials in combination with oxygen storage/release capacity (OSC) are crucial for various catalytic reactions. The direct use of hydrocarbons as fuel for the SOFC (instead of pure H2), without the necessity of reforming and purification reactors can improve global efficiency of these systems [4]. The X-ray diffraction data showed that ZrO2-x%CeO2 samples with x>50 are formed by a larger fraction of the cubic phase (spatial group Fm3m), while for x<50 the major crystalline structure is the tetragonal phase (spatial group P42/nmc). The crystallite size of the cubic phase increases with increase in ceria content. The tetragonal crystallite size decreases when ceria content increases. After impregnation, the Rietveld analysis showed a NiO content around 60wt.% for all samples. The lattice parameters for the ZrO2 tetragonal phase are lower for higher ZrO2 contents, while for all samples the cubic NiO and CeO2 parameters do not present changes. The calculated densities are higher for higher ceria content, as expected. The crystallite size of NiO are similar (~20nm) for all samples and 55nm for the NiO standard. Nitrogen adsorption experiments revealed a broader particle size distribution for higher CeO2 content. The superficial area values were around 35m2/g for all samples, the average pore diameter and pore volumes were higher when increasing ceria content. After NiO impregnation the particle size distribution was the same for all samples, with two pore sizes, the first around 3nm and a broader peak around 10nm. The superficial area increased to approximately 45m2/g for all samples, and the pore volume was also higher after impregnation and increased when ceria content increased. These results point up that the impregnation of NiO improves the textural characteristics of the pristine material. The complementary TEM/EDS images present a homogeneous coating of NiO particles over the ZrO2-x%CeO2 support, showing that these samples are excellent for catalysis applications. [1] D. Y. Zhao, J. Feng, Q. Huo, N. Melosh, G. H. Fredrickson, B. F. Chmelka, G. D. Stucky, Science 279, 548-552 (1998). [2] C. Yu, Y. Yu, D. Zhao, Chem. Comm. 575-576 (2000). [3] A. Trovarelli, M. Boaro, E. Rocchini, C. de Leitenburg, G. Dolcetti, J. Alloys Compd. 323-324 (2001) 584-591. [4] S. Larrondo, M. A. Vidal, B. Irigoyen, A. F. Craievich, D. G. Lamas, I. O. Fábregas, et al. Catal. Today 107–108 (2005) 53-59.

N-Heterocyclic carbene complexes of silver, rhodium and iron: structures, dynamics and catalysis

The research performed in the framework of this Master Thesis has been directly inspired by the recent work of an organometallic research group led by Professor Maria Cristina Cassani on a topic related to the structures, dynamics and catalytic activity of N-heterocyclic carbene-amide rhodium(I) complexes1. A series of [BocNHCH2CH2ImR]X (R = Me, X = I, 1a’; R = Bz, X = Br, 1b’; R = trityl, X = Cl, 1c’) amide-functionalized imidazolium salts bearing increasingly bulky N-alkyl substituents were synthetized and characterized. Subsequently, these organic precursors were employed in the synthesis of silver(I) complexes as intermediate compounds on a way to rhodium(I) complexes [Rh(NBD)X(NHC)] (NHC = 1-(2-NHBoc-ethyl)-3-R-imidazolin-2-ylidene; X = Cl, R = Me (3a’), R = Bz (3b’), R = trityl (3c’); X = I, R = Me (4a’)). VT NMR studies of these complexes revealed a restricted rotation barriers about the metal-carbene bond. However, while the rotation barriers calculated for the complexes in which R = Me, Bz (3a’,b’ and 4a) matched the experimental values, this was not true in the trityl case 3c’, where the experimental value was very similar to that obtained for compound 3b’ and much smaller with respect to the calculated one. In addition, the energy barrier derived for 3c’ from line shape simulation showed a strong dependence on the temperature, while the barriers measured for 3a’,b’ did not show this effect. In view of these results and in order to establish the reasons for the previously found inconsistency between calculated and experimental thermodynamic data, the first objective of this master thesis was the preparation of a series of rhodium(I) complexes [Rh(NBD)X(NHC)] (NHC = 1-benzyl-3-R-imidazolin-2-ylidene; X = Cl, R = Me, Bz, trityl, tBu), containing the benzyl substituent as a chiral probe, followed by full characterization. The second objective of this work was to investigate the catalytic activity of the new rhodium compounds in the hydrosilylation of terminal alkynes for comparison purposes with the reported complexes. Another purpose of this work was to employ the prepared N-heterocyclic ligands in the synthesis of iron(II)-NHC complexes.

N-Heterocyclic carbene complexes of rhodium: structures, dynamics and catalysis

A series of imidazolium salts of the type [BocNHCH2CH2ImR]X (Boc = t-Bu carbamates; Im = imidazole) (R = Me, X = I, 1a; R = Bn, X = Br, 1b; R = Trityl, X = Cl, 1c) and [BnImR’]X (R’ = Me, X = Br, 1d; R’ = Bn, X = Br, 1e; R’ = Trityl, X = Cl, 1g; R’ = tBu, X = Br, 1h) bearing increasingly bulky substituents were synthetized and characterized. Subsequently, these precursors were employed in the synthesis of silver(I)-N-heterocyclic (NHC) complexes as transmetallating reagents for the preparation of rhodium(I) complexes [RhX(NBD)(NHC)] (NHC = 1-(2-NHBoc-ethyl)-3-R-imidazolin-2-ylidene; X = Cl; R = Me, 4a; R = Bn, 4b; R = Trityl, 4c; X = I, R = Me, 5a; NHC = 1-Bn-3-R’-imidazolin-2-ylidene; X = Cl; R’ = Me, 4d, R’ = Bn, 4e, R’ = Trityl, 4g; R’ = tBu, 4h). VT NMR studies of these complexes revealed a restricted rotation barriers about the metal-carbene bond. While the rotation barriers calculated for the complexes in which R = Me, Bn (4a,b,d,e and 5a) matched the experimental values, this was not true for the complexes 4c,g, bearing a trityl group for which the values are much smaller than the calculated ones. Energy barriers for 4c,g, derived from a line shape simulation, showed a strong dependence on the temperature while for 4h the rotational energy barrier is stopped at room temperature. The catalytic activity of the new rhodium compounds was investigated in the hydrosilylation of terminal alkynes and in the addition of phenylboronic acid to benzaldehyde. The imidazolium salts 1d,e were also employed in the synthesis of new iron(II)-NHC complexes. Finally, during a six-months stay at the University of York a new ligand derived from Norharman was prepared and employed in palladium-mediated cross-coupling.

Hyperverzweigte Lacton-Copolymere: enzymatische Synthese, Charakterisierung und Darstellung strukturierter Polymernetzwerke = (Hyperbranched lactone copolymers by enzyme catalysis: synthesis, characterization and preparation of structured polymer networks)

Hyperverzweigte Polymere erfuhren in den letzten Jahren immer mehr Beachtung, da sie im Vergleich zu ihren linearen Analoga besondere Eigenschaften besitzen. Im Jahre 2002 wurde die erste enzymkatalysierte Darstellung hyperverzweigter Poly(epsilon-caprolacton)e (hb-PCL) beschrieben. Hier ermöglichte das Konzept der konkurrierenden ringöffnenden Polymerisation und Polykondensation die Kontrolle der Eigenschaften des dargestellten Polymers. Detaillierte Untersuchungen in Hinblick auf Grenzen und Möglichkeiten, aber auch die Synthese im Technikumsmaßstab sind wesentliche Aspekte dieser Arbeit. Außerdem wird ein neues Konzept eingeführt, das Reknitting genannt wurde. Ziel desselben ist das Recycling kommerziellen, linearen PCLs mittels Umesterung zu hb-PCL durch Enzymkatalyse. Diese hb-PCLs zeigen vergleichbare Eigenschaften zu den aus den Comonomeren dargestellten. Ausgehend von hb-PCL sollte eine geeignete Route zu methacrylierten Vernetzerverbindungen entwickelt werden. Aus Mischungen derselben mit 2-Hydroxyethylmethacrylat wurden komplexe Netzwerkarchitekturen durch Copolymerisation erhalten. Diese Netzwerke wurden in Hinblick auf ihre mechanisch physikalischen Eigenschaften untersucht. Zuletzt wurden Screeningexperimente an anderen zyklischen Estern durchgeführt, da ein Transfer des oben vorgestellten Konzepts angestrebt wurde. Zwei neue hyperverzweigte Polymerklassen, hb-Poly(delta-valerolacton) und hb-Polytrimethylencarbonat wurden detaillierter untersucht und in Ihren Eigenschaften mit hb-PCL verglichen.

First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine

We have performed a series of first-principles electronic structure calculations to examine the reaction pathways and the corresponding free energy barriers for the ester hydrolysis of protonated cocaine in its chair and boat conformations. The calculated free energy barriers for the benzoyl ester hydrolysis of protonated chair cocaine are close to the corresponding barriers calculated for the benzoyl ester hydrolysis of neutral cocaine. However, the free energy barrier calculated for the methyl ester hydrolysis of protonated cocaine in its chair conformation is significantly lower than for the methyl ester hydrolysis of neutral cocaine and for the dominant pathway of the benzoyl ester hydrolysis of protonated cocaine. The significant decrease of the free energy barrier, ∼4 kcal/mol, is attributed to the intramolecular acid catalysis of the methyl ester hydrolysis of protonated cocaine, because the transition state structure is stabilized by the strong hydrogen bond between the carbonyl oxygen of the methyl ester moiety and the protonated tropane N. The relative magnitudes of the free energy barriers calculated for different pathways of the ester hydrolysis of protonated chair cocaine are consistent with the experimental kinetic data for cocaine hydrolysis under physiologic conditions. Similar intramolecular acid catalysis also occurs for the benzoyl ester hydrolysis of (protonated) boat cocaine in the physiologic condition, although the contribution of the intramolecular hydrogen bonding to transition state stabilization is negligible. Nonetheless, the predictability of the intramolecular hydrogen bonding could be useful in generating antibody-based catalysts that recruit cocaine to the boat conformation and an analog that elicited antibodies to approximate the protonated tropane N and the benzoyl O more closely than the natural boat conformer might increase the contribution from hydrogen bonding. Such a stable analog of the transition state for intramolecular catalysis of cocaine benzoyl-ester hydrolysis was synthesized and used to successfully elicit a number of anticocaine catalytic antibodies.