Crystal and molecular structure of paclitaxel (taxol).

Paclitaxel (formerly called taxol), an important anticancer drug, inhibits cell replication by binding to and stabilizing microtubule polymers. As drug-receptor interactions are governed by the three-dimensional stereochemistries of both participants, we have determined the crystal structure of paclitaxel to identify its conformational preferences that may be related to biological activity. The monoclinic crystals contain two independent paclitaxel molecules in the asymmetric unit plus several water and dioxane solvent molecules. Taxane ring conformation is very similar in both paclitaxel molecules and is similar to the taxane ring conformation found in the crystal structure of the paclitaxel analogue docetaxel (formerly called taxotere). The two paclitaxel molecules have carbon-13 side-chain conformations that differ from each other and from that of the corresponding side chain in the docetaxel crystal structure. The carbon-13 side-chain conformation of one paclitaxel molecule is similar to what was proposed from NMR studies done in polar solvents, while that of the other paclitaxel molecule is different and hitherto unobserved. The paclitaxel molecules interact with each other and with solvent atoms through an extensive network of hydrogen bonds. Analysis of the hydrogen-bonding network together with structure-activity studies may suggest which atoms of paclitaxel are important for binding to microtubule receptors.

Definition of a metal-dependent/Li(+)-inhibited phosphomonoesterase protein family based upon a conserved three-dimensional core structure.

Inositol polyphosphate 1-phosphatase, inositol monophosphate phosphatase, and fructose 1,6-bisphosphatase share a sequence motif, Asp-Pro-(Ile or Leu)-Asp-(Gly or Ser)-(Thr or Ser), that has been shown by crystallographic and mutagenesis studies to bind metal ions and participate in catalysis. We compared the six alpha-carbon coordinates of this motif from the crystal structures of these three phosphatases and found that they are superimposable with rms deviations ranging from 0.27 to 0.60 A. Remarkably, when these proteins were aligned by this motif a common core structure emerged, defined by five alpha-helices and 11 beta-strands comprising 155 residues having rms deviations ranging from 1.48 to 2.66 A. We used the superimposed structures to align the sequences within the common core, and a distant relationship was observed suggesting a common ancestor. The common core was used to align the sequences of several other proteins that share significant similarity to inositol monophosphate phosphatase, including proteins encoded by fungal qa-X and qutG, bacterial suhB and cysQ (identical to amtA), and yeast met22 (identical to hal2). Evolutionary comparison of the core sequences indicate that five distinct branches exist within this family. These proteins share metal-dependent/Li(+)-sensitive phosphomonoesterase activity, and each predicted tree branch exhibits unique substrate specificity. Thus, these proteins define an ancient structurally conserved family involved in diverse metabolic pathways including inositol signaling, gluconeogenesis, sulfate assimilation, and possibly quinone metabolism. Furthermore, we suggest that this protein family identifies candidate enzymes to account for both the therapeutic and toxic actions of Li+ as it is used in patients treated for manic depressive disease.

CC-1065 and the duocarmycins: unraveling the keys to a new class of naturally derived DNA alkylating agents.

Key studies defining the DNA alkylation properties and selectivity of a new class of exceptionally potent, naturally occurring antitumor antibiotics including CC-1065, duocarmycin A, and duocarmycin SA are reviewed. Recent studies conducted with synthetic agents containing deep-seated structural changes and the unnatural enantiomers of the natural products and related analogs have defined the structural basis for the sequence-selective alkylation of duplex DNA and fundamental relationships between chemical structure, functional reactivity, and biological properties. The agents undergo a reversible, stereoelectronically controlled adenine-N3 addition to the least substituted carbon of the activated cyclopropane within selected AT-rich sites. The preferential AT-rich non-covalent binding selectivity of the agents within the narrower, deeper AT-rich minor groove and the steric accessibility to the alkylation site that accompanies deep AT-rich minor groove penetration control the sequence-selective DNA alkylation reaction and stabilize the resulting adduct. For the agents that possess sufficient reactivity to alkylate DNA, a direct relationship between chemical or functional stability and biological potency has been defined.

The Adsorption of Polyatomic Molecules on Carbon Surfaces

Carbon nanotubes exhibit the structure and chemical properties that make them apt substrates for many adsorption applications. Of particular interest are carbon nanotube bundles, whose unique geometry is conducive to the formation of pseudo-one-dimensional phases of matter, and graphite, whose simple planar structure allows ordered phases to form in the absence of surface effects. Although both of these structures have been the focus of many research studies, knowledge gaps still remain. Much of the work with carbon nanotubes has used simple adsorbates1-43, and there is little kinetic data available. On the other hand, there are many studies of complex molecules adsorbing on graphite; however, there is almost no kinetic data reported for this substrate. We seek to close these knowledge gaps by performing a kinetic study of linear molecules of increasing length adsorbing on carbon nanotube bundles and on graphite. We elucidated the process of adsorption of complex admolecules on carbon nanotube bundles, while at the same time producing some of the first equilibrium results of the films formed by large adsorbates on these structures. We also extended the current knowledge of adsorption on graphite to include the kinetics of adsorption. The kinetic data that we have produced enables a more complete understanding of the process of adsorption of large admolecules on carbon nanotube bundles and graphite. We studied the adsorption of particles on carbon nanotube bundles and graphite using analytical and computational techniques. By employing these methods separately but in parallel, we were able to constantly compare and verify our results. We calculated and simulated the behavior of a given system throughout its evolution and then analyzed our results to determine which system parameters have the greatest effect on the kinetics of adsorption. Our analytical and computational results show good agreement with each other and with the experimental isotherm data provided by our collaborators. As a result of this project, we have gained a better understanding of the kinetics of adsorption. We have learned about the equilibration process of dimers on carbon nanotube bundles, identifying the “filling effect”, which increases the rate of total uptake, and explaining the cause of the transient “overshoot” in the coverage of the surface. We also measured the kinetic effect of particle-particle interactions between neighboring adsorbates on the lattice. For our simulations of monomers adsorbing on graphite, we succeeded in developing an analytical equation to predict the characteristic time as a function of chemical potential and of the adsorption and interaction energies of the system. We were able to further explore the processes of adsorption of dimers and trimers on graphite (again observing the filling effect and the overshoot). Finally, we were able to show that the kinetic behaviors of monomers, dimers, and trimers that have been reported in experimental results also arise organically from our model and simulations.

Hydrogen storage in CO2-activated amorphous nanofibers and their monoliths

Amorphous carbon nanofibers (CNFs), produced by the polymer blend technique, are activated by CO2 (ACNFs). Monoliths are synthesized from the precursor and from some ACNFs. Morphology and textural properties of these materials are studied. When compared with other activating agents (steam and alkaline hydroxides), CO2 activation renders suitable yields and, contrarily to most other precursors, turns out to be advantageous for developing and controlling their narrow microporosity (< 0.7 nm), VDR(CO2). The obtained ACNFs have a high compressibility and, consequently, a high packing density under mechanical pressure which can also be maintained upon monolith synthesis. H2 adsorption is measured at two different conditions (77 K / 0.11 MPa, and 298 K / 20 MPa) and compared with other activated carbons. Under both conditions, H2 uptake depends on the narrow microporosity of the prepared ACNFs. Interestingly, at room temperature these ACNFs perform better than other activated carbons, despite their lower porosity developments. At 298 K they reach a H2 adsorption capacity as high as 1.3 wt.%, and a remarkable value of 1 wt.% in its mechanically resistant monolith form.

Tailoring the surface chemistry of zeolite templated carbon by electrochemical methods

One option to optimize carbon materials for supercapacitor applications is the generation of surface functional groups that contribute to the pseudocapacitance without losing the designed physical properties. This requires suitable functionalization techniques able to selectively introduce a given amount of electroactive oxygen groups. In this work, the influence of the chemical and electrochemical oxidation methods, on the chemical and physical properties of a zeolite templated carbon (ZTC), as a model carbon material, have been studied and compared. Although both oxidation methods generally produce a loss of the original ZTC physical properties with increasing amount of oxidation, the electrochemical method shows much better controllability and, unlike chemical treatments, enables the generation of a large number of oxygen groups (O = 11000- 3300 μmol/g), with a higher proportion of active functionalities, while retaining a high surface area (ranging between 1900-3500 m2/g), a high microporosity and an ordered 3-D structure.

Theoretical insights on electron donor-acceptor interactions involving carbon dioxide

Electron donor-acceptor (EDA) interactions are widely involved in chemistry and their understanding is essential to design new technological applications in a variety of fields ranging from material sciences and chemical engineering to medicine. In this work, we study EDA complexes of carbon dioxide with ketones using several ab initio and Density Functional Theory methods. Energy contributions to the interaction energy have been analyzed in detail using both variational and perturbational treatments. Dispersion energy has been shown to play a key role in explaining the high stability of a non-conventional structure, which can roughly be described by a cooperative EDA interaction.

Dense carbon monoliths for supercapacitors with outstanding volumetric capacitances

A commercially available dense carbon monolith (CM) and four carbon monoliths obtained from it have been studied as electrochemical capacitor electrodes in a two-electrode cell. CM has: (i) very high density (1.17 g cm−3), (ii) high electrical conductivity (9.3 S cm−1), (iii) well-compacted and interconnected carbon spheres, (iv) homogeneous microporous structure and (v) apparent BET surface area of 957 m2g−1. It presents interesting electrochemical behaviors (e.g., excellent gravimetric capacitance and outstanding volumetric capacitance). The textural characteristics of CM (porosity and surface chemistry) have been modified by means of different treatments. The electrochemical performances of the starting and treated monoliths have been analyzed as a function of their porous textures and surface chemistry, both on gravimetric and volumetric basis. The monoliths present high specific and volumetric capacitances (292 F g−1 and 342 F cm−3), high energy densities (38 Wh kg−1 and 44 Wh L−1), and high power densities (176 W kg−1 and 183 W L−1). The specific and volumetric capacitances, especially the volumetric capacitance, are the highest ever reported for carbon monoliths. The high values are achieved due to a suitable combination of density, electrical conductivity, porosity and oxygen surface content.

Electrochemical generation of oxygen-containing groups in an ordered microporous zeolite-templated carbon

Zeolite templated carbon (ZTC) was electrochemically oxidized under various conditions, and its chemistry and structural evolution were compared to those produced by conventional chemical oxidation. In both oxidation methods, a general loss of the original structure regularity and high surface area was observed with increasing amount of oxidation. However, the electrochemical method showed much better controllability and enabled the generation of a large number of oxygen functional groups while retaining the original structure of the ZTC. Unlike chemical treatments, highly microporous carbons with an ordered 3-D structure, high surface area (ranging between 1900 and 3500 m2/g) and a large number of oxygen groups (O = 11,000–3300 μmol/g), have been prepared by the electrochemical method. Some insights into the electrooxidation mechanism of carbon materials are proposed from the obtained polarization curves, using ZTC as a model carbon material.

Tailoring the porosity of chemically activated hydrothermal carbons: Influence of the precursor and hydrothermal carbonization temperature

Advanced porous materials with tailored porosity (extremely high development of microporosity together with a narrow micropore size distribution (MPSD)) are required in energy and environmental related applications. Lignocellulosic biomass derived HTC carbons are good precursors for the synthesis of activated carbons (ACs) via KOH chemical activation. However, more research is needed in order to tailor the microporosity for those specific applications. In the present work, the influence of the precursor and HTC temperature on the porous properties of the resulting ACs is analyzed, remarking that, regardless of the precursor, highly microporous ACs could be generated. The HTC temperature was found to be an extremely influential parameter affecting the porosity development and the MPSD of the ACs. Tuning of the MPSD of the ACs was achieved by modification of the HTC temperature. Promising preliminary results in gas storage (i.e. CO2 capture and high pressure CH4 storage) were obtained with these materials, showing the effectiveness of this synthesis strategy in converting a low value lignocellulosic biomass into a functional carbon material with high performance in gas storage applications.

Factors governing the adsorption of ethanol on spherical activated carbons

Ethanol adsorption on different activated carbons (mostly spherical ones) was investigated covering the relative pressure range from 0.001 to 1. Oxygen surface contents of the ACs were modified by oxidation (in HNO3 solution or air) and/or by thermal treatment in N2. To differentiate the concomitant effects of porosity and oxygen surface chemistry on ethanol adsorption, different sets of samples were used to analyze different relative pressure ranges (below 1000 ppmv concentration and close to unity). To see the effect of oxygen surface chemistry, selected samples having similar porosity but different oxygen contents were studied in the low relative pressure range. At low ethanol concentration (225 ppmv) adsorption is favored in oxidized samples, remarking the effect of the oxidizing treatment used (HNO3 is more effective than air) and the type of oxygen functionalities created (carboxyl and anhydride groups are more effective than phenolic, carbonyl and derivatives). To analyze the high relative pressure range, spherical and additional ACs were used. As the relative pressure of ethanol increases, the effect of oxygen-containing surface groups decreases and microporosity becomes the most important variable affecting the adsorption of ethanol.

The structure of a PII signaling protein from a halophilic archaeon reveals novel traits and high-salt adaptations

To obtain insights into archaeal nitrogen signaling and haloadaptation of the nitrogen/carbon/energy-signaling protein PII, we determined crystal structures of recombinantly produced GlnK2 from the extreme halophilic archaeon Haloferax mediterranei, complexed with AMP or with the PII effectors ADP or ATP, at respective resolutions of 1.49 Å, 1.45 Å, and 2.60 Å. A unique trait of these structures was a three-tongued crown protruding from the trimer body convex side, formed by an 11-residue, N-terminal, highly acidic extension that is absent from structurally studied PII proteins. This extension substantially contributed to the very low pI value, which is a haloadaptive trait of H. mediterranei GlnK2, and participated in hexamer-forming contacts in one crystal. Similar acidic N-extensions are shown here to be common among PII proteins from halophilic organisms. Additional haloadaptive traits prominently represented in H. mediterranei GlnK2 are a very high ratio of small residues to large hydrophobic aliphatic residues, and the highest ratio of polar to nonpolar exposed surface for any structurally characterized PII protein. The presence of a dense hydration layer in the region between the three T-loops might also be a haloadaptation. Other unique findings revealed by the GlnK2 structure that might have functional relevance are: the adoption by its T-loop of a three-turn α-helical conformation, perhaps related to the ability of GlnK2 to directly interact with glutamine synthetase; and the firm binding of AMP, confirmed by biochemical binding studies with ATP, ADP, and AMP, raising the possibility that AMP could be an important PII effector, at least in archaea.

Effect of the surface chemical groups of activated carbons on their surface adsorptivity to aromatic adsorbates based on π-π interactions

Three activated carbons with different surface chemical groups were used to analyse the influence of these groups on their adsorption capacities towards aromatic-type molecules whose adsorption is based on π-π interactions with surface arene centres. The three activated carbons studied were a low-functionalized carbon (Merck), an oxygen-rich carbon obtained by HNO3 oxidation of Merck, and a nitrogen-rich carbon also prepared from Merck by mild HNO3 oxidation followed by treatment with a dicyanodiamide/dimethyl formamide mixture at 300 °C. The nature of the surface chemical groups of the three activated carbons was investigated by both physical and chemical techniques (TPD, XPS, Boehm analysis and pH potentiometric titration). A systematic study of the adsorptions of a series of analogous aromatic adsorbates on the three activated carbons was carried out to study the adsorption mechanisms. In all cases the adsorption mechanism is based on π-π interactions between the aromatic moiety of the adsorbates and the arene centres of the graphite sheets. The differences in the normalized adsorption capacities of the adsorbents for a set of adsorbates indicate that the π-donor or π-withdrawing character of the functional groups have a clear influence on the basicity of the arene centres.

Non-covalent immobilization of RhDuphos on carbon nanotubes and carbon xerogels

The immobilization of the chiral complex RhDuphos, by electrostatic or π–π (adsorption) interactions, on carbon nanotubes and carbon xerogels is investigated. To promote such interactions, the supports were either oxidized or heat treated to create carboxylic type surface groups or an apolar surface, respectively. The catalysts were tested in the hydrogenation of methyl 2-acetamidoacrylate. The prepared hybrid catalysts are less active than the homogeneous RhDuphos, but most of them show a high enantioselectivity and the one prepared with the oxidized carbon xerogel is also reusable, being able to give a high substrate conversion, keeping as well a high enantioselectivity. The anchorage by electrostatic interactions is more interesting than the anchorage by π–π interactions, as the π–π adsorption method produces a modification of the metal complex structure leading to an active hybrid catalyst but without enantioselectivity. The creation of carboxylic groups on the support surface has led to some hindering of the complex leaching.

Very high methane uptake on activated carbons prepared from mesophase pitch: A compromise between microporosity and bulk density

Two petroleum residues were pyrolyzed under two different conditions to obtain pitches with low or high mesophase content. The effect of the KOH: precursor ratio and the activation temperature on the packing density and porous texture of the carbons have been studied and optimized. Activated carbons combining high micropore volume (>1 cm3/g) and high packing density (0.7 g/cm3) have been successfully prepared. Regarding excess methane adsorption capacities, the best results (160 cm3 (STP)/cm3 at 25 °C and 3.5 MPa) were obtained using the pitch with the higher content of the more organized mesophase, activated at relatively low temperature (700 °C), with a medium KOH: precursor ratio (3:1). Some of the activated carbons exhibit enhanced adsorption capacity at high pressure, giving values as high as 175 cm3 (STP)/cm3 at 25 °C and 5 MPa and 200 cm3 (STP)/cm3 at 25 °C and 10 MPa (the same amount as in an empty cylinder but at half of the pressure), indicating a contribution of large micropores and narrow mesopores to adsorption at high pressure. The density of methane in pores between 1 and 2.5 nm at pressure up to 10 MPa was estimated to understand their contribution to the total adsorption capacity.