Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design

Use of solvent mapping, based on multiple-copy minimization (MCM) techniques, is common in structure-based drug discovery. The minima of small-molecule probes define locations for complementary interactions within a binding pocket. Here, we present improved methods for MCM. In particular, a Jarvis-Patrick (JP) method is outlined for grouping the final locations of minimized probes into physical clusters. This algorithm has been tested through a study of protein-protein interfaces, showing the process to be robust, deterministic, and fast in the mapping of protein "hot spots." Improvements in the initial placement of probe molecules are also described. A final application to HIV-1 protease shows how our automated technique can be used to partition data too complicated to analyze by hand. These new automated methods may be easily and quickly extended to other protein systems, and our clustering methodology may be readily incorporated into other clustering packages.     

Catalytic Effect of Electric Fields on the Kemp Elimination Reactions with Neutral Bases

The effect of solvent reaction fields and oriented electric fields on the Kemp elimination reaction between methylamine or imidazole and 5-nitrobenzisoxazole has been theoretically studied. The Kemp reaction is the most widely used for the design of new enzymes. Our results, using the SMD continuous model for solvents, are in quite good agreement with the experimental fact that the rate of the analogous reaction with butylamine is one order of magnitude smaller in water than in acetonitrile. In the case of external electric fields, our results show that they can increase or decrease the energy barrier depending on the magnitude and orientation of the field. A duly oriented electric field may have a notable catalytic effect on the reaction. So, external electric fields and reaction fields due to the medium can contribute to the design of new enzymes. Several factors that must be taken into account to increase the catalytic effect are discussed.     

Mathematical modeling of self-oscillations in ethane oxidation over nickel

The methodology of constructing a phenomenological model for complex heterogeneous catalytic reactions is described in detail. The proposed approach is applicable to development of mathematical models describing the onset of self-oscillations in hydrocarbon oxidation on the transition metal surface. The approach is based on construction of a microkinetic scheme taking into account the formation of main reaction products and intermediates, on estimation of the heat of reaction, activation energy, and preexponential factor for elementary steps and includes development and a subsequent analysis of the corresponding mathematical model. Catalytic reactions are considered in the ideal adsorption layer approximation without taking into account the relationship between coverages and spatial coordinates. Accordingly, the mathematical model is an independent system of ordinary differential equations. This methodology is used to develop a point (lumped) model for ethane oxidation over nickel, which is based on a 36-step microkinetic scheme taking into account the oxidation and reduction of nickel and the formation of total (CO₂ and H₂O) or partial (CO and H₂) ethane oxidation products, as well as the dehydrogenation of ethane into ethylene. The proposed model predicts the onset of self-oscillations in this reaction at atmospheric pressure in the temperature range from 850 to 1400 K. The kinetic oscillations are caused by the cyclic oxidation and reduction of nickel. The self-oscillations of the reaction rate are accompanied by oscillations of the catalyst temperature. The results of modeling are compared with experimental data.     

Epoxidation and deoxygenation of single-walled carbon nanotubes: quantification of epoxide defects

Epoxidation of single-walled carbon nanotubes (SWNTs) may be carried out by the reaction of SWNTs with either trifluorodimethyldioxirane or 3-chloroperoxybenzoic acid; the resulting O-SWNTs are spectroscopically similar to those formed by ozonolysis. Quantification of the epoxide substituents is possible through the catalytic de-epoxidation reaction using MeReO3/PPh3 and the 31P NMR spectroscopy. The de-epoxidation methodology may be used to determine that wet air oxidation is preferable to either acid or O2/SF6 purification. We have demonstrated that previously assumed "pure" SWNTs are actually "doped" to a level of at least 1 oxygen per 250 carbon atoms.     

Synthesis of seven-membered lactones via nickel- and zinc-catalyzed highly regio- and stereoselective cyclization of 2-iodobenzyl alcohols with propiolates

A new class of substituted seven-membered lactones 3 were conveniently synthesized via cyclization of o-iodobenzyl alcohol 1 (o-IC(6)H(4)CH(2)OH) with various propiolates 2 (RC triple bond CCOOMe) in the presence of Ni(dppe)Br(2) and Zn powder in acetonitrile at 80 degrees C. The catalytic reaction is highly regio- and stereoselective affording seven-membered lactones in moderate to good yields. This methodology can be successfully extended to various substituted o-iodobenzyl alcohols. An intermediate 7 was obtained from the reaction of 1a with methyl 2-octynoate (2a) in the presence of Ni(dppe)Br(2) and Zn at room temperature. A mechanism involving an unusual E/Z isomerization of the carbon-carbon double bond of 7 prior to lactone formation is proposed to account for the catalytic reaction.     

Clustering of catalytic nanocompartments for enhancing an extracellular non-native cascade reaction

Compartmentalization is fundamental in nature, where the spatial segregation of biochemical reactions within and between cells ensures optimal conditions for the regulation of cascade reactions. While the distance between compartments or their interaction are essential parameters supporting the efficiency of bio-reactions, so far they have not been exploited to regulate cascade reactions between bioinspired catalytic nanocompartments. Here, we generate individual catalytic nanocompartments (CNCs) by encapsulating within polymersomes or attaching to their surface enzymes involved in a cascade reaction and then, tether the polymersomes together into clusters. By conjugating complementary DNA strands to the polymersomes'' surface, DNA hybridization drove the clusterization process of enzyme-loaded polymersomes and controlled the distance between the respective catalytic nanocompartments. Owing to the close proximity of CNCs within clusters and the overall stability of the cluster architecture, the cascade reaction between spatially segregated enzymes was significantly more efficient than when the catalytic nanocompartments were not linked together by DNA duplexes. Additionally, residual DNA single strands that were not engaged in clustering, allowed for an interaction of the clusters with the cell surface as evidenced by A549 cells, where clusters decorating the surface endowed the cells with a non-native enzymatic cascade. The self-organization into clusters of catalytic nanocompartments confining different enzymes of a cascade reaction allows for a distance control of the reaction spaces which opens new avenues for highly efficient applications in domains such as catalysis or nanomedicine.

Compartmentalization is fundamental in nature, where the spatial segregation of biochemical reactions within and between cells ensures optimal conditions for the regulation of cascade reactions.     

Synthesis of a novel multi-SO<Subscript>3</Subscript>H functionalized ionic liquid and its catalytic activities

A novel multi-SO₃H functionalized ionic liquid is synthesized and a detailed account of its catalytic activities in acetalization and acetylation is given. The results showed that the ionic liquid is very efficient in the conventional acid-catalyzed reactions with good to excellent yields within a short reaction time. Operational simplicity, small amounts required, low cost of the catalyst, high yields, scalability and reusability are the key features of this methodology, which indicates the high potentialities of the novel ionic liquid to be used in environmentally friendly processes.     

Combinatorial discovery of reusable noncovalent supports for enzyme immobilization and nonaqueous catalysis

A simple and effective method is described for the preparation of enzyme-containing materials that possess excellent catalytic activity, mechanical strength, and reusability. Uniform spherical beads were produced via the colyophilization of alpha-chymotrypsin with the support materials, leaving the active enzyme entrapped within the porous "ice-templated" support matrix. The composites were assayed for catalytic activity by monitoring a nonaqueous transesterification reaction. The mechanical strength for each composite was measured using a compression assay. Initial screens identified a set of six support materials that contributed favorably to either the enzyme activity or to the mechanical strength of the composite. A design of experiments (DoE) methodology was employed to screen 80 combinations of these six "base" materials. A model representing this formulation space was constructed which could be used to predict both the catalytic activity and mechanical strength with reasonable accuracy for any combination of the six base component materials. This model was used to predict optimized materials with an enzyme activity that was 50 times greater than that of the free enzyme. The model was also used to set a minimum acceptable mechanical stability for these composites, and the resulting materials were shown to be reusable for at least ten reaction cycles.     

Chiral nonracemic late-transition-metal organometallics with a metal-bonded stereogenic carbon atom: development of new tools for asymmetric organic synthesis

Transition-metal-catalyzed cross-coupling reactions and the Heck reaction have evolved into powerful tools for the construction of carbon-carbon bonds. In most cases, the reactive organometallic intermediates feature a carbon-transition-metal sigma bond between a sp(2)-hybridized carbon atom and the transition metal (Csp(2)--TM). New, and potentially more powerful approach to transition-metal-catalyzed asymmetric organic synthesis would arise if catalytic chiral nonracemic organometallic intermediates with a stereogenic sp(3)-hybridized carbon atoms directly bonded to the transition metal (C*sp(3)--TM bond) could be formed from racemic or achiral organic substrates, and subsequently participate in the formation of a new carbon-carbon bond (C*sp(3)-C) with retention of the stereochemical information. To date, only a few catalytic processes that are based on this concept, have been developed. In this account, both "classical" and recent studies on preparation and reactivity of stable chiral nonracemic organometallics with a metal-bonded stereogenic carbon, which provide the foundation for the future design of new synthetic transformations exploiting the outlined concept, are discussed, along with examples of relevant catalytic processes.     

Mesoscopic model for diffusion-influenced reaction dynamics

A hybrid mesoscopic multiparticle collision model is used to study diffusion-influenced reaction kinetics. The mesoscopic particle dynamics conserves mass, momentum, and energy so that hydrodynamic effects are fully taken into account. Reactive and nonreactive interactions with catalytic solute particles are described by full molecular dynamics. Results are presented for large-scale, three-dimensional simulations to study the influence of diffusion on the rate constants of the A + C <==> B + C reaction. In the limit of a dilute solution of catalytic C particles, the simulation results are compared with diffusion equation approaches for both the irreversible and reversible reaction cases. Simulation results for systems where the volume fraction phi of catalytic spheres is high are also presented, and collective interactions among reactions on catalytic spheres that introduce volume fraction dependence in the rate constants are studied.     

Reaction progress kinetic analysis: a powerful methodology for mechanistic studies of complex catalytic reactions

Reaction progress kinetic analysis to obtain a comprehensive picture of complex catalytic reaction behavior is described. This methodology employs in situ measurements and simple manipulations to construct a series of graphical rate equations that enable analysis of the reaction to be accomplished from a minimal number of experiments. Such an analysis helps to describe the driving forces of a reaction and may be used to help distinguish between different proposed mechanistic models. This Review describes the procedure for undertaking such analysis for any new reaction under study.     

Structural reorganization and preorganization in enzyme active sites: comparisons of experimental and theoretically ideal active site geometries in the multistep serine esterase reaction cycle

Many enzymes catalyze reactions with multiple chemical steps, requiring the stabilization of multiple transition states during catalysis. Such enzymes must strike a balance between the conformational reorganization required to stabilize multiple transition states of a reaction and the confines of a preorganized active site in the polypeptide tertiary structure. Here we investigate the compromise between structural reorganization during the catalytic process and preorganization of the active site for a multistep enzyme-catalyzed reaction, the hydrolysis of esters by the Ser-His-Asp/Glu catalytic triad. Quantum mechanical transition states were used to generate ensembles of geometries that can catalyze each individual step in the mechanism. These geometries are compared to each other by superpositions of catalytic atoms to find "consensus" geometries that can catalyze all steps with minimal rearrangement. These consensus geometries are found to be excellent matches for the natural active site. Preorganization is therefore found to be the major defining characteristic of the active site, and reorganizational motions often proposed to promote catalysis have been minimized. The variability of enzyme active sites observed by X-ray crystallography was also investigated empirically. A catalog of geometrical parameters relating active site residues to each other and to bound inhibitors was collected from a set of crystal structures. The crystal-structure-derived values were then compared to the ranges found in quantum mechanically optimized structures along the entire reaction coordinate. The empirical ranges are found to encompass the theoretical ranges when thermal fluctuations are taken into account. Therefore, the active sites are preorganized to a geometry that can be objectively and quantitatively defined as minimizing conformational reorganization while maintaining optimal transition state stabilization for every step during catalysis. The results provide a useful guiding principle for de novo design of enzymes with multistep mechanisms.     

Rhodium-catalyzed enantioselective diboration of simple alkenes

Enantioselective catalytic reactions that operate directly on inexpensive unactivated alkenes are extraordinarily useful for the preparation of chiral organic building blocks and new materials. While a number of such processes have been developed, our ability to meet the intensifying demand for inexpensive stereochemically complex materials will require a significant expansion of practical catalytic asymmetric reaction methodology. In this regard, the rhodium-catalyzed enantioselective diboration reaction has been developed in order to address a number of extant problems in catalytic alkene transformation simultaneously. This process provides an enantiomerically enriched reactive dimetalated intermediate which can be converted to a variety of difunctional reaction products.     

Spatial regulation of the catalyst activity enhancement for catalytic reactions with stop-effect

A kinetic model taking into account two types of active sites has been used for an analysis of factors influencing the rate of a catalytic reaction. It has been shown that the reaction rate can be significantly increased by performing the reaction with the “stop-effect” in a dual-reactor system due to the catalyst circulation between two reactors, one of which is purged with an inert gas.     

Study of a new rate increasing "base effect" in the palladium-catalyzed amination of aryl iodides

Evidence for an interphase deprotonation of Pd(II)-amine complexes with weak carbonate base has been gained for the first time. When a rate-limiting deprotonation step is involved in the catalytic cycle, controlling the structure (shape and size of the particles) and/or molar excess of the carbonate base used can significantly increase the reaction rate of Buchwald-Hartwig aminations. By taking such a "base effect" into account a general protocol for the intermolecular amination of aryl iodides with all types of amines has been developed based on a standard Pd-BINAP catalyst, using cesium carbonate as the base.     

BINOLAM,a recoverable chiral ligand for bifunctional enantioselective catalysis: the asymmetric synthesis of cyanohydrins

[reaction: see text] A new bifunctional catalytic system based on a monometallic aluminum complex is used for the efficient enantioselective cyanation of aldehydes. The ligand (S)- or (R)-2,2'-bis(diethylaminomethyl)-substituted binaphthol (BINOLAM) used is recovered for recycling. This methodology is used for the synthesis of a precursor of epothilone A.     

A systematic docking approach. Application to the α-cyclodextrin/phenyl-ethanol complex

A new approach for systematic docking is applied to the structure of the -cyclodextrin/phenyl-ethanol complex. This methodology includes systematic scanning of the possible guest positions, clustering of low energy structures into families and final refinement using molecular mechanics. The clustering was performed on internal parameters of the complex by a program named PROXIM based on a very simple proximity criterion. This program organized nearly 30 000 structures into about 100 families. Thirty conformations have been considered (10 and 20 for the complexation on the primary and secondary face respectively), the two forms of complexation encountered in the crystal packing yield the lowest energy combination.