Dynamic effects on reaction rates in a Michael addition catalyzed by chalcone isomerase. Beyond the frozen environment approach

We present a detailed microscopic study of the dynamics of the Michael addition reaction leading from 6'-deoxychalcone to the corresponding flavanone. The reaction dynamics are analyzed for both the uncatalyzed reaction in aqueous solution and the reaction catalyzed by Chalcone Isomerase. By means of rare event simulations of trajectories started at the transition state, we have computed the transmission coefficients, obtaining 0.76 +/- 0.04 and 0.87 +/- 0.03, in water and in the enzyme, respectively. According to these simulations, the Michael addition can be seen as a formation of a new intramolecular carbon-oxygen bond accompanied by a charge transfer essentially taking place from the nucleophilic oxygen to the carbon atom adjacent to the carbonyl group (C (alpha)). As for intermolecular interactions, we find a very significant difference in the evolving solvation pattern of the nucleophilic oxygen in water and in the enzyme. While in the former medium this atom suffers an important desolvation, the enzyme provides, through variations in the distances with some residues and water molecules, an essentially constant electric field on this atom along the reaction progress. Grote-Hynes (GH) theory provides a useful framework to systematically analyze all the couplings between the reaction coordinate and the remaining degrees of freedom. This theory provides transmission coefficients in excellent agreement with the Molecular Dynamics estimations. In contrast, neither the frozen environment approach nor Kramers theory gives results of similar quality, especially in the latter case, where the transmission coefficients are severely underestimated. The (unusual) failure of the frozen environment approach signals the importance of some dynamical motions. Within the context of GH theory, analysis of the friction spectrum obtained in the enzymatic environment, together with normal-mode analysis, is used to identify those motions, of both the substrate and the environment, strongly coupled to the reaction coordinate and to classify them as dynamically active or inactive.     

A quantum mechanics study on the reaction mechanism of chalcone formation from p-coumaroyl-CoA and malonyl-CoA catalyzed by chalcone synthase

Chalcone synthase catalyzes formation of phenylpropanoid chalcone from one p-coumaroyl-coenzyme A (CoA) and three malonyl-CoA molecules. In order to elucidate structural and energetic features of the reaction mechanism, we performed the quantum mechanics calculations and obtained the following results. In loading step, only a tetrahedral intermediate is located without transition state (TS). Our results indicate that His303 acts as a H₃₁ donor, but not a hydrogen bond donor, to stabilize the intermediate formation. In decarboxylation step, the reaction proceeds via a TS and is sensitive to the environment. In elongation step, a tetrahedral TS is located. All of the results above support the reaction mechanism and further complement the proposal of Noel JP et al.     

Comparative TOF-SIMS and MALDI TOF-MS analysis on different chromatographic planar substrates

A comparison is made between two high resolution, surface-based, mass spectrometric methods: time-of-flight secondary ion mass spectrometry (TOF-SIMS) and matrix-assisted laser desorption/ionisation mass spectrometry (MALDI TOF-MS) in indication of abietic and gibberellic acids molecular profiles on different chromatographic thin layers. The analytes were applied to silica gel chromatographic thin layers with SIMS on-line interfacing channel, monolithic silica gel ultra-thin layers, and thin layers specifically designed for direct Raman spectroscopic analysis. Two MALDI matrices were used in this research: ferulic acid and 2,5-dihydroxybenzoic acid. The silica gel SIMS-interfacing channel strongly supported formation of numerous different MALDI MS fragments with abietic and gibberellic acids, and ferulic acid matrix. The most intense fragments belonged to [M-OH](+) and [M](+) ions from ferulic acid. Intense conjugates were detected with gibberellic acid. The MALDI MS spectrum from the monolithic silica gel surface showed very low analyte signal intensity and it was not possible to obtain MALDI spectra from a Raman spectroscopy treated chromatographic layer. The MALDI TOF MS gibberellic acid fragmentation profile was shielded by the matrix used and was accompanied by poor analyte identification. The most useful TOF-SIMS analytical signal response was obtained from analytes separated on monolithic silica gel and a SIMS-interfacing modified silica gel surface. New horizons with nanostructured surfaces call for high resolution MS methods (which cannot readily be miniaturised like many optical and electrochemical methods) to be integrated in chip and nanoscale detection systems.     

First computational evidence for a catalytic bridging hydroxide ion in a phosphodiesterase active site.

Phosphodiesterases are clinical targets for a variety of biological disorders, because this superfamily of enzymes regulates the intracellular concentration of cyclic nucleotides that serve as the second messengers playing a critical role in a variety of physiological processes. Understanding the structure and mechanism of a phosphodiesterase will provide a solid basis for rational design of the more efficient therapeutics. Although a three-dimensional X-ray crystal structure of the catalytic domain of human phosphodiesterase 4B2B was recently reported, it is uncertain whether a critical bridging ligand in the active site is a water molecule or a hydroxide ion. The identity of this bridging ligand is theoretically determined by performing first-principles quantum chemical calculations on models of the active site. All the results obtained indicate that this critical bridging ligand in the active site of the reported X-ray crystal structure is a hydroxide ion, rather than a water molecule, expected to serve as the nucleophile to initialize the catalytic degradation of the intracellular second messengers.     

Atypical protonation states in the active site of HIV-1 protease: a computational study

The HIV protease (HIVP) is a prominent example for successful structure-based drug design. Besides its pharmaceutical impact, it is a well-studied system for which, as experimentally evidenced, protonation changes in the active site occur upon ligand binding. Therefore, it serves as an ideal candidate for a case study using our newly developed partial charge model, which was optimized toward the application of Poisson-Boltzmann based pK(a) calculations. The charge model suggests reliably experimentally determined protonation states in the active site of HIVP. Furthermore, we perform pKa calculations for two HIVP complexes with novel types of inhibitors developed and synthesized in our group. For these complexes, no experimental knowledge about the protonation states is given. For one of the compounds, containing a central pyrrolidine ring, the calculations predict that both catalytic aspartates should be deprotonated upon ligand binding.     

Relative stability of the open and closed conformations of the active site loop of streptavidin

The eight-residue surface loop, 45-52 (Ser, Ala, Val, Gly, Asn, Ala, Glu, Ser), of the homotetrameric protein streptavidin has a "closed" conformation in the streptavidin-biotin complex, where the corresponding binding affinity is one of the strongest found in nature (ΔG ～ -18 kcal∕mol). However, in most of the crystal structures of apo (unbound) streptavidin, the loop conformation is "open" and typically exhibits partial disorder and high B-factors. Thus, it is plausible to assume that the loop structure is changed from open to closed upon binding of biotin, and the corresponding difference in free energy, ΔF = F(open) - F(closed) in the unbound protein, should therefore be considered in the total absolute free energy of binding. ΔF (which has generally been neglected) is calculated here using our "hypothetical scanning molecular-dynamics" (HSMD) method. We use a protein model in which only the atoms closest to the loop are considered (the "template") and they are fixed in the x-ray coordinates of the free protein; the x-ray conformation of the closed loop is attached to the same (unbound) template and both systems are capped with the same sphere of TIP3P water. Using the force field of the assisted model building with energy refinement (AMBER), we carry out two separate MD simulations (at temperature T = 300 K), starting from the open and closed conformations, where only the atoms of the loop and water are allowed to move (the template-water and template-loop interactions are considered). The absolute F(open) and F(closed) (of loop + water) are calculated from these trajectories, where the loop and water contributions are obtained by HSMD and a thermodynamic integration (TI) process, respectively. The combined HSMD-TI procedure leads to total (loop + water) ΔF = -27.1 ± 2.0 kcal∕mol, where the entropy TΔS constitutes 34% of ΔF, meaning that the effect of S is significant and should not be ignored. Also, ΔS is positive, in accord with the high flexibility of the open loop observed in crystal structures, while the energy ΔE is unexpectedly negative, thus also adding to the stability of the open loop. The loop and the 250 capped water molecules are the largest system studied thus far, which constitutes a test for the efficiency of HSMD-TI; this efficiency and technical issues related to the implementation of the method are also discussed. Finally, the result for ΔF is a prediction that will be considered in the calculation of the absolute free energy of binding of biotin to streptavidin, which constitutes our next project.     

Do active site conformations of small ligands correspond to low free-energy solution structures?

We compare the low free energy structures of ten small, polar ligands in solution to their conformations in their respective receptor active sites. The solution conformations are generated by a systematic search and the free energies of representative structures are computed with a continuum solvation model. Based on the values of torsion angles, we find little similarity between low energy solution structures of small ligands and their active site conformations. However, in nine out of ten cases, the positions of 'anchor points' (key atoms responsible for tight binding) in the lowest energy solution structures are very similar to the positions of these atoms in the active site conformations. A metric that more closely captures the essentials of binding supports the basic premise underlying pharmacophore mapping, namely that active site conformations of small flexible ligands correspond to their low energy structures in solution. This work supports the efforts of building pharmacophore models based on the information present in solution structures of small isolated ligands.     

Refining the active site structure of iron-iron hydrogenase using computational infrared spectroscopy

Iron-iron hydrogenases ([FeFe]H2ases) are exceptional natural catalysts for the reduction of protons to dihydrogen. Future biotechnological applications based on these enzymes require a precise understanding of their structures and properties. Although the [FeFe]H2ases have been characterized by single-crystal X-ray crystallography and a range of spectroscopic techniques, ambiguities remain regarding the details of the molecular structures of the spectroscopically observed forms. We use density functional theory (DFT) computations on small-molecule computational models of the [FeFe]H2ase active site to address this problem. Specifically, a series of structural candidates are geometry optimized and their infrared (IR) spectra are simulated using the computed C-O and C-N stretching frequencies and infrared intensities. Structural assignments are made by comparing these spectra to the experimentally determined IR spectra for each form. The H red form is assigned as a mixture of an Fe(I)Fe(I) form with an open site on the distal iron center and either a Fe(I)Fe(I) form in which the distal cyanide has been protonated or a Fe(II)Fe(II) form with a bridging hydride ligand. The Hox form is assigned as a valence-localized Fe(I)Fe(II) redox level with an open site at the distal iron. The Hox(air)(ox) form is assigned as an Fe(II)Fe(II) redox level with OH(-) or OOH(-) bound to the distal iron center that may or may not have an oxygen atom bound to one of the sulfur atoms of the dithiolate linker. Comparisons of the computed IR spectra of the (12)CO and (13)CO inhibited form with the experimental IR spectra show that exogenous CO binds terminally to the distal iron center.     

Characterization of an RNA active site: interactions between a Diels-Alderase ribozyme and its substrates and products

Ribozymes have recently been shown to catalyze the stereoselective formation of carbon-carbon bonds between small organic molecules. The interactions of these Diels-Alderase ribozymes with their substrates and products have now been elucidated by chemical substitution analysis by using 44 different, systematically varied analogues. RNA-diene interaction is governed by stacking interactions, while hydrogen bonding and metal ion coordination appear to be less important. The diene has to be an anthracene derivative, and substituents at defined positions are permitted, thereby shedding light on the geometry of the binding site. The dienophile must be a five-membered maleimidyl ring with an unsubstituted reactive double bond, and a hydrophobic side chain makes a major contribution to RNA binding. The ribozyme distinguishes between different enantiomers of chiral substrates and accelerates cycloadditions with both enantio- and diastereoselectivity. The stereochemistry of the reaction is controlled by RNA-diene interactions. The RNA interacts strongly and stereoselectively with the cycloaddition products, requiring several structural features to be present. Taken together, the results highlight the intricacy of ribozyme active sites which can control chemical reaction pathways based on minute differences in substrate stereochemistry and substitution pattern.     

A DFT computational study of the bis-silylation reaction of acetylene catalyzed by palladium complexes

In this paper we have investigated at the DFT(B3LYP) level the catalytic cycle for the bis-silylation reaction of alkynes promoted by palladium complexes. A model-system formed by an acetylene molecule, a disilane molecule, and the Pd(PH(3))(2) complex has been used. The most relevant features of this catalytic cycle can be summarized as follows: (i) The first step of the cycle is an oxidative addition involving H(3)Si-SiH(3) and Pd(PH(3))(2). It occurs easily and leads to the cis (SiH(3))(2)Pd(PH(3))(2) complex that is 5.39 kcal mol(-1) lower in energy than reactants. (ii) The transfer of the two silyl groups to the C-C triple bond does not occur in a concerted way, but involves many steps. (iii) The cis (SiH(3))(2)Pd(PH(3))(2) complex, obtained from the oxidative addition, is involved in the formation of the first C-Si bond (activation barrier of 18.34 kcal mol(-1)). The two intermediates that form in this step cannot lead directly to the formation of the final bis(silyl)ethene product. However, they can isomerize rather easily (the two possible isomerizations have a barrier of 16.79 and 7.17 kcal mol(-1)) to new more stable species. In both these new intermediates the second silyl group is adjacent to the acetylene moiety and the formation of the second C-Si bond can occur rapidly leading to the (Z)-bis(silyl)ethene, as experimentally observed. (iv) The whole catalytic process is exothermic by 41.54 kcal mol(-1), in quite good agreement with the experimental estimate of this quantity (about 40 kcal mol(-1)).     

Local structure of the zeolitic catalytically active site during reaction

The structural changes of the catalytic active site that occur during catalytic reaction in an acidic zeolite are detected. The local structure of the zeolitic Br?nsted active site is a distorted tetrahedrally coordinated aluminum that has three short and one long aluminum-oxygen bond. Using in situ Al K edge X-ray absorption spectroscopy, the adsorption of a reactive intermediate in the oligomerization of ethene changed the local structure of the catalytic active site; the long aluminum oxygen bond is partially relaxed. At increasingly higher temperature, extensive coking of the catalyst frees the Br?nsted acid site from the reactive intermediate, restoring the asymmetric coordination. These measurements show that application of in situ Al K edge spectroscopy provides fundamental insight into the structure of zeolitic catalytically active sites during catalytic action.     

A dendritic active site: catalysis of the Henry reaction

[reaction: see text] Dendrimers containing an encapsulated tertiary amine were prepared by coupling tris(2-aminoethyl)amine with dendritic branches derived from L-lysine. These dendrimers were used as catalysts in the Henry (nitroaldol) reaction between 4-nitrobenzaldehyde and nitroethane, and their catalytic performance was compared with that of triethylamine. Attachment of the dendritic shell alters the rate of reaction and influences the syn:anti ratio of products. It is proposed that the dendritic shell generates an encapsulated catalytically active site, mimicking the behavior of a protein superstructure.     

Enzymatic effects on reactant and transition states. The case of chalcone isomerase

Chalcone isomerase catalyzes the transformation of chalcone to naringerin as a part of flavonoid biosynthetic pathways. The global reaction takes place through a conformational change of the substrate followed by chemical reaction, being thus an excellent example to analyze current theories about enzyme catalysis. We here present a detailed theoretical study of the enzymatic action on the conformational pre-equilibria and on the chemical steps for two different substrates of this enzyme. Free-energy profiles are obtained in terms of potentials of mean force using hybrid quantum mechanics/molecular mechanics potentials. The role of the enzyme becomes clear when compared to the counterpart equilibria and reactions in aqueous solution. The enzyme does not only favor the chemical reaction lowering the corresponding activation free energy but also displaces the conformational equilibria of the substrates toward the reactive form. These results, which can be rationalized in terms of the electrostatic interactions established in the active site between the substrate and the environment, agree with a more general picture of enzyme catalysis. According to this, an active site designed to accommodate the transition state of the reaction would also have consequences on the reactant state, stabilizing those forms which are geometrically and/or electronically closer to the transition structure.     

Synthesis of chalcone precursor via Cu(I) catalyzed 1,3-dipolar reaction of functionalized acetylene and pyrazole embedded dipole

A new class of functionalized pyrazole bearing 1,2,3-triazole has been synthesized via Cu(I) mediated 1,3-dipolar cycloaddition of pyrazole bearing azide with various aromatic/heteroaromatic bearing terminal dipolarophile (acetylene). Structures of the newly synthesized compounds were explicated by analytical and spectral analysis. All the newly synthesized compounds were evaluated for their in-vitro antibacterial and antioxidant activity. Among the synthesized compound, triazole bearing 2,5-thiazolidinone 5b (20 ± 0.70) and triazole bearing thiocarboamide 5e (19 ± 0.70) showed good antibacterial activity against Escherichia coli and Pseudomonas aeruginosa, respectively. The newly synthesized compounds further tested for their ability to bleach DPPH radical using DPPH scavenging assay. Among the synthesized compounds 1,2,3-triazole bearing 2,5-thiazolidinone 5b (58.81%) exhibited good DPPH scavenging activity compared to the rest of the compounds. From the X-ray and Hirshfield analysis, it was observed that compound 3 , crystallizes in a triclinic crystal system with a P-1 space group. The major intercontacts present in these molecules are H…H (39.7%), C…H (23.9%), N…H (20.3%).     

Mechanistic insights from reaction progress kinetic analysis of the polypeptide-catalyzed epoxidation of chalcone

[reaction: see text] Reaction progress kinetic analysis of the poly(L)-leucine (PLL)-catalyzed epoxidation of substituted chalcones 1a-1c helps to refine an earlier mechanistic proposal by demonstrating that the reaction proceeds via reversible addition of chalcone to a PLL-bound hydroperoxide, forming a fleeting hydroperoxy enolate species. Observation of an induction period offers an alternate rationalization for effects formerly attributed to substrate inhibition. Previous clues about the origin of enantioselectivity in this system are supported by this work.     

Proton catalyzed hydrolytic deamination of cytosine: a computational study

Two pathways involving proton catalyzed hydrolytic deamination of cytosine (to uracil) are investigated at the PCM-corrected B3LYP/6-311G(d,p) level of theory, in the presence of an additional catalyzing water molecule. It is concluded that the pathway involving initial protonation at nitrogen in position 3 of the ring, followed by water addition at C4 and proton transfer to the amino group, is a likely route to hydrolytic deamination. The rate determining step is the addition of water to the cytosine, with a calculated free energy barrier in aqueous solution of ΔG ^≠=140 kJ/mol. The current mechanism provides a lower barrier to deamination than previous work based on OH ^? catalyzed reactions, and lies closer to the experimental barrier derived from rate constants (E _a = 117  ±  4 kJ/mol).     

Epimerization reaction of a substituted vinylcyclopropane catalyzed by ruthenium carbenes: mechanistic analysis

A novel ruthenium carbene-catalyzed epimerization of vinylcyclopropanes is reported. The reaction rate strongly depends on the presence of ruthenium ligands in solution. When the first-generation Grubbs catalyst is employed, a 5.3:1 equilibrium ratio of epimers is established quickly, but when a first-generation Hoveyda catalyst is employed, epimerization is observed only if an additional phosphine or nitrogen ligand is added. NMR and kinetic studies suggest that the isomerization reaction occurs through the intermediacy of a ruthenacyclopentene. The observation suggests that cyclopropylmethylidene ruthenium carbenes of synthetic utility may be accessible via ruthenacyclopentenes obtained via other routes.     

Difficult substrates in the R-hydroxynitrile lyase catalyzed hydrocyanation reaction: application of the mass transfer limitation principle in a two-phase system

The application of a number of new and/or difficult substrates in the catalyzed hydrocyanation reaction by R-hydroxynitrile lyase from almonds is described. By using an aqueous–organic two-phase system and increasing the rate of the enzymatic reaction relative to the mass transfer rate, the enantiomeric purity was improved. By fine tuning the reaction parameters (temperature, pH, and the amount of enzyme) the hydrocyanation reaction was optimized for all substrates. The general principles described here can also be applied to optimize the reaction conditions for other substrates.     

A computational study of nicotine conformations in the gas phase and in water

The conformational preferences of nicotine in three protonation states and in the gas phase as well as aqueous solution are investigated using several computational procedures. Conformational aspects emphasized are N-methyl stereochemistry, relative rotation of the pyridine and pyrrolidine rings, and pyrrolidine ring conformation. All methods consistently predicted that the N-methyl trans species are most stable for all protonation states in both gas phase and in water. However, the cis/trans energy gap is significantly reduced in water. Additionally, the two pyridine ring rotamers, which are energetically equivalent in the gas phase, experience different solvation energies in water.