Theoretical modeling of enzyme catalytic power: analysis of "cratic" and electrostatic factors in catechol O-methyltransferase

A comparative theoretical study of a bimolecular reaction in aqueous solution and catalyzed by the enzyme catechol O-methyltransferase (COMT) has been carried out by a combination of two hybrid QM/MM techniques: statistical simulation methods and internal energy minimizations. In contrast to previous studies by other workers, we have located and characterized transition structures for the reaction in the enzyme active site, in water and in a vacuum, and our potential of mean force calculations are based upon reaction coordinates obtained from features of the potential energy surfaces in the condensed media, not from the gas phase. The AM1/CHARMM calculated free energy of activation for the reaction of S-adenosyl methionine (SAM) with catecholate catalyzed by COMT is 15 kcal mol(-1) lower the AM1/TIP3P free-energy barrier for the reaction of the trimethylsulfonium cation with the catecholate anion in water at 300 K, in agreement with previous estimates. The thermodynamically preferred form of the reactants in the uncatalyzed model reaction in water is a solvent-separated ion pair (SSIP). Conversion of the SSIP into a contact ion pair, with a structure resembling that of the Michaelis complex (MC) for the reaction in the COMT active site, is unfavorable by 7 kcal mol(-1), largely due to reorganization of the solvent. We have considered alternative ways to estimate the so-called "cratic" free energy for bringing the reactant species together in the correct orientation for reaction but conclude that direct evaluation of the free energy of association by means of molecular dynamics simulation with a simple standard-state correction is probably the best approach. The latter correction allows for the fact that the size of the unit cell employed with the periodic boundary simulations does not correspond to the standard state concentration of 1 M. Consideration of MC-like species allows a helpful decomposition of the catalytic effect into preorganization and reorganization phases. In the preorganization phase, the substrates are brought together into the MC-like species, either in water or in the enzyme active site. In the reorganization phase, the roles of the enzymic and aqueous environments may be compared directly because reorganization of the substrate is about the same in both cases. Analysis of the electric field along the reaction coordinate demonstrates that in water the TS is destabilized with respect to the MC-like species because the polarity of the solute diminishes and consequently the reaction field is also decreased. In the enzyme, the electric field is mainly a permanent field and consequently there is only a small reorganization of the environment. Therefore, destabilization of the TS is lower than in solution, and the activation barrier is smaller.     

Generation and intermolecular reactions of 2-indolylacyl radicals

The generation of 2-indolylacyl radicals from the corresponding phenyl selenoesters, aldehydes, and alpha-keto carboxylic acids and the scope of their participation in intermolecular addition reactions to carbon-carbon double bonds have been studied. Whereas the phenyl selenoester method has provided easy access to a variety of 1,4-dicarbonyl compounds bearing the 2-acylindole moiety, the glyoxylic acid route has been employed for the preparation of 2-indolyl pyridyl ketones.     

Reactions of triacetic acid lactone with carbonyl compounds. X-Ray structure determination of 3-acetoacetyl-2-chromenone and 3,6,9,12-tetramethyl-1H,6H,7H,12H-6,12-methanodipyrano[4,3-b:4,3-f]-dioxocin-1,7-dione

The structure of 3-acetoacetyl-2-chromenone has been definitely assigned to the product resulting from the reaction of 4-hydroxy-6-methyl-2-pyrone, 1 , with 2-hydroxybenzaldehyde. Also, the reaction of the pyrone 1 with pentane-2,4-dione in a 2:1 molar ratio gives 3,6,9,12-tetramethyl-1H,6H,7H,12H-6,12-methanodypirano[4,3-b:4,3-f]dioxocin-1,7-dione. X-Ray analyses of both products are presented.     

Synthetic Strategies To Obtain V-P-O Open Frameworks Containing Organic Species as Structural Directing Agents. Crystal Structure of the V(IV)-Fe(III) Bimetallic Phosphate [H(3)N(CH(2))(2)NH(3)](2)[H(3)N(CH(2))(2)NH(2)][Fe(III)(H(2)O)(2)(V(IV)O)(8)(OH)(4)(HPO(4))(4)(PO(4))(4)].4H(2)O

A general synthetic approach to rationalize the solution preparative chemistry of oxovanadium phosphates containing organic species as structural directing agents is presented. Careful attention is payed to the hydrolysis and condensation processes involving the ionic species in solution, and a simple restatement of the partial charge model (PCM) has been used in order to organize the experimental results. The structure of a new V(IV)-Fe(III) bimetallic oxovanadium phosphate, [H(3)N(CH(2))(2)NH(3)](2)[H(3)N(CH(2))(2)NH(2)] [Fe(III)(H(2)O)(2)(V(IV)O)(8)(OH)(4)(HPO(4))(4)(PO(4))(4)].4H(2)O, has been determined by X-ray single crystal diffraction methods. This compound crystallizes in the monoclinic system, space group P2(1)/n and the cell dimensions are as follows: a = 14.383(3) ?, b = 10.150(2) ?, c = 18.355(4) ?, and beta = 90.39(3) degrees (Z = 2). The existence of a complex intercrossing channel system, including a very large channel of 18.4 ? of diameter (in which both water molecules and ethylenediamine species are located), is the more interesting feature of this structure. Thermal decomposition, including the dehydration/rehydration process, has been studied by thermal analysis and variable temperature X-ray powder diffraction techniques. A complementary SEM study of the different intermediate decomposition products is presented.     

Comment on “Density functional theory study of 1,2‐dioxetanone decomposition in condensed phase”

In the preceding paper results are presented, which are in serious conflict with state‐of‐the‐art ab initio method. Based on these new results the authors propose a new explanation of the reason for the preferential production of a phosphorescent state. Here we show that these controversial results are flawed, since the model use exclude biradical electron structures. © 2012 Wiley Periodicals, Inc.     

Synthesis of monodentate ferrocenylphosphines and their application to the palladium-catalyzed Suzuki reaction of aryl chlorides

Racemic and enantiopure ((p)()S)-1-bromo-2-methylferrocene 6 were synthesized in 4 steps from 2-(4,4-dimethyloxazolinyl)ferrocene and (S)-2-(4-methylethyloxazolinyl)ferrocene, respectively (46 and 81% overall yield). Bromolithium exchange and addition of ClPR(2) gave the corresponding racemic or enantiopure 2-methylferrocenyl phosphine ligands 2-MeFcPR(2) 11 (R = Ph), 12 (R = Cy), and 13 (R = (t)Bu) in 28-93% yield. Use of PCl(3) gave the C(3)-symmetric phosphine (2-MeFc)(3)P 5 from ((p)()S)-6(72% yield) but racemic 6 did not lead to the formation of triferrocenyl phosphines. Combination of 5 and Pd(2)(dba)(3) gave an active catalyst for the Suzuki reaction of aryl chlorides, for example, 4-chlorotoluene and phenylboronic acid reacted at only 60 degrees C in dioxane (86% yield). Other examples are reported together with the use of 12 in this same protocol. From the X-ray crystal structure of 5 the cone angle was determined as 211 degrees. With this, and the electronic character of 11, 12, and other phosphines (derived from nu(CO) of trans-[(R(3)P)(2)Rh(CO)Cl]), an analysis is made of the steric and electronic influences on ligand activity in the Suzuki reaction.     

Direct evaluation of a mechanism for activation of the RecA nucleoprotein filament

The RecA protein of Escherichia coli controls the SOS response for DNA damage tolerance and plays a crucial role in recombinational DNA repair. The formation of a RecA.ATP.ssDNA complex initiates all RecA activities, and yet this process is not understood at the molecular level. An analysis of RecA.DNA interactions was performed using both a mutant RecA protein containing a tryptophan (Trp) reporter and oligodeoxyribonucleotides (ODNs) containing a fluorescent guanine analogue, 6-methylisoxanthopterin (6MI). Experiments using fluorescent ODNs allowed structurally distinct nucleoprotein filaments, formed in the absence and presence of ATPgammaS (a slowly hydrolyzed analogue of ATP), to be differentiated directly. Stopped-flow spectrofluorometry, combined with presteady-state kinetic analyses, revealed unexpected differences in the rates of RecA.ODN and RecA.ATPgammaS.ODN complex assembly. This is the first demonstration that such intrinsically fluorescent synthetic DNAs can be used to characterize definitively the real-time assembly and activation of RecA.ssDNA complexes. Surprisingly, the ssDNA binding event is almost 50-fold slower in the presence of the activating ATPgammaS cofactor. Furthermore, a combination of time-dependent emission changes from 6MI and Trp allowed the first direct chemical test of whether an inactive filament can isomerize to the active state. The results revealed that, unlike the hexameric motor proteins, the inactive RecA filament cannot directly convert to the active state upon ATPgammaS binding. These results have implications for understanding how a coincidence of functions--an ATP-communicated signal-like activity and an ATP-driven motorlike activity--are resolved within a single protein molecule.     

Pre-equilibrium dipole strength in charge asymmetric peripheral heavy-ion reactions

We report on the results obtained from the study of the ³²S + ⁶⁴Ni and ³²S + ⁵⁸Ni peripheral reactions at incident energies E _lab = 288 MeV and E _lab = 320 MeV, respectively. High-energy γ-rays were detected in an array of 8 seven-pack BaF₂ clusters. Coincidence with complex fragments detected in 12 three-stage telescopes ensured the selection of peripheral reaction events. All of the relevant reaction parameters were kept constant with the exception of the different initial dipole moment caused by the different entrance channel charge asymmetry. While for quasi-elastic events no N/Z effect was observed in the differential γ-ray multiplicities of the two reactions, for deep-inelastic events a larger dipole γ-ray emission occurs during the more N/Z asymmetric reaction. A theoretical interpretation based on a collective Bremsstrahlung analysis of the reaction dynamics is presented. Received: 26 September 2002 / Accepted: 13 November 2002 / Published online: 6 March 2003 RID="a" ID="a"e-mail: pierroutsakou@na.infn.it RID="b" ID="b"Present address: INFN, Laboratori Nazionali di Legnaro, Padova, Italy. Communicated by C. Signorini