Just a near attack conformer for catalysis (chorismate to prephenate rearrangements in water,antibody, enzymes,and their mutants)

Standard free energies for formation of ground-state reactive conformers (DeltaGN degrees ) and transition states (DeltaG) in the conversion of chorismate to prephenate in water, B. subtilis mutase, E. coli mutase, and their mutants, as well as a catalytic antibody, are related by DeltaG = DeltaGN degrees + 16 kcal/mol. Thus, the differences in the rate constants for the water reaction and catalysts reactions reside in the mole fraction of substrate present as reactive conformers (NACs). These results, and knowledge of the importance of transition state stabilization in other cases, suggest a proposal that enzymes utilize both NAC and transition state stabilization in the mix required for the most efficient catalysis.     

Stereodynamics of 9,11-Diphenyl-10-azatetracyclo[6.3.0.0.(4,11)0.(5,9)]undecanes. Highly Restricted Nitrogen Inversion and Isolated Phenyl Rotation. X-ray Crystallographic, Dynamic NMR, and Molecular Mechanics Studies

The (1)H NMR spectra of 10-benzyl-9,11-diphenyl-10-azatetracyclo[6.3.0.0.(4,11)0.(5,9)]undecane (BnPh(2)()) and 10-methyl-9,11-diphenyl-10-azatetracyclo[6.3.0.0.(4,11)0.(5,9)]undecane (MePh(2)()) decoalesce due to slowing inversion at nitrogen and to slowing isolated bridgehead phenyl rotation. The high nitrogen inversion barriers in MePh(2)() (DeltaG() = 12.2 +/- 0.1 kcal/mol at 250 K) and BnPh(2)() (DeltaG() = 10.6 +/- 0.1 kcal/mol at 215 K) are typical of tertiary amines in which at least one C-N-C bond angle is constrained to a small value. Compared to the minuscule rotation barriers about sp(2)-sp(3) carbon-carbon bonds in simple molecular systems, the bridgehead phenyl rotation barriers in MePh(2)() (DeltaG() = 9.8 +/- 0.1 kcal/mol at 210 K) and BnPh(2)() (DeltaG() = 9.8 +/- 0.1 kcal/mol at 210 K) are unusually high. Molecular mechanics calculations (MMX force field) suggest that the origin of the high phenyl rotation barriers lies in the close passage of an o-phenyl proton and a methyl (or benzylmethylene) proton in the transition state. BnPh(2)() crystallized from hexane as white needles in the monoclinic system Pn. Unit cell dimensions are as follows: a = 12.198(1) ?, b = 6.1399(6) ?, c = 14.938(2) ?, beta = 107.470(4) degrees, V = 1067.1(2) ?(3), Z = 2. In the crystal molecular structure, the imine bridge CNC bond angle in BnPh(2)() is constrained to a small value (96 degrees ). The benzylic phenyl group is oriented gauche to the nitrogen lone pair.     

Comparison of formation of reactive conformers (NACs) for the Claisen rearrangement of chorismate to prephenate in water and in the E. coli mutase: the efficiency of the enzyme catalysis

The Claisen rearrangements of chorismate (CHOR) in water and at the active site of E. coli chorismate mutase (EcCM) have been compared. From a total of 33 ns molecular dynamics simulation of chorismate in water solvent, seven diaxial conformers I-VII were identified. Most of the time (approximately 99%), the side chain carboxylate of the chorismate is positioned away from the ring due to the electrostatic repulsion from the carboxylate in the ring. Proximity of the two carboxylates, as seen in conformer I, is a requirement for the formation of a near attack conformer (NAC) that can proceed to the transition state (TS). In the EcCM.CHOR complex, the two carboxylates of CHOR are tightly held by Arg28 of one subunit and Arg11* of the other subunit, resulting in the side chain C16 being positioned adjacent to C5 with their motions restricted by van der Waals contacts with methyl groups of Val35 and Ile81. With the definition of NAC as the C5...C16 distance < or =3.7 A and the attack angle < or =30 degrees, it was estimated from our MD trajectories that the free energy of NAC formation is approximately 8.4 kcal/mol above the total ground state in water, whereas in the enzyme it is only 0.6 kcal/mol above the average of the Michaelis complex EcCM.CHOR. The experimentally measured difference in the activation free energies of the water and enzymatic reactions (Delta Delta G(++)) is 9 kcal/mol. It follows that the efficiency of formation of NAC (7.8 kcal/mol) at the active site provides approximately 90% of the kinetic advantage of the enzymatic reaction as compared to the water reaction. Comparison of the EcCM.TSA (transition state analogue) and EcCM.NAC simulations suggests that the experimentally measured 100 fold tighter binding of TSA compared to CHOR does not originate from the difference between NAC and the TS binding affinities, but might be due to the free energy cost to bring the two carboxylates of CHOR together to interact with Arg28 and Arg11* at the active site. The two carboxylates of TSA are fixed by a bicyclic structure. The remaining approximately 10% of Delta Delta G(++) may be attributed to a preferential interaction of Lys39-NH(3)(+) with O13 ether oxygen in the TS.     

Temperature effects on the catalytic activity of the D38E mutant of 3-oxo-Delta5-steroid isomerase: favorable enthalpies and entropies of activation relative to the nonenzymatic reaction catalyzed by acetate ion

3-oxo-Delta5-steroid isomerase (ketosteroid isomerase, KSI) catalyzes the isomerization of 5-androstene-3,17-dione (1) to 4-androstene-3,17-dione (3) via a dienolate intermediate (2-). KSI catalyzes this conversion about 13 orders of magnitude faster than the corresponding reaction catalyzed by acetate ion, a difference in activation energy (DeltaG) of approximately 18 kcal/mol. To evaluate whether the decrease in DeltaG by KSI is due to enthalpic or entropic effects, the activation parameters for the isomerization of 1 catalyzed by the D38E mutant of KSI were determined. A linear Arrhenius plot of kcat/KM versus 1/T gives the activation enthalpy (DeltaH = 5.9 kcal/mol) and activation entropy (TDeltaS = -2.6 kcal/mol). Relative to catalysis by acetate, D38E reduces DeltaH by approximately 10 kcal/mol and increases TDeltaS by approximately 5 kcal/mol. The activation parameters for the microscopic rate constants for D38E catalysis were also determined and compared to those for the acetate ion-catalyzed reaction. Enthalpic stabilization of 2- and favorable entropic effects in both chemical transition states by D38E result in an overall energetically more favorable enzymatic reaction relative to that catalyzed by acetate ion.     

Analysis of chorismate mutase catalysis by QM/MM modelling of enzyme-catalysed and uncatalysed reactions

Chorismate mutase is at the centre of current controversy about fundamental features of biological catalysts. Some recent studies have proposed that catalysis in this enzyme does not involve transition state (TS) stabilization but instead is due largely to the formation of a reactive conformation of the substrate. To understand the origins of catalysis, it is necessary to compare equivalent reactions in different environments. The pericyclic conversion of chorismate to prephenate catalysed by chorismate mutase also occurs (much more slowly) in aqueous solution. In this study we analyse the origins of catalysis by comparison of multiple quantum mechanics/molecular mechanics (QM/MM) reaction pathways at a reliable, well tested level of theory (B3LYP/6-31G(d)/CHARMM27) for the reaction (i) in Bacillus subtilis chorismate mutase (BsCM) and (ii) in aqueous solvent. The average calculated reaction (potential energy) barriers are 11.3 kcal mol(-1) in the enzyme and 17.4 kcal mol(-1) in water, both of which are in good agreement with experiment. Comparison of the two sets of reaction pathways shows that the reaction follows a slightly different reaction pathway in the enzyme than in it does in solution, because of a destabilization, or strain, of the substrate in the enzyme. The substrate strain energy within the enzyme remains constant throughout the reaction. There is no unique reactive conformation of the substrate common to both environments, and the transition state structures are also different in the enzyme and in water. Analysis of the barrier heights in each environment shows a clear correlation between TS stabilization and the barrier height. The average differential TS stabilization is 7.3 kcal mol(-1) in the enzyme. This is significantly higher than the small amount of TS stabilization in water (on average only 1.0 kcal mol(-1) relative to the substrate). The TS is stabilized mainly by electrostatic interactions with active site residues in the enzyme, with Arg90, Arg7 and Glu78 generally the most important. Conformational effects (e.g. strain of the substrate in the enzyme) do not contribute significantly to the lower barrier observed in the enzyme. The results show that catalysis is mainly due to better TS stabilization by the enzyme.     

The syntheses of pyrazino-containing sultines and their application in diels-alder reactions with electron-poor olefins and

The Diels-Alder reactions of heterocyclic o-quinodimethanes, generated in situ from 6,7-disubstituted quinoxalino[2,3-d]-[1, 2lambda(4)]oxathiine 2-oxides (6a-c), 2,3-disubstituted-8, 9-dihydro-6H-8lambda(4)-[1,2]oxathiino[4,5-g]quinoxalin-8-one (7a-c) (sultines), and pyrazinosultine (22), with electron-poor olefins and [60]fullerene are described. The heterocyclic-fused sultines 7a-c and 22 are readily prepared from the corresponding dibromides 9a-c and 24 with the commercially available Rongalite (sodium formaldehyde sulfoxylate). When heated in the presence of electron-poor dienophiles and [60]fullerene, all of the sultines underwent extrusion of SO(2), and the resulting heterocyclic o-quinodimethanes (3a-d, 4a-c, and 25) were intercepted as the 1:1 adducts in good to excellent yields. The temperature-dependent (1)H NMR spectra of fullerene derivatives 31-38 show a dynamic process for the methylene protons. The activation free energies (DeltaG(c)()) determined for the boat-to-boat inversion of these pyrazino-containing C(60) compounds (31-34 and 38) are found to be in the range of 14.1-14.8 kcal/mol, but they are in the range of 15. 2 to >17.1 kcal/mol for adducts 35-37. The activation free energies (DeltaG(c)()) are significantly affected by (1) the orientations and (2) the substituents of the quinoxaline rings and (3) the extended benzannulation in the arenes of C(60) adducts (see Table 2), which implies that both electronic interactions and steric effects between the aromatic addends and C(60) are important. Tautomerization of methylquinoxaline to its enamine is invoked as a rationalization for the lowering of DeltaG(c)() in some of the fulleroadducts.     

Entropic and enthalpic components of catalysis in the mutase and lyase activities of Pseudomonas aeruginosa PchB

The isochorismate-pyruvate lyase from Pseudomonas aeruginosa (PchB) catalyzes two pericyclic reactions, demonstrating the eponymous activity and also chorismate mutase activity. The thermodynamic parameters for these enzyme-catalyzed activities, as well as the uncatalyzed isochorismate decomposition, are reported from temperature dependence of k(cat) and k(uncat) data. The entropic effects do not contribute to enzyme catalysis as expected from previously reported chorismate mutase data. Indeed, an entropic penalty for the enzyme-catalyzed mutase reaction (ΔS(++) = -12.1 ± 0.6 cal/(mol K)) is comparable to that of the previously reported uncatalyzed reaction, whereas that of the enzyme-catalyzed lyase reaction (ΔS(++) = -24.3 ± 0.2 cal/(mol K)) is larger than that of the uncatalyzed lyase reaction (-15.77 ± 0.02 cal/(mol K)) documented here. With the assumption that chemistry is rate-limiting, we propose that a reactive substrate conformation is formed upon loop closure of the active site and that ordering of the loop contributes to the entropic penalty for converting the enzyme substrate complex to the transition state.     

On the viability of small endohedral hydrocarbon cage complexes: X@C4H4, X@C8H8, X@C8H14, X@C10H16, X@C12H12, AND X@C16H16

Small hydrocarbon complexes (X@cage) incorporating cage-centered endohedral atoms and ions (X = H(+), H, He, Ne, Ar, Li(0,+), Be(0,+,2+), Na(0,+), Mg(0,+,2+)) have been studied at the B3LYP/6-31G(d) hybrid HF/DFT level of theory. No tetrahedrane (C(4)H(4), T(d)()) endohedral complexes are minima, not even with the very small hydrogen atom or beryllium dication. Cubane (C(8)H(8), O(h)()) and bicyclo[2.2.2]octane (C(8)H(14), D(3)(h)()) minima are limited to encapsulating species smaller than Ne and Na(+). Despite its intermediate size, adamantane (C(10)H(16), T(d)()) can enclose a wide variety of endohedral atoms and ions including H, He, Ne, Li(0,+), Be(0,+,2+), Na(0,+), and Mg(2+). In contrast, the truncated tetrahedrane (C(12)H(12), T(d)()) encapsulates fewer species, while the D(4)(d)() symmetric C(16)H(16) hydrocarbon cage (see Table of Contents graphic) encapsulates all but the larger Be, Mg, and Mg(+) species. The host cages have more compact geometries when metal atoms, rather than cations, are inside. This is due to electron donation from the endohedral metals into C-C bonding and C-H antibonding cage molecular orbitals. The relative stabilities of endohedral minima are evaluated by comparing their energies (E(endo)) to the sum of their isolated components (E(inc) = E(endo) - E(cage) - E(x)) and to their exohedral isomer energies (E(isom) = E(endo) - E(exo)). Although exohedral binding is preferred to endohedral encapsulation without exception (i.e., E(isom) is always exothermic), Be(2+)@C(10)H(16) (T(d)(); -235.5 kcal/mol), Li(+)@C(12)H(12) (T(d)(); 50.2 kcal/mol), Be(2+)@C(12)H(12) (T(d)(); -181.2 kcal/mol), Mg(2+)@C(12)H(12) (T(d)(); -45.0 kcal/mol), Li(+)@C(16)H(16) (D(4)(d)(); 13.3 kcal/mol), Be(+)@C(16)H(16) (C(4)(v)(); 31.8 kcal/mol), Be(2+)@C(16)H(16) (D(4)(d)(); -239.2 kcal/mol), and Mg(2+)@C(16)H(16) (D(4)(d)(); -37.7 kcal/mol) are relatively stable as compared to experimentally known He@C(20)H(20) (I(h)()), which has an E(inc) = 37.9 kcal/mol and E(isom) = -35.4 kcal/mol. Overall, endohedral cage complexes with low parent cage strain energies, large cage internal cavity volumes, and a small, highly charged guest species are the most viable synthetic targets.     

Mechanism of homogeneous Ir(III) catalyzed regioselective arylation of olefins

The mechanism of hydroarylation of olefins by a homogeneous Ph-Ir(acac)(2)(L) catalyst is elucidated by first principles quantum mechanical methods (DFT), with particular emphasis on activation of the catalyst, catalytic cycle, and interpretation of experimental observations. On the basis of this mechanism, we suggest new catalysts expected to have improved activity. Initiation of the catalyst from the inert trans-form into the active cis-form occurs through a dissociative pathway with a calculated DeltaH(0 K)() = 35.1 kcal/mol and DeltaG(298 K)() = 26.1 kcal/mol. The catalytic cycle features two key steps, 1,2-olefin insertion and C-H activation via a novel mechanism, oxidative hydrogen migration. The olefin insertion is found to be rate determining, with a calculated DeltaH(0 K)() = 27.0 kcal/mol and DeltaG(298 K)() = 29.3 kcal/mol. The activation energy increases with increased electron density on the coordinating olefin, as well as increased electron-donating character in the ligand system. The regioselectivity is shown to depend on the electronic and steric characteristics of the olefin, with steric bulk and electron withdrawing character favoring linear product formation. Activation of the C-H bond occurs in a concerted fashion through a novel transition structure best described as an oxidative hydrogen migration. The character of the transition structure is seven coordinate Ir(V), with a full bond formed between the migrating hydrogen and iridium. Several experimental observations are investigated and explained: (a) The nature of L influences the rate of the reaction through a ground-state effect. (b) The lack of beta-hydride products is due to kinetic factors, although beta-hydride elimination is calculated to be facile, all further reactions are kinetically inaccessible. (c) Inhibition by excess olefin is caused by competitive binding of olefin and aryl starting materials during the catalytic cycle in a statistical fashion. On the basis of this insertion-oxidative hydrogen transfer mechanism we suggest that electron-withdrawing substituents on the acac ligands, such as trifluoromethyl groups, are good modifications for catalysts with higher activity.     

Contributions of conformational compression and preferential transition state stabilization to the rate enhancement by chorismate mutase

The rate enhancement provided by the chorismate mutase (CM) enzyme for the Claisen rearrangement of chorismate to prephenate has been investigated by application of the concept of near attack conformations (NACs). Using a combined QM/MM Monte Carlo/free-energy perturbation (MC/FEP) method, 82% and 100% of chorismate conformers were found to be NAC structures in water and in the CM active site, respectively. Consequently, the conversion of non-NACs to NACs does not contribute to the free energy of activation from preorganization of the substrate into NACs. The FEP calculations yielded differences in free energies of activation that well reproduce the experimental data. Additional calculations indicate that the rate enhancement by CM over the aqueous phase results primarily from conformational compression of NACs by the enzyme and that this process is enthalpically controlled. This suggests that preferential stabilization of the transition state in the enzyme environment relative to water plays a secondary role in the catalysis by CM.     

A comparative study of claisen and cope rearrangements catalyzed by chorismate mutase. An insight into enzymatic efficiency: transition state stabilization or substrate preorganization?

In this work we present a detailed analysis of the activation free energies and averaged interactions for the Claisen and Cope rearrangements of chorismate and carbachorismate catalyzed by Bacillus subtilischorismate mutase (BsCM) using quantum mechanics/molecular mechanics (QM/MM) simulation methods. In gas phase, both reactions are described as concerted processes, with the activation free energy for carbachorismate being about 10-15 kcal mol(-)(1) larger than for chorismate, at the AM1 and B3LYP/6-31G levels. Aqueous solution and BsCM active site environments reduce the free energy barriers for both reactions, due to the fact that in these media the two carboxylate groups can be approached more easily than in the gas phase. The enzyme specifically reduces the activation free energy of the Claisen rearrangement about 3 kcal mol(-)(1) more than that for the Cope reaction. This result is due to a larger transition state stabilization associated to the formation of a hydrogen bond between Arg90 and the ether oxygen. When this oxygen atom is changed by a methylene group, the interaction is lost and Arg90 moves inside the active site establishing stronger interactions with one of the carboxylate groups. This fact yields a more intense rearrangement of the substrate structure. Comparing two reactions in the same enzyme, we have been able to obtain conclusions about the relative magnitude of the substrate preorganization and transition state stabilization effects. Transition state stabilization seems to be the dominant effect in this case.     

Insights into the metathesis reaction involving M-M,C-C,and M-C triple bonds from computations employing density functional theory on model compounds M2(OH)6 and M2(SH)6, where M = Mo and W

Calculations employing density functional theory (Gaussian 98, B3LYP, LANL2DZ, 6-31G) have been undertaken to interrogate the factors influencing the metathesis reaction involving M-M, C-C, and M-C triple bonds for the model compounds M(2)(EH)(6), M(2)(EH)(6)(mu-C(2)H(2)), and [(HE)(3)M(tbd1;CH)](2), where M = Mo, W and E = O, S. Whereas in all cases the ethyne adducts are predicted to be enthalpically favored in the reactions between M(2)(EH)(6) compounds and ethyne, only when M = W and E = O is the alkylidyne product [(HO)(3)W(tbd1;CH)](2) predicted to be more stable than the alkyne adduct. For the reaction M(2)(EH)(6)(mu-C(2)H(2)) --> [(HE)(3)M(tbd1;CH)](2), the deltaG degrees values (kcal mol(-)(1)) are -6 (M = W, E = O), +5 (M = Mo, E = O), +18 (M = W, E = S), and +21 (M = Mo, E = S) and the free energies of activation are calculated to be deltaG() = +19 kcal mol(-)(1) (M = W, E = O) and +34 kcal mol(-)(1) (M = Mo, E = O), where the transition state involves an asymmetric bridged structure M(2)(OH)(4)(mu-OH)(2)(CH)(mu-CH) in which the C-C bond has broken; C.C = 1.89 and 1.98 A for W and Mo, respectively. These results are discussed in terms of the experimental observations of the reactions involving ethyne and the symmetrically substituted alkynes (RCCR, where R = Me, Et) with M(2)(O(t)()Bu)(6) and M(2)(O(t)()Bu)(2)(S(t)()Bu)(4) compounds, where M = Mo, W.     

Ab initio and experimental studies on the hetero-Diels-Alder and cheletropic additions of sulfur dioxide to (E)-1-methoxybutadiene: a mechanism involving three molecules of SO(2)

Kinetics on the cheletropic addition of sulfur dioxide to (E)-1-methoxybutadiene (1) to give the corresponding sulfolene 2 (2-methoxy-2,5-dihydrothiophene-1,1-dioxide) gave the rate law d[2]/dt = k[1][SO(2)](x)() with x = 2.6 +/- 0.2 at 198 K. Under these conditions, no sultine 3 [(2RS,6RS)-6-methoxy-3,6-dihydro-1,2-oxathiin-2-oxide] resulting from a hetero-Diels-Alder addition was observed, and the cheletropic elimination 2 --> 1 + SO(2) did not occur. Ab initio and DFT quantum calculations confirmed that the cheletropic addition 1 + SO(2) --> 2 follows two parallel mechanisms, one involving two molecules of SO(2) and the transition structure with DeltaG(++) = 18.2 +/- 0.2 kcal/mol at 198 K (exptl); 22.5-22.7 kcal/mol [B3LYP/6-31G(d,p)], the other one involving three molecules of SO(2) with DeltaG(++) = 18.9 +/- 0.1 kcal/mol at 198 K (exptl); 19.7 kcal/mol [B3LYP/6-31G(d,p)]. The mechanism involving only one molecule of SO(2) in the transition structure requires a higher activation energy, DeltaG(++) = 25.2 kcal/mol [B3LYP/6-31G(d,p)]. Comparison of the geometries and energetics of the structures involved into the 1 + SO(2) --> 2, 3 and 1 + 2SO(2) --> 2, 3 + SO(2) reactions obtained by ab initio and DFT methods suggest that the latter calculation techniques can be used to study the cycloadditions of sulfur dioxide. The calculations predict that the hetero-Diels-Alder addition 1 + SO(2) --> 3 also prefers a mechanism in which three molecules of SO(2) are involved in the cycloaddition transition structure. At 198 K and in SO(2) solutions, the entropy cost (TDeltaS(++)) is overcompensated by the specific solvation by SO(2) in the transition structures of both the cheletropic and hetero-Diels-Alder reactions of (E)-1-methoxybutadiene with SO(2).     

Theoretical studies of hetero-diels-alder reactions involving N-sulfinyl dienophiles

The gas-phase hetero-Diels-Alder reactions between butadiene and X-substituted sulfinyl dienophiles, O(-)-S(+)=N-X, are investigated theoretically at the B3LYP/6-31G level. The Z-forms of the dienophiles are found to be more stable (by 5-7 kcal mol(-)(1)) than the E-forms. Four modes of cycloadducts are considered: Z-endo; Z-exo; E(X)(-)(endo)(); E(X)(-)(exo)(). Five factors are responsible for the decreasing energetic preferences of the adducts in the order E(X)(-)(endo)() > E(X)(-)(exo)() > Z-endo > Z-exo: (i) The sigma-sigma proximate charge-transfer interactions in the TS; (ii) the relative sizes of the LUMO AO coefficients on S and N atoms; (iii) steric hindrance in the TS; (iv) the levels of the ground state and the LUMOs of the dienophile; (v) bond energies of the C-S and C-N bonds that are formed in the TS. All the reactions proceed concertedly, but the adduct formation is asynchronous. The endo-additions are favored over the exo-additions kinetically (lower DeltaG()) as well as thermodynamically (lower DeltaG degrees ). The major secondary orbital interaction determining the endo preference is that between the lone pair on N (n(N)) and the d(3) (C(3)-C(4)) sigma orbital (n(N)-sigma(d3)) interactions, whereas the larger AO lobe (LUMO) sizes on S favor a greater degree of d(5) (C-S) bond formation than d(6) (C-N) bond. The solvent, C(6)H(6), uniformly lowers the activation barriers so that the energetic preferences in the gas phase between various modes are maintained in solution.     

Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase

The controversial 'near attack conformation'(NAC) effect in the important model enzyme chorismate mutase is calculated to be 3.8-4.6 kcal mol(-1) by QM/MM free energy perturbation molecular dynamics methods, showing that the NAC effect by itself does not account for catalysis in this enzyme.     

Halogenation of cubane under phase-transfer conditions: single and double C-H-bond substitution with conservation of the cage structure.

The first highly selective C-H chlorination, bromination, and iodination of cubane (1) utilizing polyhalomethanes as halogen sources under phase-transfer (PT) conditions is described. Isomeric dihalocubanes with all possible combinations of chlorine, bromine, and iodine in ortho, meta, and para positions were also prepared by this method; m-dihalo products form preferentially. Ab initio and density functional theory (DFT) computations were used to rationalize the pronounced differences in the reactions of 1 with halogen (Hal(*)) vs carbon-centered trihalomethyl (Hal(3)C(*)) radicals (Hal = Cl, Br). For Hal(3)C radicals the C-H abstraction pathway is less unfavorable (DeltaG(double dagger)(298) = 21.6 kcal/mol for Cl(3)C(*) and 19.4 kcal/mol for Br(3)C(*) at B3LYP/6-311+G//B3LYP/6-31G) than the fragmentation of the cubane skeleton via S(H)2-attack on one of the carbon atoms of 1 (DeltaG(double dagger)(298) = 33.8 and 35.1 kcal/mol, respectively). In stark contrast, the reaction of 1 with halogen atoms preferentially follows the fragmentation pathway (DeltaG(double dagger)(298) = 2.1 and 7.5 kcal/mol) and C-H abstraction is more unfavorable (DeltaG(double dagger)(298) = 4.6 and 12.0 kcal/mol). Our computational results nicely agree with the behavior of 1 under PT halogenation conditions (where Hal(3)C(*) is involved in the activation step) and under free-radical photohalogenation with Hal(2) (Della, E. W., et al. J. Am. Chem. Soc. 1992, 114, 10730). The incorporation of a second halogen atom preferentially in the meta position of halocubanes demonstrates the control of the regioselectivity by molecular orbital symmetry.     

Thermal and photochemical rearrangement of bicyclo[3.1.0]hex-3-en-2-one to the ketonic tautomer of phenol. Computational evidence for the formation of a diradical rather than a zwitterionic intermediate

The ground state (S(0)) and lowest-energy triplet state (T(1)) potential energy surfaces (PESs) concerning the thermal and photochemical rearrangement of bicyclo[3.1.0]hex-3-en-2-one (8) to the ketonic tautomer of phenol (11) have been extensively explored using ab initio CASSCF and CASPT2 calculations with several basis sets. State T(1) is predicted to be a triplet pipi lying 66.5 kcal/mol above the energy of the S(0) state. On the S(0) PES, the rearrangement of 8 to 11 is predicted to occur via a two-step mechanism where the internal cyclopropane C-C bond is broken first through a high energy transition structure (TS1-S(0)()), leading to a singlet intermediate (10-S(0)()) lying 25.0 kcal/mol above the ground state of 8. Subsequently, this intermediate undergoes a 1,2-hydrogen shift to yield 11 by surmounting an energy barrier of only 2.7 kcal/mol at 0 K. The rate-determining step of the global rearrangement is the opening of the three-membered ring in 8, which involves an energy barrier of 41.2 kcal/mol at 0 K. This high energy barrier is consistent with the fact that the thermal rearrangement of umbellulone to thymol is carried out by heating at 280 degrees C. Regarding the photochemical rearangement, our results suggest that the most efficient route from the T(1) state of 8 to ground state 11 is the essentially barrierless cleavage of the internal cyclopropane C-C bond followed by radiationless decay to the S(0) state PES via intersystem crossing (ISC) at a crossing point (S(0)()/T(1)()-1) located at almost the same geometry as TS1-S(0)(), leading to the formation of 10-S(0)() and the subsequent low-barrier 1,2-hydrogen shift. The computed small spin-orbit coupling between the T(1) and S(0) PESs at S(0)()/T(1)()-1 (1.2 cm(-)(1)) suggests that the ISC between these PESs is the rate-determining step of the photochemical rearrangement 8 --> 11. Finally, computational evidence indicates that singlet intermediate 10-S(0)() should not be drawn as a zwitterion, but rather as a diradical having a polarized C=O bond.     

Synthetic studies towards the mulberry Diels-Alder adducts: H-bond accelerated cycloadditions of chalcones

The methyl ether derivatives 2, 4 and 6 of the mulberry Diels-Alder adducts chalcomoracin (1) and mulberrofuran C (3) and kuwanon J (5) respectively have been synthesized by a thermal [4 + 2]-cycloaddition reaction between a chalcone and dehydroprenyl diene. A H-bonded ortho OH substituent on the chalcone was found to be essential for Diels-Alder reactivity. Density functional theory calculations show that the OH group lowers the barrier for the Diels-Alder reaction by 2-3 kcal mol(-1) compared with OMe. The acceleration by the OH group is traced to two transition-state effects: a stronger diene-chalcone interaction and better planarity of the aryl-diene unit.     

Proton transfer from C-6 of uridine 5'-monophosphate catalyzed by orotidine 5'-monophosphate decarboxylase: formation and stability of a vinyl carbanion intermediate and the effect of a 5-fluoro substituent

The exchange for deuterium of the C-6 protons of uridine 5'-monophosphate (UMP) and 5-fluorouridine 5'-monophosphate (F-UMP) catalyzed by yeast orotidine 5'-monophosphate decarboxylase (ScOMPDC) at pD 6.5-9.3 and 25 °C was monitored by (1)H NMR spectroscopy. Deuterium exchange proceeds by proton transfer from C-6 of the bound nucleotide to the deprotonated side chain of Lys-93 to give the enzyme-bound vinyl carbanion. The pD-rate profiles for k(cat) give turnover numbers for deuterium exchange into enzyme-bound UMP and F-UMP of 1.2 × 10(-5) and 0.041 s(-1), respectively, so that the 5-fluoro substituent results in a 3400-fold increase in the first-order rate constant for deuterium exchange. The binding of UMP and F-UMP to ScOMPDC results in 0.5 and 1.4 unit decreases, respectively, in the pK(a) of the side chain of the catalytic base Lys-93, showing that these nucleotides bind preferentially to the deprotonated enzyme. We also report the first carbon acid pK(a) values for proton transfer from C-6 of uridine (pK(CH) = 28.8) and 5-fluorouridine (pK(CH) = 25.1) in aqueous solution. The stabilizing effects of the 5-fluoro substituent on C-6 carbanion formation in solution (5 kcal/mol) and at ScOMPDC (6 kcal/mol) are similar. The binding of UMP and F-UMP to ScOMPDC results in a greater than 5 × 10(9)-fold increase in the equilibrium constant for proton transfer from C-6, so that ScOMPDC stabilizes the bound vinyl carbanions, relative to the bound nucleotides, by at least 13 kcal/mol. The pD-rate profile for k(cat)/K(m) for deuterium exchange into F-UMP gives the intrinsic second-order rate constant for exchange catalyzed by the deprotonated enzyme as 2300 M(-1) s(-1). This was used to calculate a total rate acceleration for ScOMPDC-catalyzed deuterium exchange of 3 × 10(10) M(-1), which corresponds to a transition-state stabilization for deuterium exchange of 14 kcal/mol. We conclude that a large portion of the total transition-state stabilization for the decarboxylation of orotidine 5'-monophosphate can be accounted for by stabilization of the enzyme-bound vinyl carbanion intermediate of the stepwise reaction.