Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants

The role of tunneling for two proton-transfer steps in the reactions catalyzed by triosephosphate isomerase (TIM) has been studied. One step is the rate-limiting proton transfer from Calpha in the substrate to Glu 165, and the other is an intrasubstrate proton transfer proposed for the isomerization of the enediolate intermediate. The latter, which is not important in the wild-type enzyme but is a useful model system because of its simplicity, has also been examined in the gas phase and in solution. Variational transition-state theory with semiclassical ground-state tunneling was used for the calculation with potential energy surface determined by an AM1 method specifically parametrized for the TIM system. The effect of tunneling on the reaction rate was found to be less than a factor of 10 at room temperature; the tunneling becomes more important at lower temperature, as expected. The imaginary frequency (barrier) mode and modes that have large contributions to the reaction path curvature are localized on the atoms in the active site, within 4 A of the substrate. This suggests that only a small number of atoms that are close to the substrate and their motions (e.g., donor-acceptor vibration) directly determine the magnitude of tunneling. Atoms that are farther away influence the effect of tunneling indirectly by modulating the energetics of the proton transfer. For the intramolecular proton transfer, tunneling was found to be most important in the gas phase, to be similar in the enzyme, and to be the smallest in water. The major reason for this trend is that the barrier frequency is substantially lower in solution than in the gas phase and enzyme; the broader solution barrier is caused by the strong electrostatic interaction between the highly charged solute and the polar solvent molecules. Analysis of isotope effects showed that the conventional Arrenhius parameters are more useful as experimental criteria for determining the magnitude of tunneling than the widely used Swain-Schaad exponent (SSE). For the primary SSE, although values larger than the transition-state theory limit (3.3) occur when tunneling is included, there is no clear relationship between the calculated magnitudes of tunneling and the SSE. Also, the temperature dependence of the primary SSE is rather complex; the value of SSE tends to decrease as the temperature is lowered (i.e., when tunneling becomes more significant). For the secondary SSE, the results suggest that it is more relevant for evaluating the "coupled motion" between the secondary hydrogen and the reaction coordinate than the magnitude of tunneling. Although tunneling makes a significant contribution to the rate of proton transfer, it appears not to be a major aspect of the catalysis by TIM at room temperature; i.e., the tunneling factor of 10 is "small" relative to the overall rate acceleration by 10(9). For the intramolecular proton transfer, the tunneling in the enzyme is larger by a factor of 5 than in solution.     

Enantioselective syntheses of tremulenediol A and tremulenolide A

[reaction: see text] An enantioselective entry to the skeleton of the tremulane sesquiterpenes is described. The approach features a series of efficient transition metal-catalyzed reactions commencing with an enantioselective rhodium(II)-catalyzed intramolecular cyclopropanation followed by a regioselective allylic alkylation and a diastereoselective rhodium(I)-catalyzed [5 + 2] cycloaddition. This strategy was applied to the first enantioselective syntheses of tremulenediol A and tremulenolide A.     

A new synthesis of platinum—carbon bonds

Syntheses of cis-[PtCl(CH₂COCH₃)(PEt₃)₂], cis-[PtCl(CH₂NO₂) (PEt₃)₂], and trans-[Pt(CCPh)₂ (PEt₃)₂] are described. The procedure involves reaction of cis-[PtCl₂(PEt₃)₂] with Ag₂O and acidic CH bonds to precipitate AgC1 and generate a PtC bond. The method may represent a new general route to platinum—carbon bonds.     

Functionality map analysis of the active site cleft of human thrombin

Summary The Multiple Copy Simultaneous Search methodology has been used to construct functionality maps for an extended region of human thrombin, including the active site. This method allows the determination of energetically favorable positions and orientations for functional groups defined by the user on the three-dimensional surface of a protein. The positions of 10 functional group sites are compared with those of corresponding groups of four thrombin-inhibitor complexes. Many, but not all features, of known thrombin inhibitors are reproduced by the method. The results indicate that certain aspects of the binding modes of these inhibitors are not optimal. In addition, suggestions are made for improving binding by interaction with functional group sites on the thrombin surface that are not used by the thrombin inhibitors. Abbreviations: MCSS, multiple copy simultaneous search; PPACK, d-phenylalanyl-l-propyl-l-arginine chloromethane; NAPAP, N -(2-naphthylsulfonylglycyl)-d-para-amidinophenylalanylpiperidine; argatroban, (2R,4R)-4-methyl-1-[N -(3-methyl-1,2,3,4-tetrahydro-8-quinolinylsulfonyl)-l-arginyl]-2-piperidine carboxylic acid; rms, root mean square. The thrombin residues are numbered according to the chymotrypsin-based numbering by Bode et al. [8]. P1, P2, P3, etc., denote the peptide inhibitor residues on the amino-terminal side of the scissile peptide bond, and S1, S2, S3, etc., the corresponding subsites of thrombin     

Thermodynamic properties of hexacosane

The heat capacity of a purified sample of hexacosane, n-C₂₆H₅₄, has been measured from 13 to 358 K. The enthalpies of transition near 325.5 K and fusion at 329.25 K, and the purity of the sample have been determined; the accuracy of the results is influenced by the closeness in temperature, and overlap, of the crystal-to-crystal and crystal-to-liquid phase transitions. Thermodynamic properties have been calculated from the heat capacities and enthalpies.     

The Tricyclooctanone Approach to the Total Synthesis of Steroids. The Cyclization of the A-CD Unit

The first steps of a novel approach to the total synthesis of 9, 11-dehydroestrone via tricyclo[3.3.0.0^2,8]octan-3-one (2) are described. One route involves a tandem-type transformation of the key intermediate 3 (A-CD unit) consisting of cyclopropane cleavage and ring B closure to afford C, 18-bisnor-13 α, 17 α-estradiol derivatives. E.g. the 3-methoxy-9 ζ-hydroxy-17 α-methanesulfonyloxy derivative (-)- 6 has been synthesized in 8 steps and 10% overall yield from 1,3-cyclohexadiene. As an alternative, the A-CD type intermediate 4b has been prepared and could be used for a ring C enlargement prior to cyclization.     

Biogenetically inspired approach to the Strychnos alkaloids. Concise syntheses of (+/-)-akuammicine and (+/-)-strychnine

A linear synthesis of the indole alkaloid (+/-)-akuammicine (2) was completed by a novel sequence of reactions requiring only 10 steps from commercially available starting materials. The approach features a tandem vinylogous Mannich addition and an intramolecular hetero Diels-Alder reaction to rapidly assemble the pentacyclic heteroyohimboid derivative 8 from the readily available hydrocarboline 6. Oxidation of the E ring of 8 gave the lactone 9 that was converted into deformylgeissoschizine (11). The subsequent elaboration of 11 into 2 was effected by a biomimetically patterned transformation that involved sequential oxidation and base-induced skeletal reorganization. A variation of these tactics was then applied to the synthesis of the C(18) hydroxylated akuammicine derivative 36. Because 36 had previously been converted into strychnine (1) in four steps, its preparation constitutes a concise, formal synthesis of this complex alkaloid.     

THE PHOTOPHYSICS OF 5-METHOXYINDOLE. A NON-EXCIPLEX FORMING INDOLE: ADDITIONAL EVIDENCE FOR TWO CLASSES OF EXCIPLEXES*

Abstract— 5-Methoxyindole is a non-exciplex forming indole, and its excited state behavior is qualitatively different from that of indole and its methyl substituted derivatives. This fact supports the idea that there are two limiting classes of exciplexes, charge-transfer and dipole-dipole stabilized. The fluorescence quantum yield in water is 0.29 with a lifetime of 4.0 ns at 25d?C. The activation energy for fluorescence quenching in water is 15.9 pM 0.5 kJ/mol, which is smaller than for indole and the methyl substituted indoles which have been measured. In cyclohexane at 25d?C, the fluorescence quantum yield is 0.63 with a lifetime of 6.7 ns. The fluorescence is efficiently quenched by electron scavengers, as is the case for other indoles. Some electron ejection to solvent probably occurs in both solvents.     

Synthesis of Oncinotin-11-one,a Macrocyclic Polyamine Alkaloid from Oncinotis tenuiloba

This paper presents a short synthesis of oncinotin-11-one ( 11 ), a minor alkaloid of Oncinotis tenuiloba (Apocynaceae). Based on a disconnection approach, the spermidine portion of the key intermediate 6 was constructed consecutively by simple N-alkylations starting from ethyl piperidine-2-carboxylate ( 1 ). Treatment of 6 with in situ lithiated 2-[(10-bromodecyl)oxy]tetrahydropyran resulted in the formation of the keto moiety under simultanous deprotection of the lactam N-atom to give the amino ketone 7 in 71% yield. Cleavage of the tetrahydro-2H-pyran-2-yl(Thp) portion and Jones oxidation of the resulting alcohol 8 gave the amino acid 9 which was cyclized. Final N-debenzylation of 10 provided the natural alkaloid 11 . Only two protective groups were needed in this synthesis. The reaction of N-alkyl-lactams with organometallic reagents is discussed.     

Boundary conditions and mode jumping in the buckling of a rectangular plate

We show that mode jumping in the buckling of a rectangular plate may be explained by a secondary bifurcation — as suggested by Bauer et al. [1] — when clamped boundary conditions on the vertical displacement function are assumed. In our analysis we use the singularity theory of mappings in the presence of a symmetry group to analyse the bifurcation equation obtained by the Lyapunov-Schmidt reduction applied to the Von Kármán equations. Noteworthy is the fact that this explanation fails when the assumed boundary conditions are simply supported.Mode jumping in the presence of clamped boundary conditions was observed experimentally by Stein [9]; simply supported boundary conditions are frequently studied but are difficult — if not impossible — to realize physically. Thus, it is important to observe that the qualitative post-buckling behavior depends on which idealization for the boundary conditions one chooses.Research sponsored in part by the U.S. Army Contract DAAG29-75-C-0024 and the N.S.F. Grant MCS77-04148Research partially supported by the N.S.F. Grant MCS77-03685 and the Research Foundation of C.U.N.Y.