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.     

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.     

Effect of pyridine on the reaction of “spanned” zinc porphyrin with organic peroxides

The reaction of “spanned” zinc porphyrin with organic peroxides in the presence of pyridine at 298 K was studied. The kinetic characteristics of the reaction were obtained. The presence of pyridine favors the formation of the zinc chlorin complex. The nature of the nitrogen base affects the character and rate of the reactions of the zinc porphyrin with peroxide. The structures of the sterically strained metal porphyrin and of the chlorin complex formed in the reaction were optimized by PM3 calculations. As follows from the geometric structure of the macrocyclic compounds, the deformations of the macroring enhance in going from zinc porphyrin to zinc chlorin.     

Experimental and theoretical investigation of rate coefficients of the reaction S(3P)+OCS in the temperature range of 298-985 K

The reaction S(3P)+OCS in Ar was investigated over the pressure range of 50-710 Torr and the temperature range of 298-985 K with the laser photolysis technique. S atoms were generated by photolysis of OCS with light at 248 nm from a KrF excimer laser; their concentration was monitored via resonance fluorescence excited by atomic emission of S produced from microwave-discharged SO2. At pressures less than 250 Torr, our measurements give k(298 K)=(2.7+/-0.5)x10(-15) cm3 molecule-1 s-1, in satisfactory agreement with a previous report by Klemm and Davis [J. Phys. Chem. 78, 1137 (1974)]. New data determined for 407-985 K connect rate coefficients reported previously for T>or=860 and Tor=500 Torr, the reaction rate was enhanced. Theoretical calculations at the G2M(CC2) level, using geometries optimized with the B3LYP6-311+G(3df) method, yield energies of transition states and products relative to those of the reactants. Rate coefficients predicted with multichannel Rice-Ramsperger-Kassel-Marcus (RRKM) calculations agree satisfactorily with experimental observations. According to our calculations, the singlet channel involving formation of SSCO followed by direct dissociation into S2(a 1Deltag)+CO dominates below 2000 K; SSCO is formed via intersystem crossing from the triplet surface. At low temperature and under high pressure the stabilization of OCS2, formed via isomerization of SSCO, becomes important; its formation and further reaction with S atoms partially account for the observed increase in the rate coefficient under such conditions.     

Kinetic and thermodynamic characterization of Co(II)-substrate radical pair formation in coenzyme B12-dependent ethanolamine ammonia-lyase in a cryosolvent system by using time-resolved, full-spectrum continuous-wave electron paramagnetic resonance spectroscopy

The formation of the Co(II)-substrate radical pair catalytic intermediate in coenzyme B12 (adenosylcobalamin)-dependent ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium has been studied by using time-resolved continuous-wave electron paramagnetic resonance (EPR) spectroscopy in a cryosolvent system. The 41% v/v DMSO/water cryosolvent allows mixing of holoenzyme and substrate, (S)-2-aminopropanol, at 230 K under conditions of kinetic arrest. Temperature step from 230 to 234-248 K initiates the cleavage of the cobalt-carbon bond and the monoexponential rise (rate constant, k(obs) = tau(obs)(-1)) of the EPR-detected Co(II)-substrate radical pair state. The detection deadtime: tau(obs) ratio is reduced by >10(2), relative to millisecond rapid mixing experiments at ambient temperatures. The EPR spectrum acquisition time is 5tau(obs), the approximately 10(2)-fold slower rate of the substrate radical rearrangement reaction relative to k(obs), and the reversible temperature dependence of the amplitude indicate that the Co(II)-substrate radical pair and ternary complex are essentially at equilibrium. The reaction is thus treated as a relaxation to equilibrium by using a linear two-step, three-state mechanism. The intermediate state in this mechanism, the Co(II)-5'-deoxyadenosyl radical pair, is not detected by EPR at signal-to-noise ratios of 10(3), which indicates that the free energy of the Co(II)-5'-deoxyadenosyl radical pair state is >3.3 kcal/mol, relative to the Co(II)-substrate radical pair. Van't Hoff analysis yields DeltaH13 = 10.8 +/- 0.8 kcal/mol and DeltaS13 = 45 +/- 3 cal/mol/K for the transition from the ternary complex to the Co(II)-substrate radical pair state. The free energy difference, DeltaG13, is zero to within one standard deviation over the temperature range 234-248 K. The extrapolated value of DeltaG13 at 298 K is -2.6 +/- 1.2 kcal/mol. The estimated EAL protein-associated contribution to the free energy difference is DeltaG(EAL) = -24 kcal/mol at 240 K, and DeltaH(EAL) = -13 kcal/mol and DeltaS(EAL) = 38 cal/mol/K. The results show that the EAL protein makes both strong enthalpic and entropic contributions to overcome the large, unfavorable cobalt-carbon bond dissociation energy, which biases the reaction in the forward direction of Co-C bond cleavage and Co(II)-substrate radical pair formation.     

Experimental and theoretical investigations of rate coefficients of the reaction S(3P)+O2 in the temperature range 298-878 K

Rate coefficients of the reaction S+O(2) with Ar under 50 Torr in the temperature range 298-878 K were determined with the laser photolysis technique. S atoms were generated by photolysis of OCS with a KrF excimer laser at 248 nm; their concentration was monitored via resonance fluorescence excited by atomic emission of S produced from microwave-discharged SO(2). Our measurements show that k(298 K)=(1.92+/-0.29)x10(-12) cm(3) molecule(-1) s(-1), in satisfactory agreement with previous reports. New data determined for 505-878 K show non-Arrhenius behavior; combining our results with data reported at high temperatures, we derive an expression k(T)=(9.02+/-0.27)x10(-19)T(2.11+/-0.15) exp[(730+/-120)/T] cm(3) molecule(-1) s(-1) for 298< or =T< or =3460 K. Theoretical calculations at the G2M (RCC2) level, using geometries optimized with the B3LYP/6-311+G(3df) method, yield energies of transition states and products relative to those of the reactants. Rate coefficients predicted with multichannel RRKM calculations agree satisfactorily with experimental observations; the reaction channel via SOO(1A') dominates at T<500 K, whereas channels involving formation of SOO(3A") followed by isomerization to SO(2) before dissociation, and formation of SOO(1A") followed by direct dissociation, become important at high temperatures, accounting for the observed rapid increase in rate coefficient.     

Enzymes do what is expected (chalcone isomerase versus chorismate mutase)

Madicago sativa chalcone isomerase (CI) catalyzes the isomerization of chalcone to flavanone, whereas E. coli chorismate mutase (CM) catalyzes the pericyclic rearrangement of chorismate to prephenate. Covalent intermediates are not formed in either of the enzyme-catalyzed reactions, K(M) and k(cat) are virtually the same for both enzymes, and the rate constants (k(o)) for the noncatalyzed reactions in water are also the same. This kinetic identity of both the enzymatic and the nonenzymatic reactions is not shared by a similarity in driving forces. The efficiency (DeltaG(o)() - DeltaG(cat)()) for the CI mechanism involves transition-state stabilization through general-acid catalysis and freeing of three water molecules trapped in the E.S species. The contribution to lowering DeltaG(cat)() by an increase in near attack conformer (NAC) formation in E.S as compared to S in water is not so important. In the CM reaction, the standard free energy for NAC formation in water is 8.4 kcal/mol as compared to 0.6 kcal/mol in E.S. Because the value of (DeltaG(o)() - DeltaG(cat)()) is 9 kcal/mol, the greater percentage of NACs accounts for approximately 90% of the kinetic advantage of the CM reaction. There is no discernible transition-state stabilization in the CM reaction. These results are discussed. In anthropomorphic terms, each enzyme has had to do what it must to have a biologically relevant rate of reaction.     

Role of entropy in increased rates of intramolecular reactions

The rates of intramolecular condensation of a series of monoesters of dicarboxylic acids have been shown to be highly dependent on the nature of the intervening groups. To understand the origin of this effect, we estimated DeltaS(NAC,S), the entropy difference between the ensemble of accessible ground state conformers and a single ground state conformer having transition-state-like geometry. DeltaS(NAC,S) differs from the activation entropy for the reaction by DeltaS(TS,NAC), the difference in vibrational entropy between the selected ground state conformer and the transition state. The estimated values of DeltaS(NAC,S) correlate well (R(2) = 0.96 and 0.73 using dielectric constant values of 80 and 1, respectively) with experimentally determined reaction rate constants. Normal-mode analysis performed on minimized ground state conformations of each molecule suggests that the change in vibrational entropy makes only a small contribution to the total activation entropy. These results indicate that the conformational entropy difference between the transition and the ground states contributes significantly to the free energy of activation.     

A quantum-chemical study of the thermodynamic properties of the CNOH<Subscript>3</Subscript> isomers

The B3LYP/6-311++G(3df,3pd) DFT method was used to determine the geometry and vibrational frequencies for the formamide, formaldoxime, nitrosomethane, oxaziridine, and formimide. The potential energy functions of the hindered internal rotations were calculated. The conformers of formaldoxime and formimide were determined. For all the molecules, including the conformers, the thermodynamic characteristics Δ_f H° (298 K), S°(298 K), C _p(298 K), and Δ_f G° (298 K) were determined. The temperature dependences C _p(T) within 298–1500 K were represented in the form of cubic polynomials.     

Synthesis, characterization, and photophysical properties of a free base and a biszinc(II) complex of 1,3-bisporphyrincalix[4]arene: evidence for "tunable intramolecular open and closed conformations"

The bismacrocycle 5,17-bis[5-(2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrinyl)]-25,26,27,28-tetrapropoxycalix[4]arene (4) was synthesized in three steps from the corresponding bisaldehyde 5,17-diformyl-25,26,27,28-tetrapropoxycalix[4]arene. The biszinc(II) complex (5) was prepared as well, and the photophysical properties were measured using 2-MeTHF as solvent at 298 and 77 K. While computer modeling for 5 predicts that both pinched cone conformers, closed (porphyrins near each other) and open (porphyrins away from each other), may exist in the "gas phase", the experimental data indicate clearly that no zinc porphyrin...zinc porphyrin interactions are present in solution at 298 K, favoring the open conformer, where the two macrocycles are placed away from each other. On the other hand, clear evidence for a closed conformer is observed at 77 K. Variable-temperature (1)H NMR experiments show that 5 is fluxional between 298 and 183 K, while 4 keeps the open conformation for the whole temperature range. This behavior is unprecedented for calix[4]areneporphyrin compounds, and the relative porphyrin ring rigidity is postulated to explain this difference.     

Quasi-classical trajectory study of the S + OH → SO + H reaction: from reaction probability to thermal rate constant

First quasi-classical trajectory calculations have been carried out for the S((3)P) + OH(X?(2)Π) → SO(X?(3)Σ(-)) + H((2)S) reaction on an ab initio global potential energy surface for the ground electronic state, X?(2)A', of HSO. Cross sections, computed for collision energies up to 1 eV, show no energy threshold and decrease with the increasing collision energy. Rate constants have been calculated in the 5-500 K temperature range. The thermal rate constant is in good agreement with approximate quantum results, while a disagreement is found at 298 K with the experimental data. Product energy distributions have also been reported at four collision energies from 0.001 to 0.5 eV. The shapes of the rovibrational and angular distributions suggest the formation of an intermediate complex that is more and more long-lived as the collision energy increases.     

Experimental and modeling studies of the pressure and temperature dependences of the kinetics and the OH yields in the acetyl + O2 reaction

The acetyl + O(2) reaction has been studied by observing the time dependence of OH by laser-induced fluorescence (LIF) and by electronic structure/master equation analysis. The experimental OH time profiles were analyzed to obtain the kinetics of the acetyl + O(2) reaction and the relative OH yields over the temperature range of 213-500 K in helium at pressures in the range of 5-600 Torr. More limited measurements were made in N(2) and for CD(3)CO + O(2). The relative OH yields were converted into absolute yields by assuming that the OH yield at zero pressure is unity. Electronic structure calculations of the stationary points of the potential energy surface were used with a master equation analysis to fit the experimental data in He using the high-pressure limiting rate coefficient for the reaction, k(∞)(T), and the energy transfer parameter, (ΔE(d)), as variable parameters. The best-fit parameters obtained are k(∞) = 6.2 × 10(-12) cm(-3) molecule(-1) s(-1), independent of temperature over the experimental range, and (ΔE(d))(He) = 160(T/298?K) cm(-1). The fits in N(2), using the same k(∞)(T), gave (ΔE(d))(N(2)) = 270(T/298?K) cm(-1). The rate coefficients for formation of OH and CH(3)C(O)O(2) are provided in parametrized form, based on modified Troe expressions, from the best-fit master equation calculations, over the pressure and temperature ranges of 1 ≤ p/Torr ≤ 1.5 × 10(5) and 200 ≤ T/K ≤ 1000 for He and N(2) as the bath gas. The minor channels, leading to HO(2) + CH(2)CO and CH(2)C(O)OOH, generally have yields <1% over this range.     

Investigation of solvent effects for the Claisen rearrangement of chorismate to prephenate: mechanistic interpretation via near attack conformations

Solvent effects on the rate of the Claisen rearrangement of chorismate to prephenate have been examined in water and methanol. The preequilibrium free-energy differences between diaxial and diequatorial conformers of chorismate, which had previously been implicated as the sole basis for the observed 100-fold rate increase in water over methanol, have been reframed using the near attack conformation (NAC) concept of Bruice and co-workers. Using a combined QM/MM Monte Carlo/free-energy perturbation (MC/FEP) method, 82%, 57%, and 1% of chorismate conformers were found to be NAC structures (NACs) in water, methanol, and the gas phase, respectively. As a consequence, the conversion of non-NACs to NACs provides no free-energy contributions to the overall relative reaction rates in water versus methanol. Free-energy perturbation calculations yielded differences in free energies of activation for the two polar protic solvents and the gas phase. The rate enhancement in water over the gas phase arises from preferential hydration of the transition state (TS) relative to the reactants via increased hydrogen bonding and long-range electrostatic interactions, which accompany bringing the two negatively charged carboxylates into closer proximity. More specifically, there is an increase of 1.3 and 0.6 hydrogen bonds to the carboxylate groups and the ether oxygen, respectively, in going from the reactant to the TS in water. In methanol, the corresponding changes in hydrogen bonding with first shell solvent molecules are small; the rate enhancement arises primarily from the enhanced long-range interactions with solvent molecules. Thus, the reaction occurs faster in water than in methanol due to greater stabilization of the TS in water by specific interactions with first shell solvent molecules.     

Investigation of the mechanism of the cell wall DD-carboxypeptidase reaction of penicillin-binding protein 5 of Escherichia coli by quantum mechanics/molecular mechanics calculations

Penicillin-binding protein 5 (PBP 5) of Escherichia coli hydrolyzes the terminal D-Ala-D-Ala peptide bond of the stem peptides of the cell wall peptidoglycan. The mechanism of PBP 5 catalysis of amide bond hydrolysis is initial acylation of an active site serine by the peptide substrate, followed by hydrolytic deacylation of this acyl-enzyme intermediate to complete the turnover. The microscopic events of both the acylation and deacylation half-reactions have not been studied. This absence is addressed here by the use of explicit-solvent molecular dynamics simulations and ONIOM quantum mechanics/molecular mechanics (QM/MM) calculations. The potential-energy surface for the acylation reaction, based on MP2/6-31+G(d) calculations, reveals that Lys47 acts as the general base for proton abstraction from Ser44 in the serine acylation step. A discrete potential-energy minimum for the tetrahedral species is not found. The absence of such a minimum implies a conformational change in the transition state, concomitant with serine addition to the amide carbonyl, so as to enable the nitrogen atom of the scissile bond to accept the proton that is necessary for progression to the acyl-enzyme intermediate. Molecular dynamics simulations indicate that transiently protonated Lys47 is the proton donor in tetrahedral intermediate collapse to the acyl-enzyme species. Two pathways for this proton transfer are observed. One is the direct migration of a proton from Lys47. The second pathway is proton transfer via an intermediary water molecule. Although the energy barriers for the two pathways are similar, more conformers sample the latter pathway. The same water molecule that mediates the Lys47 proton transfer to the nitrogen of the departing D-Ala is well positioned, with respect to the Lys47 amine, to act as the hydrolytic water in the deacylation step. Deacylation occurs with the formation of a tetrahedral intermediate over a 24 kcal x mol(-1) barrier. This barrier is approximately 2 kcal x mol(-1) greater than the barrier (22 kcal x mol(-1)) for the formation of the tetrahedral species in acylation. The potential-energy surface for the collapse of the deacylation tetrahedral species gives a 24 kcal x mol(-1) higher energy species for the product, signifying that the complex would readily reorganize and pave the way for the expulsion of the product of the reaction from the active site and the regeneration of the catalyst. These computational data dovetail with the knowledge on the reaction from experimental approaches.     

Reaction dynamics of Cl+CH3SH: rotational and vibrational distributions of HCl probed with time-resolved Fourier-transform spectroscopy

Rotationally resolved infrared emission spectra of HCl(v=1-3) in the reaction of Cl+CH3SH, initiated with radiation from a laser at 308 nm, are detected with a step-scan Fourier-transform spectrometer. Observed rotational temperature of HCl(v=1-3) decreases with duration of reaction due to collisional quenching; a short extrapolation to time zero based on data in the range 0.25-4.25 micros yields a nascent rotational temperature of 1150+/-80 K. The rotational energy averaged for HCl(v=1-3) is 8.2+/-0.9 kJ mol(-1), yielding a fraction of available energy going into rotation of HCl, fr=0.10+/-0.01, nearly identical to that of the reaction Cl+H(2)S. Observed temporal profiles of the vibrational population of HCl(v=1-3) are fitted with a kinetic model of formation and quenching of HCl(v=1-3) to yield a branching ratio (68+/-5):(25+/-4):(7+/-1) for formation of HCl(v=1):(v=2):(v=3) from the title reaction and its thermal rate coefficient k(2a)=(2.9+/-0.7)x10(-10) cm(3) molecule(-1) s(-1). Considering possible estimates of the vibrational population of HCl(v=0) based on various surprisal analyses, we report an average vibrational energy 36+/-6 kJ mol(-1) for HCl. The fraction of available energy going into vibration of HCl is f(v)=0.45+/-0.08, significantly greater than a value fv=0.33+/-0.06 determined previously for Cl+H2S. Reaction dynamics of Cl+H(2)S and Cl+CH3SH are compared; the adduct CH3S(Cl)H is likely more transitory than the adduct H(2)SCl.     

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.     

Mechanism of the OH-initiated oxidation of hydroxyacetone over the temperature range 236-298 K

The mechanism of the gas-phase reaction of OH radicals with hydroxyacetone (CH3C(O)CH2OH) was studied at 200 Torr over the temperature range 236-298 K in a turbulent flow reactor coupled to a chemical ionization mass-spectrometer. The product yields and kinetics were measured in the presence of O2 to simulate the atmospheric conditions. The major stable product at all temperatures is methylglyoxal. However, its yield decreases from 82% at 298 K to 49% at 236 K. Conversely, the yields of formic and acetic acids increase from about 8% to about 20%. Other observed products were formaldehyde, CO2 and peroxy radicals HO2 and CH3C(O)O2. A partial re-formation of OH radicals (by approximately 10% at 298 K) was found in the OH + hydroxyacetone + O2 chemical system along with a noticeable inverse secondary kinetic isotope effect (k(OH)/k(OD) = 0.78 +/- 0.10 at 298 K). The observed product yields are explained by the increasing role of the complex formed between the primary radical CH3C(O)CHOH and O2 at low temperature. The rate constant of the reaction CH3C(O)CHOH + O2 --> CH3C(O)CHO + HO2 at 298 K, (3.0 +/- 0.6) x 10(-12) cm3 molecule(-1) s(-1), was estimated by computer simulation of the concentration-time profiles of the CH3C(O)CHO product. The detailed mechanism of the OH-initiated oxidation of hydroxyacetone can help to better describe the atmospheric oxidation of isoprene, in particular, in the upper troposphere.     

Catalytic mechanism of 6-phosphogluconate dehydrogenase: a theoretical investigation

Density functional calculations are employed to theoretically explore the mechanism of all elementary reaction steps involved in the catalytic reaction of 6-phosphogluconate dehydrogenase (6PGDH). The model systems we choose for the enzyme contain the essential parts of the cofactor (NADP+), the substrate 6-phosphogluconate (6PG), and some key residues (Lys183 and Glu190) in the active site of sheep liver 6PGDH. The effect of the apoenzyme electrostatic environment on the studied reaction is treated by the self-consistent reaction-field method. Our calculations demonstrate that the first step of the catalytic reaction is the formation of a 3-keto 6PG intermediate, which proceeds through a concerted transition state involving a hydride transfer from 6PG to NADP+, and a proton transfer from 6PG to Lys183. The second step is the elimination of a CO2 molecule from 6-PG, concomitant with a proton transfer from Lys183 to 6-PG. In the final step, a concerted double proton transfer (one from Glu190 to the substrate, another from the substrate to Lys183) results in the final product, the keto form of ribulose 5-phosphate (Ru5P). The rate-limiting step is the formation of a 3-keto 6PG intermediate, with a free energy barrier of 22.7 kcal/mol at room temperature in the protein environment, and all three steps are calculated to be thermodynamically favorable. These results are in good agreement with the general acid/general base mechanism suggested from previous experiments for the 6PGDH reaction.     

Calculation of relative energies of permethylated oligosilane conformers in vapor and in alkane solution

The geometries of 35 conformers of Me(SiMe2)nMe (n = 4, 1; n = 5, 2; n = 6, 3; n = 7, 4) were optimized at the MP2/VTDZ level, and CCSD(T) single-point calculations were done at three MP2/VTDZ conformer geometries of 1. The relative ground-state energies of the conformers of 1-4 in the gas phase were obtained from the MP2/VTDZ electronic energy, zero-point vibrational energy, and thermal corrections at 0, 77, and 298 K. Relative energies in an alkane solvent at 77 and 298 K were obtained by the addition of solvation energies, obtained from the SM5.42R model. The calculated energies of 26 of the conformers (n = 4-6) have been least-squares fitted to a set of 15 additive increments associated with each Si-Si bond conformation and each pair of adjacent bond conformations, with mean deviations of 0.06-0.20 kcal/mol. An even better fit for the energies of 24 conformers (mean deviations, 0.01-0.09 kcal/mol) has been obtained with a larger set of 19 increments, which also contained contributions from selected combinations of conformations of three adjacent bonds. The utility of the additive increments for the prediction of relative conformer energies in the gas phase and in solution has been tested on the remaining nine conformers (n = 6, 7). With the improved increment set, the average deviation from the SM5.42R//MP2 results for solvated conformers at 298 K was 0.18 kcal/mol, and the maximum error was 0.98 kcal/mol.     

The isomolecular exchange reaction Ga2S(g) + In2S(g) = 2 InGaS(g)

Equilibria involving the molecules Ga₂S(g), In₂S(g), and InGaS(g), by the reaction Ga₂S(g) + In₂S(g) = 12InGaS(g) were investigated between 1060–1350 K by the Knudsen-effusion, mass-spectrometric method. The reaction enthalpy at 298 K was calculated to be 0±1 kJ mol⁻¹. The enthalpy of formation of InGaS at 298 K and the enthalpy of atomization of InGaS at 298 K were calculated to be 80±18 kJ mol⁻¹ and 710±18 kJ mol⁻¹, respectively. The equilibrium constant and the enthalpy of reaction indicated that the three gaseous molecules have a bent triatomic structure in which S is a center atom and no bond between metals.