Combined QM/MM study of the mechanism and kinetic isotope effect of the nucleophilic substitution reaction in haloalkane dehalogenase

Combined QM/MM molecular dynamics simulations have been carried out for the dehalogenation reaction of the nucleophilic displacement of dichloroethane catalyzed by haloalkane dehalogenase. The computed chlorine kinetic isotope effects and free energies of activation in the wild-type and the Phe172Trp mutant enzyme are found to be consistent with experiment. In comparison with the uncatalyzed model reaction in water, the enzyme lowers the activation barrier by about 16 kcal/mol. The enormous enzymatic action was attributed to a combination of contributions from a change in the solvation effect and transition state stabilization. The unique features of tryptophan's ability to interact favorably with hydrophobic substrates and to form hydrogen bonds to the leaving group chloride ion at the transition state enable both factors to make significant contributions to the barrier lowering mechanism in the enzyme. This is in contrast to the reference reaction in water, in which hydrogen bonding interactions are weakened at the transition state because of dispersed charge distribution at the transition state relative to that in the reactant and product states.     

Dependence of transition state structure on substrate: the intrinsic C-13 kinetic isotope effect is different for physiological and slow substrates of the ornithine decarboxylase reaction because of different hydrogen bonding structures

Ornithine decarboxylase is the first and the rate-controlling enzyme in polyamine biosynthesis; it decarboxylates l-ornithine to form the diamine putrescine. We present calculations performed using a combined quantum mechanical and molecular mechanical (QM/MM) method with the AM1 semiempirical Hamiltonian for the wild-type ornithine decarboxylase reaction with ornithine (the physiological substrate) and lysine (a "slow" substrate) and for mutant E274A with ornithine substrate. The dynamical method is variational transition state theory with quantized vibrations. We employ a single reaction coordinate equal to the carbon-carbon distance of the dissociating bond, and we find a large difference between the intrinsic kinetic isotope effect for the physiological substrate, which equals 1.04, and that for the slow substrate, which equals 1.06. This shows that, contrary to a commonly accepted assumption, kinetic isotope effects on slow substrates are not always good models of intrinsic kinetic isotope effects on physiological substrates. Furthermore, analysis of free-energy-based samples of transition state structures shows that the differences in kinetic isotope effects may be traced to different numbers of hydrogen bonds at the different transition states of the different reactions.     

Borderline between E1cB and E2 mechanisms. Chlorine isotope effects in base-promoted elimination Reactions.

The chlorine leaving group isotope effect has been measured for the base-promoted elimination reaction of 1-(2-chloro-2-propyl)indene (1-Cl) in methanol at 30 degrees C: k(35)/k(37) = 1.0086 +/- 0.0007 with methoxide as the base and k(35)/k(37) = 1.0101 +/- 0.0001 with triethylamine (TEA) as the base. These very large chlorine isotope effects combined with large kinetic deuterium isotope effects of 7.1 and 8.4, respectively, are consistent not with the irreversible E1cB mechanism proposed previously (J. Am. Chem. Soc. 1977, 99, 7926) but with the E2 mechanism with transition states having large amounts of hydron transfer and very extensive cleavage of the bond to chlorine.     

Nucleophilic participation in the transition state for human thymidine phosphorylase

Recombinant human thymidine phosphorylase catalyzes the reaction of arsenate with thymidine to form thymine and 2-deoxyribose 1-arsenate, which rapidly decomposes to 2-deoxyribose and inorganic arsenate. The transition-state structure of this reaction was determined using kinetic isotope effect analysis followed by computer modeling. Experimental kinetic isotope effects were determined at physiological pH and 37 degrees C. The extent of forward commitment to catalysis was determined by pulse-chase experiments to be 0.70%. The intrinsic kinetic isotope effects for [1'-(3)H]-, [2'R-(3)H]-, [2'S-(3)H]-, [4'-(3)H]-, [5'-(3)H]-, [1'-(14)C]-, and [1-(15)N]-thymidines were determined to be 0.989 +/- 0.002, 0.974 +/- 0.002, 1.036 +/- 0.002, 1.020 +/- 0.003, 1.061 +/- 0.003, 1.139 +/- 0.005, and 1.022 +/- 0.005, respectively. A computer-generated model, based on density functional electronic structure calculations, was fit to the experimental isotope effect. The structure of the transition state confirms that human thymidine phosphorylase proceeds through an S(N)2-like transition state with bond orders of 0.50 to the thymine leaving group and 0.33 to the attacking oxygen nucleophile. The reaction differs from the dissociative transition states previously reported for N-ribosyl transferases and is the first demonstration of a nucleophilic transition state for an N-ribosyl transferase. The large primary (14)C isotope effect of 1.139 can occur only in nucleophilic displacements and is the largest (14)C primary isotope effect reported for an enzymatic reaction. A transition state structure with substantial bond order to the attacking nucleophile and leaving group is confirmed by the slightly inverse 1'-(3)H isotope effect, demonstrating that the transition state is compressed by the impinging steric bulk of the nucleophile and leaving group.     

Intrinsic primary and secondary hydrogen kinetic isotope effects for alanine racemase from global analysis of progress curves

The pyridoxal phosphate dependent alanine racemase catalyzes the interconversion of L- and D-alanine. The latter is an essential component of peptidoglycan in cell walls of Gram-negative and -positive bacteria, making alanine racemase an attractive target for antibacterials. Global analysis of protiated and deuterated progress curves simultaneously enables determination of intrinsic kinetic and equilibrium isotope effects for alanine racemase. The intrinsic primary kinetic isotope effects for Calpha hydron abstraction are 1.57 +/- 0.05 in the D --> L direction and 1.66 +/- 0.09 in the L --> D direction. Secondary kinetic isotope effects were found for the external aldimine formation steps in both the L --> D (1.13 +/- 0.05, forward; 0.90 +/- 0.03, reverse) and D --> L (1.13 +/- 0.06, forward; 0.89 +/- 0.03, reverse) directions. The secondary equilibrium isotope effects calculated from these are 1.26 +/- 0.07 and 1.27 +/- 0.07 for the L --> D and D --> L directions, respectively. These equilibrium isotope effects imply substantial ground-state destabilization of the C-H bond via hyperconjugation with the conjugated Schiff base/pyridine ring pi system. The magnitudes of the intrinsic primary kinetic isotope effects, the lower boundary on the energy of the quinonoid intermediate, and the protonation states of the active site catalytic acids/bases (K39-epsilonNH2 and Y265-OH) suggest that the pKa of the substrate Calpha-H bond in the external aldimine lies between those of the two catalytic bases, such that the proton abstraction transition state is early in the D --> L direction and late in the L --> D direction.     

The rate-determining step in the rhodium-xantphos-catalysed hydroformylation of 1-octene

The rate-determining step in the hydroformylation of 1-octene, catalysed by the rhodium-Xantphos catalyst system, was determined by using a combination of experimentally determined (1)H/(2)H and (12)C/(13)C kinetic isotope effects and a theoretical approach. From the rates of hydroformylation and deuterioformylation, a small (1)H/(2)H isotope effect of 1.2 was determined for the hydride moiety of the rhodium catalyst. (12)C/(13)C isotope effects of 1.012(1) and 1.012(3) for the alpha-carbon and beta-carbon atoms of 1-octene were determined, respectively. Both quantum mechanics/molecular mechanics (QM/MM) and full quantum mechanics calculations were carried out on the key catalytic steps, for "real-world" ligand systems, to clarify whether alkene coordination or hydride migration is the rate-determining step. Our calculations (21.4 kcal mol(-1)) quantitatively reproduce the experimental energy barrier for CO dissociation (20.1 kcal mol(-1)) starting at the (bisphosphane)RhH(CO)(2) resting state. The barrier for hydride migration lies 3.8 kcal mol(-1) higher than the barrier for CO dissociation (experimentally determined trend approximately 3 kcal mol(-1)). The computed (1)H/(2)H and (12)C/(13)C kinetic isotope effects corroborate the results of the energy analysis.     

Monitoring and evaluation of dechlorination processes using compound-specific chlorine isotope analysis

A simple, quick and sensitive method for the compound-specific stable chlorine isotope analysis of chlorinated solvents by conventional quadrupole gas chromatography/mass spectrometry (GC/MS) is presented. With this method, compound-specific stable chlorine isotope ratios of typical chlorinated solvents like tetrachloroethene (PCE) and trichloroethene (TCE) can be determined quantitatively within 30 min by direct injection. The chlorine isotope ratios of target substances are calculated from the peak areas of several selected molecular ions and fragment ions of the substances, using a set of unique mathematical equations. The precision of the method was demonstrated through reproducibility tests. An internal precision of +/-0.4 per thousand to +/-1.1 per thousand was obtained when analyzing PCE and TCE in the 10-1000 pmol range. The validity of the method was further demonstrated by determining the chlorine isotopic fractionation factor during the reductive dechlorination of TCE in a batch experiment using zero-valent iron. The chlorine isotopic fractionation factor was calculated as 0.9976 +/- 0.0011 with a correlation coefficient of 0.9469 (n = 38). The high correlation coefficient indicates that compound-specific stable chlorine isotope analysis can be performed with sufficient accuracy using conventional quadrupole GC/MS when significant fractionation takes place during a reaction. For the first time, the chlorine isotope fractionation factor of TCE during an abiotic anaerobic dechlorination process was determined using quadrupole GC/MS, without offline sample preparation.     

Isotope effect-mapping of the ionization of glucose demonstrates unusual charge sharing

Isotopic substitution is known to affect kinetic rate constants and equilibrium constants in chemistry. In this study, we have used tritium substitution and high pH to probe the glucose left harpoon over right harpoon glucose(-) + H(+) equilibrium. Passing partially ionized mixtures of [(3)H]- and [(14)C]glucose over anionic exchange resin has permitted the detection of subtle differences in pK(a). We have found that, at pH 11.7 in an anionic exchange system, [(3)H]glucose always elutes ahead of the [(14)C]glucose, and we report isotope effects of 1.051 +/- 0.0007, 1.012 +/- 1.0005, 1.014 +/- 0.0004, 1.024 +/- 0.0003, 1.014 +/- 0.0004, and 1.015 +/- 0.0014 for [1-(3)H]-, [2-(3)H]-, [3-(3)H]-, [4-(3)H]-, [5-(3)H]-, and [6,6-(3)H(2)]glucose, respectively, as compared to either [2-(14)C]-or [6-(14)C]glucose. The elevated isotope effects at H1 and H4 imply unusual charge sharing in anionic aqueous glucose. Base titration of (13)C-chemical shift changes demonstrates the dominance of pyranose forms at elevated pH, and ab initio isotope effect computations on gas-phase glucose anions are presented.     

Dihydrogen to dihydride isomerization mechanism in [(C5Me5)FeH2(Ph2PCH2CH2PPh2)]+ through the experimental and theoretical analysis of kinetic isotope effects

The isomerization of complex [Cp*Fe(dppe)(eta2-H2)]+, generated in situ by low-temperature protonation of Cp*Fe(dppe)H with either HBF4 or CF3COOH, to the dihydride tautomer trans-[Cp*Fe(dppe)(H)2]+ is irreversible and follows first-order kinetics in the -10 to +15 degrees C range with Delta H double dagger = 21.6 +/- 0.8 kcal mol(-1) and DeltaS double dagger = 5 +/- 3 eu. The isomerization rate constant is essentially independent of the nature and quantity of a strong acid. Density functional theory (DFT) calculations on various models, including the complete system at both the quantum mechanics/molecular mechanics (QM/MM) and full QM levels, probe the relative importance of steric and electronic effects for the relative stability of the nonclassical and classical isomers and identify two likely isomerization mechanisms: a "direct" pathway involving simultaneous H-H bond breaking and cis-trans isomerization and a "via Cp" pathway involving agostic C5Me5H intermediates. Both pathways are characterized by activation energies in close correspondence with the experimental value (21.3 and 22.2 kcal mol(-1), respectively). Further kinetic studies were carried out for the Cp*Fe(dppe)H + CF3COOD and Cp*Fe(dppe)D + CF3COOD systems at 273 K. The [Cp*Fe(dppe)(eta2-HD)]+ complex establishes a very rapid isotope redistribution equilibrium with the eta2-H2 and eta2-D2 analogues. The equilibrium constant value (K = 3.3 +/- 0.3) indicates a significant equilibrium isotope effect. Simulation of the rate data provides access to the individual isomerization rate constants kHH, kHD, and kDD for the three isotopomers, yielding kinetic isotope effects: kHH/kHD = 1.24 +/- 0.01 and kHD/kDD = 1.58 +/- 0.01 (and, consequently, kHH/kDD = 1.96 +/- 0.02). The analysis of the DFT-calculated frequencies, using the [Cp*Fe(dhpe)H2]+ model system, for the [Cp*Fe(dhpe)(eta2-XY)]+ isotopomers as well as transition states for the "direct" (TSdir) and "via Cp" (TSrot) pathways (X = H, D) allowed the computation of the expected isotope effects. A comparison with the experiment strongly suggests that the mechanism occurs via the "direct" pathway for the present system, although the small difference in the calculated energy barriers suggests that the "via Cp" pathway may be preferred in other cases.     

Measurement of the alpha-secondary kinetic isotope effect for the reaction catalyzed by mammalian protein farnesyltransferase

Protein farnesytransferase (FTase) catalyzes the transfer of a 15-carbon prenyl group from farnesyl diphosphate (FPP) to the cysteine residue of target proteins and is a member of the newest class of zinc metalloenzymes that catalyze sulfur alkylation. Common substrates of FTase include oncogenic Ras proteins, and therefore inhibitors are under development for the treatment of various cancers. An increased understanding of the salient features of the chemical transition state of FTase may aid in the design of potent inhibitors and enhance our understanding of the mechanism of this class of zinc enzymes. To investigate the transition state of FTase we have used transient kinetics to measure the alpha-secondary 3H kinetic isotope effect at the sensitive C1 position of FPP. The isotope effect for the FTase single turnover reaction using a peptide substrate that is farnesylated rapidly is near unity, indicating that a conformational change, rather than farnesylation, is the rate-limiting step. To look at the chemical step, the kinetic isotope effect was measured as 1.154 +/- 0.006 for a peptide that is farnesylated slowly, and these data suggest that FTase proceeds via a concerted mechanism with dissociative character.     

An altered mechanism of hydrolysis for a metal-complexed phosphate diester

Isotope effects in the nucleophile and in the leaving group were measured to gain information about the mechanism and transition state of the hydrolysis of methyl p-nitrophenyl phosphate complexed to a dinuclear cobalt complex. The complexed diester undergoes hydrolysis about 1011 times faster than the corresponding uncomplexed diester. The kinetic isotope effects indicate that this rate acceleration is accompanied by a change in mechanism. A large inverse 18O isotope effect in the bridging hydroxide nucleophile (0.937 +/- 0.002) suggests that nucleophilic attack occurs before the rate-determining step. Large isotope effects in the nitrophenyl leaving group (18Olg = 1.029 +/- 0.002, 15N = 1.0026 +/- 0.0002) indicate significant fission of the P-O ester bond in the transition state of the rate-determining step. The data indicate that in contrast to uncomplexed diesters, which undergo hydrolysis by a concerted mechanism, the reaction of the complexed diester likely proceeds via an addition-elimination mechanism. The rate-limiting step is expulsion of the p-nitrophenyl leaving group from the intermediate, which proceeds by a late transition state with extensive bond fission to the leaving group. This represents a substantial change in mechanism from the hydrolysis of uncomplexed aryl phosphate diesters.     

Competitive 15N kinetic isotope effects of nitrogenase-catalyzed dinitrogen reduction

Biological N2 fixation is achieved under ambient conditions by enzymatic catalysis. The enzyme nitrogenase has been studied extensively, but the N2 chemical reduction step is, by far, not rate limiting and hard to examine. A new method was developed that allows studying the reduction transition state within the enzyme's complex kinetic cascade by means of the 15N kinetic isotope effect on the reaction's second-order rate constant, V/K. A value of 1.7% +/- 0.2% was measured.     

Theoretical study of general base-catalyzed hydrolysis of aryl esters and implications for enzymatic reactions

In this work, the mechanism of general base-catalyzed hydrolysis of aryl esters is investigated in vacuo with density functional theory and in solutions with a polarized continuum model. The hydrolysis is found to proceed via a concerted mechanism featuring simultaneous addition and elimination steps accompanied by proton transfers, consistent with experimental evidence. Reasonable agreement with measured kinetic isotope effects provides additional validation. It is found that solvation substantially lowers the transition state energy, but has a small effect on the reaction exothermicity. An enzyme oxyanion hole, modeled by an ammonia molecule hydrogen bonded to the acyl carbonyl oxygen, is found to stabilize the near-tetrahedral transition state. Implications of these findings for the hydrolysis step of the dehalogenation reaction catalyzed by 4-chlorobenzoyl-CoA dehalogenase are discussed.     

Geometry optimization based on linear response free energy with quantum mechanical/molecular mechanical method: applications to Menshutkin-type and Claisen rearrangement reactions in aqueous solution

The authors present a method based on a linear response theory that allows one to optimize the geometries of quantum mechanical/molecular mechanical (QM/MM) systems on the free energy surfaces. Two different forms of linear response free energy functionals are introduced, and electronic wave functions of the QM region, as well as the responses of electrostatic and Lennard-Jones potentials between QM and MM regions, are self-consistently determined. The covariant matrix relating the QM charge distribution to the MM response is evaluated by molecular dynamics (MD) simulation of the MM system. The free energy gradients with respect to the QM atomic coordinates are also calculated using the MD trajectory results. They apply the present method to calculate the free energy profiles of Menshutkin-type reaction of NH3 with CH3Cl and Claisen rearrangement of allyl vinyl ether in aqueous solution. For the Menshutkin reaction, the free energy profile calculated with the modified linear response free energy functional is in good agreement with that by the free energy perturbation calculations. They examine the nonequilibrium solvation effect on the transmission coefficient and the kinetic isotope effect for the Claisen rearrangement.     

Certification of the chlorine content of the isotopic reference materials IRMM-641 and IRMM-642

The Slovak Institute of Metrology and the Institute for Reference Materials and Measurements have collaborated in the certification of the two chlorine reference materials IRMM-641 and IRMM-642. Until now no isotopically enriched chlorine isotopic reference material certified for isotopic composition and content has been available commercially. The isotopic reference materials IRMM-641 and IRMM-642 described herein are certified for isotopic composition and for chlorine content. The chlorine content of the reference material IRMM-641 was certified by use of high-precision argentometric coulometric titration at the Slovak Institute of Metrology. The base material used for IRMM-641 is NIST Standard Reference Material 975. The chlorine content of the reference material IRMM-642 was measured by isotope dilution, using negative thermal ionization mass spectrometry at the Institute for Reference Materials and Measurements. Both standard reference materials were prepared by dissolving NaCl in water. The reference material IRMM-641 contains 0.025022 +/- 0.00011 mol kg(-1) chlorine of natural isotopic composition with an n(37Cl)/n(35Cl) ratio of 0.31977 +/- 0.00082. The reference material IRMM-642 contains 0.004458 +/- 0.000028 mol kg(-1) chlorine with an n(37Cl)/n(35Cl) ratio of 0.01914 +/- 0.00088.     

Catalytic mechanism of glycosyltransferases: hybrid quantum mechanical/molecular mechanical study of the inverting N-acetylglucosaminyltransferase I

The Golgi glycosyltransferase, N-acetylglucosaminyltransferase I (GnT-I), catalyzes the transfer of a GlcNAc residue from the donor UDP-GlcNAc to the C2-hydroxyl group of a mannose residue in the trimannosyl core of the Man5GlcNAc2-Asn-X oligosaccharide. The catalytic mechanism of GnT-I was investigated using a hybrid quantum mechanical/molecular mechanical (QM/MM) method with a QM part containing 88 atoms treated with density functional theory (DFT) at the BP/TZP level. The remaining parts of a GnT-I complex, altogether 5633 atoms, were modeled using the AMBER molecular force field. A theoretical model of a Michaelis complex was built using the X-ray structure of GnT-I in complex with the donor having geometrical features consistent with kinetic studies. The QM(DFT)/MM model identified a concerted SN2-type of transition state with D291 as the catalytic base for the reaction in the enzyme active site. The TS model features nearly simultaneous nucleophilic addition and dissociation steps accompanied by the transfer of the nucleophile proton Hb2 to the catalytic base D291. The structure of the TS model is characterized by the Ob2-C1 and C1-O1 bond distances of 1.912 and 2.542 A, respectively. The activation energy for the proposed reaction mechanism was estimated to be approximately 19 kcal mol-1. The calculated alpha-deuterium kinetic isotope effect of 1.060 is consistent with the proposed reaction mechanism. Theoretical results also identified interactions between the Hb6 and beta-phosphate oxygen of the UDP and a low-barrier hydrogen bond between the nucleophile and the catalytic base D291. It is proposed that these interactions contribute to a stabilization of TS. This modeling study provided detailed insight into the mechanism of the GlcNAc transfer catalyzed by GnT-I, which is the first step in the conversion of high mannose oligosaccharides to complex and hybrid N-glycan structures.     

Chlorine isotope fractionation of a semi-volatile organochlorine compound during preparative megabore-column capillary gas chromatography

Chlorine isotope fractionation during preparative capillary gas chromatography (pcGC) was investigated using 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) as a model compound for semi-volatile organochlorine (OCl) molecules. Chlorine isotope analysis by thermal ionization mass spectrometry revealed no significant alteration of the chlorine isotope composition when the whole peaks were collected in pcGC (delta37Cl -3.2 per thousand versus -3.6 per thousand for the unprocessed DDT, +/-0.5 per thousand SD). However, distinct isotope fractionations were measured for the front (delta37Cl -5.1 per thousand) and tail (delta37Cl -1.8 per thousand) segments of partially collected samples. Isolation of individual OCls by pcGC enables accurate off-line chlorine isotope analysis, and thus facilitates the investigation of naturally occurring OCls.     

Isotope effects on the enzymatic and nonenzymatic reactions of chorismate

The important biosynthetic intermediate chorismate reacts thermally by two competitive pathways, one leading to 4-hydroxybenzoate via elimination of the enolpyruvyl side chain, and the other to prephenate by a facile Claisen rearrangement. Measurements with isotopically labeled chorismate derivatives indicate that both are concerted sigmatropic processes, controlled by the orientation of the enolpyruvyl group. In the elimination reaction of [4-2H]chorismate, roughly 60% of the label was found in pyruvate after 3 h at 60 degrees C. Moreover, a 1.846 +/- 0.057 2H isotope effect for the transferred hydrogen atom and a 1.0374 +/- 0.0005 18O isotope effect for the ether oxygen show that the transition state for this process is highly asymmetric, with hydrogen atom transfer from C4 to C9 significantly less advanced than C-O bond cleavage. In the competing Claisen rearrangement, a very large 18O isotope effect at the bond-breaking position (1.0482 +/- 0.0005) and a smaller 13C isotope effect at the bond-making position (1.0118 +/- 0.0004) were determined. Isotope effects of similar magnitude characterized the transformations catalyzed by evolutionarily unrelated chorismate mutases from Escherichia coli and Bacillus subtilis. The enzymatic reactions, like their solution counterpart, are thus concerted [3,3]-sigmatropic processes in which C-C bond formation lags behind C-O bond cleavage. However, as substantially larger 18O and smaller 13C isotope effects were observed for a mutant enzyme in which chemistry is fully rate determining, the ionic active site may favor a somewhat more polarized transition state than that seen in solution.     

Measurement of the kinetic isotope effect for the oxidation of NADH at a poly(aniline)-modified electrode

Kinetic isotope measurements using [4,4-2H2]NADH and [4-1H, 4-2H]NADH have been used to investigate the mechanism of the electrochemical oxidation of NADH at poly(aniline)-poly(vinyl sulfonate)-modified electrodes. The experiments show a primary kinetic isotope effect for the reaction of 4.2. This is consistent with literature values for the corresponding isotope effect for the oxidation of NADH by two-electron oxidants in homogeneous solution. The result demonstrates that transfer of H from NADH to the modified electrode occurs in the rate-limiting step within the reaction complex.