Probing eudesmane cation-π interactions in catalysis by aristolochene synthase with non-canonical amino acids

Stabilization of the reaction intermediate eudesmane cation (3) through interaction with Trp 334 during catalysis by aristolochene synthase from Penicillium roqueforti was investigated by site-directed incorporation of proteinogenic and non-canonical aromatic amino acids. The amount of germacrene A (2) generated by the mutant enzymes served as a measure of the stabilization of 3. 2 is a neutral intermediate, from which 3 is formed during PR-AS catalysis by protonation of the C6,C7 double bond. The replacement of Trp 334 with para-substituted phenylalanines of increasing electron-withdrawing properties led to a progressive accumulation of 2 that showed a good correlation with the interaction energies of simple cations such as Na(+) with substituted benzenes. These results provide compelling evidence for the stabilizing role played by Trp 334 in aristolochene synthase catalysis for the energetically demanding transformation of 2 to 3.     

Probing the reaction mechanism of aristolochene synthase with 12,13-difluorofarnesyl diphosphate

12,13-Difluorofarnesyl diphosphate, prepared using Suzuki-Miyaura chemistry, is a potent inhibitor of aristolochene synthase (AS), indicating that the initial cyclisation during AS catalysis generates germacryl cation in a concerted reaction.     

Synthetic efficiency in enzyme mechanisms involving carbocations: aristolochene synthase

An intramolecular proton-transfer mechanism has been proposed for the carbocationic cyclization of farnesyl pyrophosphate (FPP) to (+)-aristolochene catalyzed by aristolochene synthase. This novel mechanism, which is based on results obtained by high-level ab initio molecular orbital and density functional theory calculations, differs from the previous proposal in the key step of carbocation propagation prior to the formation of the bicyclic carbon skeleton. Previously, germacrene A was proposed to be generated as an intermediate by deprotonation of germacryl cation followed by reprotonation of the C6-C7 double bond to yield eudesmane cation. In the mechanism proposed here the direct intramolecular proton transfer has a computed barrier of about 22 kcal/mol, which is further lowered to 16-20 kcal/mol by aristolochene synthase. An alternative pathway is also possible through a proton shuttle via a pyrophosphate-bound water molecule. The mechanism proposed here is consistent with the observation that germacrene A is not a substrate of aristolochene synthase. Furthermore, the modeled substrate-enzyme complex suggests that Trp 334 and Phe 178 play key roles in positioning the substrate in the reactive orientation in the binding pocket. This is consistent with experimental findings that mutations of either residue lead to pronounced generation of aborted cyclization products.     

Templating effects in aristolochene synthase catalysis: elimination versus cyclisation

Analysis of the products generated by mutants of aristolochene synthase from P. roqueforti (PR-AS) revealed the prominent structural role played by the aliphatic residue Leu 108 in maintaining the productive conformation of farnesyl diphosphate to ensure C1-C10 (σ-bond) ring-closure and hence (+)-aristolochene production.     

The role of aristolochene synthase in diphosphate activation

Analysis of the role of amino acids involved in diphosphate binding in the Michaelis complex of aristolochene synthase from P. roqueforti (PR-AS) reveals mechanistic details about leaving group (PPi) activation and the nature of the active site acid.     

Aristolochene synthase: mechanistic analysis of active site residues by site-directed mutagenesis

Incubation of farnesyl diphosphate (1) with Penicillium roqueforti aristolochene synthase yielded (+)-aristolochene (4), accompanied by minor quantities of the proposed intermediate (S)-(-)germacrene A (2) and the side-product (-)-valencene (5) in a 94:4:2 ratio. By contrast, the closely related aristolochene synthase from Aspergillus terreus cyclized farnesyl diphosphate only to (+)-aristolochene (4). Site-directed mutagenesis of amino acid residues in two highly conserved Mg(2+)-binding domains led in most cases to reductions in both k(cat) and k(cat)/K(m) as well as increases in the proportion of (S)-(-)germacrene A (2), with the E252Q mutant of the P. roqueforti aristolochene synthase producing only (-)-2. The P. roqueforti D115N, N244L, and S248A/E252D mutants were inactive, as was the A. terreus mutant E227Q. The P. roqueforti mutant Y92F displayed a 100-fold reduction in k(cat) that was offset by a 50-fold decrease in K(m), resulting in a relatively minor 2-fold decrease in catalytic efficiency, k(cat)/K(m). The finding that Y92F produced (+)-aristolochene (4) as 81% of the product, accompanied by 7% 5 and 12% 2, rules out Tyr-92 as the active site Lewis acid that is responsible for protonation of the germacrene A intermediate in the formation of aristolochene (4).     

The protonation of allene and some heteroallenes, a computational study

Protonation of allene and seven heteroallenes, X = Y = Z, at the terminal and central positions has been studied computationally at the MP2/6-311+G**, B3LYP/6-31+G**, and G3 levels. In all but one case protonation at a terminal position is preferred thermodynamically. The exception is allene, where protonation at C2 giving allyl cation prevails by about 10 kcal/mol over end-protonation, which gives the 2-propenyl cation. In the heteroallenes, protonation at a terminal carbon is strongly favored, activated by electron donation from the other terminal atom. Transition states for identity proton-transfer reactions were found for 10 of the "end-to-end" proton transfers. When the transfer termini are heteroatoms these processes are barrier free. We found no first-order saddle point structures for "center-to-center" proton transfers. An estimate of DeltaH++ for an identity center-to-center proton transfer could be made only for the reaction between the allyl cation and allene; it is approximately 22 kcal/mol higher than DeltaH++ for the end-to-end proton transfer between the 2-propenyl cation and allene. First-order saddle points for the proton transfer from H3S+ to both C1 and C2 of allene were found. The difference in activation enthalpies is 9.9 kcal/mol favoring protonation at C1 in spite of the thermodynamic disadvantage. We infer that protonation of X = Y = Z at central atoms passes through transition states much like primary carbenium (nitrenium, oxenium) cations, poorly conjugated with the attached vinylic or heterovinylic group. Several other processes following upon center protonation were studied and are discussed in the text, special attention being given to comparison of open and cyclic isomers.     

Proton-induced lewis acidity of unsaturated iridium amides

Oxidation of Cp*Ir((rac-TsDPEN)H (DPEN = H2NCHPhCHPhNTs) with Cp2FePF6 or Ph3CPF6 in MeCN solution generates [Cp*Ir(TsDPEN)(NCMe)]PF6 ([1H(NCMe)]PF6) together with H2 and Ph3CH, respectively. Labeling studies revealed that the Ir-H was abstracted. The formation of a transient electrophilic species is implicated by the formation of a cyclometalated derivative. The labile species [1H(NCMe)]+ was also obtained by protonation of the diamido derivative Cp*Ir(TsDPEN-H) (1) in MeCN solution (BArF4- = B(C6H3-3,5-(CF3)2)4-). The unsaturated, "naked" cation [1H]BArF4 can be prepared by protonation of 1 with H(OEt2)2BArF4 in CH2Cl2 solution or by thermal elimination of MeCN from [1H(NCMe)]+. Crystallographic analysis confirms the structure of this 16e cation in [1H]BArF4. The formally unsaturated species 1 and [1H]BArF4 have strongly contrasting Lewis acidities, with the cation binding PPh3, CO, and NH3. 1 does not measurably bind these same ligands. [1H]BArF4 is reactive toward H2, at least in the absence of inhibiting donor ligands such as MeCN. [1H]BArF4 (CH2Cl2 solutions) catalyzes the addition of H2 to 1 by proton transfer from an apparent dihydrogen complex. This work demonstrates that the protonation activates the Lewis acidity of unsaturated Ir(III) amides, giving rise to novel organometallic Lewis acids.     

Regulation mechanism of spin-orbit coupling in charge-transfer-induced luminescence of imidazopyrazinone derivatives

The spin transition in the reactions of the derivatives of imidazo[1,2-a]pyrazin-3(7H)-one (1H) with a triplet molecular oxygen (3O2) has been investigated by the geometry optimization at the B3LYP/6-31+G(d) level and the evaluation of the electronic matrix elements for spin-orbit coupling (SOC) using the full Pauli-Breit SOC operator. The reductive activation for the 3O2 reaction is affected by the proton activity and solvent polarity of a surrounding reaction field. In a polar aprotic solvent, a base-prompted anionic substrate may react with 3O2 in a stepwise manner through complete electron transfer from the substrate anion to 3O2, while the irreversible concerted 3O2 addition via intersystem crossing may become complete in a less polar solvent. SOC in the thermal decomposition of a resulting peroxide adduct can be controlled by the protonation state of the substrate. There exists an optimal protonation state for the suppression of SOC in the charge-transfer-induced luminescence (CTIL) of the peroxide, which is closely related with the ability of a substituent to donate an electron. This will constitute a necessary condition for the high efficiency of chemi- and bioluminescence.     

Induced‐Fit Mechanism in Class I Terpene Cyclases

We present crystallographic and functional data of selina‐4(15),7(11)‐diene synthase (SdS) from Streptomyces pristinaespiralis in its open and closed (ligand‐bound) conformation. We could identify an induced‐fit mechanism by elucidating a rearrangement of the G1/2 helix‐break motif upon substrate binding. This rearrangement highlights a novel effector triad comprising the pyrophosphate sensor Arg178, the linker Asp181, and the effector Gly182‐O. This structural motif is strictly conserved in class I terpene cyclases from bacteria, fungi, and plants, including epi‐isozizaene synthase (3KB9), aristolochene synthase (4KUX), bornyl diphosphate synthase (1N20), limonene synthase (2ONG), 5‐epi‐aristolochene synthase (5EAT), and taxa‐4(5),11(12)‐diene synthase (3P5R). An elaborate structure‐based mutagenesis in combination with analysis of the distinct product spectra confirmed the mechanistic models of carbocation formation and stabilization in SdS.     

Formation of p-phenylenediamine-crown ether-[PMo12O40]4- salts

Electron transfer from the electron donor of p-phenylenediamine (PPD) to the electron acceptor of (H+)3[PMo12O40]3- forms a one-electron-reduced Keggin cluster of [PMo12O40]4-, bearing a S = 1/2 spin, while proton transfer from the proton donor of (H+)3[PMo12O40]3- to the proton acceptor of PPD yielded mono- and diprotonated cations of 4-aminoanilinium (HPPD+) and p-phenylenediammonium (H2PPD2+). By introduction of crown ether receptors during the crystallization process, supramolecular cations of (HPPD+)(crown ethers) and/or (H2PPD2+)(crown ethers) were successfully introduced into three new alpha-[PMo12O40]4- salts of (H2PPD2+)2([12]crown-4)4[PMo12O40]4- (1), (HPPD+)4([15]crown-5)4[PMo12O40]4- (2), and (HPPD+)2(H2PPD2+)([18]crown-6)4[PMo12O40]4- (3) as the countercation. The protonated states of PPD and molecular-assembly structures of the supramolecular cations depended on the size of the crown ethers. In salt 3, a novel mixed-protonated state of HPPD+ and H2PPD2+ was confirmed to be complexed in the cation structure. According to the changes in the cation structures, the anion arrangements were modulated from those of the two-dimensional layer for salt 1 to the isolated cluster for salts 2 and 3. The temperature-dependent magnetic susceptibilities of salts 1-3 were consistent with the isolated spin arrangements of [PMo12O40]4-. The electronic spectra of salts 1-3 indicated the intervalence optical transition from pentavalent Mo(V) to hexavalent Mo(VI) ions within the [PMo12O40]4- cluster. Temperature-dependent electron spin resonance spectra of salt 2 revealed the delocalization-localization transition of the S = 1/2 spin at 60 K. The spin on the [PMo12O40]4- cluster was localized on a specific Mo(V) site below 60 K, which was thermally activated with an activation energy of 0.015 eV.     

Stabilisation of transition states prior to and following eudesmane cation in aristolochene synthase

The mechanistic details of the cyclisation of farnesylpyrophosphate (FPP) by aristolochene synthase (AS) from Penicillium roqueforti have only recently begun to emerge, mainly through the analysis of the reaction products generated by AS-mutants. The reaction proceeds through several intermediates including germacrene A and eudesmane cation. Previous work suggested that the side chain of phenylalanine 178 promoted the conversion of eudesmane cation to aristolochene. We now report that the catalytic function of this residue during the conversion of eudesmane cation to aristolochene is mainly due to the large size of its side chain, which facilitates the hydride shift from C2 to C3, rather than its aromatic character. In addition, F178 appears to control the regioselectivity of the final deprotonation step and, together with F112, helps stabilise the developing positive charge on C1 after the expulsion of pyrophosphate from the substrate. These results complete a screen of likely active-site aromatic residues and establish their respective roles in the conversion of FPP to aristolochene.     

The reaction of dimethyltin(IV) dichloride with thiamine diphosphate (H2TDP): synthesis and structure of [SnMe2(HTDP)(H2O)]Cl.H2O, and possibility of a hitherto unsuspected role of the metal cofactor in the mechanism of vitamin-B1-dependent enzymes

The complex [SnMe(2)(HTDP)(H(2)O)]Cl.H(2)O, synthesized by reaction between dimethyltin(IV) dichloride and thiamine diphosphate hydrochloride (H(3)TDPCl) in water, was characterized by X-ray diffractometry and IR and Raman spectroscopy in the solid state, and by electrospray mass spectrometry (ESMS) and NMR spectroscopy ((1)H, (13)C, (31)P, (119)Sn and inverse-detection (1)H,(15)N HMBC) in aqueous solution. In the solid state the HTDP(-) anion chelates the metal via one oxygen atom of each phosphate group [Sn-O = 2.062(3), 2.292(3) A], and another oxygen atom belonging to the terminal phosphate links the SnMe(2)(2+) cations into chains. The tin atom has distorted octahedral coordination involving the trans methyl groups, the above-mentioned diphosphate oxygen atoms, and the oxygen atom of the coordinated water molecule. The thiamine moiety has F conformation. NMR studies suggest that the interaction between the organometallic cation and the HTDP(-) ligand persists in D(2)O solution, which is in keeping with the ESMS spectrum showing a peak corresponding to [SnMe(2)(HTDP)]. Both in the solid state and in solution, the acidic HTDP(-) proton in the complex is located on the N(1') atom of the pyrimidine ring. The enzymatic behavior of native pyruvate decarboxylase (EC 4.1.1.1, PDC), obtained from baker's yeast, was compared in a coupled assay with that shown by the "SnMe(2)-holoenzyme" created by incubation of apoPDC with [SnMe(2)(HTDP)(H(2)O)]Cl.H(2)O. The SnMe(2)-holoenzyme exhibited about 34% of the activity of the native enzyme (with a Michaelis-Menten constant of 2.7 microM, as against 6.4 microM for native PDC), so confirming the very low specificity of PDC regarding the identity of its metal ion cofactor. In view of the observed protonation of N(1'), it is suggested that the role of divalent cations in the mechanism of thiamine-diphosphate-dependent enzymes may be not only to anchor the cofactor in its binding site but also to shift the acidic proton of HTDP(-) from the diphosphate group to N(1'); protonation of N(1') is widely believed to be important for enzyme function, but the origin of the proton has never been clarified.     

Two competitive routes in the lactim-lactam phototautomerization of a hydroxypyridine derivative cation in water: dissociative mechanism versus water-assisted proton transfer

Ground-state tautomerism and excited-state proton-transfer processes of 2-(6'-hydroxy-2'-pyridyl)benzimidazolium in H2O and D2O have been studied by means of UV-vis absorption and fluorescence spectroscopy in both steady-state and time-resolved modes. In the ground state, this compound shows a tautomeric equilibrium between the lactim cation, protonated at the benzimidazole N3, and its lactam tautomer, obtained by proton translocation from the hydroxyl group to the pyridine nitrogen. Direct excitation of the lactam tautomer leads to its own fluorescence emission, while as a result of the increase of acidity of the OH group and basicity at the pyridine N upon excitation, the lactim species undergoes a proton translocation from the hydroxyl group to the nitrogen, favoring the lactam structure in the excited state. No fluorescence emission from the initially excited lactim species was detected due to the ultrafast rate of the excited-state proton-transfer processes. The lactim-lactam phototaumerization process takes place via two competitive excited-state proton-transfer routes: a one-step water-assisted proton translocation (probably a double proton transfer) and a two-step pathway which involves first the dissociation of the lactim cation to form an emissive intermediate zwitterionic species and then the acid-catalyzed protonation at the pyridine nitrogen to give rise to the lactam tautomer.     

Intramolecular proton transfer in the cyclization of geranylgeranyl diphosphate to the taxadiene precursor of taxol catalyzed by recombinant taxadiene synthase

BACKGROUND: The committed step in the biosynthesis of the anticancer drug taxol in yew (Taxus) species is the cyclization of geranylgeranyl diphosphate to taxa-4(5),11(12)-diene. The enzyme taxadiene synthase catalyzes this complex olefin cation cyclization cascade involving the formation of three rings and three stereogenic centers. RESULTS: Recombinant taxadiene synthase was incubated with specifically deuterated substrates, and the mechanism of cyclization was probed using MS and NMR analyses of the products to define the crucial hydrogen migration and terminating deprotonation steps. The electrophilic cyclization involves the ionization of the diphosphate with closure of the A-ring, followed by a unique intramolecular transfer of the C11 proton to the re-face of C7 to promote closure of the B/C-ring juncture, and cascade termination by proton elimination from the beta-face of C5. CONCLUSIONS: These findings provide insight into the molecular architecture of the first dedicated step of taxol biosynthesis that creates the taxane carbon skeleton, and they have broad implications for the general mechanistic capability of the large family of terpenoid cyclization enzymes.     

Intriguing roles of reactive intermediates in dissociation chemistry of N-phenylcinnamides

In mass spectrometry of protonated N-phenylcinnamides, the carbonyl oxygen is the thermodynamically most favorable protonation site and the added proton is initially localized on it. Upon collisional activation, the proton transfers from the carbonyl oxygen to the dissociative protonation site at the amide nitrogen atom or the α-carbon atom, leading to the formation of important reactive intermediates. When the amide nitrogen atom is protonated, the amide bond is facile to rupture to form ion/neutral complex 1, [RC(6)H(4)CH[double bond, length as m-dash]CHCO(+)/aniline]. Besides the dissociation of the complex, proton transfer reaction from the α-carbon atom to the nitrogen atom within the complex takes place, leading to the formation of protonated aniline. The presence of electron-withdrawing groups favored the proton transfer reaction, whereas electron-donating groups strongly favored the dissociation (aniline loss). When the proton transfers from the carbonyl oxygen to the α-carbon atom, the cleavage of the C(α)-CONHPh bond results in another ion/neutral complex 2, [PhNHCO(+)/RC(6)H(4)CH[double bond, length as m-dash]CH(2)]. However, in this case, electron-donating groups expedited the proton transfer reaction from the charged to the neutral partner to eliminate phenyl isocyanate. Besides the cleavage of the C(α)-CONHPh bond, intramolecular nucleophilic substitution (a nucleophilic attack of the nitrogen atom at the β-carbon) and stepwise proton transfer reactions (two 1,2-H shifts) also take place when the α-carbon atom is protonated, resulting in the loss of ketene and RC(6)H(5), respectively. In addition, the H/D exchanges between the external deuterium and the amide hydrogen, vinyl hydrogens and the hydrogens of the phenyl rings were discovered by D-labeling experiments. Density functional theory-based (DFT) calculations were performed to shed light on the mechanisms for these reactions.     

A quantum chemical study of the protonation of phenylphosphine and its halogenated derivatives

The protonation and methylation of phenylphosphine (C(6)H(5)PH(2)) and its mono-halogenated derivatives have been studied using ab initio quantum chemical calculations. Density functional theory (B3LYP) calculations using the 6-311++G(d,p) basis set consistently confirm that protonation of phenylphosphines takes place at the phosphorus atom; the C(4)-protonated phenylphosphine lying about 66 kJ mol(-1) above the P-protonated isomer. Similarly, methylation of phosphines consistently occurs at phosphorus. The proton and methyl cation affinities are estimated as follows: PA(phenylphosphine) = 863 +/- 10 kJ mol(-1) and MCA(phenylphosphine) = 515 -/+ 12 kJ mol(-1). Mono-halogen substitution appears to reduce the proton affinites by up to 20 kJ mol(-1). In this context, following P-protonation of either ameta- or a para-X-C(6)H(4)-PH(2), an elimination of the halogen X-atom under collisional activation (CA) conditions is expected to lead to a distonic radical cation, a low-energy isomer being 50 kJ mol(-1) above ionized phenylphosphine.     

Acid-Catalyzed Hydration of anti-Sesquinorbornene

The acid-catalyzed hydration of anti-sesquinorbornene (1) has been studied at 25 degrees C in 20% DME/H(2)O from 0.001 M < [HC1] < 0.05 M. The second-order rate constant for hydration is 5.35 +/- 0.07 M(-)(1) s(-)(1) which can be compared with a value of 1.38 +/- 0.06 M(-)(1) s(-)(1) for ethyl vinyl ether determined under the same conditions. The solvent deuterium kinetic isotope effect for hydration of 1 is 2.7, and a plot of the observed second-order rate constant for the hydration in a mixed solvent system of H(2)O/D(2)O against the atom fraction of deuterium (n) is bowed upward. The reaction also shows marked buffer catalysis by formic, chloroacetic, and dichloroacetic acids, the Br?nsted alpha being 1 for these three carboxylic acids: H(3)O(+) does not fit on this Br?nsted line. A mechanism for the reaction is presented which is consistent with the generally accepted one for acid-catalyzed hydration of an alkene in which the rate-limiting step involves proton transfer from H(3)O(+) to the double bond. Whether attack of a second water on the developing carbocation occurs simultaneously with protonation cannot be ascertained from the data for 1, but if so, the extent of its C-OH(2) bond formation must be small enough that there is little change in the bonding of these O-H bonds.     

Inhibition of (+)-aristolochene synthase with iminium salts resembling eudesmane cation

Trigonal iminium halides of (4aS,7S)-1,4a-dimethyl- and (4aS,7S)-4a-methyl-7-(prop-1-en-2-yl)-2,3,4,4a,5,6,7,8-octahydroquinolinium ions, aimed to mimic transition states associated with the aristolochene synthase-catalyzed cyclization of (-)-germacrene A to eudesmane cation, were evaluated under standard kinetic steady-state conditions. In the presence of inorganic diphosphate, these analogues were shown to competitively inhibit the enzyme, suggesting a stabilizing role for the diphosphate leaving group in this apparently endothermic transformation.     

Where are the protons in alpha-[H(x)W(12)O(40)](8-x)- (x = 2-4)?

The equilibria and speciation of the proton cryptate polyoxometalate alpha-(H2)W(12)O(40)]6- (1) were examined by NMR following the phase-transfer cation metathesis of aqueous Na(6)1 with Q+Br-/CH(2)Cl(2), leading to the isolation of the (n-Bu)4N+ (Q+) salts Q(6)1 and alpha-Q5[(H3)W(12)O(40)](Q(5)2). Several groups report salts of the protonated anions H(x)1 (x = 1 and 2) with no consensus on proton numbers or locations. Reported herein, a combination of 1H and 183W NMR evidence, elemental analysis, acid titration measurements, and H/D isotopomer assignments establishes that in nonaqueous media the internal cryptand cavity of 1 reversibly accommodates only one more proton to form 2. Because an external proton must transfer across the close-packed tungsten oxide surface of 1, which should constitute a substantial activation barrier, it is significant that the transformation is instantaneous by 1H NMR (1 equiv of HBr in CH(3)CN), whereas the reverse process is slow (t1/2 approximately 17.4 h; 1 equiv of Q+OH-).