Transition state analysis of acid-catalyzed dAMP hydrolysis

Multiple kinetic isotope effects (KIEs) on deoxyadenosine monophosphate (dAMP) hydrolysis in 0.1 M HCl were used to determine the transition state (TS) structure and probe its intrinsic reactivity. The experimental KIEs revealed a stepwise (SN1) mechanism, with a discrete oxacarbenium ion intermediate. This is the first direct evidence for the deoxyribosyl oxacarbenium ion in solution. In 50% methanol/0.1 M HCl the products were deoxyribose 5-phosphate (dRMP) and alpha- and beta-methyl dRMP. The alpha-Me-dRMP/beta-Me-dRMP ratio was 8.5:1. Assuming that a free oxacarbenium ion is equally susceptible to nucleophilic attack on either face, this indicated that approximately 20% proceeded through a solvent-separated ion pair complex, or free oxacarbenium ion, a DN+AN mechanism, while approximately 80% of the reaction proceeded through a contact ion pair complex. The oxacarbenium ion lifetime was estimated at 10(-11)-10(-10) s. Computational transition states were found for ANDN, DN*AN, DN*AN, and DN+AN mechanisms using hybrid density functional theory calculations. After taking into account 20% of DN+AN, there was an excellent match of calculated to experimental KIEs for 80% of the reaction having a DN*AN mechanism. That is, C-N bond cleavage is reversible, with dAMP and the {oxacarbenium ion*adenine} complex in equilibrium. The first irreversible step is water attack on the oxacarbenium ion. The calculated 1'-14C KIE for a stepwise mechanism with irreversible C-N bond cleavage (DN*AN) was 1.052, in the range previously associated only with ANDN transition states, and close to the calculated ANDN value, 1.059. The 1'-14C KIE was strongly dependent on the adenine protonation state.     

Direct preparation of allylic zirconium reagents from zirconocene-olefin complexes and alkenes

A novel method for preparation of allylic zirconium reagents directly from 1-alkenes via zirconocene-olefin complex has been developed. Selective transfer of the hydride of zirconocene allyl hydride complex, a tautomer of zirconocene-olefin complex, to diisopropyl ketone generates the corresponding zirconocene alkoxide allyl. The allylic zirconium reagents formed effects stereoselective allylation of aldehyde at 25 degrees C and -78 degrees C to provide syn- and anti-homoallyl alcohols, respectively. The anti-isomer is formed via a six-membered chair transition state under kinetic control. The syn-selectivity can be rationalized by considering isomerization of the anti-adduct by a retroallylation process.     

Rate-equilibrium relationships in hydride transfer reactions: the role of intrinsic barriers

A literature survey on the kinetics of hydride abstractions from CH-groups by carbocations reveals a general phenomenon: Variation of the hydride acceptor affects the rates of hydride transfer to a considerably greater extent than an equal change of the thermodynamic driving force caused by variation of the hydride donor. The origin of this relationship was investigated by quantum chemical calculations on various levels of ab initio and DFT theory for the transfer of an allylic hydrogen from 1-mono- and 1,1-disubstituted propenes (XYC=CH-CH(3)) to the 3-position of 1-mono- and 1,1-disubstituted allyl cations (XYC=CH-CH(2)(+)). The discussion is based on the results of the MP2/6-31+G(d,p)//RHF/6-31+G(d,p) calculations. Electron-releasing substituents X and Y in the hydride donors increase the exothermicity of the reaction, while electron-releasing substituents in the hydride acceptors decrease exothermicity. In line with Hammond's postulate, increasing exothermicity shifts the transition states on the reaction coordinate toward reactants, as revealed by the geometry parameters and the charge distribution in the activated complexes. Independent of the location of the transition state on the reaction coordinate, a value of 0.72 is found for Hammond-Leffler's alpha = deltaDeltaG/deltaDelta(r)G degrees when the hydride acceptor is varied, while alpha = 0.28 when the hydride donor is varied. The value of alpha thus cannot be related with the position of the transition state. Investigation of the degenerate reactions XYC=CH-CH(3) + XYC=CH-CH(2)(+) indicates that the migrating hydrogen carries a partial positive charge in the transition state and that the intrinsic barriers increase with increasing electron-releasing abilities of X and Y. Substituent variation in the donor thus influences reaction enthalpy and intrinsic barriers in the opposite sense, while substituent variation in the acceptor affects both terms in the same sense, in accord with the experimental findings. Marcus theory is employed to treat these effects quantitatively.     

Anionic alternating copolymerization of 3,4‐dihydrocoumarin and glycidyl ethers: A new approach to polyester synthesis

Anionic copolymerizations of 3,4‐dihydrocoumarin (DHCM) and a series of glycidyl ethers (n‐butyl glycidyl ether, tert‐butyl glycidyl ether, and allyl glycidyl ether) with 2‐ethyl‐4‐methylimidazole as an initiator proceeded in a 1:1 alternating manner to give the corresponding polyesters, whose structures were confirmed by spectroscopic analyses and reductive scission of the ester bonds in the main chain with lithium aluminum hydride, followed by detailed analyses of the resulting fragments. The polyester obtained by the copolymerization of DHCM and allyl glycidyl ether inherited the allyl groups in the side chain, whose applicability to chemical modifications of the polyester was successfully demonstrated by a platinum‐catalyzed hydrosilylation reaction. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4092–4102, 2008     

Environment-controlled interchromophore charge transfer transitions in dipeptides probed by UV Absorption and electronic circular dichroism spectroscopy

Charge transfer (CT) transitions between the C-terminal carboxylate and peptide group have been investigated for alanyl-X and X-alanine dipeptides by far-UV absorption and electronic circular dichroism (ECD) spectroscopy (where X represents different amino acid residues). The spectra used in the present study were obtained by subtracting the spectrum of the cationic species from that of the corresponding zwitterionic peptide spectrum. These spectra displayed three bands, e.g., band I between 44 and 50 kK (kK = 10(3) cm(-1)), band II at 53 kK, and band III above 55 kK, which were, respectively, assigned to a n(COO-) --> pi* CT transition, a pi(COO-) --> pi* CT transition, and a carboxylate pi --> pi* (NV1) transition, respectively By comparison of the intensity, bandwidth, and wavenumber position of band I of some of the investigated dipeptides, we found that positive charges on the N-terminal side chain (for X = K), and to a minor extent also the N-terminal proton, reduce its intensity. This can be understood in terms of attractive Coulomb interactions that stabilize the ground state over the charge transfer state. For alanylphenylalanine, we assigned band I to a n(COO-) --> pi* CT transition into the aromatic side chain, indicating that aromatic side chains interact electronically with the backbone. We also performed ECD measurements at different pH values (pH 1-6) for a selected subset of XA and AX peptides. By subtraction of the pH 1 spectrum from that observed at pH 6, the ECD spectrum of the CT transition was obtained. A titration curve of their spectra reveals a substantial dependence on the protonation state of the aspartic acid side chain of AD, which is absent in DA and AE. This most likely reflects a conformational transition of the C-terminus into a less extended state, though the involvement of a side chain --> peptide CT transition cannot be completely ruled out.     

Transition-state analysis of the DNA repair enzyme MutY

The transition state (TS) structure of MutY-catalyzed DNA hydrolysis was solved using multiple kinetic isotope effect (KIE) measurements. MutY is a base excision repair enzyme which cleaves adenine from 8-oxo-G:A mismatches in vivo, and also from G:A mismatches in vitro. TS analysis of G:A-DNA hydrolysis revealed a stepwise S(N)1 (D(N)*A(N)(double dagger)) mechanism proceeding through a highly reactive oxacarbenium ion intermediate which would have a lifetime in solution of <10(-10) s. C-N bond cleavage is reversible; the N-glycoside bond breaks and reforms repeatedly before irreversible water attack on the oxacarbenium ion. KIEs demonstrated that MutY uses general acid catalysis by protonating N7. It enforces a 3'-exo sugar ring conformation and other sugar ring distortions to stabilize the oxacarbenium ion. Combining the experimental TS structure with the previously reported crystal structure of an abortive Michaelis complex elucidates the step-by-step catalytic sequence.     

Cobalt‐Catalyzed sp2‐C−H Activation: Intermolecular Heterocyclization with Allenes at Room Temperature

The reactivity of allenes in transition‐metal‐catalyzed C?H activation chemistry is governed by the formation of either alkenyl–metal (M–alkenyl) or metal–π‐allyl intermediates. Although either protonation or a β‐hydride elimination is feasible with a M–alkenyl intermediate, cyclization has remained unexplored to date. Furthermore, due to the increased steric hindrance, the regioselectivity for the intramolecular cyclization of the metal–π‐allyl intermediate was hampered towards the more substituted side. To address these issues, a unified approach to synthesize a diverse array of biologically and pharmaceutically relevant heterocyclic moieties by cobalt‐catalyzed directed C?H functionalization was envisioned. Upon successful implementation, the present strategy led to the regioselective formation of dihydroisoquinolin‐1(2H)‐ones, isoquinolin‐1(2H)‐ones, dihydropyridones, and pyridones.     

Theoretical study on the mechanism of iron carbonyls mediated isomerization of allylic alcohols to saturated carbonyls

The conversion of allylic alcohols to enols mediated by Fe(CO)(3) has been studied through density functional theoretical calculations. From the results obtained a complete catalytic cycle has been proposed in which the first intermediate is the [(allyl alcohol)Fe(CO)(3)] complex. This intermediate evolves to the [(enol)Fe(CO)(3)] complex through two consecutive 1,3-hydrogen shifts involving a pi-allyl hydride intermediate. The highest Gibbs energy transition state corresponds to the partial decoordination ot the enol ligand prior to the coordination of a new allyl alcohol molecule that regenerates the first intermediate. Alternative processes for the [(enol)Fe(CO)(3)] complex such as [Fe(CO)(3)]-mediated enol-aldehyde transformation and enol isomerization have also been considered. The results obtained show that the former process is unfavourable, whereas the enol isomerization may compete with the enol decoordination step of the catalytic cycle.     

The effect of active-site isoleucine to alanine mutation on the DHFR catalyzed hydride-transfer

Comparison of the nature of hydride transfer in wild-type and active site mutant (I14A) of dihydrofolate reductase suggests that the size of this side chain at position 14 modulates H-tunneling.     

Rhodium(III)-Catalyzed Asymmetric [4+1] and [5+1] Annulation of Arenes and 1,3-Enynes: A Distinct Mechanism of Allyl Formation and Allyl Functionalization

We report chiral Rh^III cyclopentadienyl-catalyzed enantioselective synthesis of lactams and isochromenes through oxidative [4+1] and [5+1] annulation, respectively, between arenes and 1,3-enynes. The reaction proceeds through a C−H activation, alkenyl-to-allyl rearrangement, and a nucleophilic cyclization cascade. The mechanisms of the [4+1] annulations were elucidated by a combination of experimental and computational methods. DFT studies indicated that, following the C−H activation and alkyne insertion, a Rh^III alkenyl intermediate undergoes δ-hydrogen elimination of the allylic C−H via a six-membered ring transition state to produce a Rh^III enallene hydride intermediate. Subsequent hydride insertion and allyl rearrangement affords several rhodium(III) allyl intermediates, and a rare Rh^III η⁴ ene-allyl species with π-agostic interaction undergoes SN₂′-type external attack by the nitrogen nucleophile, instead of C−N reductive elimination, as the stereodetermining step.     

Electron attachment to the hydrogenated Watson-Crick guanine cytosine base pair (GC+H): conventional and proton-transferred structures

The anionic species resulting from hydride addition to the Watson-Crick guanine-cytosine (GC) DNA base pair are investigated theoretically. Proton-transferred structures of GC hydride, in which proton H1 of guanine or proton H4 of cytosine migrates to the complementary base-pair side, have been studied also. All optimized geometrical structures are confirmed to be minima via vibrational frequency analyses. The lowest energy structure places the additional hydride on the C6 position of cytosine coupled with proton transfer, resulting in the closed-shell anion designated 1T (G(-)C(C6)). Energetically, the major groove side of the GC pair has a greater propensity toward hydride/hydrogen addition than does the minor grove side. The pairing (dissociation) energy and electron-attracting ability of each anionic structure are predicted and compared with those of the neutral GC and the hydrogenated GC base pairs. Anion 8T (G(O6)C(-)) is a water-extracting complex and has the largest dissociation energy. Anion 2 (GC(C4)(-)) and the corresponding open-shell radical GC(C4) have the largest vertical electron detachment energy and adiabatic electron affinity, respectively. From the difference between the dissociation energy and electron-removal ability of the normal GC anion and the most favorable structure of GC hydride, it is clear that one may dissociate the GC anion and maintain the integrity of the GC hydride.     

Experimental and theoretical studies on the isomerization of allyl thiocyanate to allyl isothiocyanate

The mechanism of isomerization of allyl thiocyanate to allyl isothiocyanate has been investigated both experimentally and theoretically. The kinetic study indicates that the reaction is unimolecular and is not ionic. The entropy of activation suggests strongly that the mechanism involves a cyclic transition state. The rate of reaction was retarded to a small extent in polar solvents relative to that in nonpolar solvents. Ab initio MO calculations indicate, in agreement with the experimental results, that the reaction proceeds through a cyclic transition state, one in which the SCN moiety is almost linear. Thus, this is a [3,3] sigmatropic rearrangement. The charge separation in the transition state was substantial. The retardation of the reaction in polar solvents was attributed to the difference in solvation in the original state and in the transition state. © 1997 John Wiley & Sons, Inc.     

Coordinative Chain Transfer Polymerization of Butadiene with Functionalized Aluminum Reagents

Functionalized aluminum alkyls enable effective coordinative chain transfer polymerization with selective chain initiation by the functionalized alkyl. (ω‐Aminoalkyl)diisobutylaluminum reagents (12 examples studied) obtained by hydroalumination of α‐amino‐ω‐enes with diisobutylaluminum hydride promote the stereoselective catalytic chain growth of butadiene on aluminum in the presence of Nd(versatate)₃, Cp*₂Nd(allyl), or Cp*₂Gd(allyl) precatalysts and [PhNMe₂H⁺]/[B(C₆F₅)₄^?]. Carbazolyl‐ and indolylaluminum reagents result in efficient molecular weight control and chain initiation by the aminoalkyl rather than the isobutyl substituent bound to aluminum. As confirmed for (3‐(9H‐carbazol‐9‐yl)propyl)‐initiated polybutadiene (PBD), for example, by deuterium quenching studies, polymer chain transfer by β‐hydride transfer is negligible in comparison to back‐transfer to aluminum.     

Bivalent ability for charge transfer in process of hydrogen interaction with surfaces of transition metals

The ability for bivalent charge transfer (CT) during hydrogen adsorption on transition metal surfaces and in the course of transition metal hydride formation is discussed. The change of the dipole moment of hydrogen adatoms, caused by transition from a strongly bound adsorption state to a weakly bound state, is demonstrated. The possibility of the CT reversion between the hydrogen adsorbate and the transition metal adsorbent, caused by a change of the surface structure, is described. The CT within the adsorbate, corresponding to the distinguished steps of the process of transition metal hydride formation, is shown.     

Inhibitors of ADP-ribosylating bacterial toxins based on oxacarbenium ion character at their transition states

The bacterial exotoxins, cholera toxin (CT), pertussis toxin (PT), and diphtheria toxin (DT), interfere with specific host proteins to cause tissue damage for their respective infections. The common toxic mechanism for these agents is mono-ADP-ribosylation of specific amino acids in G(s)(alpha), G(i)(alpha), and eEF-2 proteins, respectively, by the catalytic A chains of the toxins (CTA, PTA, and DTA). In the absence of acceptor proteins, these toxins also act as NAD(+)-N-ribosyl hydrolases. The transition-state structures for NAD(+) hydrolysis and ADP-ribosylation reactions have oxacarbenium ion character in the ribose. We designed and synthesized analogues of NAD(+) to resemble their oxacarbenium ion transition states. Inhibitors with oxacarbenium mimics replacing the NMN-ribosyl group of NAD(+) show 200-620-fold increased affinity in the hydrolytic and N-ribosyl transferase reactions catalyzed by CTA. These analogues are also inhibitors for the hydrolysis of NAD(+) by PTA with K(i) values of 24-40 microM, but bind with similar affinity to the NAD(+) substrates. Inhibition of the NAD(+) hydrolysis and ADP-ribosyl transferase reactions of DTA gave K(i) values from 19 to 48 microM. Catalytic rate enhancements by the bacterial exotoxins are small, and thus transition-state analogues cannot capture large energies of activation. In the cases of DTA and PTA, analogues known to resemble the transition states bind with approximately the same affinity as substrates. Transition-state analogue interrogation of the bacterial toxins indicates that CTA gains catalytic efficiency from modest transition-state stabilization, but DTA and PTA catalyze ADP-ribosyl transferase reactions more from ground-state destabilization. pH dependence of inhibitor action indicated that both neutral and cationic forms of transition-state analogues bind to DTA with similar affinity. The origin of this similarity is proposed to reside in the cationic nature of NAD(+) both as substrate and at the transition state.     

Charge at the migrating hydrogen in the transition state of hydride transfer reactions from CH groups to hydride acceptors. Dynamics of the redox‐couple NADH‐NAD+

We consider the controversial conclusions of the charge at the migrating hydrogen in the transition state of hydride‐transfer reactions from CH‐groups to hydride acceptors. Quantum chemical calculations were performed on elementary organic reactions involving carbenium ions, which can be considered as hydride acceptors. We also discuss the biochemical hydride‐transfer reactions in which the coenzyme NADH‐NAD⁺ plays an important role. With the calculations and the experimental model systems, an answer is given for the stereospecificity of the hydride transfer. Generally, the hydride transfer occurs via a trigonal pyramidal geometry in which the transferred hydride of the CH‐group is located in the axial position. In the case of the coenzyme NADH‐NAD⁺, the hydride transfer is coupled with an out‐of‐plane orientation of the carboxamide group of the pyridinium moiety, resulting in an increased stereospecificity. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Intramolecular rearrangements in six-coordinate ruthenium and iron dihydrides

Molecular orbital calculations at the ab initio level are used to study polytopal rearrangements in H2Ru(PH3)4 and H2Fe(CO)4 as models of 18-electron, octahedral metal dihydrides. It is found that, in both cases, the transition state for these rearrangements is a dihydrogen species. For H2Fe(CO)4, this is a square pyramidal complex where the H2 ligand occupies an apical position and is rotated by 45 degrees from its original orientation. This is precisely analogous to the transition state for Fe-olefin rotation in (olefin)Fe(CO)4 complexes and has a very similar electronic origin. Another transition state very close in energy is found wherein the basic coordination geometry is a trigonal bipyramid and the H2 ligand is coordinated in the axial position. For H2Ru(PH3)4, the former stationary point lies at a much higher energy and the latter clearly serves as the transition state for hydride exchange. The reason for this difference is discussed along with the roles of electron correlation in the two compounds.     

Structural basis of the inhibition of Golgi alpha-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions

The X-ray crystal structures of mannose trimming enzyme drosophila Golgi alpha-mannosidase II (dGMII) complexed with the inhibitors mannostatin A (1) and an N-benzyl analogue (2) have been determined. Molecular dynamics simulations and NMR studies have shown that the five-membered ring of mannostatin A is rather flexible occupying pseudorotational itineraries between 2T3 and 5E, and 2T3 and 4E. In the bound state, mannostatin A adopts a 2T1 twist envelope conformation, which is not significantly populated in solution. Possible conformations of the mannosyl oxacarbenium ion and an enzyme-linked intermediate have been compared to the conformation of mannostatin A in the cocrystal structure with dGMII. It has been found that mannostatin A best mimics the covalent linked mannosyl intermediate, which adopts a 1S5 skew boat conformation. The thiomethyl group, which is critical for high affinity, superimposes with the C-6 hydroxyl of the covalent linked intermediate. This functionality is able to make a number of additional polar and nonpolar interactions increasing the affinity for dGMII. Furthermore, the X-ray structures show that the environment surrounding the thiomethyl group of 1 is remarkably similar to the arrangements around the methionine residues in the protein. Collectively, our studies contradict the long held view that potent inhibitors of glycosidases must mimic an oxacarbenium ion like transition state.     

A 3,4‐trans‐Fused Cyclic Protecting Group Facilitates α‐Selective Catalytic Synthesis of 2‐Deoxyglycosides

A practical approach has been developed to convert glucals and rhamnals into disaccharides or glycoconjugates with high α‐selectivity and yields (77–97 %) using a trans‐fused cyclic 3,4‐O‐disiloxane protecting group and TsOH?H₂O (1 mol %) as a catalyst. Control of the anomeric selectivity arises from conformational locking of the intermediate oxacarbenium cation. Glucals outperform rhamnals because the C6 side‐chain conformation augments the selectivity.     

In situ studies of phase transitions in thin discotic films

The crystalline to liquid crystalline (Cr-LC) phase transition in thin films of zone-cast hexa-peri-hexabenzocoronene sixfold substituted with dodecyl side chains (HBC-C12H25) has been studied in detail using grazing incidence X-ray diffraction (GID), electron diffraction (ED), and variable angle spectroscopic ellipsometry (VASE), When heating the material, a first minor transition is observed around 42 degrees C. This change is attributed to alterations of the crystalline alkyl chain packing, which only slightly changes the electronic properties of the material. At higher temperatures of about 90 degrees C, but still significantly below the previously reported transition temperature in bulk, the Cr-LC transition is observed. An accompanying large increase in optical anisotropy is compatible with the X-ray data, showing a transition from the as-cast herringbone-like crystalline state to a highly ordered discotic hexagonal columnar LC phase. The structural transition has the macroscopic effect of increasing the film thickness. The high structural order of the as-cast low-temperature phase is only partly recovered after cooling, and the phase transition exhibits a large hysteresis. From the ellipsometry data, the dielectric tensor of HBC-C12H25 was refined to unprecedented detail.