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.     

Probing the requirements for recognition and catalysis in Fpg and MutY with nonpolar adenine isosteres

The Escherichia coli DNA repair enzymes Fpg and MutY are involved in the prevention of mutations resulting from 7,8-dihydro-8-oxo-2'-deoxyguanosine (OG) in DNA. The nonpolar isosteres of 2'-deoxyadenosine, 4-methylbenzimidazole beta-deoxynucleoside (B), and 9-methyl-1H-imidazo[4,5-b]pyridine beta-deoxynucleoside (Q), were used to examine the importance of hydrogen bonding within the context of DNA repair. Specifically, the rate of base removal under single-turnover conditions by the MutY and Fpg glycosylases from duplexes containing OG:B and OG:Q mismatches, relative to OG:A mismatches, was evalulated. The reaction of Fpg revealed a 5- and 10-fold increase in rate of removal of OG from duplexes containing OG:B and OG:Q base pairs, respectively, relative to an OG:A mispair. These results suggest that the lack of the ability to hydrogen bond to the opposite base facilitates removal of OG. In contrast, adenine removal catalyzed by MutY was much more efficient from an OG:A mispair-containing duplex (k2 = 12 +/- 2 min(-1)) compared to the removal of B from an OG:B duplex (k(obs) < 0.002 min(-1)). Surprisingly, MutY was able to catalyze base removal from the OG:Q-containing substrate (k2 = 1.2 +/- 0.2 min(-1)). Importantly, the B and Q analogues are not deleterious to high-affinity DNA binding by MutY. In addition, the B and Q analogues are more susceptible to acid-catalyzed depurination illustrating that the enzyme-catalyzed mechanism is distinct from the nonenzymatic mechanism. Taken together, these results point to the importance of both N7 and N3 in the mechanism of adenine excision catalyzed by MutY.     

Influence of N7 protonation on the mechanism of the N-glycosidic bond hydrolysis in 2'-deoxyguanosine. A theoretical study

The influence of N7 protonation on the mechanism of the N-glycosidic bond hydrolysis in 2'-deoxyguanosine has been studied using density functional theory (DFT) methods. For the neutral system, two different pathways (with retention and inversion of configuration at the C1' anomeric carbon) have been found, both of them consisting of two steps and involving the formation of a dihydrofurane-like intermediate. The Gibbs free energy barrier for the first step is very high in both cases (53 and 46 kcal/mol for the process with inversion and with retention, respectively). However, the N7-protonated system shows a very different mechanism which consists of two steps. The first one leads to the formation of an oxacarbenium ion intermediate, with a Gibbs free energy barrier of 27 kcal/mol, and the second one corresponds to the nucleophilic attack of the water molecule to the oxacarbenium ion and takes place with a barrier of 1.3 kcal/mol. Thus, these results agree with a stepwise SN1 mechanism (DN*AN), with a discrete intermediate formed between the leaving group and the nucleophile approach, and show that N7 protonation strongly catalyzes the hydrolysis of the N-glycosidic bond, making the guanine a better leaving group. Finally, kinetic isotope effects have been calculated for the protonated system, and the results obtained are in very good agreement with experimental data for analogous systems.     

Do Glycosyl Sulfonium Ions Engage in Neighbouring‐Group Participation? A Study of Oxathiane Glycosyl Donors and the Basis for their Stereoselectivity

Neighbouring‐group participation has long been used to control the synthesis of 1,2‐trans‐glycosides. More recently there has been a growing interest in the development of similar strategies for the synthesis of 1,2‐cis‐glycosides, in particular the use of auxiliary groups that generate sulfonium ion intermediates. However, there has been some debate over the role of sulfonium ion intermediates in these reactions: do sulfonium ions actually engage in neighbouring‐group participation, or are they a resting state of the system prior to reaction through an oxacarbenium ion intermediate? Herein, we describe the reactivities and stereoselectivities of a family of bicyclic thioglycosides in which an oxathiane ring is fused to the sugar to form a trans‐decalin‐like structure. A methyl sulfonium ion derived from one such glycosyl donor is so stable that it can be crystallised from ethanol, yet it reacts with complete stereoselectivity at high temperature. The importance of a ketal group in the oxathiane ring for maintaining this high stereoselectivity is investigated using a combination of experiment and ab initio calculations. The data are discussed in terms of S_N1 and S_N2 type mechanisms. Trends in stereoselectivity across a series of compounds are more consistent with selective addition to oxacarbenium ions rather than a shift between S_N1 and S_N2 mechanisms.     

Theoretical study on the deglycosylation mechanism of rice BGlu1 β‐glucosidase

It is proposed that the catalysis of GH1 enzymes follows a double‐displacement mechanism involving a glycosylation and a deglycosylation steps. In this article, the deglycosylation step was studied using quantum mechanical/molecular mechanical (QM/MM) approach. The calculation results reveal that the nucleophilic water (Wat1) attacks to the anomeric C₁, and the deglycosylation step experiences a barrier of 21.4 kcal/mol from the glycosyl‐enzyme intermediate to the hydrolysis product, in which an oxocarbenium cation‐like transition state (TS) is formed. At the TS, the covalent glycosyl‐enzyme bond is almost broken (distance of 2.45 Å), and the new covalent bond between the attacking oxygen of the water molecule and C₁ is basically established (length of 2.14 Å). In addition, a short hydrogen bridge is observed between the nucleophilic E386 and the C₂? OH of sugar ring (distance of 1.94 Å) at the TS, which facilitates the ring changing from a chair form to half‐chair form, and stabilizes the oxocarbenium cation‐like TS. © 2013 Wiley Periodicals, Inc.     

Could diastereoselectivity in the presence of O-2 chiral nonparticipating groups be an indicator of glycopyranosyl oxacarbenium ions in glycosylation reactions?

Although long postulated, the existence of glycopyranosyl oxacarbenium ions as intermediates or transition states (TS) in chemical glycosylation reactions has not been convincingly demonstrated experimentally. It is anticipated that elucidation of such reactive species will greatly assist synthetic chemists to control the α/β stereoselectivity by rational means. Previous density functional theory (DFT) calculations from our group found that the torsion potential about C-2-O-2 in protected glycopyranosyl donors changed from a conventional 3-fold rotor to a 2-fold rotor with a strong syn (CH-2-C-2-O-2-CPg) preference once the donor was ionized to its oxacarbenium ion. This suggested to us that if CPg of the protecting group was a chiral carbon, then diastereoselectivity might be observed in glycosylation reactions that proceed through oxacarbenium ions. The hypothesis to test is as follows: if a nonparticipating O-2 racemic chiral protecting group exhibits diastereoselectivity in glycosylation reactions, then the reaction probably proceeds through an oxacarbenium ion intermediate or TS. We present data for O-2 ether-protected d-glucopyranosyl donors where the racemic protecting group 1-methyl 1'-methylcyclopropylmethyl (MCPM) provides the chirality. MCPM proves to be more activating than the O-2-benzyl ether, and in cases where the donor is otherwise deactivated, several examples of moderate diastereoselectivity are found. These results can be interpreted to indicate that a continuum of reactivity exists where some glycosyl donors form oxacarbenium ions in glycosylation reactions but more reactive donors do not. The strongly activating properties of the cyclopropylmethyl ether functionality and the ability to induce diastereoselectivity with chiral derivatives strongly suggest widespread applications.     

The impact of protonation and deprotonation of 3-methyl-2'-deoxyadenosine on N-glycosidic bond cleavage

The enzyme-substrate contacts that are believed to be involved in depurination by proton transfer have been modelled by protonation and deprotonation of 3-methyl-2'-deoxyadenosine (3-MDA) using quantum mechanical calculations in the gas-phase and solution media. The change in the charge distribution on the sugar ring and nucleobase that is introduced by the protonation and deprotonation strongly affects the N-glycosidic bond length. The unimolecular cleavage and hydrolysis of the N-glycosidic bond, involving D(N)*A(N) and A(N)D(N) pathways, have been considered at several levels of theory. The trend in the energy barriers is A(N)D(N) > cleavage > D(N)*A(N). All probable proton transfer reactions resulting from enzyme-substrate contacts do not facilitate the N-glycosidic bond cleavage of 3-MDA. The deprotonation of 3-MDA that may result from the interaction between H6 and enzyme do not facilitate bond cleavage. The protonation at N7 induces more positive charge on the sugar ring and further facilitates the depurination relative to the protonation at N1. The changes in the charges calculated on the ribose and nucleobase are in good relationship with the C1'-C2', C1'-O4', and N-glycosidic bond lengths along the cleavage. The change in energy barrier ΔE of glycosidic bond cleavage from the gas-phase to solution media strongly depends on the charge of the species.     

Theoretical study of the imidazolidinone catalyzed 1,4-addition of N,N-dimethyl-3-anisidine with α,β-unsaturated butyric aldehyde

Friedel–Crasfts alkylation reactions of α,β-unsaturated butyric aldehydes with N,N-dimethyl-3-anisidine catalyzed by a (2S,5S)-5-benzyl-2-tert-butyl-3-methylimidazolidin-4-one HCl salt have been carried out at the PCM(CH₂Cl₂)/B3LYP/6-311++G(d,p)//B3LYP/6-31G(d) level. Three reaction processes have been characterized: (I) the formation of an iminium ion intermediate; (II) the 1,4-iminium addition of the iminium ion; and (III) the hydrolysis of the addition product. Moreover, Path 1-1 is the favorable channel in the formation of the iminium ion. From the point of view of energy, the enantioselectivity is controlled by the carbon–carbon bond formation step that is involved in both the intermediate M4 and the transition state TS4. The highest energy barrier of the reaction is the H2 proton transfer from the O10 atom of a water molecule to the N1 atom of the catalyst in the hydrolysis process, which is 23.4 kcal/mol. The presented calculated results may be helpful in understanding the experimental product distribution for the title reaction, and provide a general model to help explain the mechanisms of similar reactions.     

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.     

Ring cleavage reactions of methyl α-D-allopyranoside derivatives with phenylboron dichloride and triethylsilane

In the course of our studies on the regioselective carbon-oxygen bond cleavage of the benzylidene acetal group of hexopyranosides with a reducing agent, we found that a combination of a Lewis acid and a reducing agent triggered a ring-opening reaction of the pyranose ring of methyl α-D-allopyranosides. The formation of an acyclic boronate ester by the attachment of a hydride ion at C-1 indicated that the unexpected endocyclic cleavage of the bond between the anomeric carbon atom and the pyranose ring oxygen atom proceeded via an oxacarbenium ion intermediate produced by the chelation between O5/O6 of the pyranoside and the Lewis acid, followed by nucleophile substitution with a hydride ion at C1.     

The mechanism of cis-trans isomerization of prolyl peptides by cyclophilin

The mechanism of cis-trans isomerization of prolyl peptides catalyzed by cyclophilin (CyP) was studied computationally via molecular dynamics (MD) simulations of the transition state (TS) and the cis and trans forms of the ground state (GS), when bound to CyP and when free in aqueous solution. The MD simulations include four enzyme-bound species of tetrapeptide (Suc-Ala-XC([double bond]O)-NPro-Phe-pNA; X = Gly, Trp, Ala, and Leu). In water, the prolyl amide bond is favorably planar with the presence of conformers exhibiting +/-20 degrees twist of the C-N dihedral. In the active site a hydrogen bond between the cis-prolyl amide carbonyl O and the backbone amide N-H of Asn102 retains the 20 degrees twist of the C-N dihedral. The TS structure is characterized by a 90 degrees twist of the amide C-N bond and a more favorable interaction with Asn102 due to the shorter distance between Asn102(HN) and the amide carbonyl O. The conformational change of cis --> TS also involves pyramidalization of the amide N, which results in the formation of a hydrogen bond between the amide N and the guanidino group of Arg55. Both Asn102 and Arg55 are held in the same position in CyP.cis-isomer as in CyP.TS. In the ligand-free CyP the Arg55 guanidino group is highly disorganized and Asn102 is displaced 1 A from the position in the ligand-bound CyP. Thus, the organization of Arg55 and Asn102 occurs upon substrate binding. The geometrical complimentarity of the organized enzyme structure to the TS structure is a result of preferential binding of the proline N and the amide carbonyl of the TS compared to that of GS. However, the N-terminal part (Suc-Ala) becomes repositioned in the TS such that two hydrogen bonds disappear, one hydrogen bond appears and two other hydrogen bonds becomes weaker on the conversion of CyP.cis to CyP.TS. During this conversion, total hydrophobic contact between enzyme and the peptide is preserved. Thus, the interaction energies of GS and TS with enzyme are, as a whole, much alike. This does not support the contention that TS is bound more tightly than GS by K(m)/K(TS) = 10(6) in the cis --> trans reaction. Repositioning of the N-terminal part of the peptide on CyP.TS formation becomes more pronounced when the substrate X residue is changed from Gly < Trp < Ala < Leu. We propose that the larger turning of the N-terminus is responsible for the larger value of the experimentally observed Delta S(++) and Delta H(++), which sum up to little change in Delta G(++). The positioning of the Arg55 and the degree of 20 degrees twist of the amide C-N bond are considered as criteria for Near Attack Conformers (NACs) in cis-trans isomerization. NACs account for approximately 30% of the total GS populations of the cis-isomer. Similar NAC populations were observed with four different substrates. This is consistent with the insensitivity of enzymatic activity to the nature of the X residue. Also, the NAC population in CyP.trans-AAPF was comparable to that in CyP.cis-AAPF, in accord with similar experimentally measured rates of the cis --> trans and trans --> cis reaction in CyP. These NACs, found in CyP.cis and CyP.trans, resemble only one of the four possible TS configurations in the water reaction. The identity of this TS structure (syn/exo) is in accord with experimentally determined KIE values in the enzymatic reaction. However, the geometry of the active site was also complementary to another TS structure (anti/exo) that was not detected in the active site by the same KIE measurements, implying that the geometrical fitness of the TS cannot be a single determining factor for enzymatic reactions.     

Chair-boat interconversions in cyclic seven-membered amides and related structures

The transition state to ring reversal has been examined in a series of 7-membered rings related to caprolactam. The structural changes associated with introduction of Me groups, with alteration of the nature of the CN double bond, with ring fusion, or with introduction of a second, nonconjugated N atom perturb the transition state to ring reversal. From ¹H and ¹³C NMR studies, we find that the lactam bond itself favors a different transition state from that present in cycloheptene. With some exceptions, the observed barriers are consistent with TS II, in which ring reversal begins with movement of the C₅ end of the ring, or with TS III, in which ring reversal begins with C₃-C₄ bond torsion. The conclusions are consistent with the structural changes that result from the functional and steric alterations.     

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.     

Acid-catalysed hydrolysis of N-sulphonyl sulphilimines—II

The basicity and the acid-catalysed hydrolysis of ph(R)SNTs and o-HC₆H₄(Me)SNTs sulphilimines have been studied by UV spectrophotometric and kinetic methods, respectively, in aqueous HClO₄ (1–10 M) and 1:1 (v/v) EtOH/H₂O-HClO₄ (0.5–6 M). Depending on the constitution of the substrates, sulphilimine hydrolysis can follow three different courses, according to rate-acidity profiles, Bunnett-Olsen's treatment, activation parameters and product analysis. Most typical for sulphilimines is S_N2 hydrolysis with S^IV-N bond cleavage. In this case the reaction starts with the nucleophilic addition of water and is promoted by acid-base catalysis. If a relatively stable carbenium ion can be formed from R group, an S_N1 reaction with S^IVC bond cleavage takes place. Sulphilimine with X = o-CO₂H due to neighbouring-group participation hydrolyses very rapidly via acyloxy-sulphurane and acyloxy-sulphonium ion intermediates with five-memembered ring (S_Ni reaction involving S^IVN bond cleavage).     

Synthesis and conformational analysis of bicyclic sulfonium salts. Structures related to the glycosidase inhibitor australine

The syntheses of eight sulfonium compounds with structures related to the naturally occurring pyrrolizidine alkaloid, australine, in which the bridgehead nitrogen atom is replaced by a sulfonium ion, are described. The synthetic strategy relies on the intramolecular attack of a cyclic thioether across a terminal double bond in the presence of a suitable electrophile. We postulate that these compounds, having a permanent positive charge on the sulfur atom, will mimic the highly unstable oxacarbenium ion transition state in a glycosidase-catalyzed hydrolysis reaction. The conformational preferences of these compounds, based on analysis of 1H-1H vicinal coupling constants and 1D-NOESY data, are attributed to both steric and electrostatic interactions. These compounds will be used in the study of structure-activity relationships with glycosidase enzymes.     

Unimolecular dissociation of aniline molecular ion: A theoretical study

The potential energy surface (PES) for dissociation of aniline ion was determined using density functional theory molecular orbital calculations at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d) level. On the basis of the PES obtained, kinetic analysis was performed by Rice–Ramsperger–Kassel–Marcus (RRKM) calculations. The RRKM dissociation rate constants agreed well with previous experimental data. The most favorable channel was formation of the cyclopentadiene ion by loss of HNC, occurring through consecutive ring opening and re-closure to a five-membered ring. Loss of H could compete with the HNC loss at high energy, which occurred by direct cleavage of an N–H bond or through ring expansion.     

Proton migration and tautomerism in protonated triglycine.

Proton migration in protonated glycylglycylglycine (GGG) has been investigated by using density functional theory at the B3LYP/6-31++G(d,p) level of theory. On the protonated GGG energy hypersurface 19 critical points have been characterized, 11 as minima and 8 as first-order saddle points. Transition state structures for interconversion between eight of these minima are reported, starting from a structure in which there is protonation at the amino nitrogen of the N-terminal glycyl residue following the migration of the proton until there is fragmentation into protonated 2-aminomethyl-5-oxazolone (the b(2) ion) and glycine. Individual free energy barriers are small, ranging from 4.3 to 18.1 kcal mol(-)(1). The most favorable site of protonation on GGG is the carbonyl oxygen of the N-terminal residue. This isomer is stabilized by a hydrogen bond of the type O-H.N with the N-terminal nitrogen atom, resulting in a compact five-membered ring. Another oxygen-protonated isomer with hydrogen bonding of the type O-H.O, resulting in a seven-membered ring, is only 0.1 kcal mol(-)(1) higher in free energy. Protonation on the N-terminal nitrogen atom produces an isomer that is about 1 kcal mol(-)(1) higher in free energy than isomers resulting from protonation on the carbonyl oxygen of the N-terminal residue. The calculated energy barrier to generate the b(2) ion from protonated GGG is 32.5 kcal mol(-)(1) via TS(6-->7). The calculated basicity and proton affinity of GGG from our results are 216.3 and 223.8 kcal mol(-)(1), respectively. These values are 3-4 kcal mol(-)(1) lower than those from previous calculations and are in excellent agreement with recently revised experimental values.     

Solvolyses of 2-Deoxy-alpha- and beta-D-Glucopyranosyl 4'-Bromoisoquinolinium Tetrafluoroborates

The solvolyses of 2-deoxy-alpha- and beta-D-glucopyranosyl 4'-bromoisoquinolinium tetrafluoroborates (1 and 2) were monitored in aqueous methanol, ethanol, trifluoroethanol, and binary mixtures of ethanol and trifluoroethanol. The observed rate constants are consistent with the solvolyses of 1 and 2 proceeding via dissociative (D(N) A(N)) transition states. In comparison to the alpha-anomer, solvolysis of the beta-compound gives a greater transition state charge delocalization onto the ring oxygen atom. Analysis of the solvolysis product ratios indicates that the 2-deoxyglucosyl oxacarbenium ion is not solvent-equilibrated in the solvent mixtures studied. In the solvolysis of compound 1, the solvent trifluoroethanol facilitates diffusional separation of the leaving group and, in so doing, promotes the formation of the retained trifluoroethyl glycoside.     

Theoretical studies on the hydrolysis mechanism of N-(2-oxo-1,2-dihydro-pyrimidinyl) formamide

Density functional theory (B3LYP) and ab initio (MP2) methods with the 6-31G(d,p) basis set are used to study the mechanisms for the hydrolysis of N-(2-oxo-1,2-dihydro-pyrimidinyl) formamide (PFA) in the gas phase. The direct and the water-assisted hydrolysis processes are considered, involving one and two water molecules, respectively. Three different pathways are explored in each case. In the first pathway, the O atom of water first attacks at the C atom of amide while one H atom of water transfers toward the oxygen of amide, leading to an intermediate of tetrahedral coordinated carbon with two OH groups. In the subsequent step, the hydroxyl H atom transfers to the N atom of pyrimidine ring and the C-N covalent bond of amide dissociates simultaneously. In the second path, the O and one H of water attack at the C of amide and the N of pyrimidine ring, respectively, while the C-N bond of amide dissociates. In the third path, three processes occur simultaneously: the O of water attacks at the C of amide, one H atom attacks at the N of amide, and the C-N bond of amide is broken. It is shown that the second pathway is favored for the direct hydrolysis while the first pathway is favored for the water-assisted hydrolysis. It is also shown that the water-assisted hydrolysis is slightly more favorable than the direct hydrolysis. Moreover, solvent effects on five pathways are evaluated with Monte Carlo simulation (MC) and free energy perturbation methods. It is shown that the solvent water slightly reduces the energy barrier in each pathway. The first pathway in the water-assisted hydrolysis remains the most favorable when the solvent effects of bulk water are taken into account.     

Stereoelectronic effects determine oxacarbenium vs β-sulfonium ion mediated glycosylations

Activation of a glycosyl donor protected with a 2-O-(S)-(phenylthiomethyl)benzyl ether chiral auxiliary results in the formation of an anomeric β-sulfonium ion, which can be displaced with sugar alcohols to give corresponding α-glycosides. Sufficient deactivation of such glycosyl donors by electron-withdrawing protecting groups is, however, critical to avoid glycosylation of an oxacarbenium ion intermediate. The latter type of glycosylation pathway can also be suppressed by installing additional substituents in the chiral auxiliary.