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.     

The catalytic mechanism of mouse renin studied with QM/MM calculations

Hypertension is a chronic condition that affects nearly 25% of adults worldwide. As the Renin-Angiotensin-Aldosterone System is implicated in the control of blood pressure and body fluid homeostasis, its combined blockage is an attractive therapeutic strategy currently in use for the treatment of several cardiovascular conditions. We have performed QM/MM calculations to study the mouse renin catalytic mechanism in atomistic detail, using the N-terminal His6-Asn14 segment of angiotensinogen as substrate. The enzymatic reaction (hydrolysis of the peptidic bond between residues in the 10th and 11th positions) occurs through a general acid/base mechanism and, surprisingly, it is characterized by three mechanistic steps: it begins with the creation of a first very stable tetrahedral gem-diol intermediate, followed by protonation of the peptidic bond nitrogen, giving rise to a second intermediate. In a final step the peptidic bond is completely cleaved and both gem-diol hydroxyl protons are transferred to the catalytic dyad (Asp32 and Asp215). The final reaction products are two separate peptides with carboxylic acid and amine extremities. The activation energy for the formation of the gem-diol intermediate was calculated as 23.68 kcal mol(-1), whereas for the other steps the values were 15.51 kcal mol(-1) and 14.40 kcal mol(-1), respectively. The rate limiting states were the reactants and the first transition state. The associated barrier (23.68 kcal mol(-1)) is close to the experimental values for the angiotensinogen substrate (19.6 kcal mol(-1)). We have also tested the influence of the density functional on the activation and reaction energies. All eight density functionals tested (B3LYP, B3LYP-D3, X3LYP, M06, B1B95, BMK, mPWB1K and B2PLYP) gave very similar results.     

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.     

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.     

Investigation of ethylene dimerization over faujasite zeolite by the ONIOM method.

Ethylene dimerization was investigated by using an 84T cluster of faujasite zeolite modeled by the ONIOM3(MP2/6-311++G(d,p):HF/6-31G(d):UFF) method. Concerted and stepwise mechanisms were evaluated. In the stepwise mechanism, the reaction proceeds by protonation of ethylene to form the surface ethoxide and then C--C bond formation between the ethoxide and the second ethylene molecule to give the butoxide product. The first step is rate-determining and has an activation barrier of 30.06 kcal mol(-1). The ethoxide intermediate is rather reactive and readily reacts with another ethylene molecule with a smaller activation energy of 28.87 kcal mol(-1). In the concerted mechanism, the reaction occurs in one step of simultaneous protonation and C--C bond formation. The activation barrier is calculated to be 38.08 kcal mol(-1). Therefore, the stepwise mechanism should dominate in ethylene dimerization.     

Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations

We use quantum mechanics/molecular mechanics simulations to study the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal catalysis to process nucleic acids. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA-cleavage reaction and characterize its mechanism. We find that the reaction proceeds in two steps. In a first step, catalyzed primarily by magnesium ion A and its ligands, a water molecule attacks the scissile phosphate. Consistent with thiol-substitution experiments, a water proton is transferred to the downstream phosphate group. The transient phosphorane formed as a result of this nucleophilic attack decays by breaking the bond between the phosphate and the ribose oxygen. In the resulting intermediate, the dissociated but unprotonated leaving group forms an alkoxide coordinated to magnesium ion B. In a second step, the reaction is completed by protonation of the leaving group, with a neutral Asp132 as a likely proton donor. The overall reaction barrier of ～15 kcal mol(-1), encountered in the first step, together with the cost of protonating Asp132, is consistent with the slow measured rate of ～1-100/min. The two-step mechanism is also consistent with the bell-shaped pH dependence of the reaction rate. The nonmonotonic relative motion of the magnesium ions along the reaction pathway agrees with X-ray crystal structures. Proton-transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA-cleavage reaction.     

Ab initio and density functional theory studies of the catalytic mechanism for ester hydrolysis in serine hydrolases

We present results from ab initio and density functional theory studies of the mechanism for serine hydrolase catalyzed ester hydrolysis. A model system containing both the catalytic triad and the oxyanion hole was studied. The catalytic triad was represented by formate anion, imidazole, and methanol. The oxyanion hole was represented by two water molecules. Methyl formate was used as the substrate. In the acylation step, our computations show that the cooperation of the Asp group and oxyanion hydrogen bonds is capable of lowering the activation barrier by about 15 kcal/mol. The transition state leading to the first tetrahedral intermediate in the acylation step is rate limiting with an activation barrier (ΔE₀) of 13.4 kcal/mol. The activation barrier in the deacylation step is smaller. The double-proton-transfer mechanism is energetically unfavorable by about 2 kcal/mol. The bonds between the Asp group and the His group, and the hydrogen bonds in the oxyanion hole, increase in strength going from the Michaelis complex toward the transition state and the tetrahedral intermediate. In the acylation step, the tetrahedral intermediate is a very shallow minimum on the energy surface and is not viable when molecular vibrations are included. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 69: 89–103, 1998     

MINDO-SCF-MO-berechnung der cis-trans-isomerisierung von N-methyl- und N-phenylazomethin

MINDO/2-SCF-MO calculations for the ground state properties of N-methyl- and N-phenyl-azomethin have been carried out. The calculated rotation barrier for the methyl group in N-methyl-azomethin was 0·8 kcal/mol, the eclipsed conformation being most stable. The calculated rotation barrier about the CN bond in the protonated methylazomethin was 27·9 kcal/mol. MINDO/1-SCF-MO treatment for the N-inversion barrier of the unprotonated species yielded 13·00 kcal/mol. Similar MINDO/2 calculations for N-phenylazomethin yielded 4·0 kcal/mol for the rotation barrier of the phenyl ring around the CN= bond, the perpendicular conformation of the ring to the CNC plane being most stable. For the corresponding N protonated derivative the value 27·3 kcal/mol was calculated for the rotation barrier around the CN bond. MINDO/1 treatment yielded an inversion barrier of 14·0 kcal/mol for N-phenylazomethin.     

Catalytic Mechanisms of Transfer Hydrogenation of Azobenzene with Ammonia Borane by Pincer Bismuth Complex: Crucial Role of C=N Functional Group on the Pincer Ligand

Transfer hydrogenation of azobenzene with ammonia borane mediated by pincer bismuth complex 1 was systematically investigated through density functional theory calculations. An unusual metal-ligand cooperation mechanism was disclosed, in which the saturation/regeneration of the C=N functional group on the pincer ligand plays an essential role. The reaction is initiated by the hydrogenation of the C=N bond (saturation) with ammonia borane to afford 3^CN , which is the rate-determining step with Gibbs energy barrier (ΔG^≠) and Gibbs reaction energy (ΔG) of 25.6 and −7.3 kcal/mol, respectively. 3^CN is then converted to a Bi−H intermediate through a water-bridged pathway, which is followed up with the transfer hydrogenation of azobenzene to produce the final product N,N′-diphenylhydrazine and regenerate the catalyst. Finally, the catalyst could be improved by substituting the phenyl group for the tert-butyl group on the pincer ligand, where the ΔG^≠ value (rate-determining step) decreases to 24.0 kcal/mol.     

Nitric oxide adsorption and reduction reaction mechanism on the Rh7(+) cluster: a density functional theory study

The transition metal rhodium has been proved the effective catalyst to convert from NO(x) to N(2.) In the present work, we are mainly focused on the NO adsorption and decomposition reaction mechanism on the surface of the Rh(7)(+) cluster, and the calculated results suggest that the reaction can proceed via three steps. First, the NO can adsorb on the surface of the Rh(7)(+) cluster; second, the NO decomposes to N and O atoms; finally, the N atom reacts with the second adsorbed NO and reduces to a N(2) molecule. The N-O bond breaks to yield N and O atoms in the second step, which is the rate-limiting step of the whole catalytic cycle. This step goes over a relatively high barrier (TS(12)) of 39.6 kcal/mol and is strongly driven by a large exothermicity of 55.1 kcal/mol during the formation of stable compound 3, accompanied by the N and O atoms dispersed on the different Rh atoms of the Rh(7)(+) cluster. In addition, the last step is very complex due to the different possibilities of reaction mechanism. On the basis of the calculations, in contrast to the reaction path II that generates N(2) from two nitrogen atoms coupling, the reaction path I for the formation of intermediate N(2)O is found to be energetically more favorable. Present work would provide some valuable fundamental insights into the behavior of the nitric oxide adsorption and reduction reaction mechanism on the Rh(7)(+) cluster.     

New insights into the mechanism of the Schiff base hydrolysis catalyzed by type I dehydroquinate dehydratase from S. enterica: a theoretical study

The reaction pathway of Schiff base hydrolysis catalyzed by type I dehydroquinate dehydratase (DHQD) from S. enterica has been studied by performing molecular dynamics (MD) simulations and density functional theory (DFT) calculations and the corresponding potential energy profile has also been identified. On the basis of the results, the catalytic hydrolysis process for the wild-type enzyme consists of three major reaction steps, including nucleophilic attack on the carbon atom involved in the carbon-nitrogen double bond of the Schiff base intermediate by a water molecule, deprotonation of the His143 residue, and dissociation between the product and the Lys170 residue of the enzyme. The remarkable difference between this and the previously proposed reaction mechanism is that the second step here, absent in the previously proposed reaction mechanism, plays an important role in facilitating the reaction through a key proton transfer by the His143 residue, resulting in a lower energy barrier. Comparison with our recently reported results on the Schiff base formation and dehydration processes clearly shows that the Schiff base hydrolysis is rate-determining in the overall reaction catalyzed by type I DHQD, consistent with the experimental prediction, and the calculated energy barrier of ～16.0 kcal mol(-1) is in good agreement with the experimentally derived activation free energy of ～14.3 kcal mol(-1). When the imidazole group of His143 residue is missing, the Schiff base hydrolysis is initiated by a hydroxide ion in the solution, rather than a water molecule, and both the reaction mechanism and the kinetics of Schiff base hydrolysis have been remarkably changed, clearly elucidating the catalytic role of the His143 residue in the reaction. The new mechanistic insights obtained here will be valuable for the rational design of high-activity inhibitors of type I DHQD as non-toxic antimicrobials, anti-fungals, and herbicides.     

Inversion vs retention of configuration in gas-phase ammonium ion/alcohol reactions

The potential energy surface for gas-phase reactions of ammonium ion with alcohols was examined by ab initio and DFT methods. Transition structures for inversion (S(N)2) and retention (S(N)F) mechanisms were located for 2-propanol and exo-2-norbornanol. The S(N)F (retention) process was found to be 6-8 kcal/mol higher in energy than the inversion S(N)2 counterpart for the 2-propanol system. The retention process in the 2-exo-norbornanol/ammonium ion system was favored by 1.3 kcal/mol.     

Reactivity of amino acid nucleoside phosphoramidates: a mechanistic quantum chemical study

Recent experimental evidence (Maiti et al. Chem.-Eur. J., submitted) indicates that hydrolysis of nucleoside phosphoramidates is subjected to anchimeric influence by carboxyl moieties in the leaving group but also by the base in the nucleotide. A quantum chemical analysis of these findings is presented. First the intrinsic hydrolysis mechanism is investigated for simplified model compounds, and then both amino acid and nucleoside substituents are included. It is found that hydrolysis is assisted by the α-carboxyl group via formation of a five-membered intermediate and that the barrier for the reaction of this intermediate toward the product state can be influenced by the nucleobase. The adenine base protonated on N3 interacts with the transition state and considerably lowers the barrier for hydrolysis. The influence of several base modifications is explained by calculating the pK(a) for protonation on N3.     

A theoretical analysis of the free-energy profile of the different pathways in the alkaline hydrolysis of methyl formate in aqueous solution

The free-energy profile for the different reaction pathways available to the hydroxide ion and methyl formate in aqueous solution is reported for the first time. The theoretical analysis was carried out by using the cluster-continuum method recently proposed by us for calculating the free energy of solvation of ions. Unlike the gas-phase reaction, our results are consistent with the fact that the reaction occurs mainly by nucleophilic attack of the hydroxide on the carbonyl carbon to yield a tetrahedral intermediate (B(AC)2 mechanism). However, an additional pathway, in which the hydroxide ion acts as a general base and a water molecule coordinated to this ion acts as the nucleophile, is also predicted to be important. The relative importance of these pathways is calculated to be 87 % and 13 %, respectively. The tetrahedral intermediate of the hydrolysis reaction has an estimated lifetime of 10 nanoseconds, and its conjugate acid has a pK(a) of 8.8. This tetrahedral intermediate is predicted to proceed to products by two pathways: elimination of methoxide ion (84 %) and by water catalyzed elimination of methanol (16 %). The less common reaction pathway, which involves attack of the hydroxide ion on the formyl hydrogen (decarbonylation mechanism) and leads to water, carbon monoxide, and methanol, is calculated to be only 3 kcal mol(-1) less favorable than the B(AC)2 mechanism. By comparison, direct attack of the hydroxide ion on the methyl group (B(AL)2 or S(N)2 mechanism) leading to an acyl-oxygen bond cleavage has a very high free energy of activation and is not expected to be important. The theoretically observed activation free energy at 298.15 K is calculated to be 15.5 kcal mol(-1), in excellent agreement with the experimentally measured value of 15.3 kcal mol(-1). This present model allows for a clear distinction between contributions due to solvation and those due to intrinsic (gas-phase) effects and proves to yield results in very good agreement with available experimental data.     

NMR.-Study of nitrogen inversion and conformation of 1,5-dihydro-isoalloxazines ("reduced flavin"). Studies in the flavin series, XIX

The pyramidal inversion of the N(5)-centre of several reduced flavins was measured by NMR. The inversion barrier was found to be ～10 kcal/mol in acetone solutions and to be independent of the size of the N(5) substituent. An increase of the inversion barrier of ～5 kcal/mol was observed in the case where the N(5) substituent could only be in axial position, and an increase of ～3.5 kcal/mol was observed for an acyl-like N(5) substituent. In aqueous solution the inversion barrier increases by ～3 kcal/mol. The stereochemistry of reduced flavin and its potential relevance in flavin-dependent biological dehydrogenations is discussed.     

Mechanism of the addition reaction of alkyl azides to [60]fullerene and the subsequent N2 extrusion to form monoimino-[60]fullerenes.

The 1,3-dipolar cycloaddition of methyl azide to C60 and the subsequent nitrogen elimination from the formed triazoline intermediate to yield the aziridine adduct have been studied using semiempirical and density functional methods. The results obtained show that the addition of methyl azide to C60 takes place in the ring junction between two six-membered rings leading to a closed [6,6]-trizoline intermediate with an energy barrier of about 20 kcal mol-1 and an exothermicity of ca. 2 kcal mol-1 at the B3LYP/6-31G**//AM1 level of theory. The subsequent thermal loss of N2 takes place through a stepwise mechanism in which the cleavage of the N-N single bond precedes the breaking of the N-C bond, with a total activation energy of approximately 45 kcal mol-1. The N2 loss occurs simultaneously with the formation of the new N-C bond. During the process, the steric effects of the leaving N2 molecule prevent the addition of the nitrene substituent to the [6,6]-ring junction attacked initially and force the addition to an adjacent [5,6]-ring junction.     

A revisited picture of the mechanism of glycerol dehydration

The dehydration mechanism of neutral glycerol in the gas phase was investigated by means of metadynamics simulations. Structures, vibrational frequencies, Gibbs free energy barriers, and rate constants at 800 K were computed for the different steps involved in the pyrolytic process. In this article, we provide a novel mechanism for the dehydration of neutral glycerol, proceeding via formation of glycidol with a barrier of 66.8 kcal/mol. The formation of glycidol is the rate limiting step of the overall decomposition process. Once formed, glycidol converts into 3-hydroxypropanal with a barrier of 49.5 kcal/mol. 3-Hydroxypropanal can decompose further into acrolein or into formaldehyde and vinyl-alcohol with barriers of 53.9 and 35.3 kcal/mol, respectively. These findings offer new insights to available experimental data based on glycerol pyrolysis studies performed with isotopic labeling and on the interpretation of the chemistry of glycerol and sugars in pyrolytic conditions.     

Methane-to-methanol oxidation by the hydrated iron(IV) oxo species in aqueous solution: a combined DFT and car-parrinello molecular dynamics study

Previously, we have shown that the ferryl ion ([FeIVO]2+) is easily produced from Fenton's reagent (i.e., a mixture of Fe2+ ions and H2O2 in aqueous solution), using DFT and Car-Parrinello MD calculations. To verify that the ferryl ion can indeed act as the active species in oxidation reactions with Fenton's reagent, we study in the present paper the reactivity of the ferryl ion toward an organic substrate, in particular the oxidation of methane to methanol. In the first part of this paper, we perform static DFT calculations on the reaction of CH4 with the [(H2O)5FeIVO]2+ complex in vacuo that show a strong prevalence of the oxygen-rebound mechanism over the methane coordination mechanism. This is in agreement with the static DFT results for methane oxidation by biocatalysts MMO and P450, but not with those for methane oxidation by bare metal-oxo ions, where the methane coordination mechanism prevails. The highest energy barrier in the oxygen-rebound mechanism is only 3 kcal/mol in vacuo, whereas in the methane coordination mechanism the highest barrier is 23 kcal/mol. Overall the oxidation reaction energy is downhill by 47 kcal/mol. We conclude that the ferryl ion can indeed act as the oxidative intermediate in the Fenton oxidation of organic species. In the second part of this paper, we perform a preliminary assessment of solvent effects on the oxidation by the ferryl ion in aqueous solution using the method of constrained (first principles) molecular dynamics. The free energy barrier of the H-abstraction reaction from methane by the ferryl ion (i.e., the first step in the rebound mechanism) in aqueous solution is, with 22 kcal/mol in solution, significantly higher than in vacuo. Given the fact that methane has a relatively strong C-H bond (ca. 10 kcal/mol stronger than the C-H bonds in the more typical Fenton's reagent substrates), we infer that for many organic substrates oxidation with the ferryl ion as an active intermediate may be a perfectly viable route.     

Investigation of Breaking Efficiency of N-Glycosidic Bond Between Sulfonamide and Honey

Sulfonamide residue in honey existed in a form bonded to sugar via the N-glycosidic bond.It would result in the possible underestimation of concentration of sulfonamide if it is not decomposed by chemi...     

On the mechanism of the N-glycosydic bond hydrolysis of 2��-deoxyguanosine: insights from first principles calculations

The effect of the activation of the nucleobase (leaving group) or the activation of the water molecule (nucleophile) by a general acid or a general base on the hydrolysis of the N-glycosydic bond of 2??-deoxyguanosine has been analyzed by means of density functional methods. First, we have considered two limiting cases: (1) the activation of the guanine by protonation at N7 and (2) the nucleophile attack by a hydroxyl ion, to separately evaluate the two kinds of activation. Next, we have studied the simultaneous activation of the leaving group and the nucleophile by introducing models of amino acid residues such as a formic acid (HCOOH) and imidazolium (C₃N₂H₅ ⁺), methylammonium (CH₃NH₃ ⁺) and formate (HCOO^?) ions in the system. It is shown that protonation of the nucleobase greatly catalyzes the hydrolysis of the N-glycosydic bond, the reaction occurring through a stepwise (D_N*A_N) mechanism with a discrete oxocarbenium ion intermediate. However, when a H₂O nucleophile molecule is activated by a formate anion, the reaction mechanism is a concerted A_ND_N but with different degrees of dissociative character of the transition structure depending on the acid that is activating the nucleobase.