Computational insights into the mechanism of radical generation in B12-dependent methylmalonyl-CoA mutase

ONIOM calculations have provided novel insights into the mechanism of homolytic Co-C5' bond cleavage in the 5'-deoxyadenosylcobalamin cofactor catalyzed by methylmalonyl-CoA mutase. We have shown that it is a stepwise process in which conformational changes in the 5'-deoxyadenosine moiety precede the actual homolysis step. In the transition state structure for homolysis, the Co-C5' bond elongates by approximately 0.5 Angstroms from the value found in the substrate-bound reactant complex. The overall barrier to homolysis is approximately 10 kcal/mol, and the radical products are approximately 2.5 kcal/mol less stable than the initial ternary complex of enzyme, substrate, and cofactor. The movement of the deoxyadenosine moiety during the homolysis step positions the resulting 5'-deoxyadenosyl radical for the subsequent hydrogen atom transfer from the substrate, methylmalonyl-CoA.     

Reactions of 1,3-cyclohexadiene with singlet oxygen. A theoretical study.

A thorough study of the reaction of singlet oxygen with 1,3-cyclohexadiene has been made at the B3LYP/6-31G(d) and CASPT2(12e,10o) levels. The initial addition reaction follows a stepwise diradical pathway to form cyclohexadiene endoperoxide with an activation barrier of 6.5 kcal/mol (standard level = CASPT2(12e,10o)/6-31G(d); geometries and zero-point corrections at B3LYP/6-31G(d)), which is consistent with an experimental value of 5.5 kcal/mol. However, as the enthalpy of the transition structure for the second step is lower than the diradical intermediate, the reaction might also be viewed as a nonsynchronous concerted reaction. In fact, the concertedness of the reaction is temperature dependent since entropy differences create a free energy barrier for the second step of 1.8 kcal/mol at 298 K. There are two ene reactions; one is a concerted mechanism (DeltaH(double dagger) = 8.8 kcal/mol) to 1-hydroperoxy-2,5-cyclohexadiene (5), while the other, which forms 1-hydroperoxy-2,4-cyclohexadiene (18), passes through the same diradical intermediate (9) as found on the pathway to endoperoxide. The major pathway from the endoperoxide is O-O bond cleavage (22.0 kcal/mol barrier) to form a 1,4-diradical (25), which is 13.9 kcal/mol less stable than the endoperoxide. From the diradical, two low-energy pathways exist, one to epoxyketone (29) and the other to the diepoxide (27), where both products are known to be formed experimentally with a product ratio sensitive to the nature of substitutents. A significantly higher activation barrier leads to C-C bond cleavage and direct formation of maleic aldehyde plus ethylene.     

New insight into the gas-phase bimolecular self-reaction of the HOO radical

The singlet and triplet potential energy surfaces (PESs) for the gas-phase bimolecular self-reaction of HOO*, a key reaction in atmospheric environments, have been investigated by means of quantum-mechanical electronic structure methods (CASSCF and CASPT2). All the reaction pathways on both PESs consist of a first step involving the barrierless formation of a prereactive doubly hydrogen-bonded complex, which is a diradical species lying about 8 kcal/mol below the energy of the reactants at 0 K. The lowest energy reaction pathway on both PESs is the degenerate double hydrogen exchange between the HOO* moieties of the prereactive complex via a double proton transfer mechanism involving an energy barrier of only 1.1 kcal/mol for the singlet and 3.3 kcal/mol for the triplet at 0 K. The single H-atom transfer between the two HOO* moieties of the prereactive complex (yielding HOOH + O2) through a pathway keeping a planar arrangement of the six atoms involves a conical intersection between either two singlet or two triplet states of A' and A" symmetries. Thus, the lowest energy reaction pathway occurs via a nonplanar cisoid transition structure with an energy barrier of 5.8 kcal/mol for the triplet and 17.5 kcal/mol for the singlet at 0 K. The simple addition between the terminal oxygen atoms of the two HOO* moieties of the prereactive complex, leading to the straight chain H2O4 intermediate on the singlet PES, involves an energy barrier of 7.3 kcal/mol at 0 K. Because the decomposition of such an intermediate into HOOH + O2 entails an energy barrier of 45.2 kcal/mol at 0 K, it is concluded that the single H-atom transfer on the triplet PES is the dominant pathway leading to HOOH + O2. Finally, the strong negative temperature dependence of the rate constant observed for this reaction is attributed to the reversible formation of the prereactive complex in the entrance channel rather than to a short-lived tetraoxide intermediate.     

Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study

In this ONIOM(QM:MM) study, we evaluate the role of the protein surroundings in the mechanism of H2O2 reduction catalyzed by the glutathione peroxidase enzyme, using the whole monomer (3113 atoms in 196 amino acid residues) as a model. A new optimization scheme that allows the full optimization of transition states for large systems has been utilized. It was found that in the presence of the surrounding protein the optimized active site structure bears a closer resemblance to the one in the X-ray structure than that without the surrounding protein. H2O2 reduction occurs through a two-step mechanism. In the first step, the selenolate anion (E-Se(-)) formation occurs with a barrier of 16.4 kcal/mol and is endothermic by 12.0 kcal/mol. The Gln83 residue plays the key role of the proton abstractor, which is in line with the experimental suggestion. In the second step, the O-O bond is cleaved, and selenenic acid (R-Se-OH) and a water molecule are formed. The calculated barrier for this process is 6.0 kcal/mol, and it is exothermic by 80.9 kcal/mol. The overall barrier of 18.0 kcal/mol for H2O2 reduction is in reasonable agreement with the experimentally measured barrier of 14.9 kcal/mol. The protein surroundings has been calculated to exert a net effect of only 0.70 kcal/mol (in comparison to the "active site only" model including solvent effects) on the overall barrier, which is most likely due to the active site being located at the enzyme surface.     

Methylene transfer or carbometalation? A theoretical study to determine the mechanism of lithium carbenoid-promoted cyclopropanation reactions in aggregation and solvation States

Density functional theory calculations for the lithium carbenoid-promoted cyclopropanations in aggregation and solvation states are presented in order to investigate the controversy of the mechanistic dichotomy, that is, the methylene-transfer mechanism and the carbometalation mechanism. The methylene-transfer mechanism represents the reaction reality, whereas the carbometalation pathway does not appear to compete significantly with the methylene-transfer pathway and should be ruled out as a major factor. A simple model calculation for monomeric lithium carbenoid-promoted cyclopropanations with ethylene in the gas phase is not sufficient to reflect the reaction conditions accurately or to determine the reaction mechanism since its result is inconsistent with the experimental facts. The aggregated lithium carbenoids are the most probable reactive species in the reaction system. The calculated reaction barriers of the methylene-transfer pathways are 10.1 and 8.0 kcal/mol for the dimeric (LiCH2F)2 and tetrameric (LiCH2F)4 species, respectively, compared with the reaction barrier of 16.0 kcal/mol for the monomeric LiCH2F species. In contrast, the reaction barriers of the carbometalation pathways are 26.8 kcal/mol for the dimeric (LiCH2F)2 and 33.9 kcal/mol for the tetrameric (LiCH2F)4 species, compared with the reaction barrier of 12.5 kcal/mol for the monomeric LiCH2F species. The effects of solvation were investigated by explicit coordination of the solvent molecules to the lithium centers. This solvation effect is found to enhance the methylene-transfer pathway, while it is found to impede the carbometalation pathway instead. The combined effects of the aggregation and solvation lead to barriers to reaction in the range of 7.2-9.0 kcal/mol for lithium carbenoid-promoted cyclopropanation reactions along the methylene-transfer pathway. Our computational results are in good agreement with the experimental observations.     

On the mechanism of (PCP)Ir-catalyzed acceptorless dehydrogenation of alkanes: a combined computational and experimental study

Pincer complexes of the type ((R)PCP)IrH(2), where ((R)PCP)Ir is [eta(3)-2,6-(R(2)PCH(2))(2)C(6)H(3)]Ir, are the most effective catalysts reported to date for the "acceptorless" dehydrogenation of alkanes to yield alkenes and free H(2). We calculate (DFT/B3LYP) that associative (A) reactions of ((Me)PCP)IrH(2) with model linear (propane, n-PrH) and cyclic (cyclohexane, CyH) alkanes may proceed via classical Ir(V) and nonclassical Ir(III)(eta(2)-H(2)) intermediates. A dissociative (D) pathway proceeds via initial loss of H(2), followed by C-H addition to ((Me)PCP)Ir. Although a slightly higher energy barrier (DeltaE(+ +)) is computed for the D pathway, the calculated free-energy barrier (DeltaG(+ +)) for the D pathway is significantly lower than that of the A pathway. Under standard thermodynamic conditions (STP), C-H addition via the D pathway has DeltaG(o)(+ +) = 36.3 kcal/mol for CyH (35.1 kcal/mol for n-PrH). However, acceptorless dehydrogenation of alkanes is thermodynamically impossible at STP. At conditions under which acceptorless dehydrogenation is thermodynamically possible (for example, T = 150 degrees C and P(H)2 = 1.0 x 10(-7) atm), DeltaG(+ +) for C-H addition to ((Me)PCP)Ir (plus a molecule of free H(2)) is very low (17.5 kcal/mol for CyH, 16.7 kcal/mol for n-PrH). Under these conditions, the rate-determining step for the D pathway is the loss of H(2) from ((Me)PCP)IrH(2) with DeltaG(D)(+ +) approximately DeltaH(D)(+ +) = 27.2 kcal/mol. For CyH, the calculated DeltaG(o)(+ +) for C-H addition to ((Me)PCP)IrH(2) on the A pathway is 35.2 kcal/mol (32.7 kcal/mol for n-PrH). At catalytic conditions, the calculated free energies of C-H addition are 31.3 and 33.7 kcal/mol for CyH and n-PrH addition, respectively. Elimination of H(2) from the resulting "seven-coordinate" Ir-species must proceed with an activation enthalpy at least as large as the enthalpy change of the elimination step itself (DeltaH approximately 11-13 kcal/mol), and with a small entropy of activation. The free energy of activation for H(2) elimination (DeltaG(A)(+ +)) is hence found to be greater than ca. 36 kcal/mol for both CyH and n-PrH under catalytic conditions. The overall free-energy barrier of the A pathway is calculated to be higher than that of the D pathway by ca. 9 kcal/mol. Reversible C-H(D) addition to ((R)PCP)IrH(2) is predicted to lead to H/D exchange, because the barriers for hydride scrambling are extremely low in the "seven-coordinate" polyhydrides. In agreement with calculation, H/D exchange is observed experimentally for several deuteriohydrocarbons with the following order of rates: C(6)D(6) > mesitylene-d(12) > n-decane-d(22) > cyclohexane-d(12). Because H/D exchange in cyclohexane-d(12) solution is not observed even after 1 week at 180 degrees C, we estimate that the experimental barrier to cyclohexane C-D addition is greater than 36.4 kcal/mol. This value is considerably greater than the experimental barrier for the full catalytic dehydrogenation cycle for cycloalkanes (ca. 31 kcal/mol). Thus, the experimental evidence, in agreement with calculation, strongly indicates that the A pathway is not kinetically viable as a segment of the "acceptorless" dehydrogenation cycle.     

Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K

Molecular dynamics simulations using a combined QM/MM potential have been performed to study the catalytic mechanism of human cathepsin K, a member of the papain family of cysteine proteases. We have determined the two-dimensional free energy surfaces of both acylation and deacylation steps to characterize the reaction mechanism. These free energy profiles show that the acylation step is rate limiting with a barrier height of 19.8 kcal/mol in human cathepsin K and of 29.3 kcal/mol in aqueous solution. The free energy of activation for the deacylation step is 16.7 kcal/mol in cathepsin K and 17.8 kcal/mol in aqueous solution. The reduction of free energy barrier is achieved by stabilization of the oxyanion in the transition state. Interestingly, although the "oxyanion hole" has been formed in the Michaelis complex, the amide units do not donate hydrogen bonds directly to the carbonyl oxygen of the substrate, but they stabilize the thiolate anion nucleophile. Hydrogen-bonding interactions are induced as the substrate amide group approaches the nucleophile, moving more than 2 A and placing the oxyanion in contact with Gln19 and the backbone amide of Cys25. The hydrolysis of peptide substrate shares a common mechanism both for the catalyzed reaction in human cathepsin K and for the uncatalyzed reaction in water. Overall, the nucleophilic attack by Cys25 thiolate and the proton-transfer reaction from His162 to the amide nitrogen are highly coupled, whereas a tetrahedral intermediate is formed along the nucleophilic reaction pathway.     

A multilayered representation,quantum mechanical and molecular mechanics study of the CH3F + OH− reaction in water

The bimolecular nucleophilic substitution (S_N2) reaction of CH₃F + OH^? in aqueous solution was investigated using a combined quantum mechanical and molecular mechanics approach. Reactant complex, transition state, and product complex along the reaction pathway were analyzed in water. The potentials of mean force were calculated using a multilayered representation with the DFT and CCSD(T) level of theory for the reactive region. The obtained free energy activation barrier for this reaction at the CCSD(T)/MM representation is 18.3 kcal/mol which agrees well with the experimental value at ～21.6 kcal/mol. Both the solvation effect and solute polarization effect play key roles on raising the activation barrier height in aqueous solution, with the former raising the barrier height by 3.1 kcal/mol, the latter 1.5 kcal/mol. © 2013 Wiley Periodicals, Inc.     

Theoretical studies on the electrocyclic reactions of bis(allene) and vinylallene. Role of allene group

The reaction mechanisms of the electrocyclic ring closure of bis(allene) and vinylallene were studied by ab initio MO methods. The conrotatory and disrotatory pathways of the electrocyclic reactions from bis(allene) to bis(methylene)cyclobutene were determined by a CASSCF method. The transition state on the conrotatory pathway is 26.8 kcal/mol above bis(allene) and about 23 kcal/mol lower than that on the disrotatory pathway at a MRMP calculation level. The activation energy on the conrotatory pathway is lower by 23 kcal/mol than that of the electrocyclic reaction of butadiene. This lower energy barrier comes from the interactions of the "side pi orbitals" of the allene group. The interaction of the "vertical pi orbitals" of the allene group is predominant at the early stage of the reaction. The activation energy of the electrocyclic reaction of vinylallene is about 8.5 kcal/mol higher than that on the conrotatory pathway of bis(allene).     

Quantum mechanical study of the ring-closing reaction of the hexatriene radical cation

The ring-closing reaction of hexatriene radical cation 1(*)(+) to 1,3-cyclohexadiene radical cation 2(*)(+) was studied computationally at the B3LYP/6-31G* and QCISD(T)/6-311G*//QCISD/6-31G* levels of theory. Both, concerted and stepwise mechanisms were initially considered for this reaction. Upon evaluation at the B3LYP level of theory, three of the possible pathways-a concerted C(2)-symmetric via transition structure 3(*)(+) and stepwise C(1)-symmetric pathways involving three-membered ring intermediate 5(*)(+) and four-membered ring intermediate 6(*)(+)-were rejected due to high-energy stationary points along the reaction pathway. The two remaining pathways were found to be of competing energy. The first proceeds through the asymmetric, concerted transition structure 4(*)(+) with an activation barrier E(a) = 16.2 kcal/mol and an overall exothermicity of -23.8 kcal/mol. The second pathway, beginning from the cis,cis,trans rotamer of 1(*)(+), proceeds by a stepwise pathway to the cyclohexadiene product with an overall exothermicity of -18.6 kcal/mol. The activation energy for the rate-determining step in this process, the formation of the intermediate bicyclo[3.1.0]hex-2-ene via transition structure 9(*)(+), was found to be 20.4 kcal/mol. More rigorous calculations of a smaller subsection of the potential energy hypersurface at the QCISD(T)//QCISD level confirmed these findings and emphasized the importance of conformational control of the reactant.     

Aromatic dienophiles. 1. A theoretical study of an inverse-electron demand Diels-Alder reaction between 2-aminopyrrole and 1,3,5-triazine

This study is devoted to a detailed theoretical study of an inverse-electron demand Diels-Alder reaction (IDA) with 1,3,5-triazine as the diene and 2-aminopyrrole 1A(alpha) as the dienophile, which is a key step in a cascade reaction for the one-pot synthesis of purine analogues. Geometries were optimized with the B3LYP/6-31G* method and energies were evaluated with the MP2/6-311++G** method. This IDA reaction occurs through a stepwise mechanism, where the first step corresponds to the nucleophilic attack of 2-aminopyrrole to triazine to form a zwitterionic intermediate, which is in equilibrium with a neutral intermediate through a hydrogen transfer process, followed by a rate-determining ring-closure step. It is shown that the B3LYP method significantly overestimates the activation energy, whereas the MP2 method offers a reasonable activation barrier of 27.9 kcal/mol in the gas phase. The solvation effect has been studied by the PCM model. In DMSO, the calculated activation energy of the IDA reaction is decreased to 24.0 kcal/mol with a strong endothermicity of 17.4 kcal/mol due to the energy penalty of transforming two aromatic reactants into a nonaromatic IDA adduct. The possible stepwise [2+2] pathway is ruled out based on its higher activation and reaction energies than those of the [4+2] pathway. By comparing the IDA reactions of triazine to 2-aminopyrrole and pyrrole, we address two crucial roles of the alpha-amino substituent in lowering activation and reaction energies and controlling the reaction regiochemistry.     

Methane activation on Pt and Pt4: a density functional theory study

The activation mechanisms of a methane molecule on a Pt atom (CH4-Pt) and on a Pt tetramer (CH4-Pt4) were investigated using density functional theory (B3LYP and PW91) calculations. The results from these two functionals are different mostly in predicting the reaction barrier, in particular for the CH4-Pt system. A new lower energy pathway was identified for the CH4 dehydrogenation on a Pt atom. In the new pathway, the PtCH2 + H2 products were formed via a transition state, in which the Pt atom forms a complex with carbene and both dissociated hydrogen atoms. We report here the first theoretical study of methane activation on a Pt4 cluster. Among the five single steps toward dehydrogenation, our results show that the rate-limiting step is the third step, that is, breaking the second C-H bond, which requires overcoming an energy barrier of 28 kcal/mol. On the other hand, the cleavage of the first C-H bond, that is, the first reaction step, requires overcoming an energy barrier of 4 kcal/mol.     

Theoretical research on Pd cluster catalysts for the direct dehydrogenation of propane to propylene

In this article, the feasibility of catalytic dehydrogenation of propane by Pd clusters (Pd₇, Pd₆C, Pd₆Si, Pd₆Ge, and Pd₆Sn) was investigated by using density functional theory (DFT). It was found that Pd₆Sn has the strongest electron mobility and the ability to activate C H bonds, and the highest adsorption barrier (−75.16 kcal/mol) with propylene. The first pathway of the Pd₆Sn-catalyzed primary reaction has the lowest decisive step barrier (16.65 kcal/mol), and the second pathway of the secondary reaction has the highest decisive step barrier (62.25 kcal/mol). It was demonstrated that both the catalyst's electron-leaping ability and the ability to activate C H bonds were the key factors affecting the activity, and the adsorption strength of the catalyst to the product was the main factor affecting the selectivity. It was shown that Pd cluster-catalyzed PDH is theoretically feasible and Pd₆Sn is likely to be a potential cluster catalyst for propane dehydrogenation.     

DFT study of the glutathione peroxidase-like activity of phenylselenol incorporating solvent-assisted proton exchange

Modeling of the glutathione peroxidase-like activity of phenylselenol has been accomplished using density-functional theory and solvent-assisted proton exchange (SAPE). SAPE is a modeling technique intended to mimic solvent participation in proton transfer associated with chemical reaction. Within this method, explicit water molecules incorporated into the gas-phase model allow relay of a proton through the water molecules from the site of protonation in the reactant to that in the product. The activation barriers obtained by SAPE for the three steps of the GPx-like mechanism of PhSeH fall within the limits expected for a catalytic system at physiological temperatures (DeltaG(1)++ = 19.1 kcal/mol; DeltaG(2)++= 6.6 kcal/mol; G(3)++ = 21.7 kcal/mol) and are significantly lower than studies which require direct proton transfer. The size of the SAPE network is also considered for the model of the reduction of the selenenic acid, step 2 of the GPx-like cycle. Use of a four-water network better accommodates the reaction pathway and reduces the activation barrier by 5 kcal/mol over the two-water model.     

Theoretical analysis of concerted and stepwise mechanisms of the hetero-Diels–Alder reaction of butadiene with formaldehyde and thioformaldehyde

The concerted and stepwise mechanisms of the hetero-Diels–Alder reaction of butadiene with formaldehyde and thioformaldehyde were studied by a CASSCF molecular orbital method. The energy barrier of the concerted reaction of butadiene with formaldehyde is about 21 kcal/mol higher than that of butadiene with thioformaldehyde at the CAS-MP2 calculation level. For the stepwise reaction paths, the energy barrier for the first step process of the reaction of butadiene with formaldehyde is about 17 kcal/mol above that of butadiene with thioformaldehyde. The concerted pathways for both systems are more favorable by 9–12 kcal/mol than the stepwise pathways. The electronic mechanisms for the concerted reactions of both reaction systems are also discussed by a CiLC analysis.     

Theoretical studies of proton-transfer reactions of 2-hydroxypyridine--(H2O)n (n = 0-2) in the ground and excited states

The potential energy profiles for proton-transfer reactions of 2-hydroxypyridine and its complexes with water were determined by MP2, CASSCF and MR-CI calculations with the 6-31G** basis set. The tautomerization reaction between 2-hydroxypyridine (2HP) and 2-pyridone (2PY) does not take place at room temperature because of a barrier of approximately 35 kcal/mol for the ground-state pathway. The water-catalyzed enol-keto tautomerization reactions in the ground state proceed easily through the concerted proton transfer, especially for the two-water complex. The S1 tautomerization between the 2HP and 2PY monomers has a barrier of 18.4 kcal/mol, which is reduced to 5.6 kcal/mol for the one-water complex and 6.4 kcal/mol for the two-water complex. The results reported here predict that the photoinduced tautomerization reaction between the enol and keto forms involves a cyclic transition state having one or two water molecules as a bridge.     

Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9

To elucidate enzyme catalysis through computer simulation, a prerequisite is to reliably compute free energy barriers for both enzyme and solution reactions. By employing on-the-fly Born-Oppenheimer molecular dynamics simulations with the ab initio quantum mechanical/molecular mechanical approach and the umbrella sampling method, we have determined free energy profiles for the methyl-transfer reaction catalyzed by the histone lysine methyltransferase SET7/9 and its corresponding uncatalyzed reaction in aqueous solution, respectively. Our calculated activation free energy barrier for the enzyme catalyzed reaction is 22.5 kcal/mol, which agrees very well with the experimental value of 20.9 kcal/mol. The difference in potential of mean force between a corresponding prereaction state and the transition state for the solution reaction is computed to be 30.9 kcal/mol. Thus, our simulations indicate that the enzyme SET7/9 plays an essential catalytic role in significantly lowering the barrier for the methyl-transfer reaction step. For the reaction in solution, it is found that the hydrogen bond network near the reaction center undergoes a significant change, and there is a strong shift in electrostatic field from the prereaction state to the transition state, whereas for the enzyme reaction, such an effect is much smaller and the enzyme SET7/9 is found to provide a preorganized electrostatic environment to facilitate the methyl-transfer reaction. Meanwhile, we find that the transition state in the enzyme reaction is a little more dissociative than that in solution.