Fundamental reaction pathway and free energy profile for inhibition of proteasome by Epoxomicin

First-principles quantum mechanical/molecular mechanical free energy calculations have been performed to provide the first detailed computational study on the possible mechanisms for reaction of proteasome with a representative peptide inhibitor, Epoxomicin (EPX). The calculated results reveal that the most favorable reaction pathway consists of five steps. The first is a proton transfer process, activating Thr1-O(γ) directly by Thr1-N(z) to form a zwitterionic intermediate. The next step is nucleophilic attack on the carbonyl carbon of EPX by the negatively charged Thr1-O(γ) atom, followed by a proton transfer from Thr1-N(z) to the carbonyl oxygen of EPX (third step). Then, Thr1-N(z) attacks on the carbon of the epoxide group of EPX, accompanied by the epoxide ring-opening (S(N)2 nucleophilic substitution) such that a zwitterionic morpholino ring is formed between residue Thr1 and EPX. Finally, the product of morpholino ring is generated via another proton transfer. Noteworthy, Thr1-O(γ) can be activated directly by Thr1-N(z) to form the zwitterionic intermediate (with a free energy barrier of only 9.9 kcal/mol), and water cannot assist the rate-determining step, which is remarkably different from the previous perception that a water molecule should mediate the activation process. The fourth reaction step has the highest free energy barrier (23.6 kcal/mol) which is reasonably close to the activation free energy (～21-22 kcal/mol) derived from experimental kinetic data. The obtained novel mechanistic insights should be valuable for not only future rational design of more efficient proteasome inhibitors but also understanding the general reaction mechanism of proteasome with a peptide or protein.     

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.     

Ab initio and density functional theory evidence on the rate-limiting step in the Morita-Baylis-Hillman reaction

The first ab initio and DFT studies on the mechanism of the MBH reaction show that the rate-limiting step involves an intramolecular proton transfer in the zwitterionic intermediate generated by the addition of enolate to electrophile. The activation barrier for the C-C bond-formation is found to be 20.2 kcal/mol lower than the proton-transfer step for the MBH reaction between methyl vinyl ketone and benzaldehyde catalyzed by DABCO.     

MCSCF study of singlet oxygen addition to ethenol—a model of photooxidation reactions of unsaturated and aromatic compounds bearing hydroxy groups

The reaction path of singlet (¹Δ_g) oxygen addition to ethenol (vinyl alcohol)—a model of the reactions of singlet oxygen with aromatic and unsaturated compounds bearing the hydroxy groups—has been studied by means of MCSCF calculations, using various active spaces and basis sets. The effects of dynamic correlation (at the PT2 level) and basis set superposition error (BSSE) on relative energies were also investigated. It was found that including polarization functions is necessary to obtain geometries of the oxygen moiety consistent with the available experimental data. Two possible reaction products were considered: 1-hydroxy-1,2-dioxethane (peroxide) and 2-hydroperoxyethanal-1 (hydroperoxide); their energies are 24.1 and 36.6 kcal/mol (44.1 and 78.2 kcal/mol with the PT2 contribution and BSSE correction) below the dissociation limit, respectively (all energies reported here refer to the 6-31G** basis set and an active space composed of eight orbitals and ten electrons). A common stage of both reactions is the formation of a peralcoxyl intermediate with one of the oxygen atoms attached to the unsubstituted carbon atom; the energies of the respective transition state and that of the intermediate are 30.2 and 18.7 kcal/mol (15.9 and 10.3 kcal/mol with the PT2 contribution and BSSE correction) above the dissociation limit, respectively. The energy of this transition state is the dominant energy barrier to the reaction. The intermediate can then undergo conversion to the dioxethane product, to the perepoxide intermediate, or via a proton transfer, directly to the hydroperoxide, the last route being the most probable one. The perepoxide intermediate, after a proton transfer, also readily gives the hydroperoxide. It was also found that the unimolecular conversion from dioxethane to hydroperoxide via a proton transfer from the hydroxy group accompanied with ring cleavage requires an activation energy of at least 56 kcal/mol, making this reaction path highly improbable. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1668–1681, 1997     

Cooperative and competitive effects of substituents at C1 and C4 on the barriers to ring inversion of 5,5-difluorobicyclo[2.1.0]pentanes

To identify the reasons for the very low barrier that has been measured for ring inversion of 1,4,5,5-tetrafluorobicyclo[2.1.0]pentane (deltaG(double dagger) = 6.8 +/- 0.2 kcal/mol), CASSCF and CASPT2 calculations have been performed on ring inversion in this and other bicyclo[2.1.0]pentanes. The results of the calculations show that a cooperative interaction between the geminal fluorines at C2 and the fluorines at C1 and C3 in the singlet cyclopentane-1,3-diyl transition structure (TS) contributes 3.7 kcal/mol to lowering the barrier to ring inversion in the tetrafluoro compound. In contrast, a competitive substituent effect in the TS for ring inversion of 1,4-dicyano-5,5-difluorobicyclo[2.1.0]pentane is predicted to raise the barrier height by 6.1 kcal/mol. The origin of these cooperative and competitive substituent effects is discussed.     

The electronic structure and energetics of V(+)-benzene half-sandwiches of different multiplicities: Comparative multireference and single-reference theoretical study

Multireference [complete active space self-consistent field (CASSCF) and multiconfigurational quasidegenerate perturbation theory (MCQDPT)] and single-reference ab initio (Moller-Plesset second order perturbation theory (MP2) and coupled clusters with singles, doubles and noniterative triples [CCSD(T)]) and density functional theory (PBE and B3LYP) electronic structure calculations of V(C(6)H(6))(+) half-sandwich in the states of different multiplicities are described and compared. Detailed analyses of the geometries and electronic structures of the all found states are given; adiabatic and diabatic dissociation energies are estimated. The lowest electronic state of V(C(6)H(6))(+) half-sandwich was found to be the quintet (5)B(2) state with a slightly deformed upside-down-boat-shaped benzene ring and d(4) configuration of V atom, followed by a triplet (3)A(2) state lying about 4 kcal/mol above. The lowest singlet state (1)A(1)(d(4)) lies much ( approximately 28 kcal/mol) higher. MCQDPT calculated adiabatic dissociation energy (53.6 kcal/mol) for the lowest (5)B(2)(d(4)) state agrees well with the current 56.4 (54.4) kcal/mol experimental estimate, giving a preference to the lower one. Compared to MCQDPT, B3LYP hybrid exchange-correlation functional provides the best results, while CCSD(T) performs usually worse. Gradient-corrected PBE calculations tend to systematically overestimate metal-benzene binding in the row quintet相似文献   

New model for a theoretical density functional theory investigation of the mechanism of the carbonic anhydrase: how does the internal bicarbonate rearrangement occur?

A theoretical density functional theory (DFT, B3LYP) investigation has been carried out on the catalytic cycle of the carbonic anhydrase. A model system including the Glu106 and Thr199 residues and the "deep" water molecule has been used. It has been found that the nucleophilic attack of the zinc-bound OH on the CO(2) molecule has a negligible barrier (only 1.2 kcal mol(-1)). This small value is due to a hydrogen-bond network involving Glu106, Thr199, and the deep water molecule. The two usually proposed mechanisms for the internal bicarbonate rearrangement have been carefully examined. In the presence of the two Glu106 and Thr199 residues, the direct proton transfer (Lipscomb mechanism) is a two-step process, which proceeds via a proton relay network characterized by two activation barriers of 4.4 and 9.0 kcal mol(-1). This pathway can effectively compete with a rotational mechanism (Lindskog mechanism), which has a barrier of 13.2 kcal mol(-1). The fast proton transfer found here is basically due to the effect of the Glu106 residue, which stabilizes an intermediate situation where the Glu106 fragment is protonated. In the absence of Glu106, the barrier for the proton transfer is much larger (32.3 kcal mol(-1)) and the Lindskog mechanism becomes favored.     

Structure and stability of the [TCNE](2)(2-) dimers in dichloromethane solution: a computational study

The solution behavior of [TCNE](.-), which forms long-living pi-[TCNE]22- dimers, is computationally studied by B3LYP and MCQDPT/CASSCF(2,2) calculations (a multiconfigurational quasi-degenerate perturbative calculation using a CASSCF(2,2) wavefunction, which properly accounts for the dispersion interaction). B3LYP calculations indicate minimum-energy [TCNE](2)(2-)(dichloromethane)(4) aggregates, a solvent where pi-[TCNE](2)(2-) dimers are spectroscopically observed. Their existence is attributed to [TCNE](.-)...solvent interactions that exceed the [TCNE](.-)...[TCNE](.-) repulsion. The lowest energy minimum at the B3LYP level corresponds to an open-shell singlet electronic structure, a metastable minimum where the shortest interanion C...C distance is 5.23 A. A slightly less stable minimum is also found for the closed-shell singlet when double-occupancy of the orbitals is imposed, but it converts into the open-shell singlet minimum when the double occupancy is relaxed. At the MCQDPT/CASSCF(2,2) level, the only minimum is for the closed-shell singlet (24.0 kcal/mol (101 kJ/mol) more stable than the dissociation products), consistent with experimental enthalpy of dimerization of [TCNE](.-) in dichloromethane solutions. It has an interanion C...C distance of 2.75 A and is in accord with the UV-vis experimental properties of the [TCNE](.-) solutions.     

A theoretical study on the catalytic mechanism of Mus musculus adenosine deaminase

The catalytic mechanism of Mus musculus adenosine deaminase (ADA) has been studied by quantum mechanics and two‐layered ONIOM calculations. Our calculations show that the previously proposed mechanism, involving His238 as the general base to activate the Zn‐bound water, has a high activation barrier of about 28 kcal/mol at the proposed rate‐determining nucleophilic addition step, and the corresponding calculated kinetic isotope effects are significantly different from the recent experimental observations. We propose a revised mechanism based on calculations, in which Glu217 serves as the general base to abstract the proton of the Zn‐bound water, and the protonated Glu217 then activates the substrate for the subsequent nucleophilic addition. The rate‐determining step is the proton transfer from Zn‐OH to 6‐NH₂ of the tetrahedral intermediate, in which His238 serves as a proton shuttle for the proton transfer. The calculated kinetic isotope effects agree well with the experimental data, and calculated activation energy is also consistent with the experimental reaction rate. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Mechanism of water oxidation to molecular oxygen with osmocene as photocatalyst: a theoretical study

In the present work, photoinduced O(2) evolution from the [Cp(2)Os-OH](+) complex in aqueous solution has been studied by the DFT, CASSCF, and CASPT2 methods. The CASPT2//CASSCF calculations predict that the S(3) state is initially populated and the subsequent deprotonation of [Cp(2)Os-OH](+) proceeds very easily along the T(1) pathway as a result of the efficient S(3) → T(1) intersystem crossing. It is found that the O-O bond is formed via the acid-base mechanism, which is different from the direct oxo-oxo coupling mechanism suggested in the experimental study. Formation of the O-O bond is the rate-determining step and has an activation energy and activation free energy of 81.3 and 90.4 kcal/mol, respectively. This is consistent with the low quantum yield observed for generating molecular oxygen upon irradiation at 350 nm (~ 82 kcal/mol). The O(2) release from an intermediate complex has to overcome a small barrier on the triplet pathway first and then pass through the triplet-singlet intersection, generating the O(2) molecules in either the lowest singlet or triplet state. The formed (3)O(2) molecule can be converted into the (1)O(2) molecule by the heavy atom effect in the Os complexes, which is probably the reason only the (1)O(2) molecule was detected experimentally.     

Ab initio model study on acetylcholinesterase catalysis: potential energy surfaces of the proton transfer reactions

Ab initio molecular orbital (MO) and hybrid density functional theory (DFT) calculations have been applied to the initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE), which is the nucleophiric addition of Ser200 in catalytic triads to a neurotransmitter acetylcholine (ACh). We focus our attention mainly on the effects of oxyanion hole and Glu327 on the potential energy surfaces (PESs) for the proton transfer reactions in the catalytic triad Ser200-His440-Glu327. The activation barrier for the addition reaction of Ser200 to ACh was calculated to be 23.4 kcal/mol at the B3LYP/6-31G(d)//HF/3-21G(d) level of theory. The barrier height under the existence of oxyanion hole, namely, Ser200-His440-Glu327-ACh-(oxyanion hole) system, decreased significantly to 14.2 kcal/mol, which is in reasonable agreement with recent experimental value (12.0 kcal/mol). Removal of Glu327 from the catalytic triad caused destabilization of both energy of transition state for the reaction and tetrahedral intermediate (product). PESs calculated for the proton transfer reactions showed that the first proton transfer process is the most important in the stabilization of tetrahedral intermediate complex. The mechanism of addition reaction of ACh was discussed on the basis of theoretical results.     

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.     

Investigation of the mechanism of the cell wall DD-carboxypeptidase reaction of penicillin-binding protein 5 of Escherichia coli by quantum mechanics/molecular mechanics calculations

Penicillin-binding protein 5 (PBP 5) of Escherichia coli hydrolyzes the terminal D-Ala-D-Ala peptide bond of the stem peptides of the cell wall peptidoglycan. The mechanism of PBP 5 catalysis of amide bond hydrolysis is initial acylation of an active site serine by the peptide substrate, followed by hydrolytic deacylation of this acyl-enzyme intermediate to complete the turnover. The microscopic events of both the acylation and deacylation half-reactions have not been studied. This absence is addressed here by the use of explicit-solvent molecular dynamics simulations and ONIOM quantum mechanics/molecular mechanics (QM/MM) calculations. The potential-energy surface for the acylation reaction, based on MP2/6-31+G(d) calculations, reveals that Lys47 acts as the general base for proton abstraction from Ser44 in the serine acylation step. A discrete potential-energy minimum for the tetrahedral species is not found. The absence of such a minimum implies a conformational change in the transition state, concomitant with serine addition to the amide carbonyl, so as to enable the nitrogen atom of the scissile bond to accept the proton that is necessary for progression to the acyl-enzyme intermediate. Molecular dynamics simulations indicate that transiently protonated Lys47 is the proton donor in tetrahedral intermediate collapse to the acyl-enzyme species. Two pathways for this proton transfer are observed. One is the direct migration of a proton from Lys47. The second pathway is proton transfer via an intermediary water molecule. Although the energy barriers for the two pathways are similar, more conformers sample the latter pathway. The same water molecule that mediates the Lys47 proton transfer to the nitrogen of the departing D-Ala is well positioned, with respect to the Lys47 amine, to act as the hydrolytic water in the deacylation step. Deacylation occurs with the formation of a tetrahedral intermediate over a 24 kcal x mol(-1) barrier. This barrier is approximately 2 kcal x mol(-1) greater than the barrier (22 kcal x mol(-1)) for the formation of the tetrahedral species in acylation. The potential-energy surface for the collapse of the deacylation tetrahedral species gives a 24 kcal x mol(-1) higher energy species for the product, signifying that the complex would readily reorganize and pave the way for the expulsion of the product of the reaction from the active site and the regeneration of the catalyst. These computational data dovetail with the knowledge on the reaction from experimental approaches.     

Cyanil](2)(2-) dimers possess long, two-electron ten-center (2e(-)/10c) multicenter bonding

A long, two-electron ten-center (2e(-)/10c) [8 carbon plus 2 oxygen] bond in diamagnetic dimers of radical-anion tetracyano-1,4-benzoquinoneide (cyanil, [Q] (-)), [Q](2)(2-), is described by B3LYP and CASSCF(2,2)/MCQDPT calculations.     

Elimination of water from the carboxyl group of GlyGlyH+

The elimination of water from the carboxyl group of protonated diglycine has been investigated by density functional theory calculations. The resulting structure is identical to the b(2) ion formed in the mass spectrometric fragmentation of protonated peptides (therefore named "b2" in this study). The most stable geometry of the fragment ion ("b2") is an O-protonated diketopiperazine. However, its formation is kinetically disfavored as it requires a free energy of 58.2 kcal/mol. The experimentally observed N-protonated oxazolone is 3.0 kcal/mol less stable. The lowest energy pathway for the formation of the "b2" ion requires a free energy of 37.5 kcal/mol and involves the proton transfer from the amide oxygen of protonated diglycine to the hydroxyl oxygen. Fragmentation initiated by proton transfer from the terminal nitrogen has also a comparable free energy of activation (39.4 kcal/mol). Proton transfer initiating the fragmentation, from the highly basic terminal nitrogen or amide oxygen to the less basic hydroxyl oxygen is feasible at energies reached in usual mass spectrometric experiments. Amide N-protonated diglycine structures are precursors of mainly y(1) ions rather than "b2" ions. In the lowest energy fragmentation channels, proton transfer to the hydroxylic oxygen, bond breaking and formation of an oxazolone ring occur concertedly but asynchronously. Proton transfer to hydroxyl oxygen and cleavage of the corresponding C-O bond take place at the early stages of the fragmentation step, while ring closure to form an oxazolone geometry occurs at the later stages of the transition. The experimentally observed low kinetic energy release is expected to be due to the existence of a strongly hydrogen bonded protonated oxazolone-water complex in the exit channel. Whereas the threshold energy for "b2" ion formation (37.1 kcal/mol) is lower than for the y(1) ion (38.4 kcal/mol), the former requires a tight transition state with an activation entropy, DeltaS++ = -1.2 cal/mol.K and the latter has a loose transition state with DeltaS++ = +8.8 cal/mol.K. This leads to y(1) being the major fragment ion over a wide energy range.     

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.     

Mechanisms of acid decomposition of dithiocarbamates. 4. Theoretical calculations on the water-catalyzed reaction

A theoretical study of the water-catalyzed dithiocarbamic acid cleavage has been performed using N-methyl- (MeDTC) and N-phenyldithiocarbamic acid (PhDTC) as model molecules. Calculations have been carried out within the Density Functional Theory (DFT) formalism, using the B3LYP hybrid functional together with medium-sized basis sets, both in gas phase and by considering solvent effects through dielectric continuum methods. According to the results obtained, both in gas phase and in solution, MeDTC decomposes through a proton-transfer step assisted by a water molecule (this being the rate-determining step), leading to a zwitterionic intermediate, followed by a fast N-C bond-breaking process. In the case of PhDTC, the theoretical results point to a one-step mechanism in which the N-C bond breaking takes place in a concerted manner with the proton transfer. The calculated Delta Delta G(++) of the proton-transfer step for MeDTC and PhDTC is 4.0 kcal mol(-1), which is similar to the experimental values. For both compounds the water-assisted intramolecular proton transfer occurs with a twisting of the CS(2) group that inhibits the resonance of the thiocarbamic group, making the nitrogen more basic and therefore favoring the proton transfer. The difference in the torsional barrier has been calculated to be ca. 5 kcal mol(-1), and it is therefore concluded that most of the activation barrier of the reaction is due to the torsional barrier of the CS(2) group.     

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.     

Arginine zwitterion is more stable than the canonical form when solvated by a water molecule

We present calculations for the Arg-H2O system and predict that the zwitterionic Arg is thermodynamically more stable than the canonical form in the gas phase under the influence of a single water molecule because of the strongly basic guanidine side chain. Canonical conformers of Arg-H2O are found to isomerize to the zwitterionic forms via a small barrier (approximately 6 kcal/mol).