QM/MM study of the taxadiene synthase mechanism

Combined quantum mechanics/molecular mechanics (QM/MM) calculations were used to investigate the reaction mechanism of taxadiene synthase (TXS). TXS catalyzes the cyclization of geranylgeranyl diphosphate (GGPP) to taxadiene (T) and four minor cyclic products. All these products originate from the deprotonation of carbocation intermediates. The reaction profiles for the conversion of GGPP to T as well as to minor products were calculated for different configurations of relevant TXS carbocation complexes. The QM region was treated at the M06-2X/TZVP level, while the CHARMM27 force field was used to describe the MM region. The QM/MM calculations suggest a reaction pathway for the conversion of GGPP to T, which slightly differs from previous proposals regarding the number of reaction steps and the conformation of the carbocations. The QM/MM results also indicate that the formation of minor products via water-assisted deprotonation of the carbocations is highly exothermic, by about −7 to −23 kcal/mol. Curiously, however, the computed barriers and reaction energies indicate that the formation of some of the minor products is more facile than the formation of T. Thus, the present QM/MM calculations provide detailed insights into possible reaction pathways and into the origin of the promiscuity of TXS, but they do not reproduce the product distribution observed experimentally. © 2019 Wiley Periodicals, Inc.     

QM/MM Methods for Biomolecular Systems

Two are better than one : Quantum mechanics/molecular mechanics (QM/MM) methods are the state‐of‐the‐art computational technique for treating reactive and other “electronic” processes in biomolecular systems. This Review presents the general methodological aspects of the QM/MM approach, its use within optimization and simulation techniques, and its areas of application, always with a biomolecular focus.

     

Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide

Methodology is discussed for mixed ab initio quantum mechanics/molecular mechanics modeling of systems where the quantum mechanics (QM) and molecular mechanics (MM) regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree–Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by “breaking” bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. Results from tests of the method to find relative conformational energies and geometries of alanine dipeptides and alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1468–1494, 1999     

Transition structure selectivity in enzyme catalysis: a QM/MM study of chorismate mutase

Two different transition structures (TSs) have been located and characterized for the chorismate conversion to prephenate in Bacillus subtilis chorismate mutase by means of hybrid quantum-mechanical/molecular-mechanical (QM/MM) calculations. GRACE software, combined with an AM1/CHARMM24/TIP3P potential, has been used involving full gradient relaxation of the position of ca. 3300 atoms. These TSs have been connected with their respective reactants and products by the intrinsic reaction coordinate (IRC) procedure carried out in the presence of the protein environment, thus obtaining for the first time a realistic enzymatic reaction path for this reaction. Similar QM/MM computational schemes have been applied to study the chemical reaction solvated by ca. 500 water molecules. Comparison of these results together with gas phase calculations has allowed understanding of the catalytic efficiency of the protein. The enzyme stabilizes one of the TSs (TS_OHout) by means of specific hydrogen bond interactions, while the other TS (TS_OHin) is the preferred one in vacuum and in water. The enzyme TS is effectively more polarized but less dissociative than the corresponding solvent and gas phase TSs. Electrostatic stabilization and an intramolecular charge-transfer process can explain this enzymatically induced change. Our theoretical results provide new information on an important enzymatic transformation and the key factors responsible for efficient selectivity are clarified. Received: 25 March 2000 / Accepted: 7 August 2000 / Published online: 23 November 2000     

The Jahn-Teller effect of the TiIII ion in aqueous solution: extended ab initio QM/MM molecular dynamics simulations.

Combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, including only the first and the first and second hydration shells in the QM region, were performed for TiIII in aqueous solution. The hydration structure of TiIII is discussed in terms of radial distribution functions, coordination-number distributions and several angle distributions. Dynamical properties, such as librational and vibrational motions and TiIII-O vibrations, were evaluated. A fast dynamical Jahn-Teller effect of TiIII(aq) was observed in the QM/MM simulations, in particular when the second hydration shell was included into the QM region. The results justify the computational effort required for the inclusion of the second hydration shell into the QM region and show the importance of this effort for obtaining accurate hydration-shell geometries, dynamical properties, and details of the Jahn-Teller effect.     

QM/MM modeling of enantioselective pybox-ruthenium- and box-copper-catalyzed cyclopropanation reactions: scope, performance, and applications to ligand design

An extensive comparison of full-QM (B3LYP) and QM/MM (B3LYP:UFF) levels of theory has been made for two enantioselective catalytic systems, namely, Pybox-Ru and Box-Cu complexes, in the cyclopropanation of alkenes (ethylene and styrene) with methyl diazoacetate. The geometries of the key reaction intermediates and transition structures calculated at the QM/MM level are generally in satisfactory agreement with full-QM calculated geometries. More importantly, the relative energies calculated at the QM/MM level are in good agreement with those calculated at the full-QM level in all cases. Furthermore, the QM/MM energies are often in better agreement with the stereoselectivity experimentally observed, and this suggests that QM/MM calculations can be superior to full-QM calculations when subtle differences in inter- and intramolecular interactions are important in determining the selectivity, as is the case in enantioselective catalysis. The predictive value of the model presented is validated by the explanation of the unusual enantioselectivity behavior exhibited by a new bis-oxazoline ligand, the stereogenic centers of which are quaternary carbon atoms.     

Cover picture: transition-metal-catalyzed unzipping of single-walled carbon nanotubes into narrow graphene nanoribbons at low temperature (angew. Chem. Int. Ed. 35/2011)

Narrow, smooth-edged graphene nanoribbons are needed for graphene electronics to replace the current silicon technology. In their Communication on page?8041?ff., J. Wang, F. Ding, et?al. report a smart strategy for cutting single-walled carbon nanotubes (gray) into narrow graphene nanoribbons in H(2) gas (green) with a single transition-metal atom (Cu, red) as the chemical scissors.     

Study of the oxidative half‐reaction catalyzed by a non‐heme ferrous catalytic center by means of structural and computational methodologies

Deacetoxycephalosporin C synthase (DAOCS) is a mononuclear ferrous enzyme that catalyzes the expansion of the five‐membered thiazolidine ring of the penicillin nucleus into the six‐membered dihydrothiazine ring of the cephalosporins. In the first half‐reaction with dioxygen and 2‐oxoglutarate, a reactive iron–oxygen species is produced that can subsequently react with the penicillin substrate to yield the cephalosporin. We describe quantum mechanical calculations of the first part of the reaction based on the high‐resolution structures of the active site of DAOCS and its complexes with ligands. These studies are aimed at understanding how the reactive species can be produced and contained in the active site of the enzyme. The results demonstrate the priming of the active site by the co‐substrate for oxygen binding and hint to the presence of a stable iron–peroxo intermediate in equilibrium with a more reactive ferryl species and the formation of CO₂ as a leaving group by decarboxylation of 2‐oxoglutarate. A conclusion from these studies is that substitution of CO₂ by the penicillin substrate triggers the oxidation reaction in a booby‐trap‐like mechanism. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

A QM/MM Investigation of Thymine Dimer Radical Anion Splitting Catalyzed by DNA Photolyase

On the mend : The repair reaction of the thymine dimer by DNA photolyase (see picture) is studied by hybrid quantum mechanical/molecular mechanical dynamics simulations based on the X‐ray structure of the enzyme–DNA complex. The dynamics of splitting of the thymine dimer radical anion within the DNA photolyase active site is characterized. The model includes the protein environment.

     

New Insights into the Jahn–Teller Effect through ab initio Quantum-Mechanical/Molecular-Mechanical Molecular Dynamics Simulations of CuII in Water

The Cu^II hydration shell structure has been studied by means of classical molecular dynamics (MD) simulations including three-body corrections and hybrid quantum-mechanical/molecular-mechanical (QM/MM) molecular dynamics (MD) simulations at the Hartree–Fock level. The copper(II ) ion is found to be six-fold coordinated and [Cu(H₂O)₆]²⁺ exhibits a distorted octahedral structure. The QM/MM MD approach reproduces correctly the experimentally observed Jahn–Teller effect but exhibits faster inversions (<200 fs) and a more complex behaviour than expected from experimental data. The dynamic Jahn–Teller effect causes the high lability of [Cu(H₂O)₆]²⁺ with a ligand-exchange rate constant some orders of magnitude higher than its neighbouring ions Ni^II and Zn^II. Nevertheless, no first-shell water exchange occurred during a 30-ps simulation. The structure of the hydrated ion is discussed in terms of radial distribution functions, coordination numbers, and various angular distributions and the dynamical properties as librational and vibrational motions and reorientational times were evaluated, which lead to detailed information about the first hydration shell. Second-shell water-exchange processes could be observed within the simulation time scale and yielded a mean ligand residence time of ≈20 ps.     

First detection of a selenenyl fluoride ArSe-F by NMR spectroscopy: the nature of Ar2Se2/XeF2 and ArSe-SiMe3/XeF2 reagents

Arylselenenyl fluorides ArSeF are obtained from diselenides Ar2Se2 or arylselenotrimethylsilanes ArSe-SiMe3, and XeF2. They are detected by low-temperature 19F and 77Se NMR spectroscopy. Substitution in the ortho position of the aromatic ring to provide electronic or steric protection is a requirement for their formation. ArSe--F compounds decompose according to 3 ArSe-F-->[ArSe-SeF2Ar]+ArSe-F-->ArSeF3+Ar2Se2. Reaction energies for this disproportionation as well as that of the sulfur and tellurium homologues have been calculated with MP2, CCSD(T,) and B3 LYP methods. They were found to be increasingly exothermic in the sequence S相似文献   

How Frustrated Lewis Acid/Base Systems Pass through Transition‐State Regions: H2 Cleavage by [tBu3P/B(C6F5)3]

We investigate the transition‐state (TS) region of the potential energy surface (PES) of the reaction tBu₃P+H₂+B(C₆F₅)₃→tBu₃P‐H⁽⁺⁾+^(?)H?B(C₆F₅)₃ and the dynamics of the TS passage at room temperature. Owing to the conformational inertia of the phosphane???borane pocket involving heavy tBu₃P and B(C₆F₅)₃ species and features of the PES E(P???H, B???H | B???P) as a function of P???H, B???H, and B???P distances, a typical reactive scenario for this reaction is a trajectory that is trapped in the TS region for a period of time (about 350 fs on average across all calculated trajectories) in a quasi‐bound state (scattering resonance). The relationship between the timescale of the TS passage and the effective conformational inertia of the phosphane???borane pocket leads to a prediction that isotopically heavier Lewis base/Lewis acid pairs and normal counterparts could give measurably different reaction rates. Herein, the predicted quasi‐bound state could be verified in molecular collision experiments involving femtosecond spectroscopy.     

Introducing Mutations to Modify the C13/C9 Ratio in Linoleic Acid Oxygenations Catalyzed by Rabbit 15‐Lipoxygenase: A QM/MM and MD Study

Lipoxygenases (LOs) are a family of nonheme iron‐containing enzymes that catalyze the hydroperoxidation of several polyunsaturated fatty acids with a huge regio‐ and stereospecificity. Mammalian 15‐LO‐1 yields almost exclusively oxygenation at the C13 position of the linoleic acid (LA), its preferred substrate. This is very important because metabolites derived from oxidation in distinct positions produce opposite physiological effects. We have combined here quantum mechanics/molecular mechanics calculations with molecular dynamics simulations to show how a suitable mutation of the rabbit 15‐LO‐1 enzyme can produce a significant amount of products derived from oxygenation at the C9 position of LA. In effect, the Leu597Val or Leu597Ala mutants are predicted to lead to a diminution of the oxygenation C13/C9 ratio in LA as huge as five orders of magnitude. This shows that the conserved residue Leu597 actually drives the regiospecific hydroperoxidation of LA catalyzed by 15‐LO‐1 enzyme.     

Mechanism of proteolysis in matrix metalloproteinase‐2 revealed by QM/MM modeling

The mechanism of enzymatic peptide hydrolysis in matrix metalloproteinase‐2 (MMP‐2) was studied at atomic resolution through quantum mechanics/molecular mechanics (QM/MM) simulations. An all‐atom three‐dimensional molecular model was constructed on the basis of a crystal structure from the Protein Data Bank (ID: 1QIB), and the oligopeptide Ace‐Gln‐Gly～Ile‐Ala‐Gly‐Nme was considered as the substrate. Two QM/MM software packages and several computational protocols were employed to calculate QM/MM energy profiles for a four‐step mechanism involving an initial nucleophilic attack followed by hydrogen bond rearrangement, proton transfer, and C? N bond cleavage. These QM/MM calculations consistently yield rather low overall barriers for the chemical steps, in the range of 5–10 kcal/mol, for diverse QM treatments (PBE0, B3LYP, and BB1K density functionals as well as local coupled cluster treatments) and two MM force fields (CHARMM and AMBER). It, thus, seems likely that product release is the rate‐limiting step in MMP‐2 catalysis. This is supported by an exploration of various release channels through QM/MM reaction path calculations and steered molecular dynamics simulations. © 2015 Wiley Periodicals, Inc.