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.
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 (TSOHout) by means of specific hydrogen bond interactions, while the other TS (TSOHin) 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 相似文献
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. 相似文献
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. 相似文献
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. 相似文献
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.
The CuII 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 NiII and ZnII. 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. 相似文献
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
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. 相似文献
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. 相似文献