A Priori Evaluation of Aqueous Polarization Effects through Monte Carlo QM-MM Simulations

Gao, Jiali; Xia, Xinfu

doi:10.1126/science.1411573

Cited by 608 publications

(634 citation statements)

References 54 publications

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“…In the present study, we use a combined QM/MM potential in molecular dynamics simulations, 7,42 in which the solute is represented explicitly by an electronic structure method and the solvent is approximated by the three-point charge TIP3P model for water. 43 The details have been described in a number of articles.…”

Section: Computational Details Potential Energy Functionmentioning

confidence: 99%

Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

2007

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An integrated Feynman path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method has been used to investigate the kinetic isotope effects (KIEs) in the proton transfer reaction between nitroethane and acetate ion in water. In the present study, both nuclear and electronic quantum effects are explicitly treated for the reacting system. The nuclear quantum effects are represented by bisection sampling centroid path integral simulations, while the potential energy surface is described by a combined quantum mechanical and molecular mechanical (QM/MM) potential. The accuracy essential for computing KIEs is achieved by a FEP technique that transforms the mass of a light isotope into a heavy one, which is equivalent to the perturbation of the coordinates for the path integral quasiparticle in the bisection sampling scheme. The PI-FEP/UM method is applied to the proton abstraction of nitroethane by acetate ion in water through molecular dynamics simulations. The rule of the geometric mean and the Swain-Schaad exponents for various isotopic substitutions at the primary and secondary sites have been examined. The computed total deuterium KIEs are in accord with experiments. It is found that the mixed isotopic Swain-Schaad exponents are very close to the semiclassical limits, suggesting that tunneling effects do not significantly affect this property for the reaction between nitroethane and acetate ion in aqueous solution.

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Section: Computational Details Potential Energy Functionmentioning

confidence: 99%

Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

2007

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“…These require a combination of quantum chemical and molecular dynamics calculations. Many efforts are being invested at present into merging molecular dynamics and quantum chemistry techniques [81,83,91,87,90,84,92]. The importance of combining these two major tools of computational chemistry is now being realized to a large extent by both the molecular dynamics and the quantum chemistry communities.…”

Section: Further Developmentsmentioning

confidence: 99%

“…Later, various techniques were developed which allow for the self-consistent ab initio treatment of a molecule embedded in a dielectric continuum [75,76,77]. At present, there exist a number of ab initio as well as semi-empirical techniques which try to account for the realistic atomic structure and charge distribution of the environment via explicit incorporation of protein (or solution) point charges in the electronic Hamiltonian of the quantum chemically treated substrate [78,79,80,81,82,83].…”

Section: Quantum Chemistry Of In Situ Retinalmentioning

confidence: 99%

“…It has been observed that modification of protein groups in the vicinity of the retinal Schiff base shifts considerably the bR absorption spectrum [69] and affects drastically the rates of both thermally- [70] and photo- [71,72] [75,76,77]. At present, there exist a number of ab initio as well as semi-empirical techniques which try to account for the realistic atomic structure and charge distribution of the environment via explicit incorporation of protein (or solution) point charges in the electronic Hamiltonian of the quantum chemically treated substrate [78,79,80,81,82,83].In our study, the refined structure of bacteriorhodopsin reported in [31] was used as a starting point for all the computations. This structure, corresponding to the bR 568 pigment, is depicted in Figures 2a and 5b.…”

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confidence: 99%

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Quantum Chemistry of in situ Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin

Logunov

Schulten

1996

Quantum Mechanical Simulation Methods for Studying Biological Systems

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1A combination of molecular dynamics and quantum chemistry techniques have been employed to study the electronic excitation and conformational potential surface of retinal in the binding site of bacteriorhodopsin (bR). The CASSCF(6,9)/6-31G level of ab initio calculations (within Gaussian92) has been used for the treatment of both the ground (S0) and excited (S1) states of retinal. Charges of all atoms in the protein are represented by spherical Gaussians and explicitly included in the electronic Hamiltonian of retinal. Spectral properties have been analyzed for the native bR pigment as well as for its D85N mutant.The calculated relative shift in the absorption maxima between the two pigments is in better agreement with experiment than the computed absolute parameters of the absorption line shapes. The dark adaptation processes in bacteriorhodopsin (which involves rotation around the 13-14 and the 15-N retinal double bonds) has been modelled by following the pre-defined reaction coordinate. Our simulations support the notion that the isomerization process is catalyzed by the protonation of an aspartic acid (Asp85) side group of bacteriorhodopsin. 2 IntroductionBacteriorhodopsin (bR) spans the cell membrane of Halobacterium halobium and functions as a light-driven proton pump. bR contains seven α-helices which enclose the prosthetic group, all-trans retinal, bound via a protonated Schiff base linkage to Lys-216. Figure 1a shows the chemical structure of retinal and its conventional numbering scheme. The bR structure is presented in Fig. 2a. Retinal absorbs light and undergoes a photoisomerization process; the thermal reversal of this reaction is coupled to transfer of a proton from the cytoplasmic side (top in Fig. 2a) to the extracellular side (bottom in Fig. 2a) of the protein.Recent reviews that discuss the structure and function of bR are [1,2,3,4,5,6,7]. Figure 1 here Bacteriorhodopsin accomplishes its function through a cyclic process initiated by absorption of a photon. This photon triggers an isomerization of retinal, which proceeds then through several intermediate states identified by their absorption spectra. An accepted kinetic scheme for this cycle is an unbranched series of intermediates, shown in Fig. 3. Photoisomerization occurs in the bR 568 → J 625 transition. During the L 550 → M 412 transition the Schiff base proton is transferred to Asp-85 and, subsequently, to the outside of the cell [8,9,10,11,12,13]. During the M 412 → N 520 transition, a proton is transferred to the Schiff base from Asp-96, which then takes up a proton from the cytoplasmic environment [13]. The reaction cycle is completed as the protein returns to bR 568 via the O 640 intermediate. Figure 2 here When bR is allowed to equilibrate in the dark, it converts within an hour to a 2:1 mixture containing 13-cis retinal and all-trans retinal bR [14]. The protein containing the 13-cis retinal isomer of bRis referred to as the dark adapted (DA) pigment of bR, bR 548 , which absorbs at 548 nm. bR 548 contains, actually, retinal in a 1...

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“…[6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21] The portion of the system in which the reaction is taking place (the acid site and the reacting molecule) is modeled by quantum-chemical methods, and the rest of the system is treated with classical force fields. This allows for the inclusion of geometric and electrostatic effects of the rest of the lattice into quantum-chemical models of the catalytic reaction at little additional computational cost.…”

Section: Introductionmentioning

confidence: 99%

Zeolite Structure and Reactivity by Combined Quantum-Chemical−Classical Calculations

et al. 1999

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Proton-energy differences, ammonia adsorption, and D/H-exchange barriers for methane at selected isolated Brønsted sites in zeolites FAU, MFI, BEA, ERI, and CHA are studied by combined quantum-chemicalclassical (QM/MM) calculations in an attempt to understand the factors that determine the reactivity at these Brønsted sites. The barrier of the D/H-exchange reaction for methane was found to correlate well with the calculated ammonia chemisorption energy, but even better with the O-Al-O angle of the free zeolite Brønsted site the reaction is taking place on, provided the Si-O-Al-O-Si moiety over which the reaction takes place is more or less collinear. The barrier is considerably higher if this collinearity is weaker, which may be explained by the necessity of costly backbone distortions to accommodate the geometrical requirements of the transition state. This is confirmed by similarly strong correlations with the O-Al-O angle change going from the free acid site to zeolite-ammonium ion bidentate structures, which may be thought of as a measure of the backbone distortion. A new measurement of the D/H-exchange barrier in BEA is also reported. It was found to be 88 ( 18 kJ/mol, lower than the experimental barriers in both FAU and MFI.

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A Priori Evaluation of Aqueous Polarization Effects through Monte Carlo QM-MM Simulations

Cited by 608 publications

References 54 publications

Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water

Quantum Chemistry of in situ Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin

Zeolite Structure and Reactivity by Combined Quantum-Chemical−Classical Calculations

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