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Weitao Yang - One of the best experts on this subject based on the ideXlab platform.
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a combined explicit implicit method for high accuracy Reaction Path integration
Journal of Chemical Physics, 2006Co-Authors: Steven K Burger, Weitao YangAbstract:We present the use of an optimal combined explicit-implicit method for following the Reaction Path to high accuracy. This is in contrast to most purely implicit Reaction Path integration algorithms, which are only efficient on stiff ordinary differential equations. The defining equation for the Reaction Path is considered to be stiff, however, we show here that the Reaction Path is not uniformly stiff and instead is only stiff near stationary points. The optimal algorithm developed in this work is a combination of explicit and implicit methods with a simple criterion to switch between the two. Using three different chemical Reactions, we combine and compare three different integration methods: the implicit trapezoidal method [C. Gonzalez and H. Schlegel, J. Chem. Phys. 90, 2154 (1989)], an explicit stabilized third order algorithm [A. A. Medovikov, BIT 38, 372 (1998)] implemented in the code DUMKA3 and the traditional explicit fourth order Runge-Kutta method written in the code RKSUITE. The results for hi...
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nuclear quantum effects on an enzyme catalyzed Reaction with Reaction Path potential proton transfer in triosephosphate isomerase
Journal of Chemical Physics, 2006Co-Authors: Mingliang Wang, Weitao YangAbstract:Nuclear quantum mechanical effects have been examined for the proton transfer Reaction catalyzed by triosephosphate isomerase, with the normal mode centroid Path integral molecular dynamics based on the potential energy surface from the recently developed Reaction Path potential method. In the simulation, the primary and secondary hydrogens and the C and O atoms involving bond forming and bond breaking were treated quantum mechanically, while all other atoms were dealt classical mechanically. The quantum mechanical activation free energy and the primary kinetic isotope effects were examined. Because of the quantum mechanical effects in the proton transfer, the activation free energy was reduced by 2.3 kcal/mol in comparison with the classical one, which accelerates the rate of proton transfer by a factor of 47.5. The primary kinetic isotope effects of kH/kD and kH/kT were estimated to be 4.65 and 9.97, respectively, which are in agreement with the experimental value of 4+/-0.3 and 9. The corresponding Swain-Schadd exponent was predicted to be 3.01, less than the semiclassical limit value of 3.34, indicating that the quantum mechanical effects mainly arise from quantum vibrational motion rather than tunneling. The Reaction Path potential, in conjunction with the normal mode centroid molecular dynamics, is shown to be an efficient computational tool for investigating the quantum effects on enzymatic Reactions involving proton transfer.
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Reaction Path determination for quantum mechanical molecular mechanical modeling of enzyme Reactions by combining first order and second order chain of replicas methods
Journal of Chemical Physics, 2005Co-Authors: Andres G Cisneros, Haiyan Liu, Weitao YangAbstract:A two-step procedure for the determination of Reaction Paths in enzyme systems is presented. This procedure combines two chain-of-states methods: a quantum mechanical/molecular mechanical (QM/MM) implementation of the nudged elastic band (NEB) method and a second order parallel Path optimizer method both recently developed in our laboratory. In the first step, a Reaction Path determination is performed with the NEB method, along with a restrained minimization procedure for the MM environment to obtain a first approximation to the Reaction Path. In the second step, the calculated Path is refined with the parallel Path optimizer method. By combining these two methods the Reaction Paths are determined accurately, and in addition, the number of Path optimization iterations are significantly reduced. This procedure is tested by calculating both steps of the isomerization of 2-oxo-4-hexenedioate by 4-oxalocrotonate tautomerase, which have been previously determined by our group. The calculated Paths agree with the previously reported results and we obtain a reduction of 45%–55% in the number of Path optimization cycles.
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transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the Reaction Path potential method
Journal of Chemical Physics, 2004Co-Authors: Mingliang Wang, Zhenyu Lu, Weitao YangAbstract:A global potential energy surface has been constructed through interpolation of our recently developed Reaction Path potential for chemical Reactions in enzymes which is derived from combined ab initio quantum mechanical and molecular mechanical calculations. It has been implemented for the activated molecular dynamics simulations of the initial proton transfer Reaction catalyzed by triosephosphate isomerase. To examine the dynamical effects on the rate constants of the enzymatic Reaction, the classical transmission coefficient κ(t) is evaluated to be 0.47 with the reactive flux approach, demonstrating considerable deviations from transition state theory. In addition, the fluctuations of protein environments have small effects on the barrier recrossing, and the transmission coefficient κ(t) strongly depends on the fluctuations of atoms near the active site of the enzyme.
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Reaction Path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations
Journal of Chemical Physics, 2004Co-Authors: Weitao YangAbstract:Combined ab initio quantum mechanical and molecular mechanical calculations have been widely used for modeling chemical Reactions in complex systems such as enzymes, with most applications being based on the determination of a minimum energy Path connecting the reactant through the transition state to the product in the enzyme environment. However, statistical mechanics sampling and Reaction dynamics calculations with a combined ab initio quantum mechanical (QM) and molecular mechanical (MM) potential are still not feasible because of the computational costs associated mainly with the ab initio quantum mechanical calculations for the QM subsystem. To address this issue, a Reaction Path potential energy surface is developed here for statistical mechanics and dynamics simulation of chemical Reactions in enzymes and other complex systems. The Reaction Path potential follows the ideas from the Reaction Path Hamiltonian of Miller, Handy and Adams for gas phase chemical Reactions but is designed specifically for large systems that are described with combined ab initio quantum mechanical and molecular mechanical methods. The Reaction Path potential is an analytical energy expression of the combined quantum mechanical and molecular mechanical potential energy along the minimum energy Path. An expansion around the minimum energy Path is made in both the nuclear and the electronic degrees of freedom for the QM subsystem internal energy, while the energy of the subsystem described with MM remains unchanged from that in the combined quantum mechanical and molecular mechanical expression and the electrostatic interaction between the QM and MM subsystems is described as the interaction of the MM charges with the QM charges. The QM charges are polarizable in response to the changes in both the MM and the QM degrees of freedom through a new response kernel developed in the present work. The input data for constructing the Reaction Path potential are energies, vibrational frequencies, and electron density response properties of the QM subsystem along the minimum energy Path, all of which can be obtained from the combined quantum mechanical and molecular mechanical calculations. Once constructed, it costs much less for its evaluation. Thus, the Reaction Path potential provides a potential energy surface for rigorous statistical mechanics and Reaction dynamics calculations of complex systems. As an example, the method is applied to the statistical mechanical calculations for the potential of mean force of the chemical Reaction in triosephosphate isomerase.
Josep Maria Bofill - One of the best experts on this subject based on the ideXlab platform.
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a restricted quantum Reaction Path hamiltonian theory discrete variable representation propagation algorithm and applications
Journal of Chemical Physics, 2009Co-Authors: Javier González, Xavier Giménez, Josep Maria BofillAbstract:A derivation of a quantum Reaction Path Hamiltonian is proposed, which is based on a reformulation of the classical version of Gonzalez et al. [J. Phys. Chem. A 105, 5022 (2001)], and the resulting equations are solved by means of a discrete variable representation approach, leading to a well-suited algorithm for the calculation of quantum dynamics of chemical Reactions involving polyatomic molecules. General expressions for any type of Reaction Path are presented with special interest in the intrinsic Reaction coordinate, which have been used to study selected cases, including a one-dimensional Eckart barrier, for which results are shown to be exact, two bidimensional systems, namely, a Muller–Brown potential energy surface, which is characteristic of polyatomic isomerization processes, and the collinear H+H2 chemical Reaction, and finally the tridimensional, J=0, F+H2 Reaction. Results for the specific chemical systems are shown to be in quite good agreement with exact two- and three-dimensional quantum...
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Generalized Reaction-Path Hamiltonian dynamics
Theoretical Chemistry Accounts, 2004Co-Authors: Javier González, Xavier Giménez, Josep Maria BofillAbstract:The Reaction-Path Hamiltonian is reformulated in a form that is independent of the specific choice of guiding Path. A necessary and sufficient condition for a given curve to satisfy Reaction-Path Hamiltonian requirements is derived, showing that any curve with no explicit dependence on the independent parameter does give rise to a formally acceptable Reaction-Path Hamiltonian. Numerical calculations have also been performed, comparing some Reaction-Path choices with the exact classical dynamics, evidencing the physically ground basis of most Reaction Path approaches.
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a Reaction Path liouville approach to the rate constant for polyatomic chemical Reactions
Physical Chemistry Chemical Physics, 2002Co-Authors: Javier González, Xavier Giménez, Josep Maria BofillAbstract:An approximate, computationally feasible expression for the rate constant is derived in terms of a generalized formulation of the Reaction Path Hamiltonian, plus a distributed gaussian expansion scheme to the solution of the Liouville equation for the phase space distribution function. This scheme is shown to yield a rigorous upper bound to the exact classical rate constant, which is in turn lower than, or at most equal to, that given by transition state theory. The method is tested with the Muller–Brown model system, giving rise to fairly accurate results.
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On the Reaction Path Hamiltonian for Polyatomic Molecules
The Journal of Physical Chemistry A, 2001Co-Authors: Javier González, ‡ Xavier Giménez, Josep Maria BofillAbstract:The classical Reaction Path Hamiltonian formulation of Miller, Handy, and Adams is reformulated using a linear expansion of the gradient in internal coordinates. It leads to a correspondence betwee...
Javier González - One of the best experts on this subject based on the ideXlab platform.
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a restricted quantum Reaction Path hamiltonian theory discrete variable representation propagation algorithm and applications
Journal of Chemical Physics, 2009Co-Authors: Javier González, Xavier Giménez, Josep Maria BofillAbstract:A derivation of a quantum Reaction Path Hamiltonian is proposed, which is based on a reformulation of the classical version of Gonzalez et al. [J. Phys. Chem. A 105, 5022 (2001)], and the resulting equations are solved by means of a discrete variable representation approach, leading to a well-suited algorithm for the calculation of quantum dynamics of chemical Reactions involving polyatomic molecules. General expressions for any type of Reaction Path are presented with special interest in the intrinsic Reaction coordinate, which have been used to study selected cases, including a one-dimensional Eckart barrier, for which results are shown to be exact, two bidimensional systems, namely, a Muller–Brown potential energy surface, which is characteristic of polyatomic isomerization processes, and the collinear H+H2 chemical Reaction, and finally the tridimensional, J=0, F+H2 Reaction. Results for the specific chemical systems are shown to be in quite good agreement with exact two- and three-dimensional quantum...
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Generalized Reaction-Path Hamiltonian dynamics
Theoretical Chemistry Accounts, 2004Co-Authors: Javier González, Xavier Giménez, Josep Maria BofillAbstract:The Reaction-Path Hamiltonian is reformulated in a form that is independent of the specific choice of guiding Path. A necessary and sufficient condition for a given curve to satisfy Reaction-Path Hamiltonian requirements is derived, showing that any curve with no explicit dependence on the independent parameter does give rise to a formally acceptable Reaction-Path Hamiltonian. Numerical calculations have also been performed, comparing some Reaction-Path choices with the exact classical dynamics, evidencing the physically ground basis of most Reaction Path approaches.
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a Reaction Path liouville approach to the rate constant for polyatomic chemical Reactions
Physical Chemistry Chemical Physics, 2002Co-Authors: Javier González, Xavier Giménez, Josep Maria BofillAbstract:An approximate, computationally feasible expression for the rate constant is derived in terms of a generalized formulation of the Reaction Path Hamiltonian, plus a distributed gaussian expansion scheme to the solution of the Liouville equation for the phase space distribution function. This scheme is shown to yield a rigorous upper bound to the exact classical rate constant, which is in turn lower than, or at most equal to, that given by transition state theory. The method is tested with the Muller–Brown model system, giving rise to fairly accurate results.
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On the Reaction Path Hamiltonian for Polyatomic Molecules
The Journal of Physical Chemistry A, 2001Co-Authors: Javier González, ‡ Xavier Giménez, Josep Maria BofillAbstract:The classical Reaction Path Hamiltonian formulation of Miller, Handy, and Adams is reformulated using a linear expansion of the gradient in internal coordinates. It leads to a correspondence betwee...
Eric H Oelkers - One of the best experts on this subject based on the ideXlab platform.
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Reaction Path modelling of in situ mineralisation of co2 at the carbfix site at hellisheidi sw iceland
Geochimica et Cosmochimica Acta, 2018Co-Authors: Sandra O Snaebjornsdottir, Sigurdur R Gislason, Iwona Galeczka, Eric H OelkersAbstract:Abstract Results from injection of 175 tonnes of CO2 into the basaltic subsurface rocks at the CarbFix site in SW-Iceland in 2012 show almost complete mineralisation of the injected carbon in less than two years (Matter et al., 2016; Snaebjornsdottir et al., 2017). Reaction Path modelling was performed to illuminate the rate and extent of CO2-water-rock Reactions during and after the injection. The modelling calculations were constrained by the compositions of fluids sampled prior to, during, and after the injection, as reported by Alfredsson et al. (2013) and Snaebjornsdottir et al. (2017). The pH of the injected fluid, prior to CO2 dissolution was ∼9.5, whereas the pH of the background waters in the first monitoring well prior to the injections was ∼9.4. The pH of the sampled fluids used in the modelling ranged from ∼3.7 at the injection well to as high as 8.2 in the first monitoring well. Modelling results suggest that CO2-rich water-basalt interaction is dominated by crystalline basalt dissolution along a faster, high permeability flow Path, but by basaltic glass dissolution along a slower, pervasive flow Path through which the bulk of the injected fluid flows. Dissolution of pre-existing calcite at the onset of the injection does not have a net effect on the carbonation, but does contribute to a rapid early pH rise during the injection, and influences which carbonate minerals precipitate. At low pH, Mg, and Fe are preferentially released from crystalline basalts due to the higher dissolution rates of olivine, and to lesser extent pyroxene, compared to plagioclase and glass (Gudbrandsson et al., 2011). This favours the formation of siderite and Fe-Mg carbonates over calcite during early mineralisation. The model suggests the formation of the following carbonate mineral sequences: siderite at pH 5, and calcite at higher pH. Other minerals forming with the carbonates are Al- and Fe-hydroxides and chalcedony, and zeolites and smectites at elevated pH. The most efficient carbonate formation is when the pH is high enough for formation of carbonates, but not so high that zeolites and smectites start to form, which compete with carbonates over both cations and pore space. The results of Reaction Path modelling at the CarbFix site in SW-Iceland indicate that this “sweet spot” for mineralisation of CO2 is at pH from ∼5.2 to 6.5 in basalts at low temperature (20–50 °C).
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Reaction Path modelling of in-situ mineralisation of CO2 at the CarbFix site at Hellisheidi, SW-Iceland
2018Co-Authors: Snæbjörnsdóttir S, Iwona Galeczka, Eric H OelkersAbstract:Results from injection of 175 tonnes of CO 2 into the basaltic subsurface rocks at the CarbFix site in SW-Iceland in 2012 show almost complete mineralisation of the injected carbon in less than two years (Matter et al., 2016; Snæbjörnsdóttir et al., 2017). Reaction Path modelling was performed to illuminate the rate and extent of CO 2 -water-rock Reactions during and after the injection. The modelling calculations were constrained by the compositions of fluids sampled prior to, during, and after the injection, as reported by Alfredsson et al. (2013) and Snæbjörnsdóttir et al. (2017). The pH of the injected fluid, prior to CO 2 dissolution was ∼9.5, whereas the pH of the background waters in the first monitoring well prior to the injections was ∼9.4. The pH of the sampled fluids used in the modelling ranged from ∼3.7 at the injection well to as high as 8.2 in the first monitoring well. Modelling results suggest that CO 2 -rich water-basalt interaction is dominated by crystalline basalt dissolution along a faster, high permeability flow Path, but by basaltic glass dissolution along a slower, pervasive flow Path through which the bulk of the injected fluid flows. Dissolution of pre-existing calcite at the onset of the injection does not have a net effect on the carbonation, but does contribute to a rapid early pH rise during the injection, and influences which carbonate minerals precipitate. At low pH, Mg, and Fe are preferentially released from crystalline basalts due to the higher dissolution rates of olivine, and to lesser extent pyroxene, compared to plagioclase and glass (Gudbrandsson et al., 2011). This favours the formation of siderite and Fe-Mg carbonates over calcite during early mineralisation. The model suggests the formation of the following carbonate mineral sequences: siderite at pH < 5, Mg-Fe-carbonates and Ca-Mg-Fe-carbonates at pH > 5, and calcite at higher pH. Other minerals forming with the carbonates are Al- and Fe-hydroxides and chalcedony, and zeolites and smectites at elevated pH. The most efficient carbonate formation is when the pH is high enough for formation of carbonates, but not so high that zeolites and smectites start to form, which compete with carbonates over both cations and pore space. The results of Reaction Path modelling at the CarbFix site in SW-Iceland indicate that this “sweet spot” for mineralisation of CO 2 is at pH from ∼5.2 to 6.5 in basalts at low temperature (20–50 °C)
Mingliang Wang - One of the best experts on this subject based on the ideXlab platform.
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nuclear quantum effects on an enzyme catalyzed Reaction with Reaction Path potential proton transfer in triosephosphate isomerase
Journal of Chemical Physics, 2006Co-Authors: Mingliang Wang, Weitao YangAbstract:Nuclear quantum mechanical effects have been examined for the proton transfer Reaction catalyzed by triosephosphate isomerase, with the normal mode centroid Path integral molecular dynamics based on the potential energy surface from the recently developed Reaction Path potential method. In the simulation, the primary and secondary hydrogens and the C and O atoms involving bond forming and bond breaking were treated quantum mechanically, while all other atoms were dealt classical mechanically. The quantum mechanical activation free energy and the primary kinetic isotope effects were examined. Because of the quantum mechanical effects in the proton transfer, the activation free energy was reduced by 2.3 kcal/mol in comparison with the classical one, which accelerates the rate of proton transfer by a factor of 47.5. The primary kinetic isotope effects of kH/kD and kH/kT were estimated to be 4.65 and 9.97, respectively, which are in agreement with the experimental value of 4+/-0.3 and 9. The corresponding Swain-Schadd exponent was predicted to be 3.01, less than the semiclassical limit value of 3.34, indicating that the quantum mechanical effects mainly arise from quantum vibrational motion rather than tunneling. The Reaction Path potential, in conjunction with the normal mode centroid molecular dynamics, is shown to be an efficient computational tool for investigating the quantum effects on enzymatic Reactions involving proton transfer.
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transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the Reaction Path potential method
Journal of Chemical Physics, 2004Co-Authors: Mingliang Wang, Zhenyu Lu, Weitao YangAbstract:A global potential energy surface has been constructed through interpolation of our recently developed Reaction Path potential for chemical Reactions in enzymes which is derived from combined ab initio quantum mechanical and molecular mechanical calculations. It has been implemented for the activated molecular dynamics simulations of the initial proton transfer Reaction catalyzed by triosephosphate isomerase. To examine the dynamical effects on the rate constants of the enzymatic Reaction, the classical transmission coefficient κ(t) is evaluated to be 0.47 with the reactive flux approach, demonstrating considerable deviations from transition state theory. In addition, the fluctuations of protein environments have small effects on the barrier recrossing, and the transmission coefficient κ(t) strongly depends on the fluctuations of atoms near the active site of the enzyme.
