Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase

We compare free energy calculations for the methyl transfer reaction catalyzed by catechol O-methyltransferase using the quantum mechanical/molecular mechanical free energy method with implicit and explicit solvents. An analogous methylation reaction in a solution is also studied. For the explicit solvent model, we use the three-point transferable intermolecular potential model, and for the implicit model, we use the generalized Born molecular volume model as implemented in CHARMM. We find that activation and reaction free energies calculated with the two models are very similar, despite some structural differences that exist. A significant change in the polarization of the environment occurs as the reaction proceeds. This is more pronounced for the reaction in a solution than for the enzymatic reaction. For the enzymatic reaction, most of the changes take place in the protein rather than in the solvent, and, hence, the benefit of having an instantaneous relaxation of the solvent degrees of freedom is less pronounced for the enzymatic reaction than for the reaction in a solution. This is a likely reason why energies of the enzyme reaction are less sensitive to the choice of atomic radii than are energies of the reaction in a solution.     

Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9

To elucidate enzyme catalysis through computer simulation, a prerequisite is to reliably compute free energy barriers for both enzyme and solution reactions. By employing on-the-fly Born-Oppenheimer molecular dynamics simulations with the ab initio quantum mechanical/molecular mechanical approach and the umbrella sampling method, we have determined free energy profiles for the methyl-transfer reaction catalyzed by the histone lysine methyltransferase SET7/9 and its corresponding uncatalyzed reaction in aqueous solution, respectively. Our calculated activation free energy barrier for the enzyme catalyzed reaction is 22.5 kcal/mol, which agrees very well with the experimental value of 20.9 kcal/mol. The difference in potential of mean force between a corresponding prereaction state and the transition state for the solution reaction is computed to be 30.9 kcal/mol. Thus, our simulations indicate that the enzyme SET7/9 plays an essential catalytic role in significantly lowering the barrier for the methyl-transfer reaction step. For the reaction in solution, it is found that the hydrogen bond network near the reaction center undergoes a significant change, and there is a strong shift in electrostatic field from the prereaction state to the transition state, whereas for the enzyme reaction, such an effect is much smaller and the enzyme SET7/9 is found to provide a preorganized electrostatic environment to facilitate the methyl-transfer reaction. Meanwhile, we find that the transition state in the enzyme reaction is a little more dissociative than that in solution.     

Solution of the master equation for Wigner's quasiprobability distribution in phase space for the Brownian motion of a particle in a double well potential

Quantum effects in the Brownian motion of a particle in the symmetric double well potential V(x)=ax(2)2+bx(4)4 are treated using the semiclassical master equation for the time evolution of the Wigner distribution function W(x,p,t) in phase space (x,p). The equilibrium position autocorrelation function, dynamic susceptibility, and escape rate are evaluated via matrix continued fractions in the manner customarily used for the classical Fokker-Planck equation. The escape rate so yielded has a quantum correction depending strongly on the barrier height and is compared with that given analytically by the quantum mechanical reaction rate solution of the Kramers turnover problem. The matrix continued fraction solution substantially agrees with the analytic solution. Moreover, the low-frequency part of the spectrum associated with noise assisted Kramers transitions across the potential barrier may be accurately described by a single Lorentzian with characteristic frequency given by the quantum mechanical reaction rate.     

Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface

To accurately determine the reaction path and its energetics for enzymatic and solution-phase reactions, we present a sequential sampling and optimization approach that greatly enhances the efficiency of the ab initio quantum mechanics/molecular mechanics minimum free-energy path (QM/MM-MFEP) method. In the QM/MM-MFEP method, the thermodynamics of a complex reaction system is described by the potential of mean force (PMF) surface of the quantum mechanical (QM) subsystem with a small number of degrees of freedom, somewhat like describing a reaction process in the gas phase. The main computational cost of the QM/MM-MFEP method comes from the statistical sampling of conformations of the molecular mechanical (MM) subsystem required for the calculation of the QM PMF and its gradient. In our new sequential sampling and optimization approach, we aim to reduce the amount of MM sampling while still retaining the accuracy of the results by first carrying out MM phase-space sampling and then optimizing the QM subsystem in the fixed-size ensemble of MM conformations. The resulting QM optimized structures are then used to obtain more accurate sampling of the MM subsystem. This process of sequential MM sampling and QM optimization is iterated until convergence. The use of a fixed-size, finite MM conformational ensemble enables the precise evaluation of the QM potential of mean force and its gradient within the ensemble, thus circumventing the challenges associated with statistical averaging and significantly speeding up the convergence of the optimization process. To further improve the accuracy of the QM/MM-MFEP method, the reaction path potential method developed by Lu and Yang [Z. Lu and W. Yang, J. Chem. Phys. 121, 89 (2004)] is employed to describe the QM/MM electrostatic interactions in an approximate yet accurate way with a computational cost that is comparable to classical MM simulations. The new method was successfully applied to two example reaction processes, the classical SN2 reaction of Cl-+CH3Cl in solution and the second proton transfer step of the reaction catalyzed by the enzyme 4-oxalocrotonate tautomerase. The activation free energies calculated with this new sequential sampling and optimization approach to the QM/MM-MFEP method agree well with results from other simulation approaches such as the umbrella sampling technique with direct QM/MM dynamics sampling, demonstrating the accuracy of the iterative QM/MM-MFEP method.     

Potentiometric determination of bromate using an Fe(III)-Fe(II) potential buffer by circulatory flow-injection analysis.

A method for the potentiometric determination of bromate by circulatory flow injection analysis (CFIA) is described. The procedure involves the use of an Fe(III)-Fe(II) potential buffer solution, which is recycled via a reservoir. The analytical method is based on a linear relationship between the concentration of bromate and a very transient potential change in the electrode potential due to the generation of intermediate bromine during the reaction of bromate with the Fe(III)-Fe(II) potential buffer solution, which also contains NaBr, (NH4)6Mo7O24 and H2SO4. An aliquot (5 microl) of a bromate sample solution was injected into the stream of the potential buffer solution, 100 ml of which was circulated at a flow rate of 1 ml/min; the potential buffer solution stream was then returned to the reservoir after passing through a flow-through redox electrode detector. A potential change due to the reaction of the injected sample with the potential buffer in a reaction coil was measured with the detector in the form of a peak signal. The effects of the bromide, sulfuric acid and Fe(III)-Fe(II) concentrations in the potential buffer, and length of the reaction coil on the peak heights were examined in order to optimize the proposed CFIA method. The analytical sensitivities to bromate were 5.6 mV/microM for 1 x 10(-2) M and 30.9 mV/microM for 1 x 10(-3) M in the concentration of Fe(III)-Fe(II) in a potential buffer solution containing 0.35 M NaBr, 0.2% (NH4)6Mo7O24 and 1 M H2SO4. The detection limit of bromate obtained by a 1 x 10(-3) M Fe(III)-Fe(II) potential buffer solution was 0.02 microM (2.5 ppb). The numbers of repetitive determinations in which the relative sensitivities within 5% were regarded as being tolerated were ca. 4000 and 2000 for the use of only 100 ml of 1 x 10(-2) M and 1 x 10(-3) M Fe(III)-Fe(II) potential buffer solution, respectively.     

Effect of Preparation Method on the Structural Characteristics of NiO-ZrO2 Oxygen Carriers for Chemical-looping Combustion

Chemical-looping combustion(CLC) offers an effective approach for power generation and CO₂ capture. In this work, an NiO-ZrO₂ oxygen carrier prepared by three methods was subjected to an optimal reaction temperature test, an optimal flow test and a cyclic redox reaction test to explore the most suitable reaction conditions. Through comparative analysis, it is noted that the coprecipitation method is not suitable for the preparation of this NiO-ZrO₂ oxygen carrier, while the oxygen carrier prepared by the mechanical mixing method and solution combustion method obtained a higher CH₄ conversion rate and CO₂ selectivity. In addition, these two oxygen carriers also showed high stability during successive CLC testing. Therefore, both the mechanical mixing method and the solution combustion method can be used to prepare NiO-ZrO₂ oxygen carriers.     

Hybrid quantum mechanical and molecular mechanics study of the S(N)2 Reaction of CCl4 + OH- in aqueous solution: the potential of mean force, reaction energetics, and rate constants

The bimolecular nucleophilic substitution reaction of CCl(4) and OH(-) in aqueous solution was investigated on the basis of a combined quantum mechanical and molecular mechanics method. A multilayered representation approach is employed to achieve high accuracy results at the CCSD(T) level of theory. The potential of mean force calculations at the DFT level and CCSD(T) level of theory yield reaction barrier heights of 22.7 and 27.9 kcal/mol, respectively. Both the solvation effects and the solvent-induced polarization effect have significant contributions to the reaction energetics, for example, the solvation effect raises the saddle point by 10.6 kcal/mol. The calculated rate constant coefficient is 8.6 × 10(-28) cm(3) molecule(-1) s(-1) at the standard state condition, which is about 17 orders magnitude smaller than that in the gas phase. Among the four chloromethanes (CH(3)Cl, CH(2)Cl(2), CHCl(3), and CCl(4)), CCl(4) has the lowest free energy activation barrier for the reaction with OH(-) in aqueous solution, confirming the trend that substitution of Cl by H in chloromethanes diminishes the reactivity.     

Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations

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.     

An optimum strategy for solution chemistry using semiempirical molecular orbital method: Importance of description of charge distribution

For the purpose to execute direct dynamics calculation in solution chemistry, we propose an optimum strategy for solution chemistry using semiempirical molecular orbital (MO) method with neglect of diatomic differential overlap (NDDO) approximation with specific solution reaction parameters (SSRP), i.e., the NDDO‐SSRP method. In this strategy, the empirical parameters of the semi‐empirical MO method were optimized individually for target molecule or ion by reference to the ab initio MO calculation data for many configurations on the potential energy surface near the reaction path. For demonstration, the NDDO‐SSRP method was applied to two molecules and two ions (OH^?, H₂O, NH₃, NH₄⁺) at their equilibrium states in aqueous solution, respectively. Accordingly, it was verified that both the potential energy surface and the charge distribution of these solutes in aqueous solution are dramatically improved to reproduce themselves accurately at ab initio MO calculation level. In conclusion, it is expected that the NDDO‐SSRP method should become quite useful for dynamic and statistical applications to chemical reaction systems in solution. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

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

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.     

Nonuniform charge scaling (NUCS): a practical approximation of solvent electrostatic screening in proteins

In molecular mechanics calculations, electrostatic interactions between chemical groups are usually represented by a Coulomb potential between the partial atomic charges of the groups. In aqueous solution these interactions are modified by the polarizable solvent. Although the electrostatic effects of the polarized solvent on the protein are well described by the Poisson--Boltzmann equation, its numerical solution is computationally expensive for large molecules such as proteins. The procedure of nonuniform charge scaling (NUCS) is a pragmatic approach to implicit solvation that approximates the solvent screening effect by individually scaling the partial charges on the explicit atoms of the macromolecule so as to reproduce electrostatic interaction energies obtained from an initial Poisson--Boltzmann analysis. Once the screening factors have been determined for a protein the scaled charges can be easily used in any molecular mechanics program that implements a Coulomb term. The approach is particularly suitable for minimization-based simulations, such as normal mode analysis, certain conformational reaction path or ligand binding techniques for which bulk solvent cannot be included explicitly, and for combined quantum mechanical/molecular mechanical calculations when the interface to more elaborate continuum solvent models is lacking. The method is illustrated using reaction path calculations of the Tyr 35 ring flip in the bovine pancreatic trypsin inhibitor.     

Dispersity and stability of foams obtained from poly(vinyl alcohol) solution and the properties of resulting foamed cryogels

Foams have been generated from aqueous poly(vinyl alcohol) solution by two different methods: dispersion (mechanical) method, i.e., by bubbling a gas through a porous medium into the aqueous poly(vinyl alcohol) solution, and the condensation (chemical) method, i.e., by performing a gas-generating reaction directly in the polymer solution. The effect of the formation method on foam stability and dispersity has been studied. The foam produced by the condensation method of foaming the aqueous poly(vinyl alcohol) solution with nitrogen is more stable and finely dispersed and has a higher expansion ratio than that obtained by bubbling the gas through the polymer solution. Foamed cryogels have been formed by freezing-thawing the foam resulting from the chemical reaction in the polymer solution. The values of the elasticity modulus, melting temperature, and thermal conductivity of the cryogels have been determined.     

微流控纺丝制备葡萄糖响应凝胶纤维

葡萄糖响应凝胶纤维在血糖监测传感器开发中有着潜在的应用前景。本文基于微流控纺丝方法和自由基聚合反应制备了化学交联和物理交联的葡萄糖响应聚(N-异丙基丙烯酰胺/3-丙烯酰胺基苯硼酸)(P(NIPAM-co-AAPBA))凝胶纤维。通过傅里叶变换红外光谱、扫描电子显微镜和力学性能测试等技术手段表征了凝胶纤维的结构和形态、力学性能、溶胀度动力学与葡萄糖响应性。结果表明,凝胶纤维具有多孔的微观结构,通过改变芯层与壳层溶液的流速可以调控凝胶纤维的直径。随着AAPBA质量分数的增加,凝胶纤维的溶胀速率和平衡溶胀度均有所降低,但葡萄糖响应性能提高。与化学交联的凝胶纤维相比,物理交联的凝胶纤维具有良好的力学性能。     

Potentiometric flow-injection determination of trace hydrogen peroxide based on its induced reaction in iron(III)-iron(II) potential buffer containing bromide and molybdenum(VI)

A rapid and highly sensitive potentiometric flow-injection method for the determination of trace hydrogen peroxide was developed by use of an Fe(III)-Fe(II) potential buffer solution containing bromide and Mo(VI). The analytical method was based on a linear relationship between a concentration of hydrogen peroxide and a largely transient potential change of an oxidation-reduction potential electrode due to bromine generated by the reaction of hydrogen peroxide with the potential buffer solution. The oxidation of bromide to bromine by hydrogen peroxide occurred very rapidly with the assistance of Mo(VI) when Fe(II) existed in the potential buffer solution. It was estimated by batchwise experiments that hydroxyl radical, OH., was generated by the reaction of hydrogen peroxide with Fe(II) as an intermediate, and subsequently oxidized bromide to bromine. In a flow system, analytical sensitivities to hydrogen peroxide obtained by the detection of the transient change of potential were enhanced about 75 fold compared with those obtained by using the potential change caused by the reaction of hydrogen peroxide with the potential buffer solution without bromide and Mo(VI). Sensitivities increased with decreasing concentration of the Fe(III)-Fe(II) buffer in the reagent solution. The detection limit (S/N = 3) of 4 x 10(-7) M (13.6 ppb) was achieved by using the 1 x 10(-4) M Fe(III)-Fe(II) buffer containing 0.4 M NaBr, 1.0 M H(2)SO(4) and 0.5% (NH(4))(6)Mo(7)O(24). Analytical throughput was approximately 40 h(-1) and the RSD (n = 6) was 0.6% for measurement of 4 x 10(-6) M hydrogen peroxide. The proposed method was applied to the determination of hydrogen peroxide in real rainwater samples, and was found to provide a good recovery for H(2)O(2) added to rainwater samples.     

Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase

Elucidating the role of nuclear quantum mechanical (NQM) effects in enzyme catalysis is a topic of significant current interest. Despite the great experimental progress in this field it is important to have theoretical approaches capable of evaluating and analyzing nuclear quantum mechanical contributions to catalysis. In this study, we use the catalytic reaction of lipoxygenase, which is characterized by an extremely large kinetic isotope effect, as a challenging test case for our simulation approach. This is done by applying the quantum classical path (QCP) method with an empirical valence bond potential energy surface. Our computational strategy evaluates the relevant NQM corrections and reproduces the large observed kinetic isotope effect and the temperature dependence of the H atom transfer reaction while being less successful with the D atom transfer reaction. However, the main point of our study is not so much to explore the temperature dependence of the isotope effect but rather to develop and validate an approach for calculations of nuclear quantum mechanical contributions to activation free energies. Here, we find that the deviation between the calculated and observed activation free energies is small for both H and D at all investigated temperatures. The present study also explores the nature of the reorganization energy in the enzyme and solution reactions. It is found that the outer-sphere reorganization energy is extremely small. This reflects the fact that the considered reaction involves a very small charge transfer. The implication of this finding is discussed in the framework of the qualitative vibronic model. The main point of the present study is, however, that the rigorous QCP approach provides a reliable computational tool for evaluating NQM contributions to catalysis even when the given reaction includes large tunneling contributions. Interestingly, our results indicate that the NQM effects in the lipoxygenase reaction are similar in the enzyme and in the reference solution reactions, and thus do not contribute to catalysis. We also reached similar conclusions in studies of other enzymes.     

A surface hopping method for chemical reaction dynamics in solution described by diabatic representation: an analysis of tunneling and thermal activation

We present a surface hopping method for chemical reaction in solution based on diabatic representation, where quantum mechanical time evolution of the vibrational state of the reacting nuclei as well as the reaction-related electronic state of the system are traced simultaneously together with the classical motion of the solvent. The method is effective in describing the system where decoherence between reactant and product states is rapid. The diabatic representation can also give a clear picture for the reaction mechanism, e.g., thermal activation mechanism and a tunneling one. An idea of molecular orbital theory has been applied to evaluate the solvent contribution to the electronic coupling which determines the rate of reactive transition between the reactant and product potential surfaces. We applied the method to a model system which can describe complex chemical reaction of the real system. Two numerical examples are presented in order to demonstrate the applicability of the present method, where the first example traces a chemical reaction proceeded by thermal activation mechanism and the second examines tunneling mechanism mimicking a proton transfer reaction.     

Periodic change of viscosity and density in an oscillating chemical reaction

It was found that the periodic change of the solution viscosity and density was generated in the Belousov-Zhabotinsky (BZ) reaction. This rhythmic phenomenon was observed in both the iron catalyst [[Fe(Phen)(3)](2+)-[Fe(Phen)(3)](3+)] and the cerium catalyst [Ce(III)-Ce(IV)] system, where the solution viscosity and density were synchronized with the redox potential in the in-phase mode. However, the time delay existed between the redox potential and the solution viscosity and density. The behavior of the BZ reaction was also monitored in the presence of the nonionic surfactant. This experiment revealed that, beyond the critical micelle concentration, the phase between the redox potential and the solution viscosity and density was synchronized into the antiphase mode. We suggested that the variation of the catalyst drove the oscillation of the solution viscosity and density in the BZ reaction.     

Potentiometric flow injection determination of amylase activity by using hexacyanoferrate(III)-hexacyanoferrate(II) potential buffer

A highly sensitive potentiometric flow injection determination of amylase activity was carried out, utilizing a redox reaction of hexacyanoferrate(III) in alkaline media with reducing sugar as product of the enzymatic hydrolysis reaction of starch with amylase. The analytical method is based on the potential change detection of a flow-through type redox electrode detector due to the composition change of a [Fe(CN)(6)](3-)-[Fe(CN)(6)](4-) potential buffer solution, which is caused by the redox reaction with the product of the enzymatic reaction. A linear relationship exists between the potential change (peak height) and the activity of amylase. Amylase of a wide activity range from 2.5x10(-2) to 1.2x10(-4) U ml(-1) can be determined by the changing the concentrations of the [Fe(CN)(6)](3-)-[Fe(CN)(6)](4-) potential buffer from 10(-3) to 10(-5) M. The lower detection limit of amylase activity is 6.0x10(-5) U ml(-1). The sampling rate and relative standard deviation are 15 h(-1) and 0.9% (n=5) for 3.8x10(-3) U ml(-1) of amylase. The present method was successfully applied to determine amylase activity in real samples (commercial digestive medicines) with an accuracy of 4% compared with analytical results obtained using the present method with those achieved using the conventional titration method.     

几种Cardo聚芳醚砜的合成与表征

酚酞型聚芳醚砜(PES-C)是综合性能优异的热塑性工程塑料,可通过溴化、磺化等改性.本文用一步法,K₂C0₃存在下以二甲基亚矾为介质,合成了不同取代烷基的聚合物.     

掺硼金刚石膜电极表面产生羟基自由基的原位ESR研究

建立了原位电化学-电子顺磁共振(ESR)方法,系统研究了掺硼金刚石(BDD)膜电极表面在水溶液中的羟基自由基(·OH)产生规律.结果表明,在高于析氧电位时,·OH的生成速率随着阳极电位的升高、电流密度的增加而增大,增加速率逐渐减缓.与此同时,与氢终端的BDD膜电极相比,氧终端的BDD膜电极表面因具有较好的亲水性而具有更高的·OH产生能力.在电化学氧化处理有机废水的过程中,电极表面处于氧终端的状态,有利于·OH产生并保持较高的活性.溶液pH值也在一定程度上影响·OH生成反应,酸性溶液中,BDD膜电极表面的·OH产生能力强于在中性或碱性溶液中.进一步研究发现,BDD膜电极表面还可能生成O3-·0自由基.本研究为深入探索BDD膜电极表面·OH的产生机制提供了研究手段,为阐述BDD膜电极电极在污染物处理中高效性的本质提供了有效的证据.