Modeling the catalysis of anti-cocaine catalytic antibody: competing reaction pathways and free energy barriers

The competing reaction pathways and the corresponding free energy barriers for cocaine hydrolysis catalyzed by an anti-cocaine catalytic antibody, mAb15A10, were studied by using a novel computational strategy based on the binding free energy calculations on the antibody binding with cocaine and transition states. The calculated binding free energies were used to evaluate the free energy barrier shift from the cocaine hydrolysis in water to the antibody-catalyzed cocaine hydrolysis for each reaction pathway. The free energy barriers for the antibody-catalyzed cocaine hydrolysis were predicted to be the corresponding free energy barriers for the cocaine hydrolysis in water plus the calculated free energy barrier shifts. The calculated free energy barrier shift of -6.87 kcal/mol from the dominant reaction pathway of the cocaine benzoyl ester hydrolysis in water to the dominant reaction pathway of the antibody-catalyzed cocaine hydrolysis is in good agreement with the experimentally derived free energy barrier shift of -5.93 kcal/mol. The calculated mutation-caused shifts of the free energy barrier are also reasonably close to the available experimental activity data. The good agreement suggests that the protocol for calculating the free energy barrier shift from the cocaine hydrolysis in water to the antibody-catalyzed cocaine hydrolysis may be used in future rational design of possible high-activity mutants of the antibody as anti-cocaine therapeutics. The general strategy of the free energy barrier shift calculation may also be valuable in studying a variety of chemical reactions catalyzed by other antibodies or proteins through noncovalent bonding interactions with the substrates.     

Diffusive dynamics on multidimensional rough free energy surfaces

The dynamics of processes relevant to chemistry and biophysics on rough free energy landscapes is investigated using a recently developed algorithm to solve the Smoluchowski equation. Two different processes are considered: ligand rebinding in MbCO and protein folding. For the rebinding dynamics of carbon monoxide (CO) to native myoglobin (Mb) from locations around the active site, the two-dimensional free energy surface (FES) is constructed using extensive molecular dynamics simulations. The surface describes the minima in the A state (bound MbCO), CO in the distal pocket and in the Xe4 pocket, and the transitions between these states and allows to study the diffusion of CO in detail. For the folding dynamics of protein G, a previously determined two-dimensional FES was available. To follow the diffusive dynamics on these rough free energy surfaces, the Smoluchowski equation is solved using the recently developed hierarchical discrete approximation method. From the relaxation of the initial nonequilibrium distribution, experimentally accessible quantities such as the rebinding time for CO or the folding time for protein G can be calculated. It is found that the free energy barrier for CO in the Xe4 pocket and in the distal pocket (B state) closer to the heme iron is approximately 6 kcal/mol which is considerably larger than the inner barrier which separates the bound state and the B state. For the folding of protein G, a barrier of approximately 10 kcal/mol between the unfolded and the folded state is consistent with folding times of the order of milliseconds.     

Preorganization and protein dynamics in enzyme catalysis

Recently, an alternative has been offered to the concept of transition state (TS) stabilization as an explanation for rate enhancements in enzyme-catalyzed reactions. Instead, most of the rate increase has been ascribed to preorganization of the enzyme active site to bind substrates in a geometry close to that of the TS, which then transit the activation barrier impelled by motions along the reaction coordinate. The question as to how an enzyme achieves such preorganization and concomitant TS stabilization as well as potential coupled motions along the reaction coordinate leads directly to the role of protein dynamic motion. Dihydrofolate reductase (DHFR) is a paradigm in which the role of dynamics in catalysis continues to be unraveled by a wealth of kinetic, structural, and computational studies. DHFR has flexible loop regions adjacent to the active site whose motions modulate passage through the kinetically preferred pathway. The participation of residues distant from the DHFR active site in enhancing the rate of hydride transfer, however, is unanticipated and may signify the importance of long range protein motions. The general significance of protein dynamics in understanding other biological processes is briefly discussed.     

Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations

An efficient method for the calculation of minimum free energy pathways and free energy profiles for conformational transitions is presented. Short restricted perturbation-targeted molecular dynamics trajectories are used to generate an approximate free energy surface. Approximate reaction pathways for the conformational change are constructed from one-dimensional line segments on this surface using a Monte Carlo optimization. Accurate free energy profiles are then determined along the pathways by means of one-dimensional adaptive umbrella sampling simulations. The method is illustrated by its application to the alanine "dipeptide." Due to the low computational cost and memory demands, the method is expected to be useful for the treatment of large biomolecular systems.     

Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase

The controversial 'near attack conformation'(NAC) effect in the important model enzyme chorismate mutase is calculated to be 3.8-4.6 kcal mol(-1) by QM/MM free energy perturbation molecular dynamics methods, showing that the NAC effect by itself does not account for catalysis in this enzyme.     

High-dimensional ab initio potential energy surfaces for reaction dynamics calculations

There has been great progress in the development of potential energy surfaces (PESs) for reaction dynamics that are fits to ab initio energies. The fitting techniques described here explicitly represent the invariance of the PES with respect to all permutations of like atoms. A review of a subset of dynamics calculations using such PESs (currently 16 such PESs exist) is then given. Bimolecular reactions of current interest to the community, namely, H + CH(4) and F + CH(4), are focused on. Unimolecular reactions are then reviewed, with a focus on the photodissociation dynamics of H(2)CO and CH(3)CHO, where so-called "roaming" pathways have been discovered. The challenges for electronically non-adiabatic reactions, and associated PESs, are presented with a focus on the OH* + H(2) reaction. Finally, some thoughts on future directions and challenges are given.     

Interfacial energy exchange and reaction dynamics in collisions of gases on model organic surfaces

Molecular beam scattering experiments and molecular dynamics simulations have been combined to develop an atomic-level understanding of energy transfer, accommodation, and reactions during collisions between gases and model organic surfaces. The work highlighted in this progress report has been motivated by the scientific importance of understanding fundamental interfacial chemical reactions and the relevance of reactions on organic surfaces to many areas of environmental chemistry. The experimental investigations have been accomplished by molecular beam scattering from ω-functionalized self-assembled monolayers (SAMs) on gold. Molecular beams provide a source of reactant molecules with precisely characterized collision energy and flux; SAMs afford control over the order, structure, and chemical nature of the surface. The details of molecular motion that affect energy exchange and scattering have been elucidated through classical-trajectory simulations of the experimental data using potential energy surfaces derived from ab initio calculations. Our investigations began by employing rare-gas scattering to explore how alkanethiol chain length and packing density, terminal group relative mass, orientation, and chemical functionality influence energy transfer and accommodation at organic surfaces. Subsequent studies of small molecule scattering dynamics provided insight into the influence of internal energy, molecular orientation, and gas–surface attractive forces in interfacial energy exchange. Building on the understanding of scattering dynamics in non-reactive systems, our work has recently explored the reaction probabilities and mechanisms for O₃ and atomic fluorine in collisions with a variety of functionalized SAM surfaces. Together, this body of work has helped construct a more comprehensive understanding of reaction dynamics at organic surfaces.     

Chiral proton catalysis: a catalytic enantioselective direct aza-Henry reaction

Despite Nature's longstanding ability to use a proton, the most prevalent Lewis acid, to both activate and orient a substrate during an enantioselective reaction, this work represents the first example of this phenomenon outside of a protein. A chiral, nonracemic BisAMidine (BAM) ligand was designed, synthesized, and complexed to the proton of a Br?nsted acid. The resulting coordination compound catalyzed the production of enantioenriched product from the combination of a Schiff base and nitroalkane (the aza-Henry reaction). This particular reaction is also considered a model for many analogous carbon-carbon bond-forming reactions catalyzed by enzymes (e.g., the Mannich reaction). This discovery suggests the use of ionic hydrogen bonds in asymmetric catalysis may not only be more general than previously thought, but also a viable "green" approach to single-enantiomer organic compounds.     

能源催化材料的电化学合成

电催化是发展可持续洁净能源技术的基础科学,是电化学能源转换和物质转化的关键环节.精准合成催化活性纳米结构是制约很多电催化反应走向实际应用的重要挑战.与湿化学合成、固相合成和气相沉积等传统方法相比,电化学合成是一种简单、快速、廉价及可控的高效催化材料制备方法,也是一种最为直接的一体化电极制备方法.本文综述了近年来利用电化...     

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.     

Reaction dynamics on bifurcating potential energy surfaces

Classical trajectories were run on a local fit to the bifurcating transition region of the Valtazanos and Ruedenberg ab initio potential energy surface for the cyclopropylidene to allene reaction, and also on several variations of this local surface. The trajectory results were analyzed to determine the outcome as a function of initial conditions, and several plots of these are presented.Camille and Henry Dreyfus Teacher-Scholar; Alfred P. Sloan Foundation fellow     

Molecular dynamics of apo-adenylate kinase: a distance replica exchange method for the free energy of conformational fluctuations

A large domain motion in adenylate kinase from E. coli (AKE) is studied with molecular dynamics. AKE undergoes a large-scale rearrangement of its lid and AMP-binding domains when the open form closes over its substrates, AMP, and Mg2+-ATP, whereby the AMP-binding and lid domains come closer to the core. The third domain, the core, is relatively stable during this motion. A reaction coordinate that monitors the distance between the AMP-binding and core domains is selected to be able to compare with the results of energy transfer experiments. Sampling along this reaction coordinate is carried out by using a distance replica exchange method (DREM), where systems that differ by a restraint potential enforcing different reaction coordinate values are independently simulated with periodic attempts at exchange of these systems. Several methods are used to study the efficiency and convergence properties of the DREM simulation and compared with an analogous non-DREM simulation. The DREM greatly accelerates the rate and extent of configurational sampling and leads to equilibrium sampling as measured by monitoring collective modes obtained from a principal coordinate analysis. The potential of mean force along the reaction coordinate reveals a rather flat region for distances from the open to a relatively closed AKE conformation. The potential of mean force for smaller distances has a distinct minimum that is quite close to that found in the closed form X-ray structure. In concert with a decrease in the reaction coordinate distance (AMP-binding-to-core distance) the lid-to-core distance of AKE also decreases. Therefore, apo AKE can fluctuate from its open form to conformations that are quite similar to its closed form X-ray structure, even in the absence of its substrates.     

Stabilization of surface reaction intermediates by added metal atoms on metal surfaces of low free energy

Dynamic restructuring of the Ag(111) surface occurs during the reaction of sulfur dioxide with Ag(111)-p(4 x 4)-O at 300 K, resulting in the incorporation of added silver atoms into the unit cells of both adsorbed sulfite and sulfate. This result clearly demonstrates that incorporation of metal atoms into the structures of adsorbates and reaction intermediates is not restricted to more open, higher free energy single crystal planes. These observations indicate that the participation of added metal atoms must be considered in the theoretical treatment of metal catalyzed reactions.     

Electrophilic bromination of gaseous aromatic compounds: Mechanism and linear free energy effects on reaction rates

Electrophilic bromination of monosubstituted aromatic compounds is effected in a pentaquadrupole mass spectrometer using BrCO⁺ and CH₃NH₂Br⁺ as mass-selected reagent ions. Reaction normally occurs at the ring and the brominated product can be mass selected in turn and caused to dissociate by Br˙ loss upon collision-induced dissociation. Linear free energy correlations with Brown substituent σ⁺ constants describe the extent of gas-phase bromine cation addition under the non-equilibrium, low-pressure and solvent-free conditions which pertain in quadruple collision cells. The electrophilic addition reaction proceeds via a σ-complex to the ring as suggested by MS³ spectra, except in the case of nitrobenzene, where substituent bromination is suggested by the occurrence of a competitive process in which the nitrosubstituent is displaced by bromine. The reactivity parameters ρ are ?0.23 and ?0.56 for the gaseous reagents, BrCO⁺ and CH₃NH₂Br⁺, respectively. Both values are much less negative than corresponding values for bromination in solution. The greater reactivity of BrCO⁺ is evident by the fact that it reacts even with the strongly deactivated substrates and this is consistent with a weak Br? CO bond. Competitive protonation occurs in the case of CH₃NH₂Br⁺ and, unlike bromination, the rate of this reaction does not correlate with σ⁺ values. This is suggested to be a consequence of protonation at the ring in some cases and at the substituent in others, including acetophenone and benzonitrile. Evidence for this is that, in contrast to its lack of correlation with substituent constants, the rate of protonation correlates linearly with proton affinity.     

Metadynamics in essential coordinates: free energy simulation of conformational changes

We propose an approach that combines an extraction of collective motions of a molecular system with a sampling of its free energy surface. A recently introduced method of metadynamics allows exploration of the free energy surface of a molecular system by means of coarse-grained dynamics with flooding of free energy minima. This free energy surface is defined as a function of a set of collective variables (e.g., interatomic distances, angles, torsions, and others). In this study, essential coordinates determined by essential dynamics (principle component analysis) were used as collective variables in metadynamics. First, dynamics of the model system (explicitly solvated alanine dipeptide, Ace-Ala-Nme) was simulated by a classical molecular dynamics simulation. The trajectory (1 ns) was then analyzed by essential dynamics to obtain essential coordinates. The free energy surface as a function of the first and second essential coordinates was then explored by metadynamics. The resulting free energy surface is in agreement with other studies of this system. We propose that a combination of these two methods (metadynamics and essential dynamics) has great potential in studies of conformational changes in peptides and proteins.     

Surface modification by substitution: Changing topology of conformational potential energy surfaces

It is shown for compounds XS-CHCH-CHO that chemical substitution (X = H → F and X = H → Li) results in the change of conformational potential energy surfaces not only in the quantitative but in the qualitative sense as well. Qualitative change always implied a modified surface topology, i.e. critical points are either created by “split-ups” or annihilated by “collapse”. It appears that some kind of “selection rule” might be operative in the “creation” and “annihilation” of critical points during the change of surface topology as the result of chemical substitution.     

Molecular dynamics simulations and free energy calculations on the enzyme 4‐hydroxyphenylpyruvate dioxygenase

4‐Hydroxyphenylpyruvate dioxygenase is a relevant target in both pharmaceutical and agricultural research. We report on molecular dynamics simulations and free energy calculations on this enzyme, in complex with 12 inhibitors for which experimental affinities were determined. We applied the thermodynamic integration approach and the more efficient one‐step perturbation. Even though simulations seem well converged and both methods show excellent agreement between them, the correlation with the experimental values remains poor. We investigate the effect of slight modifications on the charge distribution of these highly conjugated systems and find that accurate models can be obtained when using improved force field parameters. This study gives insight into the applicability of free energy methods and current limitations in force field parameterization. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011     

Size dependent interface energy and catalytic kinetics on non-ideal surfaces

Thermodynamic analysis is applied to describe the size dependent kinetics on surfaces with lateral interactions. A two-step sequence, often used in heterogeneous catalysis to account for catalytic kinetics, was modified to include the dependency of interfacial free energy on the particle size.