Dynamics of an enzymatic substitution reaction in haloalkane dehalogenase

Reactive flux molecular dynamics simulations have been carried out using a combined QM/MM potential to study the dynamics of the nucleophilic substitution reaction of dichloroethane by a carboxylate group in haloalkane dehalogenase and in water. We found that protein dynamics accelerates the reaction rate by a factor of 2 over the uncatalyzed reaction. Compared to the thermodynamic effect in barrier reduction, protein dynamic contribution is relatively small. However, analyses of the friction kernel reveal that the origins of the reaction dynamics in water and in the enzyme are different. In aqueous solution, there is significant electrostatic solvation effect, which is reflected by the slow reorganization relaxation of the solvent. On the other hand, there is no strong electrostatic coupling in the enzyme and the major effect on reaction coordinate motion is intramolecular energy relaxation.     

Influence of interparticle interactions on the kinetics of self-assembly and mechanical strength of nanoparticulate aggregates

Computer simulations based on Discrete Element Method have been performed in order to investigate the influence of interparticle interactions on the kinetics of self-assembly and the mechanical strength of nanoparticle aggregates.Three different systems have been considered.In the first system the interaction between particles has been simulated using the JKR (Johnson,Kendall and Roberts) contact theory,while in the second and third systems the interaction between particles has been simulated using van der Waals and electrostatic forces respectively.In order to compare the mechanical behaviour of the three systems,the magnitude of the maximum attractive force between particles has been kept the same in all cases.However,the relationship between force and separation distance differs from case to case and thus,the range of the interparticle force.The results clearly indicate that as the range of the interparticle force increases,the self-assembly process is faster and the work required to produce the mechanical failure of the assemblies increases by more than one order of magnitude.     

Combined QM/MM study of the mechanism and kinetic isotope effect of the nucleophilic substitution reaction in haloalkane dehalogenase

Combined QM/MM molecular dynamics simulations have been carried out for the dehalogenation reaction of the nucleophilic displacement of dichloroethane catalyzed by haloalkane dehalogenase. The computed chlorine kinetic isotope effects and free energies of activation in the wild-type and the Phe172Trp mutant enzyme are found to be consistent with experiment. In comparison with the uncatalyzed model reaction in water, the enzyme lowers the activation barrier by about 16 kcal/mol. The enormous enzymatic action was attributed to a combination of contributions from a change in the solvation effect and transition state stabilization. The unique features of tryptophan's ability to interact favorably with hydrophobic substrates and to form hydrogen bonds to the leaving group chloride ion at the transition state enable both factors to make significant contributions to the barrier lowering mechanism in the enzyme. This is in contrast to the reference reaction in water, in which hydrogen bonding interactions are weakened at the transition state because of dispersed charge distribution at the transition state relative to that in the reactant and product states.     

Performance of slotted pores in particle manufacture using rotating membrane emulsification

This paper addresses the use of different slotted pores in rotating membrane emulsification technology.Pores of square and rectangular shapes were studied to understand the effect of aspect ratio (1-3.5) and their orientation on oil droplet formation.Increasing the membrane rotation speed decreased the droplet size,and the oil droplets produced were more uniform using slotted pores as compared to circular geometry.At a given rotation speed,the droplet size was mainly determined by the pore size and the fluid velocity of oil through the pore (pore fluid velocity).The ratio of droplet diameter to the equivalent diameter of the slotted pore increased with the pore fluid velocity.At a given pore fluid velocity and rotation speed,pore orientation significantly influences the droplet formation rate: horizontally disposed pores (with their longer side perpendicular to the membrane axis) generate droplets at double the rate of vertically disposed pores.This work indicates practical benefits in the use of slotted membranes over conventional methods.     

Semiempirical QM/MM potential with simple valence bond (SVB) for enzyme reactions. Application to the nucleophilic addition reaction in haloalkane dehalogenase

 We present a method for the correction of errors in combined QM/MM calculations using a semiempirical Hamiltonian for enzyme reactions. Since semiempirical models can provide a reasonable representation of the general shape of the potential energy surface for chemical reactions, we introduce a simple valence bond-like (SVB) term to correct the energies at critical points on the potential energy surface. The present SVB term is not a stand-alone potential energy function, but it is used purely for introducing small energy corrections to the semiempirical Hamiltonian to achieve the accuracy needed for modeling enzymatic reactions. We show that the present coupled QM-SVB/MM approach can be parameterized to reproduce experimental and ab initio results for model reactions, and have applied the PM3-SVB/MM potential to the nucleophilic addition reaction in haloalkane dehalogenase. In a preliminary energy minimization study, the PM3-SVB/MM results are reasonable, suggesting that it may be used in free energy simulations to assess enzymatic reaction mechanism. Received: 1 November 2001 / Accepted: 6 September 2002 / Published online: 19 February 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: Lakshmi S. Devi-Kesavan e-mail: kesavan@chem.umn.edu Acknowledgments. The work is partially supported by the NIH and the NSF.     

Predicting thermal conductivity of liquid suspensions of nanoparticles (nanofluids) based on rheology

A methodology is proposed for predicting the effective thermal conductivity of dilute suspensions of nanoparticles (nanofluids) based on rheology.The methodology uses the rheological data to infer microstructures of nanoparticles quantitatively,which is then incorporated into the conventional Hamilton-Crosser equation to predict the effective thermal conductivity of nanofluids.The methodology is experimentally validated using four types of nanofluids made of titania nanoparticles and titanate nanotubes dispersed in water and ethylene glycol.And the modified Hamilton-Crosser equation successfully predicted the effective thermal conductivity of the nanofluids.     

Nanoporous metal organic framework materials for hydrogen storage

Hydrogen is expected to play an important role in future transportation as a promising alternative clean energy source to carbon-based fuels.One of the key challenges to commercialize hydrogen energy is to develop appropriate onboard hydrogen storage systems,capable of charging and discharging large quantities of hydrogen with fast enough kinetics to meet commercial requirements.Metal organic framework (MOF) is a new type of inorganic and organic hybrid nanoporous particulate materials.Its diverse networks can enhance hydrogen storage through tuning the structure and property of MOFs.The MOF materials so far developed adsorb hydrogen through weak disperston interactions,which allow significant quantity of hydrogen to be stored at cryogenic temperatures with fast kinetics.Novel MOFs are being developed to strengthen the interactions between hydrogen and MOFs in order to store hydrogen under ambient conditions.This review surveys the development of such candidate materials,their performance and future research needs.     

Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K

Molecular dynamics simulations using a combined QM/MM potential have been performed to study the catalytic mechanism of human cathepsin K, a member of the papain family of cysteine proteases. We have determined the two-dimensional free energy surfaces of both acylation and deacylation steps to characterize the reaction mechanism. These free energy profiles show that the acylation step is rate limiting with a barrier height of 19.8 kcal/mol in human cathepsin K and of 29.3 kcal/mol in aqueous solution. The free energy of activation for the deacylation step is 16.7 kcal/mol in cathepsin K and 17.8 kcal/mol in aqueous solution. The reduction of free energy barrier is achieved by stabilization of the oxyanion in the transition state. Interestingly, although the "oxyanion hole" has been formed in the Michaelis complex, the amide units do not donate hydrogen bonds directly to the carbonyl oxygen of the substrate, but they stabilize the thiolate anion nucleophile. Hydrogen-bonding interactions are induced as the substrate amide group approaches the nucleophile, moving more than 2 A and placing the oxyanion in contact with Gln19 and the backbone amide of Cys25. The hydrolysis of peptide substrate shares a common mechanism both for the catalyzed reaction in human cathepsin K and for the uncatalyzed reaction in water. Overall, the nucleophilic attack by Cys25 thiolate and the proton-transfer reaction from His162 to the amide nitrogen are highly coupled, whereas a tetrahedral intermediate is formed along the nucleophilic reaction pathway.