Reaction mechanism of the mandelate anion racemization catalyzed by mandelate racemase enzyme: a QM/MM molecular dynamics free energy study

The present work studies the reaction mechanism of the racemization of mandelate substrate by mandelate racemase enzyme. The reaction has some intriguing aspects such as the deprotonation of a nonacid hydrogen and the achievement of the pseudosymmetry necessary to obtain the racemic mixture. We will make use of a QM/MM potential energy surface to compute the free energy profiles associated with the reaction. The most favorable reaction mechanism consists of two proton transfers and the configuration inversion of the stereogenic carbon taking place in a concerted manner. We have also designed a suitable reaction coordinate to compute the free energy profiles for this rather complicated reaction. In addition, analysis of the electrostatic effects and bond distances along the reaction will explain how the enzyme accomplishes the catalysis. Finally, the enzymatic reaction will be compared to a model of the uncatalyzed reaction and the catalytic effect of mandelate racemase will be evaluated.     

Reaction mechanism of soluble epoxide hydrolase: insights from molecular dynamics simulations

Molecular dynamics simulations have been performed to gain insights into the catalytic mechanism of the hydrolysis of epoxides to vicinal diols by soluble epoxide hydrolase (sEH). The binding of a substrate, 1S,2S-trans-methylstyrene oxide, was studied in two conformations in the active site of the enzyme. It was found that only one is likely to be found in the active enzyme. In the preferred conformation the phenyl group of the substrate is pi-sandwiched between two aromatic residues, Tyr381 and His523, whereas the other conformation is pi-stacked with only one aromatic residue, Trp334. Two simulations were carried out to 1 ns for each conformation to evaluate the protonation state of active site residue His523. It was found that a protonated histidine is essential for keeping the active site from being disrupted. Long time scale, 4 ns, molecular dynamics simulation was done for the structure with the most likely combination of binding conformation and protonation state of His523. Near Attack Conformers (NACs) are present 5.3% of the time and nucleophilic attack on either epoxide carbon atom, approximately 75% on C(1) and approximately 25% on C(2), is found. A maximum of one hydrogen bond between the epoxide oxygen and either of the active site tyrosines, Tyr465 and Tyr381, is present, in agreement with experimental mutagenesis results that reveal a slight loss in activity if one tyrosine is mutated and essential loss of all activity upon double mutation of the two tyrosines in question. It was found that a hydrogen bond from Tyr465 to the substrate oxygen is essential for controlling the regioselectivity of the reaction. Furthermore, a relationship between the presence of this hydrogen bond and the separation of reactants was found. Two groups of amino acid segments were identified each as moving collectively. Furthermore, an overall anti-correlation was found between the movements of these two individually collectively moving groups, made up by parts of the cap-region, including the two tyrosines, and the site of the catalytic triad, respectively. This overall anti-correlated collective domain motion is, perhaps, involved in the conversion of E.NAC to E.TS.     

Probing the neutral graphene-ionic liquid interface: insights from molecular dynamics simulations

We study basic mechanisms of the interfacial layer formation at the neutral graphite monolayer (graphene)-ionic liquid (1,3-dimethylimidazolium chloride, [dmim][Cl]) interface by fully atomistic molecular dynamics simulations. We probe the interface area by a spherical probe varying the charge (-1e, 0, +1e) as well as the size of the probe (diameter 0.50 nm and 0.38 nm). The molecular modelling results suggest that: there is a significant enrichment of ionic liquid cations at the surface. This cationic layer attracts Cl(-) anions that leads to the formation of several distinct ionic liquid layers at the surface. There is strong asymmetry in cationic/anionic probe interactions with the graphene wall due to the preferential adsorption of the ionic liquid cations at the graphene surface. The high density of ionic liquid cations at the interface adds an additional high energy barrier for the cationic probe to come to the wall compared to the anionic probe. Qualitatively the results from probes with diameter 0.50 nm and 0.38 nm are similar although the smaller probe can approach closer to the wall. We discuss the simulation results in light of available experimental data on the interfacial structure in ionic liquids.     

A detailed reaction mechanism for hexamethyldisiloxane combustion via experiments and ReaxFF molecular dynamics simulations

Hexamethyldisiloxane (HMDSO) is one of the main impurities in the syngas produced from sewage and landfill plants. In order to utilize this syngas or control the characteristics of the generated silica particles, it is crucial to understand the chemical kinetics of HMDSO combustion. This study investigated the process of HMDSO combustion using synchrotron radiation mass spectrometry (SRMS), gas chromatography (GC), and ReaxFF molecular dynamics simulations. First, the force field used for ReaxFF simulation was validated by comparing the energies of different bond lengths, bond angles, and dihedral angles with the ones from DFT calculations. Good agreements were found. Then, ReaxFF simulations of HMDSO combustion with this force field were conducted under various conditions, which include different equivalence ratios (0.67, 1.0, and 1.5) and temperatures ranging from 2000 to 3500 K. The oxidation characteristics of HMDSO were analyzed, including the evolution of gas products and particle formation. Finally, based on the results from experiments and ReaxFF simulations, the reaction pathways, reaction lists, and reaction kinetics data during HMDSO combustion were obtained. A detailed reaction mechanism was proposed and validated by applying it in modeling the H₂/HMDSO/O₂ combustion systems. The temperature and part of the gas products such as CO and CO₂ as well as SiO could be well predicted.     

Insights into the acylation mechanism of class A beta-lactamases from molecular dynamics simulations of the TEM-1 enzyme complexed with benzylpenicillin

Herein, we present results from molecular dynamics MD simulations ( approximately 1 ns) of the TEM-1 beta-lactamase in aqueous solution. Both the free form of the enzyme and its complex with benzylpenicillin were studied. During the simulation of the free enzyme, the conformation of the Omega loop and the interresidue contacts defining the complex H-bond network in the active site were quite stable. Most interestingly, the water molecule connecting Glu166 and Ser70 does not exchange with bulk solvent, emphasizing its structural and catalytic relevance. In the presence of the substrate, Ser130, Ser235, and Arg244 directly interact with the beta-lactam carboxylate via H-bonds, whereas the Lys234 ammonium group has only an electrostatic influence. These interactions together with other specific contacts result in a very short distance ( approximately 3 A) between the attacking hydroxyl group of Ser70 and the beta-lactam ring carbonyl group, which is a favorable orientation for nucleophilic attack. Our simulations also gave insight into the possible pathways for proton abstraction from the Ser70 hydroxyl group. We propose that either the Glu166 carboxylate-Wat1 or the substrate carboxylate-Ser130 moieties could abstract a proton from the nucleophilic Ser70.     

The fragmentation-recombination mechanism of the enzyme glutamate mutase studied by QM/MM simulations

The radical mechanism of the conversion of glutamate to methylaspartate catalyzed by glutamate mutase is studied with quantum mechanical/molecular mechanical (QM/MM) simulations based on density functional theory (DFT/MM). The hydrogen transfer between the substrate and the cofactor is found to be rate limiting with a barrier of 101.1 kJ mol(-1). A careful comparison to the uncatalyzed reaction in water is performed. The protein influences the reaction predominantly electrostatically and to a lesser degree sterically. Our calculations shed light on the atomistic details of the reaction mechanism. The well-known arginine claw and Glu 171 ( Clostridium cochlearium notation) are found to have the strongest influence on the reaction. However, a catalytic role of Glu 214, Lys 322, Gln 147, Glu 330, Lys 326, and Met 294 is found as well. The arginine claw keeps the intermediates in place and is probably responsible for the enantioselectivity. Glu 171 temporarily accepts a proton from the glutamyl radical intermediate and donates it back at the end of the reaction. We relate our results to experimental data when available. Our simulations lead to further understanding of how glutamate mutase catalyzes the carbon skeleton rearrangement of glutamate.     

Unfolding the conformational behavior of peptide dendrimers: insights from molecular dynamics simulations

We present here the first comprehensive structural characterization of peptide dendrimers using molecular simulation methods. Multiple long molecular dynamics simulations are used to extensively sample the conformational preferences of five third-generation peptide dendrimers, including some known to bind aquacobalamine. We start by analyzing the compactness of the conformations thus sampled using their radius of gyration profiles. A more detailed analysis is then performed using dissimilarity measures, principal coordinate analysis, and free energy landscapes, with the aim of identifying groups of similar conformations. The results point to a high conformational flexibility of these molecules, with no clear "folded state", although two markedly distinct behaviors were found: one of the dendrimers displayed mostly compact conformations clustered into distinct basins (rough landscape), while the remaining dendrimers displayed mainly noncompact conformations with no significant clustering (downhill landscape). This study brings new insight into the conformational behavior of peptide dendrimers and may provide better routes for their functional design. In particular, we propose a yet unsynthesized peptide dendrimer that might exhibit enhanced ability to coordinate aquocobalamin.     

Structure of liquid formic acid investigated by first principle and classical molecular dynamics simulations

The structure of liquid formic acid has been investigated by Car-Parrinello and classical molecular dynamics simulations, focusing on the characterization of the H-bond network and on the mutual arrangement of pairs of bonded molecules. In agreement with previous computational studies, two levels of H-bonded structures have been found. Small clusters, characterized by O-H...O bonds, are held together by weak C-H...O bonds to form large branched structures. From the ab initio simulation we infer the importance of cyclic H-bond dimer configurations, typical of the gas phase. Most of these dimer structures are however found to be embedded into H-bonded chains. When only O-H...O bonds are taken into account, linear H-bond chains are detected as basic structures of the liquid. More branched structures occur when C-H...O bonds are also considered. Regarding the arrangement of molecular pairs, we observed that O-H...O bonds favor the occurrence of configurations with parallel molecular planes, whereas no preferential orientation is observed for molecules forming C-H...O bonds.     

Kinetic insights into the role of the solvent in the polymorphism of 5-fluorouracil from molecular dynamics simulations

We investigate the fundamental factors controlling polymorphism in 5-fluorouracil by performing molecular dynamics simulations of solutions of the compound in water, nitromethane, and wet nitromethane. Analysis of the effect of solvent on the initial aggregation of 5-fluorouracil molecules shows that the strong binding of water to the 5-fluorouracil molecule hinders the formation of the doubly hydrogen-bonded dimer and, by default, promotes close hydrophobic F...F interactions that are a feature of the unusual (Z' = 4) structure of form I. In contrast, doubly hydrogen-bonded dimers are observed to form readily in solution in dry nitromethane, consistent with the crystallization of the doubly hydrogen-bonded ribbon structure of form II from this solvent. When nitromethane is doped with water, the water forms hydrogen bonds to the solute, interfering with the formation of the doubly hydrogen-bonded dimers, which is consistent with the crystallization of form I from this hygroscopic solvent when it is not dried. Overall, the molecular dynamics simulations provide an atomistic picture of how solvent-solute interactions can significantly affect the initial association of 5-fluorouracil molecules to the extent that they determine the polymorphic outcome of the crystallization.     

Wax inhibition by comb-like polymers: support of the incorporation-perturbation mechanism from molecular dynamics simulations

Deposition of wax on a cold surface is a serious problem in oil production. Progress in developing more effective wax inhibitors has been impeded by the lack of an established mechanism connecting the molecular structure to inhibitor efficiency. Some comb-like polymers having long alkyl side chains are known to decrease the rate of wax formation. Among several possible mechanisms, we investigate here the incorporation-perturbation mechanism. According to this mechanism, the inhibitor molecules in oil are preferentially partitioned (incorporation) toward the wax-rich (amorphous) wax deposits (soft wax), which then serves as a perturbation to slow down the ordering transition of soft amorphous wax into more stable but problematic hard wax crystals. Indeed, molecular dynamics simulations on an effective inhibitor molecule in both the oil phase and in the amorphous wax phase support the idea that the oil-to-wax partition of the inhibitor is energetically favorable. With the inhibitor molecule embedded, the structure of wax crystal is disturbed, significantly decreasing the order and significantly lowering the cohesive energy density relative to that of the pure wax crystal, supporting the slower transition from soft wax to hard wax. Thus, in the presence of an effective wax inhibitor, crystallization (formation of hard wax) is slowed dramatically, so that there is time to flush out the soft wax with a high-pressure flow inside the pipeline. This suggests design principles for developing improved wax inhibitors.     

Theoretical insights into enantioselective catalysis: the mechanism of the Kharasch-Sosnovsky reaction

The mechanism of the Kharasch-Sosnovsky reaction has been investigated using B3 LYP/6-31G* calculations on a chiral reaction model [cyclohexene+tert-butyl perbenzoate-->cyclohex-2-enyl benzoate+tert-butyl alcohol, catalyzed by a chiral bisoxazoline-copper(I) complex]. Although two previous reaction mechanisms have been considered, the results are consistent with a new mechanistic pathway. This path involves ligand exchange between the catalyst-cyclohexene complex with tert-butyl perbenzoate to give a catalyst-perester complex, which undergoes an (either one- or two-step) oxidative addition reaction to yield a copper(III) complex. The limiting step of the Kharasch-Sosnovsky reaction consists of an intramolecular step involving the abstraction of an allylic hydrogen from cyclohexene [which is pi-bound to the copper(III) complex]. The resulting allyl-copper(III) complex (subsequent to the loss of tert-butanol) can undergo a haptotropic rearrangement by means of an eta1-allyl/eta3-allyl equilibrium, leading to scrambling between vinylic and allylic positions when an isotopically labeled substrate is used. The allyl-copper(III) ion undergoes a stereospecific reductive elimination involving the pi-bond migration to yield a reaction product-catalyst complex, which can regenerate the alkene-copper(I) complex by ligand exchange. The proposed reaction mechanism is consistent with all known experimental results (including enantioselectivity data).     

Insights into the phosphoryl-transfer mechanism of cAMP-dependent protein kinase from quantum chemical calculations and molecular dynamics simulations

To investigate the molecular details of the phosphoryl-transfer mechanism catalyzed by cAMP-dependent protein kinase, we performed quantum mechanical (QM) calculations on a cluster model of the active site and molecular dynamics (MD) simulations of a ternary complex of the protein with Mg(2)ATP and a 20-residue peptide substrate. Overall, our theoretical results confirm the participation of the conserved aspartic acid, Asp(166), as an acid/base catalyst in the reaction mechanism catalyzed by protein kinases. The MD simulation shows that the contact between the nucleophilic serine side chain and the carboxylate group of Asp(166) is short and dynamically stable, whereas the QM study indicates that an Asp(166)-assisted pathway is structurally and energetically feasible and is in agreement with previous experimental results.     

A proficient enzyme: insights on the mechanism of orotidine monophosphate decarboxylase from computer simulations

Decarboxylation of orotidine 5'-monophosphate (Omp) to uridine 5'-monophosphate by orotidine 5'-monophosphate decarboxylase (ODCase) is currently the object of vivid debate. Here, we clarify its enzymatic activity with long time scale classical molecular dynamics and hybrid ab initio Car-Parrinello/molecular mechanics simulations. The lack of structural (experimental) information on the ground state of ODCase/Omp complex is overcome by a careful construction of the model and the analysis of three different strains of the enzyme. We find that the ODCase/substrate complex is characterized by a very stable charged network Omp-Lys-Asp-Lys-Asp, which is incompatible with the previously proposed direct decarboxylation driven by a ground-state destabilization. A direct decarboxylation induced by a transition-state electrostatic stabilization is consistent with our findings. The calculated activation free energy for the direct decarboxylation with the formation of a C6 carboanionic intermediate yields an overall rate enhancement by the enzyme (k(cat)/k(wat) = 3.5 x 10(16)) in agreement with experiments (k(cat)/k(wat) = 1.7 x 10(17)). The decarboxylation is accompanied by the movement of a fully conserved lysine residue toward the developing negative charge at the C6 position.     

Dynamic mechanism for the autophosphorylation of CheA histidine kinase: molecular dynamics simulations

The two-component system (TCS) is an important signal transduction component for most bacteria. This signaling pathway is mediated by histidine kinases via autophosphorylation between P1 and P4 domains. Taking chemotaxis protein CheA as a model of TCS, the autophosphorylation mechanism of the TCS histidine kinases has been investigated in this study by using a computational approach integrated homology modeling, ligand-protein docking, protein-protein docking, and molecular dynamics (MD) simulations. Four nanosecond-scale MD simulations were performed on the free P4 domain, P4-ATP, P4-TNPATP, and P1-P4-ATP complexes, respectively. Upon its binding to the binding pocket of P4 with a folded conformation, ATP gradually extends to an open state with help from a water molecule. Meanwhile, ATP forms two hydrogen bonds with His413 and Lys494 at this state. Because of the lower energy of the folded conformations, ATP shrinks back to its folded conformations, leading to the rupture of the hydrogen bond between ATP and Lys494. Consequently, Lys494 moves away from the pocket entrance, resulting in an open of the ATP lid of P4. It is the open state of P4 that can bind tightly to P1, where the His45 of P1 occupies a favorable position for its autophosphorylation from ATP. This indicates that ATP is not only a phosphoryl group donor but also an activator for CheA phosphorylation. Accordingly, a mechanism of the autophosphorylation of CheA is proposed as that the ATP conformational switch triggers the opening of the ATP lid of P4, leading to P1 binding tightly, and subsequently autophosphorylation from ATP to P1.     

Atomistic insights on the LCST behavior of PMEO2MA in water by molecular dynamics simulations

Fully atomistic molecular dynamics simulations of poly(2‐[2‐methoxyethoxy]ethyl methacrylate) (PMEO₂MA) in water at temperatures below and above its lower critical solution temperature (LCST) were performed to improve the understanding of its LCST behavior. Atomic trajectories were used to calculate various structural and dynamic properties. Simulation results show that PMEO₂MA undergo a distinct coil‐to‐globule transition above LCST. Detailed analyses of the number of first hydration shell water molecules around various atomic regions are revealed that the water solubility of PMEO₂MA below LCST is mainly provided by the hydrophobic hydration around the side chain carbon atoms. This is achieved by the cage‐like water network formations which are disrupted when the temperature is increased above LCST, accompanied by significant amount of water molecule release and local water‐ordering reduction, which leads to the LCST phase transition. Furthermore, other analyses such as the number of hydrogen bonds and hydrogen bond lifetimes suggest that intermolecular hydrogen bondings between polymer and water molecules have little effect on the phase transition. Our results will contribute to a better understanding on the LCST phase transition of oligo(ethylene glycol) methyl ether methacrylate (OEGMA)‐based homopolymers at atomistic level that will be useful when designing homo‐ and co‐polymers of OEGMAs with desired properties. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 429–441     

New insights into the mechanism of asymmetric hydrogenation catalysed by monophosphonite-rhodium complexes

The solvento complex [Rh(L)2(S)2]+ where L=tBuP(R-binaphthoxo) is shown to be in equilibrium with an eta-arene dirhodium complex and only weak, monodentate binding of alkenes is observed; in addition, an intermediate Rh alkyl hydride complex containing two coordinated monophosphonites is unambiguously characterised by NMR.     

New insights into the mechanism of the Schiff base hydrolysis catalyzed by type I dehydroquinate dehydratase from S. enterica: a theoretical study

The reaction pathway of Schiff base hydrolysis catalyzed by type I dehydroquinate dehydratase (DHQD) from S. enterica has been studied by performing molecular dynamics (MD) simulations and density functional theory (DFT) calculations and the corresponding potential energy profile has also been identified. On the basis of the results, the catalytic hydrolysis process for the wild-type enzyme consists of three major reaction steps, including nucleophilic attack on the carbon atom involved in the carbon-nitrogen double bond of the Schiff base intermediate by a water molecule, deprotonation of the His143 residue, and dissociation between the product and the Lys170 residue of the enzyme. The remarkable difference between this and the previously proposed reaction mechanism is that the second step here, absent in the previously proposed reaction mechanism, plays an important role in facilitating the reaction through a key proton transfer by the His143 residue, resulting in a lower energy barrier. Comparison with our recently reported results on the Schiff base formation and dehydration processes clearly shows that the Schiff base hydrolysis is rate-determining in the overall reaction catalyzed by type I DHQD, consistent with the experimental prediction, and the calculated energy barrier of ～16.0 kcal mol(-1) is in good agreement with the experimentally derived activation free energy of ～14.3 kcal mol(-1). When the imidazole group of His143 residue is missing, the Schiff base hydrolysis is initiated by a hydroxide ion in the solution, rather than a water molecule, and both the reaction mechanism and the kinetics of Schiff base hydrolysis have been remarkably changed, clearly elucidating the catalytic role of the His143 residue in the reaction. The new mechanistic insights obtained here will be valuable for the rational design of high-activity inhibitors of type I DHQD as non-toxic antimicrobials, anti-fungals, and herbicides.     

Structure and vibrational spectroscopy of salt water/air interfaces: predictions from classical molecular dynamics simulations

We report the sum frequency generation (SFG) spectra of aqueous sodium iodide interfaces computed with the methodology outlined by Morita and Hynes (J. Phys. Chem. B 2002, 106, 673), which is based on molecular dynamics simulations. The calculated spectra are in qualitative agreement with experiment. Our simulations show that the addition of sodium iodide to water leads to an increase in SFG intensity in the region of 3400 cm(-1), which is correlated with an increase in ordering of hydrogen-bonded water molecules. Depth-resolved orientational distribution functions suggest that the ion double layer orders water molecules that are approximately one water layer below the Gibbs dividing surface. We attribute the increase in SFG intensity to these ordered subsurface water molecules that are present in the aqueous sodium iodide/air interfaces but are absent in the neat water/air interface.     

New insights into the reaction mechanism and the rate-determining step of n-butane hydroisomerisation over reduced MoO3 catalysts

The comparison of the proportions of the minor products formed during the hydroisomerisation of n-butane over reduced MoO3 with thermodynamic data demonstrates that a bifunctional mechanism operates and that the rate-determining step is the isomerisation of the linear butene intermediates to iso-butene.