Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis

QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies.     

Three‐dimensional wave impact on a rigid structure using smoothed particle hydrodynamics

Navier–Stokes computations of a wave–structure interaction are performed with the aim of assessing the potential of smoothed particle hydrodynamics to accurately estimate impact loading time history. A three‐dimensional dam‐break flow with a rectangular column located downstream is considered. The net force and impulse exerted on the column is monitored throughout the simulation with the results correlating well with existing experimental data. Initial and boundary conditions and numerical parameters are varied and their effect on the column load investigated. The column load is found to be most sensitive to the choice of boundary treatment. Copyright © 2011 John Wiley & Sons, Ltd.     

Effect of annealing on hydrophobic stability of plasma deposited fluoropolymer coatings

Fluorinated amorphous carbon (a-C:F) films e.g. plasma polymerised perfluorocyclobutane have long attracted much consideration due to their low surface energy, hydrophobicity, low refractive index, good electrical and thermal insulation and good thermal stability. Although a-C:F films have many advantages, hydrophobic stability over time in air and water remains a major concern. In this study, the effects of weathering conditions on the hydrophobicity of fluorocarbon films prepared from perfluorocyclobutane precursors were examined using water contact angle measurements. It was found that the high initial hydrophobicity of as-deposited films degrades rapidly in humid conditions. The stability of hydrophobicity can be significantly improved when a suitable treatment such as annealing is employed. The mechanism of weathering was explained with the help of a number of morphological and chemical characterisation techniques such as Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), Fourier Transform Infrared Spectroscopy (FTIR) and X-ray Photoelectron Spectroscopy (XPS). In particular, XPS results demonstrated that a reduction in the overall amount of -CF₃ radical, oxygenation of surface fluorides and the formation of an overlayer all influence the degradation of fluorocarbon in aquatic environment.     

Structural Characterization of Some Acylisoxazolone Extractants

From IR, UV, ³¹P, ¹H, and ¹³C NMR spectroscopic data, it is shown that the three 3-phenyl-4-acyl-isoxazol-5-ones, HPXI (HPBI, HPTI, and HPtbBI with acyl-, benzoyl-, toluoyl-, and para-(tert-butyl)benzoyl-, respectively), promising extractants of actinides, appear under the same major tautomeric forms, both in the solid and in solutions in various solvents: the diketo-enamine form in methanol, a -ketoenolic form in the solid, and in chloroform, benzene, and toluene. The radiocrystallographic structures of HPTI and HPtbBI have been determined. They appear as 3-phenyl-4-(-hydroxybenzylidene)isoxazol-5-ones, forming intramolecular chelates through H-bonds. -Aryl interactions might influence the relative positions of the -ketoenolic oxygen atoms and, hence, the bite angle and the cone angle of these ligands. Spectroscopic data give evidence of strong TOPO–HPXI interactions (TOPO: tri-n-octylphosphine oxide) in toluene, of the same order of magnitude for the three acylisoxazolones, in the order: HPBI > HPTI > HPtbBI.     

Expression of the prohelicity of bis-cyclomanganated 2,3-diphenylquinoxaline through reactions with diaryldiazomethanes

The reactions of bis-cyclomanganated 2,3-diphenylquinoxaline with diazodiphenylmethane and 9-diazofluorene allowed the formation of a new oligomeric and dinuclear manganospiralene and the ready preparation of a pentacyclic helix comprising two (eta 5-fluorenyl)Mn(CO)3 fragments, whose helicity can be locked upon one-dimensional linear coordination to silver cation.     

Adventitious formation of a new oxopentadienyl Mn(I) tricarbonyl complex: Structural study and bonding investigation of (η-CH2C(Fc)CHC(Fc)O)Mn(CO)3

A Mn(I) tricarbonyl complex of a 1,3-diferrocenyl-1-oxopentadienyl ligand was synthesised adventitiously by what seems to be an in-situ aldol-like condensation of two acetylferrocene units promoted by benzyl-Mn(CO)₅. X-ray structural analysis of this unexpected product confirms the η⁵ coordination of the 1,3-diferrocenyl-1-oxopentadienyl ligand to the Mn(CO)₃ moiety. The nature of the metal-ligand bonding relationship was studied by theoretical calculations; it outlines the charge unbalance (polarisation) at the oxopentadienyl moiety as well as the lack of ketone character of the latter Mn-bound ligand.     

Mechanistic aspects of biological redox reactions involving NADH 2: A combined semiempirical and ab initio study of hydride-ion transfer between the NADH analogue, 1-methyl-dihydronicotinamide,and folate and dihydrofolate analogue substrates of dihydrofolate reductase

As part of a study of factors controlling biological redox reactions of nicotinamide cofactors [nicotinamide adenine dinucleotide (phosphate) NAD(P)H], we have investigated the effect on a model reaction of the conformational state (cis or trans) of the carboxamide side chain, using quantum chemical methods. The reaction is that for the enzyme dihydrofolate reductase between the NADPH analogue, 1-methyl-dihydronicotinamide, and the protonated forms of the folate and dihydrofolate substrate analogues, pyrazine and dihydropyrazine. Some calculations on pterin and dihydropterin substrate analogues were also carried out in order to gauge the effects of inter-ring coupling. The influence of carboxamide side-chain conformation of nicotinamide on the energetics of the hydride-ion transfer, and on the structures of the transition states and stable intermolecular-interaction complexes, are examined as a function of the orientation of approach of the reactants. These approach geometries include those corresponding to the observed binding of cofactor and either substrate or inhibitor in the enzyme active site. Reactant, product, reactants-complex, and transition-state geometries were optimized at the semiempirical AM1 level, while ab initio SCF/STO-3G and SCF/3-21G single-point calculations were carried out at the AM1 optimized geometries for all species, as well as full geometry optimizations for isolated reactants and products. The results show that reactants-complex and transition-state energies are lower for the trans conformer of dihydronicotinamide than for the cis conformer, due to more favorable H-bonding or electrostatic interactions with the protonated substrate. Also, consideration of the structural parameters, including reaction coordinate bond lengths, ring geometries, and charge distributions, indicate that the trans transition states are more product-like than those for the cis. For the (trans) approaches corresponding to the enzymic orientation for substrate, the intermolecular interaction for the folate reaction lacks the stabilizing influence of the formal H-bond which is present for the dihydrofolate reaction, and consequently the reactants-complex and transition state are less stable.     

Compound prioritization methods increase rates of chemical probe discovery in model organisms

Preselection of compounds that are more likely to induce a phenotype can increase the efficiency and reduce the costs for model organism screening. To identify such molecules, we screened ~81,000 compounds in Saccharomyces cerevisiae and identified ~7500 that inhibit cell growth. Screening these growth-inhibitory molecules across a diverse panel of model organisms resulted in an increased phenotypic hit-rate. These data were used to build a model to predict compounds that inhibit yeast growth. Empirical and in silico application of the model enriched the discovery of bioactive compounds in diverse model organisms. To demonstrate the potential of these molecules as lead chemical probes, we used chemogenomic profiling in yeast and identified specific inhibitors of lanosterol synthase and of stearoyl-CoA 9-desaturase. As community resources, the ~7500 growth-inhibitory molecules have been made commercially available and the computational model and filter used are provided.