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.     

Recent progress in nanomaterial-enhanced fluorescence polarization/anisotropy sensors

In this review, we summarize the number of scientific publications in the field of FP/FA sensor in recent five years, and introduce the recent progress of FP/FA sensor based on nanomaterial. The various analytical applications of FP/FA sensor based on nanomaterial are discussed. We also provide perspectives on the current challenges and future prospects in the promising field.     

Comparative study of three immunoassays based on monoclonal antibodies for detection of the pesticide parathion-methyl in real samples

Three immunoassay systems: indirect, direct competitive enzyme-linked immunosorbent assay (IC-ELISA and DC-ELISA), fluorescence polarization immunoassay (FPIA) based on monoclonal antibodies for the detection of parathion-methyl (PM) were developed and optimized. Several PM derivatives (haptens) were conjugated to proteins and fluoresceinthiocarbamyl ethylenediamine (EDF) to obtain immunogens and competitors. The influence of immunogen and competitor structures on the assay performance was investigated. IC-ELISA was the most sensitive of all techniques developed, with a detection limit of 0.08 ng ml⁻¹, but assay time was the longest (3.5 h per 96-well microtitre plate). DC-ELISA was easier to perform and quicker (1.5 h per 96-well microtitre plate) but less sensitive than IC-ELISA (detection limit was 0.5 ng ml⁻¹). FPIA was the fastest and simplest (7 min per 10 samples) but the least sensitive (detection limit was 15 ng ml⁻¹) technique. The methods were characterized by high specificity and reproducibility. The cross-reactivity for parathion-ethyl was around 30-40% for IC-ELISA and FPIA, but significantly higher (125%) for DC-ELISA. The immunoassays were applied to the analysis of PM residues in different food and environmental matrices. Methanol extracts of vegetable, fruit and soil samples were used for the analysis. Recoveries for most spiked samples averaged between 85 and 110%. The methods developed can be used for screening of food and environmental samples for PM residues without complicated clean-up.     

Neue Kupferkomplexe mit Phosphaalkenliganden. Molekülstruktur von [Cu{P(Mes*)C(NMe2)2}2]BF4 (Mes* = 2,4,6‐tBu3C6H2)

New Copper Complexes Containing Phosphaalkene Ligands. Molecular Structure of [Cu{P(Mes*)C(NMe₂)₂}₂]BF₄ (Mes* = 2,4,6‐tBu₃C₆H₂) Reaction of equimolar amounts of the inversely polarized phosphaalkene tBuP=C(NMe₂)₂ ( 1a ) and copper(I) bromide or copper(I) iodide, respectively, affords complexes [Cu₃X₃{μ‐P(tBu)C(NMe₂)₂}₃] ( 2 ) (X =Br) and ( 3 ) (X = I) as the formal result of the cyclotrimerization of a 1:1‐adduct. Treatment of 1a with [Cu(L)Cl] (L = PiPr₃; SbiPr₃) leads to the formation of compounds [CuCl(L){P(tBu)C(NMe₂)₂}] ( 4a ) (L = PiPr₃) and ( 4b ) (L = SbiPr₃), respectively. Reaction of [(MeCN)₄Cu]BF₄ with two equivalents of PhP=C(NMe₂)₂ ( 1b ) yields complex [Cu{P(Ph)C(NMe₂)₂}₂]BF₄ ( 5b ). Similarly, compounds [Cu{P(Aryl)C(NMe₂)₂}₂]BF₄ ( 5c (Aryl = Mes and 5d (Aryl = Mes*)) are obtained from ArylP=C(NMe₂)₂ ( 1c : Aryl = Mes; 1d : Mes*) and [(MeCN)₄Cu]BF₄ in the presence of SbiPr₃. Complexes 2 , 3 , 4a , 4b , and 5b‐5d are characterized by means of elemental analyses and spectroscopy (¹H‐, ¹³C{¹H}‐, ³¹P{¹H}‐NMR). The molecular structure of 5d is determined by X‐ray diffraction analysis.     

Effect of the Electrode Potential on the Oxygen Reaction Rate in the Electrode System O2, Au/La0.88Sr0.12Ga0.82Mg0.18O2.85

The polarization dependences of a porous gold electrode in contact with a solid electrolyte of the composition La_0.88Sr_0.12Ga_0.82Mg_0.18O_2.85 are studied at 600–800°C and oxygen pressures of 2 × 10⁻²-1 atm. It is shown that the rate of cathodic reduction of oxygen out of the gas phase depends on the preliminary treatment of the sample. The activation energy is equal to 110–135 kJ mol⁻¹ at a low polarization. After increasing the polarization, the activation energy for the cathodic reduction of oxygen equals 75–85 kJ mol⁻¹ and depends on the oxygen pressure as a power function with a power index of 1/4. The rate of the anodic evolution of oxygen is dependent neither on the preliminary treatment of the sample nor on the oxygen pressure in the gas phase and the polarization curve has a characteristic segment, which corresponds to a limiting overvoltage.__________Translated from Elektrokhimiya, Vol. 41, No. 8, 2005, pp. 954–962.Original Russian Text Copyright © 2005 by Shkerin, Sokolova, Beresnev.     

电化学石英晶体微天平研究界面电场对DNA杂交的影响

采用电化学石英晶体微天平, 现场监测不同界面电场下完全匹配的靶标DNA和不完全匹配的靶标DNA分别与寡聚核苷酸探针分子杂交的过程. 结果表明, 电极表面荷正电时DNA表观杂交效率比电极表面荷负电时高, 但假阳性比较显著; 而电极表面荷负电时能有效地抑制错配杂交. 探讨了引入界面电场后探针分子取向和微观作用力对DNA杂交的影响.     

Investigation on corrosion inhibition and adsorption mechanism of azomethine derivatives at mild steel/0.5 ​M ​H2SO4 solution interface: Gravimetric,electrochemical, SEM and EDX studies

The inhibition performance of five azomethine derivatives such as: 1-(4-Methyloxy phenylimino)-1-(phenylhydrazono)-propan-2-one (SB₁), 1-(4-Methylphenylimino)-1-(phenylhydrazono) propan-2-one (SB₂), 1-(phenylimino)-1(phenylhydrazono)-propan-2-one (SB₃), 1-(4-Bromo phenylimino)-1(phenylhydrazono)-propan-2-one (SB₄) and 1-(4-Chlorophenylimino)-1(phenylhydrazono) -propan-2-on (SB₅) as corrosion inhibitors for mild steel in sulfuric acid 0.5 ?M were investigated using different methods. All experimental results demonstrate that these compounds are eficients inhibitors. The inhibition efficiencies ($IE$) increase with inhibitors concentration. At 7.5 $\times$ 10^?5 ?M, the $IE$ was 97.27%, 96.31%, 94.23%, 93.19 and 91.64% for SB₁, SB₂, SB₃, SB₄ and SB₅, respectively. The potentiodynamic polarization results indicated that all the studied inhibitors act as mixed type. The adsorption process on mild steel surface obeyed Langmuir isotherm. The associated activation parameters and thermodynamic have been calculated and discussed. The adsorbed film formed on the metal surface was characterized by SEM and EDX.     

A Procedure for Transforming Impedance Spectra for the Determination of Mechanism of Electrochemical Reactions

Transformation of impedance spectra into relaxation time spectra (RTS) is used for determining contributions of individual processes of the oxygen electroreduction reaction (OER) to the polarization resistance of the electrochemical cell. The transformation technique involves the solution of the convolution equation found with the aid of a modified Van Cittert iteration algorithm checked on model impedance spectra. The technique, when used to analyze impedance spectra of electrochemical cells air|Pt|YSZ|YSZ + Pt|air, shows that the conversion of a globular structure of the YSZ + Pt cermet layer to a columnar one is accompanied by a change of peak amplitudes in RTS. The revealed RTS dynamics when heated to 750°C is compared with peculiarities of individual processes in OER.     

Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations

This study examines the contribution of electrostatic and polarization to the interaction energy in a variety of molecular complexes. The results obtained from the Kitaura-Morokuma (KM) energy decomposition analysis at the HF/6-31G(d) level indicate that, for intermolecular distances around the equilibrium geometries, the polarization energy can be determined as the addition of the polarization energies of interacting blocks, as the mixed polarization term is typically negligible. Comparison of KM and QM/MM results shows that the electrostatic energy determined in the KM method is underestimated (in absolute value) by QM/MM methods. The reason of such underestimation can be attributed to the simplified representation of treating the interaction between overlapping charge distribution by the interaction of a QM molecule with a set of point charges. Nevertheless, the polarization energies calculated by KM and QM/MM methods are in close agreement. Finally, a consistent, automated strategy to derive charge distributions that include implicitly polarization effects in pairwise, additive force fields is presented. The strategy relies in the simultaneous fitting of electrostatic and polarization energies computed by placing a suitable perturbing particle at selected points around the molecule. The suitability of these charges to describe molecular interactions is discussed.