A recently characterized cytochrome P450 isozyme GcoA activates lignin components through a selective O-demethylation or alternatively an acetal formation reaction. These are important reactions in biotechnology and, because lignin is readily available; it being the main component in plant cell walls. In this work we present a density functional theory study on a large active site model of GcoA to investigate syringol activation by an iron(IV)-oxo heme cation radical oxidant (Compound I) leading to hemiacetal and acetal products. Several substrate-binding positions were tested and full energy landscapes calculated. The study shows that substrate positioning determines the product distributions. Thus, with the phenol group pointing away from the heme, an O-demethylation is predicted, whereas an initial hydrogen-atom abstraction of the weak phenolic O-H group would trigger a pathway leading to ring-closure to form acetal products. Predictions on how to engineer P450 GcoA to get more selective product distributions are given. 相似文献
The entropy of vaporization at a liquid’s boiling point is well approximated by Trouton’s rule and even more accurately by Hildebrand’s rule. A cell method is used here to calculate the entropy of vaporization for a range of liquids by subtracting the entropy of the gas from that of the liquid. The liquid’s entropy is calculated from the force magnitudes measured in a molecular dynamics simulation based on the harmonic approximation. The change in rotational entropy is not accounted for except in the case of liquid water. The predicted entropies of vaporization agree well with experiment and Trouton’s and Hildebrand’s rules for most liquids and for water except other liquids with hydrogen bonds. This supports the idea that molecular rotation is close to ideal at a liquid’s boiling point if hydrogen bonds are absent; if they are present, then the rotational entropy gain must be included. The method provides a molecular interpretation of those rules by providing an equation in terms of a molecule’s free volume in a liquid which depends on the force magnitudes. Free volumes at each liquid’s boiling point are calculated to be ~1 Å3 for liquids lacking hydrogen bonds, lower at ~0.3 Å3 for those with hydrogen bonds, and they decrease weakly with increasing molecular size. 相似文献
A method to calculate the classical and quantum free energy of a liquid from a computer simulation by using cell theory [J. Chem. Phys. 2007, 126, 064504] is tested for liquid water and ice Ih against experiment as a function of temperature. This fast and efficient method reproduces reasonably well the experimental values of entropy, enthalpy, and free energy of a liquid across the supercooled, stable, and superheated range of temperatures considered. There are small differences between classical and quantum results of water at 298 K, necessitating a small correction term to reproduce water's enthalpy of vaporisation. Only at higher temperatures is entropy underestimated by up to 9 J K(-1) mol(-1) as verified by thermodynamic integration calculations. Satisfactory agreement for ice, however, is only obtained by using the quantum formulation. Even then, at higher temperatures, the entropies exceed experiment by up to 15 J K(-1) mol(-1). Further insight into the quantum nature of water is provided by inspecting the temperature dependence of the frequencies. The harmonic approximation is further supported by the harmonic force and torque distributions and the very similar entropies obtained from the force and torque variances. All these results suggest that the single molecule harmonic oscillator approximation for water, although not exact, provides a rapid, insightful, and useful means to evaluate the thermodynamic properties of water from a computer simulation in a way that can account for the quantization of water's energy levels. 相似文献
Two new methods are assessed for determining the location of hydration sites around proteins from computer simulation. Current methods extract hydration sites from peaks in the water density constructed in the protein frame. However, the dynamic nature of the water molecules, the nearby protein residues, and the protein reference frame as a whole tend to smear out the water density, making it more difficult to resolve sites. Two techniques are introduced to better resolve the water density. The first is to construct the water density from the time-averaged position of each water molecule in the protein frame while the water remains within a given distance of this averaged position. The second technique is to construct the water density from the time-averaged position of each water in the reference frame only of the nearby residues. Criteria for determining hydration sites from the water density are examined. Both techniques are found to significantly improve the detail in the water density and the number of hydration sites detected. 相似文献
A host-guest optical sensor for the determination of aliphatic amines as exemplified by octylamine is proposed. It is based on the reversible fluorescence enhancement of heptakis(2,6-di-O-isobutyl)-β-cyclodextrin(DOB-β-CD) hosting tetraphenylporphyrin (TPP) immobilized in poly(vinyl chloride) (PVC) membrane by aliphatic amine extracted from aqueous phase into membrane phase. The optimum membrane contained 1.15 wt % TPP, 6.15 wt % DOB-β-CD as sensing reagent and other membrane materials. The fluorescence enhancement of the membrane resulted from the formation of a stable three-component complex among DOB-β-CD, TPP, and aliphatic amines. With the optimum conditions described, the fluorescence response of the sensor to octylamine shows a good correlation with the theoretically derived equation in the range 1.0 × 10–6 to 8.0 × 10–4 mol/L. The response characteristics including reversibility, response time, reproducibility and lifetime and selectivity of this optical device are also discussed in detail. This sensor has also been applied for the determination of octylamine in water samples containing interferents with satisfactory recovery. 相似文献
We present studies of novel nanocomposites of BiNi impregnated into the structure of opals as well as inverse opals. Atomic force microscopy and high resolution elemental analyses show
a highly ordered structure and uniform distribution of the BiNi filler in the matrix. These BiNi-based nanocomposites are
found to exhibit distinct ferromagnetic-like ordering with transition temperature of about 675 K. As far as we know there
exists no report in literature on any BiNi compound which is magnetic. 相似文献
A method to calculate the free energy of water from computer simulation is presented. Based on cell theory, it approximates the potential energy surface sampled in the simulation by an anisotropic six-dimensional harmonic potential to model the three hindered translations and three hindered rotations of a single rigid water molecule. The potential is parametrized from the magnitude of the forces and torques measured in the simulation. The entropy of these six harmonic oscillators is calculated and summed with a conformational term to give the total entropy. Combining this with the simulation enthalpy yields the free energy. The six water models examined are TIP3P, SPC, TIP4P, SPC/E, TIP5P, and TIP4P-Ew. The results reproduce experiment well: free energies for all models are within 1.6 kJ mol(-1) and entropies are within 3.6 J K(-1) mol(-1). Approximately two-thirds of the entropy comes from translation, a third from rotation, and 5% from conformation. Vibrational frequencies match those in the experimental infrared spectrum and assist in their assignment. Intermolecular quantum effects are found to be small, with free energies for the classical oscillator lying 0.5-0.7 kJ mol(-1) higher than in the quantum case. Molecular displacements and vibrational and zero point energies are also calculated. Altogether, these results validate the harmonic oscillator as a quantitative model for the liquid state. 相似文献
Partition coefficients quantify a molecule’s distribution between two immiscible liquid phases. While there are many methods to compute them, there is not yet a method based on the free energy of each system in terms of energy and entropy, where entropy depends on the probability distribution of all quantum states of the system. Here we test a method in this class called Energy Entropy Multiscale Cell Correlation (EE-MCC) for the calculation of octanol–water logP values for 22 N-acyl sulfonamides in the SAMPL7 Physical Properties Challenge (Statistical Assessment of the Modelling of Proteins and Ligands). EE-MCC logP values have a mean error of 1.8 logP units versus experiment and a standard error of the mean of 1.0 logP units for three separate calculations. These errors are primarily due to getting sufficiently converged energies to give accurate differences of large numbers, particularly for the large-molecule solvent octanol. However, this is also an issue for entropy, and approximations in the force field and MCC theory also contribute to the error. Unique to MCC is that it explains the entropy contributions over all the degrees of freedom of all molecules in the system. A gain in orientational entropy of water is the main favourable entropic contribution, supported by small gains in solute vibrational and orientational entropy but offset by unfavourable changes in the orientational entropy of octanol, the vibrational entropy of both solvents, and the positional and conformational entropy of the solute.