Formation of the iron-oxo hydroxylating species in the catalytic cycle of aromatic amino acid hydroxylases

The first part of the catalytic cycle of the pterin‐dependent, dioxygen‐using nonheme‐iron aromatic amino acid hydroxylases, leading to the Fe^IV?O hydroxylating intermediate, has been investigated by means of density functional theory. The starting structure in the present investigation is the water‐free Fe? O₂ complex cluster model that represents the catalytically competent form of the enzymes. A model for this structure was obtained in a previous study of water‐ligand dissociation from the hexacoordinate model complex of the X‐ray crystal structure of the catalytic domain of phenylalanine hydroxylase in complex with the cofactor (6R)‐L ‐erythro‐5,6,7,8‐tetrahydrobiopterin (BH₄) (PAH‐Fe^II‐BH₄). The O? O bond rupture and two‐electron oxidation of the cofactor are found to take place via a Fe‐O‐O‐BH₄ bridge structure that is formed in consecutive radical reactions involving a superoxide ion, O₂^?. The overall effective free‐energy barrier to formation of the Fe^IV?O species is calculated to be 13.9 kcal mol^?1, less than 2 kcal mol^?1 lower than that derived from experiment. The rate‐limiting step is associated with a one‐electron transfer from the cofactor to dioxygen, whereas the spin inversion needed to arrive at the quintet state in which the O? O bond cleavage is finalized, essentially proceeds without activation.     

Ultrathin spin-coated dioleoylphosphatidylcholine lipid layers in dry conditions: a combined atomic force microscopy and nanomechanical study

Atomic force microscopy (AFM) has been used to study the structural and mechanical properties of low concentrated spin-coated dioleoylphosphatidylcholine (DOPC) layers in dry environment (RH ≈ 0%) at the nanoscale. It is shown that for concentrations in the 0.1-1 mM range the structure of the DOPC spin-coated samples consists of an homogeneous lipid monolayer ～1.3 nm thick covering the whole substrate on top of which lipid bilayer (or multilayer) micro- and nanometric patches and rims are formed. The thickness of the bilayer structures is found to be ～4.5 nm (or multiples of this value for multilayer structures), while the lateral dimensions range from micrometers to tens of nanometer depending on the lipid concentration. The force required to break a bilayer (breakthrough force) is found to be ～0.24 nN. No dependence of the mechanical values on the lateral dimensions of the bilayer structures is evidenced. Remarkably, the thickness and breakthrough force values of the bilayers measured in dry environment are very similar to values reported in the literature for supported DOPC bilayers in pure water.     

An Assessment of Computational Methods for Obtaining Structural Information of Moderately Flexible Biomolecules from Ion Mobility Spectrometry

When utilized in conjunction with modeling, the collision cross section (Ω) from ion mobility spectrometry can be used to deduce the gas phase structures of analyte ions. Gas phase conformations are determined computationally, and their Ω calculated using an approximate method, the results of which are compared with experimental data. Though prior work has focused upon rigid small molecules or large biomolecules, correlation of computational and experimental Ω has not been thoroughly examined for analytes with intermediate conformational flexibility, which constitute a large fraction of the molecules studied in the field. Here, the computational paradigm for calculating Ω has been tested for the tripeptides WGY, YGW, and YWG (Y = tyrosine, W = tryptophan, G = glycine). Experimental data indicate that Ω_exp (YWG) > Ω_exp (WGY) ≈ Ω_exp (YGW). The energy distributions of conformations obtained from tiers of simulated annealing molecular dynamics (SAMD) were analyzed using a wide array of density functionals. These quantum mechanical energy distributions do not agree with the MD data, which leads to structural differences between the SAMD and DFT conformations. The latter structures are obtained by reoptimization of the SAMD geometries, and are the only suite of structures that reproduce the experimental trend in analyte separability. In the absence of fitting Lennard Jones potentials that reproduce experimental results for the Trajectory Method, the Exact Hard Sphere Scattering method produced numerical values that are in best agreement with the experimental cross sections obtained in He drift gas.     

Solid state and solution structures of alkaline-earth complexes with lariat ethers containing aniline and benzimidazole pendants

Herein we report the synthesis and structural characterization of Mg(II), Ca(II), Sr(II) and Ba(II) complexes with bibracchial lariat ethers derived from 1,7-diaza-15-crown-5 and 1,7-diaza-12-crown-4 containing aniline or benzimidazole pendant arms. The solid state structures of most of them have been determined by using single crystal X-ray crystallography. A coordination number of seven was observed for the Mg(II) complexes in the solid state, while the Ca(II), Sr(II) and Ba(II) complexes are 8-, 9- and 11-coordinate, respectively. The Ca(II), Sr(II) and Ba(II) complexes show a syn conformation, with the two pendant arms of the ligand disposed on the same side of the macrocyclic mean plane. However, the Mg(II) complex with the largest ligand derived from 1,7-diaza-15-crown-5 containing benzimidazole pendants presents an anti conformation in the solid state. ¹H and ¹³C NMR spectroscopy reveal that this conformation is maintained in acetonitrile solution.     

On the Relationship between Hydrogen Bond Strength and the Formation Energy in Resonance-Assisted Hydrogen Bonds

Resonance-assisted hydrogen bonds (RAHB) are intramolecular contacts that are characterised by being particularly energetic. This fact is often attributed to the delocalisation of π electrons in the system. In the present article, we assess this thesis via the examination of the effect of electron-withdrawing and electron-donating groups, namely −F, −Cl, −Br, −CF₃, −N(CH₃)₂, −OCH₃, −NHCOCH₃ on the strength of the RAHB in malondialdehyde by using the Quantum Theory of Atoms in Molecules (QTAIM) and the Interacting Quantum Atoms (IQA) analyses. We show that the influence of the investigated substituents on the strength of the investigated RAHBs depends largely on its position within the π skeleton. We also examine the relationship between the formation energy of the RAHB and the hydrogen bond interaction energy as defined by the IQA method of wave function analysis. We demonstrate that these substituents can have different effects on the formation and interaction energies, casting doubts regarding the use of different parameters as indicators of the RAHB formation energies. Finally, we also demonstrate how the energy density can offer an estimation of the IQA interaction energy, and therefore of the HB strength, at a reduced computational cost for these important interactions. We expected that the results reported herein will provide a valuable understanding in the assessment of the energetics of RAHB and other intramolecular interactions.     

HPLC enantioseparation of alkaloid malacitanine using fluorimetric/polarimetric detection

This work reports two methods developed for the separation and determination of the enantiomers of the new alkaloid malacitanine (MLC) and the determination of the enantiomeric purity in mixtures. First, the isomers were separated using a Chirex 3020 (250 mm × 4.6 mm, 5 μm) chiral column with a mobile phase of cyclohexane–1,2‐dichloroethane–ethanol–trifluoroacetic acid (64:30:6:0.6, v/v/v/v) at a flow rate of 1 mL/min and fluorimetric detection. Obtained retention times were 12.4 and 15.9 min (+ and ?) with a resolution Rs of 1.13. Relative standard deviations (RSDs) were 2.5 and 2.4% at the 0.5‐μg level (four determinations). Second, a nonenantioselective procedure for the determination of enantiomeric purity of MLC using a Lichrospher ® Si‐60 (250 mm × 5 mm, 5 μm) normal phase with a mobile phase of 100% ethanol at a flow rate of 0.9 mL/min coupled to two detectors in series, fluorimetric and polarimetric. RSD of 3.3% was obtained. Calculated enantiomeric purity by chiral chromatography gave 48.6% (?)‐MLC in the near racemic product. Using polarimetric signal of the nonseparated enantiomers and comparing the slopes of the calibration curves (enantiomers) from the racemic product gave 47.8% (?)‐MLC content. A study of accuracy of (?)‐MLC gave recoveries from 98.3 to 100.7%.     

Density functional analysis of ancillary ligand electronic contributions to metal-mediated enediyne cyclization

Density functional theory (DFT) has been used to study electronic perturbations induced by ancillary halogen ligation within metalloenediyne constructs, and the subsequent affect upon thermal Bergman cyclization temperatures. To isolate electronic from geometric components of Bergman cyclization thermodynamics, model diamine- and diphosphine-enediynes (L = 1,6-diamino- or 1,6-diphosphino-cis-1,5-hexadiyne-3-ene) of Mn(II), Cu(II), Zn(II), and Pd(II) with ancillary chloride ligands have been examined computationally and compared to more complex ethylenediamine-based metalloenediyne frameworks of the form MLX(2) (X = Cl, Br, I; L = 1,4-dibenzyl-1,4-diaza-cyclododec-8-ene-6,10-diyne) with distorted square-planar (Cu(II)), T(d) (Zn(II)), and D(4h) (Pd(II)) geometries. In the latter systems, the ethylenediamine linkage restricts the conformation of the enediyne backbone, causing the alkyne termini separation to be nearly independent of metal geometry (3.75-3.82 A). Within the Zn(II) family, steric effects are shown to induce conformational changes on the cyclization potential energy surface (PES) prior to the Bergman transition state, introducing distinct electron-electron repulsive interactions. Multiple metal and ligand conformations are also observed on the Cu(II) metalloenediyne cyclization PES. In contrast, square-planar Pd(II) compounds exhibit overlap between the out-of-plane halogen lone pairs and metal d orbitals, as well as the enediyne pi system, reminiscent of an organometallic "push-pull" reaction mechanism. These systems have significantly higher predicted activation barriers toward cycloaromatization due to enhanced electron repulsion.     

Non-linear oscillations of elastic orthotropic annular plates of variable thickness

A computational analysis of the non-linear oscillations of elastic orthotropic annular plates of variable thickness is presented. The non-linear boundary value problem is converted into a corresponding eigenvalue problem by using a Kantorovich time-averaging method. Then, by a Newton-Raphson iteration scheme in conjunction with the concept of analytical continuation, the solution to the non-linear oscillations of elastic orthotropic annular plates of variable thickness are obtained.     

A TDDFT description of the low-energy excited states of copper and zinc metalloenediynes

Time-dependent density functional theory shows that the photoreactivities of copper and zinc metalloenediynes derive from multi-configurational excited states involving the enediyne and pyridine pi systems.     

Comparison of micellar electrokinetic chromatography, liquid chromatography, and microbiologic assay for analysis of cephalexin in oral suspensions

Two well-accepted methodologies, based on a microbiologic assay (MA) and liquid chromatography (LC), and a novel methodology using micellar electrokinetic chromatography (MEKC), were compared for the determination of cephalexin in commercially available and simulated samples of oral suspensions. The MA, described in the Brazilian Pharmacopeia, was performed with a strain of Staphylococcus aureus ATCC 6538 as the test organism, following the cylinder-plate method. The LC analysis followed the European Pharmacopoeia, 3rd Ed., and was used with minor modifications. The MEKC analysis was based on a previous work of the group. Estimates of the repeatability relative standard deviations of the MA, LC, and MEKC methods in the analysis of a commercial sample were 0.34, 0.42, and 0.37%, respectively. The recovery obtained with LC was 99.90 +/- 1.11%; for MEKC, it was 100.09 +/- 0.56%. Although the 3 methodologies were statistically equivalent for the determination of cephalexin in oral suspensions, MA gave suitable repeatability despite being nonspecific and time-consuming. MEKC provided faster analysis and higher column efficiency, whereas LC presented superior sensitivity. The results indicated that MEKC can be used as an alternative method to MA and LC in routine quality control laboratories.