Using quaternions to calculate RMSD

A widely used way to compare the structures of biomolecules or solid bodies is to translate and rotate one structure with respect to the other to minimize the root-mean-square deviation (RMSD). We present a simple derivation, based on quaternions, for the optimal solid body transformation (rotation-translation) that minimizes the RMSD between two sets of vectors. We prove that the quaternion method is equivalent to the well-known formula due to Kabsch. We analyze the various cases that may arise, and give a complete enumeration of the special cases in terms of the arrangement of the eigenvalues of a traceless, 4 x 4 symmetric matrix. A key result here is an expression for the gradient of the RMSD as a function of model parameters. This can be useful, for example, in finding the minimum energy path of a reaction using the elastic band methods or in optimizing model parameters to best fit a target structure.     

Reactivity of the indole ring in palladium(II) complexes of 2N1O-donor ligands: cyclopalladation and pi-cation radical formation

The Pd(II) complexes of new 2N1O-donor ligands containing a pendent indole, 3-[N-2-pyridylmethyl-N-2-hydroxy-3,5-di(tert-butyl)benzylamino]ethylindole (Htbu-iepp), 1-methyl-3-[N-2-pyridylmethyl-N-2-hydroxy-3,5-di(tert-butyl)benzylamino]ethylindole (Htbu-miepp), 3-[N-2-pyridylmethyl-N-2-hydroxy-3,5-di(tert-butyl)benzylamino]methylindole (Htbu-impp), and 3-(N-2-pyridylmethyl-N-4-hydroxybenzylamino)ethylindole (Hp-iepp) (H denotes a dissociable proton), were synthesized, and the structures of [Pd(tbu-iepp)Cl] (1a), [Pd(tbu-iepp-c)Cl] (1b), [Pd(tbu-miepp)Cl] (3), and [Pd(p-iepp-c)Cl] (4) (tbu-iepp-c and p-iepp-c denote tbu-iepp and p-iepp bound to Pd(II) through a carbon atom, respectively) were determined by X-ray analysis. Complexes 1a prepared in CH(2)Cl(2)/CH(3)CN and 3 prepared in CH(3)CN have a pyridine nitrogen, an amine nitrogen, a phenolate oxygen, and a chloride ion in the coordination plane. Complex 1b prepared in CH(3)CN has the same composition as 1a and was revealed to have the C2 atom of the indole ring bound to Pd(II) with the Pd(II)-C2 distance of 1.973(2) A. The same Pd(II)-indole C2 bonding was revealed for 4. Interconversion between 1a and 1b was observed for their solutions, the equilibrium being dependent on the solvent used. Reaction of 1b and 4 with 1 equiv of Ce(IV) in DMF gave the corresponding one-electron-oxidized species, which exhibited an ESR signal at g = 2.004 and an absorption peak at approximately 550 nm, indicating the formation of the Pd(II)-indole pi-cation radical species. The half-life, t(1/2), of the indole radical species at room temperature was calculated to be 20 s (k(obs) = 3.5 x 10(-)(2) s(-)(1)) for 1b. The cyclic voltammogram for 1b in DMF gave two irreversible oxidation peaks at E(pa) = 0.68 and 0.80 V (vs Ag/AgCl), which were ascribed to the oxidation processes of the coordinated indole and phenolate moieties, respectively.     

High performance liquid chromatography with an electrochemical detector in the cathodic mode as a tool for the determination of p-nitrophenol and assay of acid phosphatase in urine samples

Utilizing a commercially available helium-purging device and PEEK tubes for all tubing, especially for connection between the mobile phase and pump, high performance liquid chromatography with an electrochemical detector (ECD/HPLC) at the cathodic mode is a simple and precise method for the determination of p-nitrophenol (NP). Studies with cyclic and hydrodynamic voltammetry indicated that 25% aqueous MeOH containing 0.1% (v/v) CF(3)CO(2)H and -0.8 V vs. Ag/AgCl are the best mobile phase and detection potential for cathodic ECD/HPLC. With the present system, the limits of detection and determination were 0.2 and 0.25 microM, respectively, and up to 50 microM, a linear calibration curve was afforded. Within-day precisions for the analysis of 5 and 50 microM NP were 0.8 and 0.7% (n=6), respectively, and between-day precisions (n=6) for these samples were 3.5 and 2.2%, respectively. Compared with the commonly used Bessey-Lowry-Brock method, cathodic ECD/HPLC was useful for the assay of acid phosphatase in urine samples with p-nitrophenyl phosphate disodium salt as a substrate.     

Recognition of chiral catechols using oxo-titanium phthalocyanine

Oxo-titanium phthalocyanine (TiOPc) derivatives of catechin and hematoxylin (natural ortho-diol type chiral compounds) have been prepared and characterized by spectral and chromatographic techniques. It is demonstrated that the TiOPc unit is an excellent template for chiral recognition through its isolated Q-transitions. The formation of a helical dimeric complex with hematoxylin induces strong CD-activity in the Q-band region. Ab initio geometry optimizations were combined with a Kuhn-Kirkwood coupled-oscillator mechanism to obtain the absolute configuration of hematoxylin. In addition, it is shown that the described chiroptical recognition method is sensitive to slight conformational changes.     

Single-particle light scattering study of polyethyleneglycol-grafted poly(ureaurethane) microcapsule in ethanol

Microcapsules having polyethyleneglycol-grafted poly(ureaurethane) (PUU) membrane and di-2ethylhexyl phthalate core have been prepared, and the structure when they were suspended in dispersing ethanol have been studied by means of single-particle light scattering method. The PUU membrane was synthesized from monomers with aromatic functional groups (microcapsule MC110) and hexamethylene functional groups (microcapsule MC160). Because the outer and inner solvent passed through the membrane easily, the outside and inside of the membrane were the same at the equilibrium state. The thickness of the wall membrane was significantly smaller than that calculated from the overall weight ratio of the wall-forming material and the core solvents. It was attributed to low affinity of PUU membranes and ethanol.     

Nanosize-induced drastic drop in equilibrium hydrogen pressure for hydride formation and structural stabilization in pd-rh solid-solution alloys

We have synthesized and characterized homogeneous solid-solution alloy nanoparticles of Pd and Rh, which are immiscible with each other in the equilibrium bulk state at around room temperature. The Pd-Rh alloy nanoparticles can absorb hydrogen at ambient pressure and the hydrogen pressure of Pd-Rh alloys for hydrogen storage is dramatically decreased by more than 4 orders of magnitude from the corresponding pressure in the metastable bulk state. The solid-solution state is still maintained in the nanoparticles even after hydrogen absorption/desorption, in contrast to the metastable bulks which are separated into Pd and Rh during the process.     

Rapid fermentation of beer using an immobilized yeast multistage bioreactor

The characteristics of yeast sulfite metabolism in a multistage bioreactor system for beer fermentation were investigated. No sulfite was produced in the continuous stirred-tank reactor (CSTR). However, large amounts were produced in the packed-bed reactor (PBR). Production of sulfite in the PBR seems to be inevitable when it is operated continuously. In order to control the sulfite level in the young beer, the yeast needs to be reactivated into the growth phase. One possible strategy to achieve this is to aerate and periodically remove yeast clogged in the reactor once every 6–7 months before the sulfite level exceeds a given concentration (e.g., 20 mg/L). It was confirmed that sulfite production is closely related to the growth condition of the yeast and is therefore important to consider in the control strategy for sulfite when using the immobilized yeast reactor for beer production.     

Internal Rotation of the Methyl Group in Cations of Toluene Derivatives

The potential of the internal rotation of the methyl group was determined for o-, m-, and p-fluorotoluene cations by pulsed field ionization spectroscopy. The potential of the internal rotational motion was also surveyed for other toluene derivative cations. It was found that the barrier height generally increases by ionization. The increase in the barrier height has been discussed in connection with the reduction of the internal rotational constant B by ionization. The geometrical distortion of the methyl group during the internal rotation has been suggested.     

Chemical constituents of Blumea balsamifera of Indonesia and their protein tyrosine phosphatase 1B inhibitory activity

A methanol extract of the leaves of Blumea balsamifera (L.) DC. (Asteraceae) afforded a new guaian-type sesquiterpene, epiblumeaene K (1), together with four known guaian-type sesquiterpenes (2-5), three known sesquiterpenes (6-8), and nine known flavonoids (9-17) by a combination of chromatography and preparative TLC techniques. Their structures were elucidated by extensive spectroscopic methods and comparison with the literature data. Among the isolated compounds, a known sesquiterpene, beta-caryophyllene 8R,9R-oxide (6), exhibited a significant PTP1B inhibitory activity in a dose-dependent manner, with an IC50 value of 25.8 microM (5.62 microg/mL).     

Substrate specificity of fluoroacetate dehalogenase: an insight from crystallographic analysis, fluorescence spectroscopy, and theoretical computations

The high substrate specificity of fluoroacetate dehalogenase was explored by using crystallographic analysis, fluorescence spectroscopy, and theoretical computations. A crystal structure for the Asp104Ala mutant of the enzyme from Burkholderia sp. FA1 complexed with fluoroacetate was determined at 1.2 ? resolution. The orientation and conformation of bound fluoroacetate is different from those in the crystal structure of the corresponding Asp110Asn mutant of the enzyme from Rhodopseudomonas palustris CGA009 reported recently (J. Am. Chem. Soc. 2011, 133, 7461). The fluorescence of the tryptophan residues of the wild-type and Trp150Phe mutant enzymes from Burkholderia sp. FA1 incubated with fluoroacetate and chloroacetate was measured to gain information on the environment of the tryptophan residues. The environments of the tryptophan residues were found to be different between the fluoroacetate- and chloroacetate-bound enzymes; this would come from different binding modes of these two substrates in the active site. Docking simulations and QM/MM optimizations were performed to predict favorable conformations and orientations of the substrates. The F atom of the substrate is oriented toward Arg108 in the most stable enzyme-fluoroacetate complex. This is a stable but unreactive conformation, in which the small O-C-F angle is not suitable for the S(N)2 displacement of the F(-) ion. The cleavage of the C-F bond is initiated by the conformational change of the substrate to a near attack conformation (NAC) in the active site. The second lowest energy conformation is appropriate for NAC; the C-O distance and the O-C-F angle are reasonable for the S(N) 2 reaction. The activation energy is greatly reduced in this conformation because of three hydrogen bonds between the leaving F atom and surrounding amino acid residues. Chloroacetate cannot reach the reactive conformation, due to the longer C-Cl bond; this results in an increase of the activation energy despite the weaker C-Cl bond.