“Enzyme Test Bench,” a high‐throughput enzyme characterization technique including the long‐term stability

A new high throughput technique for enzyme characterization with specific attention to the long term stability, called “Enzyme Test Bench,” is presented. The concept of the Enzyme Test Bench consists of short term enzyme tests in 96‐well microtiter plates under partly extreme conditions to predict the enzyme long term stability under moderate conditions. The technique is based on the mathematical modeling of temperature dependent enzyme activation and deactivation. Adapting the temperature profiles in sequential experiments by optimal non‐linear experimental design, the long term deactivation effects can be purposefully accelerated and detected within hours. During the experiment the enzyme activity is measured online to estimate the model parameters from the obtained data. Thus, the enzyme activity and long term stability can be calculated as a function of temperature. The engineered instrumentation provides for simultaneous automated assaying by fluorescent measurements, mixing and homogenous temperature control in the range of 10–85 ± 0.5°C. A universal fluorescent assay for online acquisition of ester hydrolysis reactions by pH‐shift is developed and established. The developed instrumentation and assay are applied to characterize two esterases. The results of the characterization, carried out in microtiter plates applying short term experiments of hours, are in good agreement with the results of long term experiments at different temperatures in 1 L stirred tank reactors of a week. Thus, the new technique allows for both: the enzyme screening with regard to the long term stability and the choice of the optimal process temperature regarding such process parameters as turn over number, space time yield or optimal process duration. The comparison of the temperature dependent behavior of both characterized enzymes clearly demonstrates that the frequently applied estimation of long term stability at moderate temperatures by simple activity measurements after exposing the enzymes to elevated temperatures may lead to suboptimal enzyme selection. Thus, temperature dependent enzyme characterization is essential in primary screening to predict its long term behavior. Biotechnol. Bioeng. 2009;103: 305–322. © 2008 Wiley Periodicals, Inc.     

Spectrofluorimetric determination of aluminium using 2‐hydroxy‐1‐naphthylidene‐(8‐aminoquinoline)

A sensitive and selective spectrofluorimetric method has been developed for the rapid determination of aluminium. This method is based on the complex formation between aluminium and 2‐hydroxy‐1‐naphthylidene‐(8‐aminoquinoline) (HNAQ). The optimum conditions for the complex formation were a metal‐to‐ligand (M : L) stoichiometric ratio of 1:1, a pH of 5.5 and a 0.20 m acetate buffer. The fluorescence of the complex was monitored at an emission wavelength of 502 nm with excitation at 438 nm. Under these conditions, linear calibration curves were obtained in the ranges 0.05–1 and 1–5 ppm. The detection limit was 3.4 ppb for the former and 13.5 ppb for the latter. The maximum relative standard deviation of the method for an aluminium standard of 200 ppb was 1.5% (n = 5). This method was successfully applied for the determination of aluminium in drinking water, pharmaceutical antacid tablets and suspension samples. Copyright © 2010 John Wiley & Sons, Ltd.     

Determination of nucleic acid by [tetra‐(3‐methoxy‐4‐hydroxyphenyl)]–Tb3+ porphyrin as the fluorescence spectral probe in bis(2‐ethylhexyl)sulfosuccinate sodium salt micelle system

A new system for the determination of nucleic acid by rare earth metallic porphyrin of [tetra‐(3‐methoxy‐4‐hydroxyphenyl)]–Tb³⁺ [T(3‐MO‐4HP)–Tb³⁺] porphyrin as fluorescence spectral probe has been developed in this paper. Nucleic acid can enhance the fluorescence intensity of the T(3‐MO‐4HP)–Tb³⁺ porphyrin in the presence of bis(2‐ethylhexyl)sulfosuccinate sodium salt(AOT) micelle. In pH 8.00 Tris–HCl buffer solution, under optimum conditions, the enhanced fluorescence intensity is in proportion to the concentration of nucleic acids in the range of 0.05–3.00 µg mL^?1 for calf thymus DNA (ct DNA) and 0.03–4.80 µg mL^?1 for fish sperm DNA(fs DNA). Their detection limits are 0.03 and 0.01 µg mL^?1, respectively. In addition, the binding interaction mechanism between T(3‐MO‐4HP)–Tb³⁺ porphyrin and ct DNA is also investigated by resonance scattering and fluorescence spectra. The maximum binding number is calculated by molar ratio method. The new system can be used for the determination of nucleic acid in pig liver, yielding satisfactory results. Copyright © 2009 John Wiley & Sons, Ltd.     

K‐Birnessite Electrode Obtained by Ion Exchange for Potassium‐Ion Batteries: Insight into the Concerted Ionic Diffusion and K Storage Mechanism

Novel and low‐cost rechargeable batteries are of considerable interest for application in large‐scale energy storage systems. In this context, K‐Birnessite is synthesized using a facile solid‐state reaction as a promising cathode for potassium‐ion batteries. During synthesis, an ion exchange protocol is applied to increase K content in the K‐Birnessite electrode, which results in a reversible capacity as high as 125 mAh g^?1 at 0.2 C. Upon K⁺ exchange the reversible phase transitions are verified by in situ X‐ray diffraction (XRD) characterization. The underlying mechanism is further revealed to be the concerted K⁺ ion diffusion with quite low activation energies by first‐principle simulations. These new findings provide new insights into electrode process kinetics, and lay a solid foundation for material design and optimization of potassium‐ion batteries for large‐scale energy storage.     

Application of information theory to a three‐body coarse‐grained representation of proteins in the PDB: Insights into the structural and evolutionary roles of residues in protein structure

Knowledge‐based methods for analyzing protein structures, such as statistical potentials, primarily consider the distances between pairs of bodies (atoms or groups of atoms). Considerations of several bodies simultaneously are generally used to characterize bonded structural elements or those in close contact with each other, but historically do not consider atoms that are not in direct contact with each other. In this report, we introduce an information‐theoretic method for detecting and quantifying distance‐dependent through‐space multibody relationships between the sidechains of three residues. The technique introduced is capable of producing convergent and consistent results when applied to a sufficiently large database of randomly chosen, experimentally solved protein structures. The results of our study can be shown to reproduce established physico‐chemical properties of residues as well as more recently discovered properties and interactions. These results offer insight into the numerous roles that residues play in protein structure, as well as relationships between residue function, protein structure, and evolution. The techniques and insights presented in this work should be useful in the future development of novel knowledge‐based tools for the evaluation of protein structure. Proteins 2014; 82:3450–3465. © 2014 Wiley Periodicals, Inc.     

Single‐molecule force spectroscopy applied to heparin‐induced thrombocytopenia

Heparin‐induced thrombocytopenia (HIT), occurring up to approximately 1% to 5% of patients receiving the antithrombotic drug heparins, has a complex pathogenesis involving multiple partners ranging from small molecules to cells/platelets. Recently, insights into the mechanism of HIT have been achieved by using single‐molecule force spectroscopy (SMFS), a methodology that allows direct measurements of interactions among HIT partners. Here, the potential of SMFS in unraveling the mechanism of the initial steps in the pathogenesis of HIT at single‐molecule resolution is highlighted. The new findings ranging from the molecular binding strengths and kinetics to the determination of the boundary between risk and non‐risk heparin drugs or platelet‐surface and platelet‐platelet interactions will be reviewed. These novel results together have contributed to elucidate the mechanisms underlying HIT and demonstrate how SMFS can be applied to develop safer drugs with a reduced risk profile.     

Study on the resonance Rayleigh scattering and resonance non‐linear scattering spectra of ion‐association complexes of [PdI4]2−‐protein systems and their analytical applications

In an acid medium solution, proteins such as bovine serum albumin, human serum albumin, ovalbumin, hemoglobin, lysozyme, γ‐globulin, α‐chymotrypsin and papain could react with [PdI₄]^2? by virtue of electrostatic attraction and hydrophobic force to form ion‐association complexes. As a result, the resonance Rayleigh scattering (RRS) and resonance nonlinear scattering such as second‐order scattering (SOS) and frequency doubling scattering (FDS) intensities were enhanced greatly and new scattering spectra appeared. The maximum scattering peaks of RRS, SOS and FDS were at 367, 720 and 370 nm, respectively. The enhanced RRS, SOS and FDS intensities were directly proportional to the concentrations of proteins. The detection limits for the different proteins were 2.4–11.8 ng/mL for RRS method, 9.5–47.9 ng/mL for SOS method and 4.6–18.5 ng/mL for FDS method. In this work, the influences of the interaction of [PdI₄]^2? with proteins on spectral characteristics of RRS, SOS and FDS were investigated and the optimum conditions were tested. Meanwhile, the effects of coexisting substances were tested and the results showed that the method exhibited a good selectivity. Based on the above research, a highly sensitive, simple and rapid method for the determination of trace amounts of proteins by resonance light scattering technique has been developed. It can be applied to the determination of proteins in tablet, human serum and urine samples. Copyright © 2009 John Wiley & Sons, Ltd.     

Two liquid chromatographic approaches for the simultaneous determination of xipamide and its degradation product (2,6‐xylidine) using time‐programmed fluorescence detection

A study of the performance of reversed‐phase chromatography with a programmable multiwavelength fluorimetric technique using either conventional hydro‐organic or micellar eluent is established for the determination of xipamide (XIP) in the presence of its degradation product, 2,6‐xylidine (XY). In conventional liquid chromatography (CLC), the analyses were carried out on a Promosil ODS 100 Å column (250 mm × 4.6 mm i.d., 5 μm) using a mobile phase consisting of methanol/0.1 M phosphate buffer (65: 35, v/v) at pH 4.0. For micellar liquid chromatography (MLC), a short Spherisorb column (150 mm × 4.6 mm i.d., 5 μm) was employed in conjunction with a greener mobile phase (pH 5.0) containing 0.1 M sodium dodecyl sulfate and 15% n‐propanol. CLC proved to be superior to MLC in terms of sensitivity for the determination of the degradation product because it could detect trace amounts down to 10.0 ng/ml of XY as a degradation product in XIP. However, MLC represents an eco‐friendly approach for the simultaneous determination of XIP and XY. In addition, the opportunity for the direct introduction of biological matrices into the chromatographic system is one of the distinctive benefits of MLC. The proposed methods were applied for the determination of XIP in its tablets, human urine and content uniformity testing. The results of the proposed methods were statistically compared with those obtained using the comparison fluorimetric method, revealing no significant differences in the performance of the methods regarding accuracy and precision.     

Nonheterocytous cyanobacteria from Brazilian saline‐alkaline lakes

Saline‐alkaline lakes are extreme environments that limit the establishment and development of life. The Nhecolândia, a subregion of the Pantanal wetland in Brazil, is characterized by the existence of ~500 saline‐alkaline lakes, which support an underexplored and rich diversity of microorganisms. In this study, unicellular and homocytous cyanobacteria from five saline‐alkaline lakes were accessed by culture‐dependent approaches. Morphological evaluation and analyses of near complete sequences (~1400 nt) of the 16S rRNA genes were applied for phylogenetic and taxonomic placement. This polyphasic approach allowed for the determination of the taxonomic position of the isolated strains into the following genera: Cyanobacterium, Geminocystis, Phormidium, Leptolyngbya, Limnothrix, and Nodosilinea. In addition, fourteen Pseudanabaenales and Oscillatoriales representatives of putative novel taxa were found. These sequences fell into five new clades that could correspond to new generic units of the Pseudanabaenaceae and Phormidiaceae families.     

A Novel Oxy‐Oxonia(Azonia)‐Cope Reaction: Serendipitous Discovery and Its Application to the Synthesis of Macrocyclic Musks

This brief review, including new experimental results, is the summary of a talk at the GDCh conference ‘flavors & fragrances 2013’ in Leipzig, Germany, 11th–13th September, 2013. Musk odorants are indispensable in perfumery to lend sensuality to fine fragrances, a nourishing effect to cosmetics, and a comforting feeling to laundry. We have recently found serendipitously a new oxy‐oxonia‐Cope rearrangement. In this account, we review the background of oxonia‐sigmatropic rearrangements and the discovery of this novel reaction. Special attention is focused on the versatile lactone and lactam formation reactions via [n+4] ring enlargement and the macrocyclization in the synthesis of new macrocyclic musks. The synthesized structures provide new insights into the structure? odor relationships of musks.     

Molecular tweezers for enantiodiscrimination in NMR: Di‐(R,R)‐1‐[10‐(1‐hydroxy‐2,2,2‐trifluoroethyl)‐9‐anthryl]‐2,2,2‐trifluoroethyl benzenedicarboxylates

A series of new chiral molecular tweezers, di‐(R,R)‐1‐[10‐(1‐hydroxy‐2,2,2‐trifluoroethyl)‐9‐anthryl]‐2,2,2‐trifluoroethyl phthalate (2), isophthalate (3) and terephthalate (4), were synthesized and their structure studied by NMR and molecular mechanics. Their effectiveness as chiral solvating agents for the determination of the enantiomeric purity of chiral compounds using NMR was demonstrated. Chirality 2010. © 2009 Wiley‐Liss, Inc.     

Identification of N‐octylnortadalafil and its Stereoisomers in Dietary Supplements with Chiral Liquid Chromatography–Circular Dichroism

A direct chiral liquid chromatography–circular dichroism (LC‐CD) method was developed for the simple and rapid identification of N‐octylnortadalafil [(6R, 12aR)‐6‐(1,3‐benzodioxol‐5‐yl)‐2‐octyl‐2,3,6,7,12,12a‐hexahydropyrazino[1’,2’:1,6]pyrido[3,4‐b]indole‐1,4‐dione; RR‐OTDF] and its stereoisomers in dietary supplements. Samples were extracted with methanol. Compounds were then separated by chiral LC‐CD using Chiralcel OD‐RH (4.6 × 1 50 mm, 5 µm) with 5 mM ammonium formate (pH 3)/0.1% formic acid in acetonitrile (95:5, v/v) mixture solution (mobile phase A) and 0.1% formic acid in acetonitrile (mobile phase B). The isocratic elution used was mobile phase A / mobile phase B (3:7, v/v) at a flow rate of 1 ml/min. The column temperature was held at 30°C. RR‐OTDF and its stereoisomers were separated within 20 min with the resolution factors being over 2.0. Using this method, RR‐OTDF and (6R, 12aS)‐6‐(1,3‐benzodioxol‐5‐yl)‐2‐octyl‐2,3,6,7,12,12a‐hexahydropyrazino[1’,2’:1,6]pyrido[3,4‐b]indole‐1,4‐dione were detected in a dietary supplement. Chirality 28:204–208, 2016. © 2016 Wiley Periodicals, Inc.     

Efficient approximate k‐fold and leave‐one‐out cross‐validation for ridge regression

In model building and model evaluation, cross‐validation is a frequently used resampling method. Unfortunately, this method can be quite time consuming. In this article, we discuss an approximation method that is much faster and can be used in generalized linear models and Cox’ proportional hazards model with a ridge penalty term. Our approximation method is based on a Taylor expansion around the estimate of the full model. In this way, all cross‐validated estimates are approximated without refitting the model. The tuning parameter can now be chosen based on these approximations and can be optimized in less time. The method is most accurate when approximating leave‐one‐out cross‐validation results for large data sets which is originally the most computationally demanding situation. In order to demonstrate the method's performance, it will be applied to several microarray data sets. An R package penalized, which implements the method, is available on CRAN.     

Enantiomeric assay of escitalopram S(+)‐enantiomer and its “in‐process impurities” using two different techniques

The enantiomeric purity of escitalopram oxalate ESC and its “in‐process impurities,” namely, ESC‐N‐oxide, ESC‐citadiol, and R(?)‐enantiomer were studied in drug substance and products using high‐performance liquid chromatography (HPLC)‐UV (Method I), synchronous fluorescence spectroscopy (SFS) (Method IIA), and first derivative SFS (Method IIB). Method I describes as an isocratic HPLC‐UV for the direct resolution and determination of enantiomeric purity of ESC and its “in‐process impurities.” The proposed method involved the use of α_l‐acid glycoprotein (AGP) chiral stationary phase. The regression plots revealed good linear relationships of concentration range of 0.25 to 100 and 0.25 to 10 μg mL^?1 for ESC and its impurities. The limits of detection and quantifications for ESC were 0.075 and 0.235 μg mL^?1, respectively. Method II involves the significant enhancement of the fluorescence intensities of ESC and its impurities through inclusion complexes formation with hydroxyl propyl‐β‐cyclodextrin as a chiral selector in Micliavain buffer. Method IIA describes SFS technique for assay of ESC at 225 nm in presence of its impurities: R(?)‐enantiomer, citadiol, and N‐oxide at ?λ of 100 nm. This method was extended to (Method IIB) to apply first derivative SFS for the simultaneous determination of ESC at 236 nm and its impurities: the R(?)‐enantiomer, citadiol, and N‐oxide at 308, 275, and 280 nm, respectively. Linearity ranges were found to be 0.01 to 1.0 μg mL^?1 for ESC and its impurities with lower detection and quantification limits of 0.033/0.011 and 0.038/0.013 μg mL^?1 for SFS and first derivative synchronous fluorescence spectra (FDSFS), respectively. The methods were used to investigate the enantiomeric purity of escitalopram.     

4‐alkoxyethoxy‐N‐octadecyl‐1,8‐naphthalimide fluorescent sensor for human serum albumin and other major blood proteins: design,synthesis and solvent effect

A series of 4‐alkoxyethoxy‐N‐octadecyl‐1,8‐naphthalimides with intense blue fluorescence were designed and synthesized as polarity and spectrofluorimetric probes for the determination of proteins. In solvents of different polarities, the Stokes shifts of two dyes increased with increasing solvent polarity and fluorescence quantum yields decreased significantly, suggesting that electronic transiting from ground to excited states was π–π^* in character. Dipole moment changes were estimated from solvent‐dependent Stokes shift data using a solvatochromic method based on bulk solvent polarity functions and the microscopic solvent polarity parameter (). These results were generally consistent with semi‐empirical molecular orbital calculations and were found to be quite reliable based on the fact that the correlation of the solvatochromic Stokes shifts with was superior to that obtained using bulk solvent polarity functions. Fluorescence data revealed that the fluorescence quenching of human serum albumin (HSA) by dyes was the result of the formation of a Dye–HSA complex. The method was applied to the determination of total proteins (HSA + immunoglobulins) in human serum samples and results were in good agreement with those reported by the research institute. Copyright © 2012 John Wiley & Sons, Ltd.     

Organocatalyzed Domino Synthesis of New Thiazole‐Based Decahydroacridine‐1,8‐diones and Dihydropyrido[2,3‐d : 6,5‐d′]‐ dipyrimidines in Water as Antimicrobial Agents

Organopromoter, 2‐aminoethanesulfonic acid was used to catalyze the synthesis of a series of structurally intriguing new hybrids thiazolyl acridine‐1,8(2H,5H)‐diones and dihydropyrido[2,3‐d : 6,5‐d′]dipyrimidine‐2,4,6,8(1H,3H,5H,7H)‐tetraones for the first time. 2‐Aminoethanesulfonic acid is a biobased organopromoter, used to generate four new bonds for the synthesis of new coupled thiazole‐based decahydroacridine‐1,8‐diones. Superior green credentials, operational simplicity, easy work‐up and recyclability of the catalyst are the key strengths of this method. The broad substrate scope, mild reaction conditions, short reaction time, cost effectiveness, high atom economy and good to excellent yields make the present method a distinct improvement over existing methods. Spectral (IR, ¹H‐NMR,¹³C‐NMR, Mass) data and elemental analyses confirmed the structures of the titled products. A series of thiazolyl acridine‐1,8(2H,5H)‐diones and dihydropyrido[2,3‐d : 6,5‐d′]dipyrimidine‐2,4,6,8(1H,3H,5H,7H)‐tetraones were screened for their antimicrobial activity against four bacterial and three fungal strains.     

Polymer‐in‐“Quasi‐Ionic Liquid” Electrolytes for High‐Voltage Lithium Metal Batteries

Due to the limited oxidation stability (<4 V) of ether oxygen in its polymer structure, polyethylene oxide (PEO)‐based polymer electrolytes are not compatible with high‐voltage (>4 V) cathodes, thus hinder further increases in the energy density of lithium (Li) metal batteries (LMBs). Here, a new type of polymer‐in‐“quasi‐ionic liquid” electrolyte is designed, which reduces the electron density on ethereal oxygens in PEO and ether solvent molecules, induces the formation of stable interfacial layers on both surfaces of the LiNi_1/3Mn_1/3Co_1/3O₂ (NMC) cathode and the Li metal anode in Li||NMC batteries, and results in a capacity retention of 88.4%, 86.7%, and 79.2% after 300 cycles with a charge cutoff voltage of 4.2, 4.3, and 4.4 V for the LMBs, respectively. Therefore, the use of “quasi‐ionic liquids” is a promising approach to design new polymer electrolytes for high‐voltage and high‐specific‐energy LMBs.     

Chemoenzymatic Approach to Optically Active 4‐Hydroxy‐5‐alkylcyclopent‐2‐en‐1‐one Derivatives: An Application of a Combined Circular Dichroism Spectroscopy and DFT Calculations to Assignment of Absolute Configuration

A series of representative optically active derivatives of 4‐hydroxy‐5‐alkylcyclopent‐2‐en‐1‐one were prepared from the respective 2‐furyl methyl carbinols via the Piancatelli rearrangement followed by the enzymatic kinetic resolution of racemates. Applicability of chiroptical methods (experimental and calculated electronic circular dichroism [ECD] and vibrational circular dichroism [VCD] spectra) to determine the absolute configuration of both stereogenic centers in 4‐hydroxy‐5‐methylcyclopent‐2‐en‐1‐one was demonstrated. It was also demonstrated that the concurrent application of ECD and VCD spectroscopy can be used for the determination of the configuration of two stereogenic centers. Chirality 26:300–306, 2014. © 2014 Wiley Periodicals, Inc.     

New bioluminescence pyrophosphate assay for high‐sensitivity detection of food‐borne pathogens

Traditional methods of identifying food‐borne pathogens are time consuming and laborious, so innovative methods for their rapid identification must be developed. Testing for bioluminescence pyrophosphate is a convenient and fast method of detecting pathogens without complex equipment. However, the sensitivity of the method is not as high as that of other methods, and it has a very high detection limit. In this study, the method was optimized to improve its sensitivity. The shortcomings of the method were first identified and corrected using dATPαS instead of dATP for the polymerase chain reaction (PCR), therefore reducing the background signal. Also, when the DNA template extracted from the food‐borne pathogens was purified, the new bioluminescence pyrophosphate assay had a limit of detection of <10 copy/μl or 10 colony‐forming units/ml, and its sensitivity was higher than that of fluorescent real‐time quantitative PCR. Moreover, a single copy of a food‐borne pathogen could be detected when a single DNA template was included in the PCR. Salmonella was detected in and isolated from 60 samples of broiler chicken, and the accuracy of the results was verified using a culture method (GB 4789.4–2010). These results showed that the new bioluminescence pyrophosphate assay has the advantages of an intuitive detection process, convenient operation, and rapid measurements. Therefore, it can be used for the rapid detection of pathogenic bacteria and probiotics in various fields.     

Chiral Molecular Science: How were the absolute configurations of chiral molecules determined? “Experimental results and theories”

Molecular chirality is a key concept in chemistry, bioscience, and molecular technology, like the invention of a light‐powered chiral molecular motor explained in this review. Thus, the primary research subject is how to determine the absolute configuration (AC) of chiral compounds. This review article focuses on the principle, theory, and practice of the nonempirical methods for determining ACs of chiral compounds, i.e., the Bijvoet method in X‐ray crystallography and the circular dichroism (CD) exciton chirality method, together with the historical aspects of AC determination. The theoretical equations of X‐ray crystallography and exciton CD spectroscopy are explained in detail, and these equations are useful for readers to understand the principle and mechanism of these methods. This review also focuses on the relative methods, where the internal reference with known AC is used and the relative configuration is determined by X‐ray crystallography and/or ¹H nuclear magnetic resonance (NMR) diamagnetic anisotropy method. In these cases, CSDP acid and MαNP acid are useful for the chiral resolution of racemic alcohols, where their diastereomeric esters are easily separable by high‐performance liquid chromatography (HPLC) on silica gel. Thus, these methods are useful for the preparation of enantiopure compounds and simultaneous determination of their ACs. In this review article, the above methods are explained mainly based on the author's own research results.