Is the assessment of interlaboratory comparison results for a small number of tests and limited number of participants reliable and rational?

Tests and/or test items can sometimes be expensive, unique, or only performed in a few laboratories. There can be cases where assigned values are unknown, there is no information, or only poor information on the probability density function attributed to the test result. Sometimes there are neither reference materials nor the ability to establish consensus values due to a lack of experts. It can be impossible to repeat a test on the same item because it is destroyed during the test itself, or the homogeneity of tested items is unknown and no criteria can be established. Specified technical requirements concerning proficiency testing and interlaboratory comparison schemes are generally not applicable in this situation. However, interlaboratory comparison could allow laboratories to have more confidence in their results. The present paper discusses three statistical methods of assessing interlaboratory comparison results obtained in such conditions. Two methods are based on an assigned value determined from participant results through robust analysis. The third is based on the compatibility of results assessed using the ζ parameter. This paper focuses on an interlaboratory comparison for two laboratories, each testing three samples. The use of statistical methods turns out to be high risk, particularly in terms of falsely accepting results. Additionally, is shown that methods dedicated to small samples are also not efficient in detecting discrepancies of test results.     

Is it possible to estimate the enantioselectivity of a chiral catalyst from its racemic mixture?

The evaluation of a racemic catalyst was investigated in the case of oxazaborolidine (OAB)-catalyzed borane reduction of 1,5-diphenyl-1,5-pentanedione, giving the corresponding diol. On the basis of the diastereoselectivity of the diols, it is possible to estimate the enantioselectivity (ee) of the first step, which correlates well with the ee in the reaction of the structurally similar phenyl n-pentyl ketone with enantiopure OAB catalyst. The measure of diastereoselectivity could be a tool for screening racemic catalysts without the need for resolving the individual enantiomers, if in the second step of the process there is no substrate control and no catalyst scrambling.     

Is it common for charge recombination to be faster than charge separation?

Attaining long-lived charge-transfer (CT) states is of the utmost importance for energy science, photocatalysis, and materials engineering. When charge separation (CS) is slower than consequent charge recombination (CR), formation of a CT state is not apparent, yet the CT process provides parallel pathways for deactivation of electronically excited systems. The nuclear, or Franck-Condon (FC), contributions to the CT kinetics, as implemented by various formalisms based on the Marcus transition-state theory, provide an excellent platform for designing systems that produce long-lived CT states. Such approaches, however, tend to underestimate the complexity of alternative parameters that govern CT kinetics. Here we show a comparative analysis of two systems that have quite similar FC CT characteristics but manifest distinctly different CT kinetics. A decrease in the donor-acceptor electronic coupling during the charge-separation step provides an alternative route for slowing down undesired charge recombination. These examples suggest that, while infrequently reported and discussed, cases where CR is faster than CS are not necessarily rare occurrences.     

How different is pyrimidine as a core component of DNA base from its diazine isomers: A DFT study?

Recent photoemission spectroscopic (X‐ray photoemission spectra) study revealed less dramatic chemical changes for pyrimidine (PyM, 1, 3‐diazine) with in its ionization potential. Present systematic study using density functional theory calculations shows that PyM is indeed quite different from its diazine isomers (PyD, 1, 2‐diazine and PyA, 1, 4‐diazine). It is discovered that the most stable isomer PyM is relaxed from C_2V to C₁ point symmetry with a total electronic energy deduction of ?15.86 kcal.mol^?1. Although not substantial, PyM has the smallest molecule shape (electronic spatial extent) and the largest HOMO‐LUMO energy gap of 5.65 eV; only one absorption band in the region of 200–300 nm of the UV‐Vis spectrum but three clusters of chemical shift in the carbon and hydrogen NMR spectra. The energy decomposition analyses revealed that the interaction energy (ΔE_Int) of PyM is preferred over PyA by 4.08 kcal.mol^?1 and over PyD by 22.32 kcal.mol^?1, with the preferred N? C? N bond revealed by graph theory.     

Does the DNA Binding Mode of a Molecule Affect its Ability to Interact With Singlet Oxygen?

Singlet oxygen is known to be a potent mutagenic agent and several biologically relevant molecules have been proposed to act as scavengers for this noxious species. However, numerous studies have been conducted in homogenous solution and the reactivity of singlet oxygen scavengers known to bind DNA has never been investigated in double-stranded DNA. In the following paper, we present the results obtained regarding the interaction between 4',6-diamidino-2-phenylindole (DAPI) and singlet oxygen. We show the molecule to be a potent scavenger of singlet oxygen in aqueous solution with an absolute rate constant (chemical and physical quenching of singlet oxygen) of (1.7 ± 0.3) × 10⁷  m ⁻¹ s⁻¹. In addition, we demonstrate that the binding mode of a singlet oxygen scavenger to DNA can strongly influence its reactivity toward singlet oxygen. In the case of DAPI, while the molecule exhibits a chemical reaction with singlet oxygen when the molecule is free in aqueous solution or intercalated in GC sequences of DNA, DAPI becomes chemically unreactive toward singlet oxygen when bound in the minor groove of DNA AT sequences.     

Preparation of PLL-PEG-PLL and its application to DNA encapsulation

With the successful sequencing of Human Genome, it would be possible to cure all diseases by gene ther- apy in the near future. However, one of the major problems in gene therapy is the development of gene vectors. To date, there are two kinds of gene vectors, namely, viral and non-viral gene vectors. Viruses are widely used as vectors in gene therapy, with the trans- fection efficiency being relatively high, but they have the safety problems such as immunogenicity, non- biocompatibility and …     

Is it possible to predict the average surface hydrophobicity of a protein using only its amino acid composition?

Hydrophobicity is one of the most important physicochemical properties of proteins. Moreover, it plays a fundamental role in hydrophobic interaction chromatography, a separation technique that, at present time, is used in most industrial processes for protein purification as well as in laboratory scale applications. Although there are many ways of assessing the hydrophobicity value of a protein, recently, it has been shown that the average surface hydrophobicity (ASH) is an important tool in the area of protein separation and purification particularly in protein chromatography. The ASH is calculated based on the hydrophobic characteristics of each class of amino acid present on the protein surface. The hydrophobic characteristics of the amino acids are determined by a scale of aminoacidic hydrophobicity. In this work, the scales of Cowan-Whittaker and Berggren were studied. However, to calculate the ASH, it is necessary to have the three-dimensional protein structure. Frequently this data does not exist, and the only information available is the amino acid sequence. In these cases it would be desirable to estimate the ASH based only on properties extracted from the protein sequence. It was found that it is possible to predict the ASH from a protein to an acceptable level for many practical applications (correlation coefficient > 0.8) using only the aminoacidic composition. Two predictive tools were built: one based on a simple linear model and the other on a neural network. Both tools were constructed starting from the analysis of a set of 1982 non-redundant proteins. The linear model was able to predict the ASH for an independent subset with a correlation coefficient of 0.769 for the case of Cowan-Whittaker and 0.803 for the case of Berggren. On the other hand, the neural model improved the results shown by the linear model obtaining correlation coefficients of 0.831 and 0.836, respectively. The neural model was somewhat more robust than the linear model particularly as it gave similar correlation coefficients for both hydrophobicity scales tested, moreover, the observed variabilities did not overcome 6.1% of the mean square error. Finally, we tested our models in a set of nine proteins with known retention time in hydrophobic interaction chromatography. We found that both models can predict this retention time with correlation coefficients only slightly inferior (11.5% and 5.5% for the linear and the neural network models, respectively) than models that use the information about the three-dimensional structure of proteins.     

What is the minimum number of water molecules required to dissolve a potassium chloride molecule?

This work answers an unsolved question that consists of determining the least number of water molecules necessary to separate a potassium chloride molecule. The answer based on accurate quantum chemical calculations suggests that tetramers are the smallest clusters necessary to dissociate KCl molecules. The study was made with Møller‐Plesset second‐order perturbation theory modified with the cluster theory having single, double, and perturbative triple excitations. With this extensive study, the dissociation of KCl molecule in different water clusters was evaluated. The calculated results show that four water molecules stabilize a solvent separated K⁺/Cl^? ion‐pair in prismatic structure and with six water molecules further dissociation was observed. Attenuated total reflection infrared spectroscopy of KCl dissolved in water establishes that clusters are made of closely bound ions with a mean of five water molecules per ion‐pair [K⁺(H₂O)₅Cl^?]. (Max and Chapados, Appl Spectrosc 1999, 53, 1601; Max and Chapados, J Chem Phys 2001, 115, 2664.) The calculated results tend to support that five water molecules leads toward the formation of contact ion‐pair. The structures, energies, and infrared spectra of KCl molecules in different water clusters are also discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

What governs the charge transfer in DNA? The role of DNA conformation and environment

Charge transfer in DNA has received much attention in the last few years due to its role in oxidative damage and repair in DNA and also due to possible applications of DNA in nanoelectronics. Despite intense experimental and theoretical efforts, the mechanism underlying long-range hole transport is still unresolved. This is in particular due to the sensitive dependence of charge transfer on the complex structure and dynamics of DNA and the interaction with the solvent, which could not be addressed adequately in the modeling approaches up to now. In this work, we study the factors governing hole transfer in detail, using a DFT-based fragment-orbital method, which allows to compute the charge transfer parameters along multinanosecond molecular dynamics simulations. Environmental effects are captured using a hybrid quantum mechanics-molecular mechanics (QM/MM) coupling scheme. This methodology allows to analyze several factors responsible for charge transfer in DNA in detail. The fluctuation of counterions, strongly counterbalanced by the surrounding water, leads to large oscillations of onsite energies, which govern the energetics of hole propagation along the DNA strand. In contrast, the electronic couplings depend only on DNA conformation and are not affected by the solvent. In particular, the onsite energies are strongly correlated between neighboring nucleobases, indicating that a conformational-gating type of mechanism may be induced by the collective environmental degrees of freedom.     

How are small ions involved in the compaction of DNA molecules?

DNA is a genetic material found in all life on Earth. DNA is composed of four types of nucleotide subunits, and forms a double-helical one-dimensional polyelectrolyte chain. If we focus on the microscopic molecular structure, DNA is a rigid rod-like molecule. On the other hand, with coarse graining, a long-chain DNA exhibits fluctuating behavior over the whole molecule due to thermal fluctuation. Owe to its semiflexible nature, individual giant DNA molecule undergoes a large discrete transition in the higher-order structure. In this folding transition into a compact state, small ions in the solution have a critical effect, since DNA is highly charged. In the present article, we interpret the characteristic features of DNA compaction while paying special attention to the role of small ions, in relation to a variety of single-chain morphologies generated as a result of compaction.     

Is Genetic Engineering a Route to Enhance Microalgae-Mediated Bioremediation of Heavy Metal-Containing Effluents?

Contamination of the biosphere by heavy metals has been rising, due to accelerated anthropogenic activities, and is nowadays, a matter of serious global concern. Removal of such inorganic pollutants from aquatic environments via biological processes has earned great popularity, for its cost-effectiveness and high efficiency, compared to conventional physicochemical methods. Among candidate organisms, microalgae offer several competitive advantages; phycoremediation has even been claimed as the next generation of wastewater treatment technologies. Furthermore, integration of microalgae-mediated wastewater treatment and bioenergy production adds favorably to the economic feasibility of the former process—with energy security coming along with environmental sustainability. However, poor biomass productivity under abiotic stress conditions has hindered the large-scale deployment of microalgae. Recent advances encompassing molecular tools for genome editing, together with the advent of multiomics technologies and computational approaches, have permitted the design of tailor-made microalgal cell factories, which encompass multiple beneficial traits, while circumventing those associated with the bioaccumulation of unfavorable chemicals. Previous studies unfolded several routes through which genetic engineering-mediated improvements appear feasible (encompassing sequestration/uptake capacity and specificity for heavy metals); they can be categorized as metal transportation, chelation, or biotransformation, with regulation of metal- and oxidative stress response, as well as cell surface engineering playing a crucial role therein. This review covers the state-of-the-art metal stress mitigation mechanisms prevalent in microalgae, and discusses putative and tested metabolic engineering approaches, aimed at further improvement of those biological processes. Finally, current research gaps and future prospects arising from use of transgenic microalgae for heavy metal phycoremediation are reviewed.     

How strong can the bend be on a DNA helix from cisplatin? DFT and MP2 quantum chemical calculations of cisplatin-bridged DNA purine bases

The B3LYP/6-31G(d) level of theory was used for the optimization of [Pt(NH(3))(4)](2+), [Pt(NH(3))(3)(H(2)O)](2+), cis-[Pt(NH(3))(2)(H(2)O)(2)](2+), and related platinum complexes. In addition, water or ammonium ligands were replaced by DNA purine bases so that finally cis-diammineplatinum with two bases (Pt-bridged complexes) is obtained. Single point calculations using the MP2/6-31+G(d) method were performed on the obtained reference geometries and were utilized for estimating bond dissociation energies (BDEs) and stabilization energies, and for electron density analyses. After reoptimization, IR spectra were determined from HF second derivatives. It was found that replacement of both water and ammonium by the DNA base is an exothermic process (20-50 kcal/mol depending on the ligands present in the complex). Asymmetric structures with one interbase H-bond were obtained for cis-diammine[bond](N(7),N(7)'-diadenine)[bond]platinum and mixed cis-diammine[bond](N(7)-adenine)[bond](N(7)-guanine)[bond]platinum complexes. In the case of the diguanine Pt-bridge, a symmetrical complex with two ammonium...O(6) H-bonds was found. The higher stabilization energy of the di-guanine complex is linked to a larger component of the Coulombic interaction. However, the BDE of Pt[bond]N(7)(G) is smaller in this complex than the BDE of Pt[bond]N(7)(G) from the mixed Pt[bond]AG complex. Also, steric repulsion of the ligands is about 10 kcal/mol smaller for the asymmetrical Pt[bond]AA and Pt[bond]AG bridges. The influence of the trans effect on DBE can be clearly seen. Adenine exhibits the largest trans effect, followed by guanine, ammonium, and water. The strength of the H-bond can be determined from the IR spectra. The strongest H-bond is the interbase H-bridge between adenine and guanine in the mixed Pt[bond]AG complex; otherwise, the H-bonds of adenine complexes are weaker than in guanine complexes. BDE can be traced in the guanine-containing complexes. The nature of the covalent bonding is analyzed in terms of partial charges and MO. A general explanation of the lower affinity of transition metals to oxygen than nitrogen can be partially seen in the less favorable geometrical orientation of lone electron pairs of oxygen.     

Structures and stability of lithium monosilicide clusters SiLin (n = 4–16): What is the maximum number,magic number,and core number for lithium coordination to silicon?

In the coordination, hypervalent and cluster chemistry, three important characteristic properties are the maximum coordination number, magic number, and core coordination number. Yet, few studies have considered these three numbers at the same time for an ML(n) cluster with n larger than 8. In this article, we systematically studied the three properties of SiLi(n) (n = 4-16) clusters at the B3LYP/6-31G(d), B3LYP/6-311++G(2d), and CCSD(T)/6-311++G(3df)//B3LYP/6-311++G(2d) (for energy only) levels. Various isomeric forms with different symmetries were calculated. For each SiLi(n) (n = 4-9), silicon cohesive energy (cE) from SiLi(n) --> Si + Li(n) reaction, vertical ionization potential (vIP), and vertical electron affinity (vEA) were obtained for the lowest-energy isomer. We found that the maximum Li-coordination number of Si is 9, which is the largest number among the known MLi(n) clusters. All cE, vIP, and vEA values predicted that 6 is the magic Li-coordination number of Si. For small SiLi(n) (n < or = 6) clusters, Li atoms favor direct coordination to Si, whereas for larger SiLi(n) (n > or = 7) clusters, there is a core cluster that is surrounded by excessive Li atoms. The core Li-coordination number is 6 for SiLi(n) (n = 7,8), 7 for SiLi(n) (n = 9,10), 8 for SiLi(n) (n = 11-15) and 9 for SiLi(n) (n > or = 16). Through the calculations, we verified the relationship between the structure and stability of SiLi(n) with the maximum coordination number, magic number, and core coordination number.     

Interaction of graphene with antipsychotic drugs: Is there any charge transfer process?

Antipsychotics represent an effective therapy for schizophrenia (a chronic mental disorder). Their benefits are related to the interaction of the drugs with dopamine D2 receptor (D2R). Antipsychotics are classified as agonists or antagonists. One of the working hypotheses is that there is a charge transfer process between the drugs and the receptors, which is different for agonists and antagonists. To have more insight into the nature of the interaction of these molecules and the differences between agonists and antagonists, we analyze the interaction of graphene with three molecules: dopamine, pramipexole (an agonist of dopamine), and risperidone (an antagonist of dopamine). The idea is to use graphene as a simple model to analyze the charge transfer process of these three drugs. Optimized structures, atomic charges, and Density of States results indicate that global charges of dopamine and pramipexole are similar, while for risperidone, it is more than double. Pramipexole is an agonist, and the charge transfer process is similar to that of dopamine. Risperidone is an antagonist, and the charge transfer process is different from dopamine. The charge transfer is more significant with risperidone than with dopamine, and this could be related to the mechanism of action. This is in agreement with the working hypotheses that establish that it is possible to distinguish between agonists and antagonists since they have different capacity to transfer charge.     

Is the dynamical polarization a significant part of the contribution of the triples to the correlation energy?

One may call dynamical polarization of doubly excited configurations the energy lowering of these configurations under the response of the other electrons to the so-created fluctuation of the electric field. This contribution of triply excited configurations may be identified and calculated through a computation that only requires a computation time proportional to the sixth power of the number of molecular orbitals (MOs), instead of the seventh power for the total contribution of the triples. Its amplitude depends on the choice of the MOs and becomes important when localized MOs are used.     

Synthesis of a New Cobalt （Ⅱ） Complex and its Interaction with DNA

A new complex of bis(N-benzyl benzotriazole-N^3) dichloro Co(Ⅱ) (Co(Ⅱ)L2Cl2) was synthesized and its crystal was characterized. The interaction of this new complex with fs-DNA was studied by electrochemical and UV spectrophotometric method. In 0.01 mol/L pH 4.2 Tris-HCl buffer solution Co(Ⅱ)L2Cl2 has two reductive peaks with peak potentials at 0.38 V and 0.27 V, respectively, and an oxidative peak at 1.05 V. After the addition of DNA, the peak currents decrease and the peak potential at 0.27 V shifts negatively. The UV spectrophotometric experiment indicates that the maximum absorbance of Co(Ⅱ)L2Cl2 at 204 nm decreases and exhibits bathochromic shift after the addition of DNA. All the results reveal that Co(Ⅱ)L2Cl2binds with DNA by intercalation as well as electrostatic interaction.     

Synthesis of a New Cobalt (II) Complex and its Interaction with DNA

The interaction of metal complexes with DNA has been widely studied by differentmethods such as spectrophotometry, light scattering technique, fluorometry1-3. Manycomplexes such as Co(phen)2 ,Co(en)2 ,Fe(EDTA)2- etc.4,5 have been synthesized and 3+ 3+their effect on DNA has been studied in order to further explain the mechanism of genemutation, anti-cancer or cancer-induced reason and DNA targeted drugs. In this paper,a new cobalt complex was synth…     

Is cellulose degradation due to β-elimination processes a threat in mass deacidification of library books?

As papers become acidic and brittle over time, libraries apply mass deacidification processes to their collections in order to neutralize acids and deposit an alkaline reserve in the paper. Books commonly treated by mass deacidification have undergone natural aging of up to 150?years. The risk of alkali-induced degradation of cellulosic material upon mass deacidification remains uncertain. In the present study, the extent of β-elimination-type degradation reactions was investigated by comparing deacidified and non-deacidified counterparts, using deacidified library materials and identical issues of non-deacidified books from second-hand book shops. The study dealt with only naturally-aged papers focusing on investigation of immediate effects of mass deacidification rather than a long-term impact. Gel permeation chromatography coupled with carbonyl group labeling gave insight into cellulose chain cleavage as well as into the behavior of oxidized functionalities. Processes occurring under natural aging conditions were compared to those upon artificial oxidation of model pulps. Library books did not show a significant reduction in molecular weight after mass deacidification compared to the non-deacidified controls, which stands in contrast to oxidized model pulps. The models showed a more pronounced loss of molecular weight upon deacidification treatments. A decrease in carbonyl groups other than reducing ends was found to occur. Thus, oxidized functionalities were found to be reactive in mass-deacidification reactions; the different behavior was traced down to particular regions of oxidative damage along the cellulose chains. In general, β-elimination processes did not pose a large risk factor upon mass deacidification treatments of the naturally-aged library material tested.     

Application of magnetic and core–shell nanoparticles to determine enrofloxacin and its metabolite using laser induced fluorescence microscope

A unique analytical method using nanoparticles and laser-induced fluorescence microscopy (LIFM) was developed to determine enrofloxacin in this work. For sample pretreatment, two different kinds of particles, i.e., synthesized dye-doped core–shell silica nanoparticles and magnetic micro-particles (MPs), were used for fluorescent tagging and concentrating the enrofloxacin, respectively. The antibody of enrofloxacin was immobilized on the synthesized FITC-doped core–shell nanoparticles, and the enrofloxacin target was extracted by the MPs. At this moment, the average number of antibodies on each core–shell silica nanoparticle was ∼0.9, which was determined by the fluorescence ratiometric method. The described method was demonstrated for a meat sample to determine enrofloxacin using LIFM, and the result was compared with enzyme-linked immunosorbent assay (ELISA). The developed technique allowed the simplified analytical procedure, improved the detection limit about 54-fold compared to ELISA.