4<Emphasis Type="Italic">p</Emphasis><Superscript>2</Superscript> resonances in photoionization from 4<Emphasis Type="Italic">s</Emphasis>4<Emphasis Type="Italic">p</Emphasis> levels in neutral zinc

In neutral zinc the 4p ² configuration lies above the 3d ¹⁰4s ionization limit and its levels become perturbers in the continuum. Lines have been identified in the Zn I spectrum for the multiplet, whereas no lines have been found for transitions to 4p ^{2 1} D or ¹ S. In this paper, cross sections for photoionization from 4s4p levels are reported that reveal the positions and widths of the 4p ² resonances. Calculations were performed using the multiconfiguration Hartree-Fock (MCHF) and B-spline R-matrix (BSR) method. Results from Breit–Pauli calculations that ignore the background continua are also presented. Included in the latter are energies for the levels and transition data (transition energies, line strengths, f-values, and A-rates) for all E1 transitions between these levels. Transition energies and the agreement in the length and velocity values, particularly for allowed transitions, indicate the accuracy of the computational model. Line widths are compared with other estimates. Contribution to the Serafin Fraga Memorial Issue.     

The unsubstituted <Emphasis Type="Italic">ortho</Emphasis>-amidino benzoic acid: crystal structure,characterization and p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> determination

The simplest o-amidino benzoic acid—2-(amino(imino)methyl)benzoic acid—has been isolated in 23 % yield as a side product of the reaction of phthalonitrile and ammonia along with desired 1-imino-1H-isoindol-3-amine. This amidino acid was fully characterized by nuclear magnetic resonance, IR spectroscopy, mass spectrometry; pK_a values were also determined. X-ray diffraction study and quantum chemical calculations revealed that in the solid state it exists as a zwitterion that is stabilized by intermolecular hydrogen bonds.     

Splitting of the <Emphasis Type="Italic">d</Emphasis><Superscript><Emphasis Type="Italic">N</Emphasis></Superscript> atomic states in icosahedral 3<Emphasis Type="Italic">d</Emphasis> metal endofullerenes M@C<Subscript>60</Subscript>

Group-theoretical and quantum-chemical investigations of the spectrum of low-lying excited states have been performed by the ROHF and FCI-RAS (Full CI in Restricted Active Space) methods for 3d metal endofullerenes (MEFs) M@C₆₀ (M =Mn, Cr, and Fe) in different charged states. The major purpose of this study is quantum-chemical verification of the anomalous (“non-Bethe’s”) character of splitting of the d ^N atomic states in an electrostatic field with icosahedral symmetry, predicted previously within the theory of integral invariants theory. The interrelation between the integral invariants theory and the quantumchemical methods applied in this work is considered in detail. Our calculations suggest that the d ^N atomic states in the icosahedral field generated by fullerene C60 (I _h ) on a metal atom (ion) remain non-split for different charged states of the metal and C₆₀. Reasons for this phenomenon and other possible approaches to verification of the prediction are discussed. It is demonstrated that the d ^N states of the encapsulated metal are split in icosahedral 3d MEFs only under very strong compression of these structures.     

Nickel catalysis for hydrogenation of <Emphasis Type="Italic">p</Emphasis>-dinitrobenzene to <Emphasis Type="Italic">p</Emphasis>-phenylenediamine

The activity of supported nickel catalysts (5–20% Ni) in the hydrogenation of p-dinitrobenzene to p-phenylenediamine was investigated. The catalysts were obtained by ureainduced precipitation. Activated carbon, alumina, titania, and silica gel were evaluated as supports. The most active catalysts, 5%Ni/TiO₂ and 20%Ni/SiO₂, provided 50–54% yields of p-phenylenediamine at complete dinitrobenzene conversion.     

Glutaraldehyde-modified electrode for nonlabeling voltammetric detection of <Emphasis Type="Italic">p16</Emphasis><Superscript><Emphasis Type="Italic">INK4A</Emphasis></Superscript> gene

A nonlabeling electrochemical detection method for analyzing the polymerase-chain-reaction-amplified sequence-specific p16 ^INK4A gene, in which the basis for the covalent immobilization of deoxyribonucleic acid (DNA) probe is described, has been developed. The self-assembly process was based on the covalent coupling of glutaraldehyde (GA) as an arm molecule onto an amino-functional surface. The p16 ^INK4A gene was used as the model target for the methylation detection of early cancer diagnosis. An amino-modified DNA probe was successfully assembled on the GA-coupling surface through the formation of Schiff base under potential control. The hybridization of amino-modified DNA probes with the target was investigated by means of electrochemical measurements, including cyclic voltammetry and square wave voltammetry. Furthermore, the functions of GA coupling for sequence-specific detection were compared with those obtained based on mercaptopropionic acid. Hybridization experiments indicated that the covalent coupling of GA was suitable for the immobilization of DNA probe and was sensitive to the electrochemical detection of single-base mismatches of label-free DNA targets in hybridization. Moreover, reported probe-modified surfaces exhibited excellent stability, and the hybridization reactions were found to be completely reversible and highly specific for recognition in subsequent hybridization processes. The strategy provided the potential for taking full advantage of existing modified electrode technologies and was verified in microarray technology, which could be applied as a useful and powerful tool in electrochemical biosensor and microarray technology.     

Estimation of uncertainty in p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values determined by potentiometric titration

A procedure is presented for estimation of uncertainty in measurement of the pK(a) of a weak acid by potentiometric titration. The procedure is based on the ISO GUM. The core of the procedure is a mathematical model that involves 40 input parameters. A novel approach is used for taking into account the purity of the acid, the impurities are not treated as inert compounds only, their possible acidic dissociation is also taken into account. Application to an example of practical pK(a) determination is presented. Altogether 67 different sources of uncertainty are identified and quantified within the example. The relative importance of different uncertainty sources is discussed. The most important source of uncertainty (with the experimental set-up of the example) is the uncertainty of pH measurement followed by the accuracy of the burette and the uncertainty of weighing. The procedure gives uncertainty separately for each point of the titration curve. The uncertainty depends on the amount of titrant added, being lowest in the central part of the titration curve. The possibilities of reducing the uncertainty and interpreting the drift of the pK(a) values obtained from the same curve are discussed.     

Interactions of Puerarin with Micelles: p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> Shifts and Thermodynamics

In this paper, the effect of varying hydrophobic chain lengths on the acid-base equilibrium of an isoflavone, puerarin, in cationic micelles has been studied. The interaction of puerarin with three types of micelles of identical positively charged head groups and varying tail lengths, viz., DTAB, TTAB and CTAB, shows that there is a shift in the apparent pK _a in the direction that favors the displacement of the acid-base equilibrium of puerarin towards the base form. The relative location depth of puerarin in micelles is determined according to their dielectric values (D) taking into account that lower D values correspond to deeper location. It is evident that the reduction of polarity favors the deprotonation of puerarin. The isothermal titration calorimetry measurements show that the effect of puerarin on the thermodynamic properties of micellization is enhanced in the order CTAB>TTAB>DTAB and the results illustrate that puerarin has more affinity for micelles with greater chain length.     

Synthesis of epothilones molecule fragment (15<Emphasis Type="Italic">R</Emphasis>)-C<Superscript><Emphasis Type="Italic">13</Emphasis></Superscript>-C<Superscript><Emphasis Type="Italic">21</Emphasis></Superscript> from D-mannitol

Efficient synthesis of an epothilone molecules fragment (15R)-C¹³-C²¹ was carried out from D-mannitol through its conversion into methyl 2,3-O-cyclohexylidene-D-glycerate followed by the cyclopropanation of the ester group with ethylmagnesium bromide in the presence of titanium(IV) isopropoxide and the transformation of the obtained cyclopropanol into the corresponding 2-substituted allyl bromide. The coupling of the latter catalyzed by copper with 2-methylthiazolyl-4-magnesium bromide, the shift of a double carbon-carbon bond in the product obtained into the position, conjugated with the thiazole ring, and the common transformation of the protected 1,2-diol function afforded the target compound in 15% yield.     

Outliers detection in the statistical accuracy test of a p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> prediction

The regression diagnostics algorithm REGDIA in S-Plus is introduced to examine the accuracy of pK _a predicted with four programs: PALLAS, MARVIN, PERRIN and SYBYL. On basis of a statistical analysis of residuals, outlier diagnostics are proposed. Residual analysis of the ADSTAT program is based on examining goodness-of-fit via graphical diagnostics of 15 exploratory data analysis plots, such as bar plots, box-and-whisker plots, dot plots, midsum plots, symmetry plots, kurtosis plots, differential quantile plots, quantile-box plots, frequency polygons, histograms, quantile plots, quantile-quantile plots, rankit plots, scatter plots, and autocorrelation plots. Outliers in pK _a relate to molecules which are poorly characterized by the considered pK _a program. Of the seven most efficient diagnostic plots (the Williams graph, Graph of predicted residuals, Pregibon graph, Gray L–R graph, Index graph of Atkinson measure, Index graph of diagonal elements of the hat matrix and Rankit Q–Q graph of jackknife residuals) the Williams graph was selected to give the most reliable detection of outliers. The six statistical characteristics, F_exp,R²,R_P²,MEP,AIC{F_{\rm exp},R^{2},R_{\rm P}^{2},{\it MEP},{\it AIC}}, and s in pK _a units, successfully examine the specimen of 25 acids and bases of a Perrin’s data set classifying four pK _a prediction algorithms. The highest values F_exp,R²,R_P²{F_{\rm exp},R^{2},R_{\rm P}^{2}} and the lowest value of MEP and s and the most negative AIC have been found for PERRIN algorithm of pK _a prediction so this algorithm achieves the best predictive power and the most accurate results. The proposed accuracy test of the REGDIA program can also be extended to test other predicted values, as log P, log D, aqueous solubility or some physicochemical properties.     

Spatial structure and stability of Mo<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript>Si<Subscript><Emphasis Type="Italic">m</Emphasis></Subscript> nanoparticles

By means of the ab initio DMol³ method Mo _n Si _m nanoparticles and fragments of Mo₃Si and MoSi₂ crystal lattices are theoretically modeled. For both crystals a few neutral Mo₄Si₆ and Mo₆Si₆ fragments of different shapes and symmetry are considered. In each case, after cluster separation its geometry is optimized, as a result of which the geometric structure noticeably changes and its stability increases. In order to theoretically search for the spatial configurations of Mo₄Si₆ and Mo₆Si₆ nanoparticle, two approaches are used: 1) in the most stable Fe₄C₆ and Fe₆C₆ isomers found previously, iron and carbon atoms are replaced by molybdenum and silicon respectively and then the geometry is optimized to obtain new equilibrium distances and angles; 2) the search for main Mo₄Si₆ and Mo₆Si₆ configurations is performed using the binominal scheme, starting from Mo₂, MoSi, and Si₂ dimers. The nanoparticle structures are found to contain metal atom chains and isolated pairs and triples of silicon atoms. In most cases, the nanoparticle stability proves to be higher than that of the crystal clusters.     

Conducting materials prepared by the oxidation of <Emphasis Type="Italic">p</Emphasis>-phenylenediamine with <Emphasis Type="Italic">p</Emphasis>-benzoquinone

p-Phenylenediamine was oxidized with p-benzoquinone in the aqueous solutions of methanesulfonic acid (MSA). The conductivity of the products increased with increasing concentration of MSA from 1.5?×?10^?12 S cm^?1 in 0.1 M MSA up to 3.4?×?10^?4 S cm^?1 in 5 M MSA. The low-molecular-weight products are basically composed of one p-benzoquinone and two p-phenylenediamine molecules. Their molecular structure is discussed on the basis of mass, Fourier-transform infrared, Raman, NMR and electron paramagnetic resonance (EPR) spectroscopies. The formation of 2,5-di(p-phenylenediamine)-p-benzoquinone protonated with methanesulfonic acid best complies with the information provided by spectroscopic techniques. Its conversion to hydroquinone tautomer explains the formation of unpaired spins observed by EPR and their potential contribution to the conduction.     

Heat capacity and phonon spectra of <Emphasis Type="Italic">A</Emphasis><Superscript>III</Superscript>N

The low temperature heat capacities of three A ^IIInitrides, A ^III=Al, Ga and In, were measured by relaxation method in the temperature range 2–300 K and the corresponding entropies at the reference temperature 298.15 K were evaluated from the experimental data. The lattice heat capacity at constant volume was also assessed theoretically within harmonic crystal approximation by direct method using a combination of VASP software package to obtain the Hellmann-Feynman forces and the Phonon program to calculate the phonon spectra. The experimental data were analyzed by means of a Debye-Einstein model taking use of the calculated heat capacity and involving additionally an anharmonic contribution.     

Oxidation of <Emphasis Type="Italic">p</Emphasis>-Xylene

The review discusses the main procedures for producing terephthalic acid from p-xylene (primarily the Amoco process with the participation of Co, Mn, and Br salts), the oxidation mechanisms, alternative processes, and perspectives.     

Photolysis of <Emphasis Type="Italic">p</Emphasis>-benzoquinone and <Emphasis Type="Italic">p</Emphasis>-chloranil in aqueous sodium sulfite solution

Photosubstitution of the sulfo group for hydrogen (chlorine in chloranil) is observed under irradiation of sulfonated derivatives of hydroquinone formed upon dissolving of p-benzoquinone and p-chloranil in aqueous solutions of sodium sulfite. The quantum yield of the photochemical reaction is 0.18 ± 0.02 for p-benzoquinone. The rate constant of the thermal reaction of substitution is 5.5 × 10⁻⁴ l mol⁻¹ s⁻¹. The substitution reaction is sensitized by eosin upon irradiation with visible light. During the course of irradiation of sulfohydroquinones, the formation of a product with an absorption maximum at 235 nm was found. The product decays with a rate constant of 0.005 s⁻¹.     

Molecular structure of <Emphasis Type="Italic">N</Emphasis>-(<Emphasis Type="Italic">o</Emphasis>-and <Emphasis Type="Italic">p</Emphasis>-hydroxybenzyl)cytisine

The molecular structures of N-(o-and p-hydroxybenzyl)cytisine were investigated by NMR spectroscopy, x-ray structure analysis, and molecular modeling. It was found that NMR resonances of the OH and aromatic protons in N-(o-hydroxybenzyl)cytisine were doubled because of the presence of two conformers in solution. __________ Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 165–168, March–April, 2008.     

The group-theoretical structure of the atomic g shell: connection with the alternating group <Emphasis Type="Italic">A</Emphasis><Subscript>6</Subscript> as <Emphasis Type="Italic">L</Emphasis><Subscript>2</Subscript>(9)

The special projective linear groups PSL(2ℓ + 1) or L ₂(2ℓ + 1) of order 2ℓ(2ℓ + 1)(ℓ + 1) can be used to study atomic shells of electrons with angular momentum quantum number ℓ corresponding to the atomic p, d, f, and g shells for ℓ = 1, 2, 3, 4, respectively. For the atomic g shell the group L ₂(9) is isomorphic with the alternating group A ₆ on six objects of order 360 or the symmetry group of the 5-dimensional simplex, a 5-dimensional analogue of the tetrahedron with 6 vertices and 15 edges. This leads to the subgroup chain SO(9) ⊃ SO(5) ⊃ L ₂(9) for the atomic g shell analogous to the subgroup chain SO(7) ⊃ G ₂ ⊃ L ₂(7) ≈⁷ O for the atomic f shell. In the L ₂(9) group only the representations of spherical harmonics or sums thereof, Γ(Y_ℓ), with dimensions dim Γ(Y_ℓ) or dim Γ(Y_ℓ) ± 1 divisible by 9 are found to be individually reducible to irreducible representations (irreps) or sums of irreps of L ₂(9). This leads to term groupings such as S, PD, G, PF, DH, L, PK, DI, FH, M, FI, PO, DN, HK, R, etc., of increasing total dimension for the irreps of SO(9) for various g ⁿ configurations in the atomic g shell.     

The SAMPL6 challenge on predicting aqueous p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values from EC-RISM theory

The “embedded cluster reference interaction site model” (EC-RISM) integral equation theory is applied to the problem of predicting aqueous pK_a values for drug-like molecules based on an ensemble of tautomers. EC-RISM is based on self-consistent calculations of a solute’s electronic structure and the distribution function of surrounding water. Following-up on the workflow developed after the SAMPL5 challenge on cyclohexane-water distribution coefficients we extended and improved the methodology by taking into account exact electrostatic solute–solvent interactions taken from the wave function in solution. As before, the model is calibrated against Gibbs energies of hydration from the “Minnesota Solvation Database” and a public dataset of acidity constants of organic acids and bases by adjusting in total 4 parameters, among which only 3 are relevant for predicting pK_a values. While the best-performing training model yields a root-mean-square error (RMSE) of 1 pK unit, the corresponding test set prediction on the full SAMPL6 dataset of macroscopic pK_a values using the same level of theory exhibits slightly larger error (1.7 pK units) than the best test set model submitted (1.7 pK units for corresponding training set vs. test set performance of 1.6). Post-submission analysis revealed a number of physical optimization options regarding the numerical treatment of electrostatic interactions and conformational sampling. While the experimental test set data revealed after submission was not used for reparametrizing the methodology, the best physically optimized models consequentially result in RMSEs of 1.5 if only improved electrostatic interactions are considered and of 1.1 if, in addition, conformational sampling accounts for quantum-chemically derived rankings. We conclude that these numbers are probably near the ultimate accuracy achievable with the simple 3-parameter model using a single or the two best-ranking conformations per tautomer or microstate. Finally, relations of the present macrostate approach to microstate pK_a results are discussed and some illustrative results for microstate populations are presented.     

Reaction of transsilylation of <Emphasis Type="Italic">N</Emphasis>-methyl-<Emphasis Type="Italic">N</Emphasis>-trimethylsilylacetamide with silanes ClCH<Subscript>2</Subscript>SiR<Superscript>1</Superscript>R<Superscript>2</Superscript>Cl

The reaction of N-methyl-N-trimethylsilylacetamide with silanes ClCH₂SiR¹R²Cl (R¹, R² = H, Me; H, Ph; Ph₂) leads to the formation of (O→Si) chelate compounds with pentacoordinate silicon: N-[chloro(methyl)-silyl]methyl-, N-[chloro(phenyl)silyl]methyl-, and N-[chloro(diphenyl)silyl]methyl-N-methylacetamides. From the data of multinuclear NMR spectroscopy, the intermediates of the reaction of N-methyl-N-trimethylsilylacetamide with ClCH₂SiPhHCl and ClCH₂SiPh²Cl are stable in CDCl₃ solution at room temperature during several days and slowly rearrange to the final (O–Si) chelate compounds.     

A <Emphasis Type="Italic">k</Emphasis>-nearest neighbor classification of hERG K<Superscript>+</Superscript> channel blockers

A series of 172 molecular structures that block the hERG K⁺ channel were used to develop a classification model where, initially, eight types of PaDEL fingerprints were used for k-nearest neighbor model development. A consensus model constructed using Extended-CDK, PubChem and Substructure count fingerprint-based models was found to be a robust predictor of hERG activity. This consensus model demonstrated sensitivity and specificity values of 0.78 and 0.61 for the internal dataset compounds and 0.63 and 0.54 for the external (PubChem) dataset compounds, respectively. This model has identified the highest number of true positives (i.e. 140) from the PubChem dataset so far, as compared to other published models, and can potentially serve as a basis for the prediction of hERG active compounds. Validating this model against FDA-withdrawn substances indicated that it may even be useful for differentiating between mechanisms underlying QT prolongation.     

Determination of tyrosine using <Emphasis Type="Italic">p</Emphasis>-sulfonated calix[<Emphasis Type="Italic">n</Emphasis>]arene modified electrode

Cyclic voltammetry was used to detect p-sulfonated calix[n]arenas (SCnA) how to immobilize on gold surface. P-sulfonated calix[n]arenes not only increased the specific surface area of the modified electrode, but also improved the enrichment ability of tyrosine. This led to a significant increase in peak current, and improved the sensitivity of tyrosine determination on the p-sulfonated calix[n]arenes-modified electrode. The modified electrode showed good catalytic ability of l-tyrosine oxidation reaction. The peak current of l-tyrosine increased and the oxidation peak potential shifted negatively with cavity size of the SCnA-modified electrode, which indicated that the catalytic ability of the modified electrode to l-tyrosine oxidation reaction was also enhanced. For the tyrosine guest molecule, the order of electrochemical activity and magnitude of catalytic ability of the oxidation reaction of the three modified gold electrodes was as follows: SC4A?>?SC6A?>?SC8A. The electrode had high selectivity and stability for the determination of tyrosine, with a wide linear range, low detection limit and high sensitivity at different concentrations under different pH values. This resulted in an accurate, fast, sensitive electrochemical method for the determination of tyrosine. The sensor was used for the determination of tyrosine in human urine with satisfactory results.