Development of a highly selective molecular topological index

The highly selective molecular topological indices EAID and 2‐EAID were extended in order to further improve their discrimination capability. The new 3‐EAID index is obtained as a combination of extended EAID index and the Wiener index. They were tested by screening three data sets of structures comprising over 36 million alkane trees with 25 vertices, 15 million benzenoids with 14 benzene rings, and 20 million compounds taken from real data sets. While EAID index respectively exhibited 75, 29, and 10 pair degeneracies in the three data sets, and 2‐EAID index respectively exhibited 15, 1, and 2 pair degeneracies, the 3‐EAID index could discriminate all unique molecules in virtual and real data sets with >107 million compounds including the molecules stated eralier. Therefore, the new index possesses not only significance in theory but also the practical application value for confirming new compounds (the number of registered substances in Chemical Abstracts Service in June 2015 is over 99 million). Also, 3‐EAID and 2‐EAID, as well as EAID could be used for administration of chemical information systems such as large structural data sets, evaluation of organic structures, and computer‐aided synthesis. Copyright © 2015 John Wiley & Sons, Ltd.     

Development and validation of RP‐HPLC‐fluorescence method for quantitative determination of quinidine,a probe substrate for P‐glycoprotein inhibition assay using Caco‐2 cell monolayer

A simple, sensitive and specific reverse‐phase high‐performance liquid chromatographic (RP‐HPLC) method with fluorescence detection was developed for quantitation of quinidine from HBSS buffer. The method was applicable in the bi‐directional transport assay for evaluation of the inhibitory effect of test compounds on P‐glycoprotein‐mediated quinidine transport; quinidine was used as a probe P‐glycoprotein substrate. The calibration curve was linear (correlation coefficient ≥99) in the range 0.30–100.00 nm. The method was validated and is specific and sensitive with limit of quantitation of 300 pm for quinidine. The method was found to be accurate and precise in the working calibration range. Stability studies were carried out at different storage conditions where the analyte was found to be stable. The applicability and reliability of the analytical method was evaluated by successful demonstration of efflux ratio (P_appB → A/P_appA → B) in the Caco‐2 cell monolayer efflux assay. The efflux ratio for quinidine (100 nm) alone was 10.8, which reduced to less than 2 in the presence of the classical P‐gp inhibitors verapamil and ketoconazole (100 μm each). Copyright © 2009 John Wiley & Sons, Ltd.     

On a new semi‐empirical electrotopological index for QSRR models

A new semi‐empirical electrotopological index, I_SET, for quantitative structure–retention relationships (QSRR) models was developed based on the refinement of the previously published semi‐empirical topological index, I_ET. We demonstrate that the values of C_i fragments that were firstly attributed from the experimental chromatographic retention and theoretical deductions have an excellent relationship with the net atomic charge of the carbon atoms. Thus, the values attributed to the vertices in the hydrogen‐suppressed graph of carbon atoms (C_i) are calculated from the correlation of the net atomic charge in each carbon atom, which is obtained from quantum chemical semi‐empirical calculations, and the C_i fragments for primary, secondary, tertiary and quaternary carbon atoms (1.0, 0.9, 0.8 and 0.7, respectively) obtained from the experimental values. This shows that I_ET encoded this quantum physical reality and that it is possible to calculate a new I_SET (the semi‐empirical electrotopological index) through the net atomic charge values obtained from a Mulliken population analysis using the semi‐empirical AM1 method and their correlation with the values attributed to the different types of carbon atoms. This demonstrates that the I_SET encodes information on the charge distribution of the solute on which dispersive and electrostatic interactions between the solute (alkanes and alkenes) and the stationary phase strongly depend. Thus, this new method can be considered as an initial step towards forthcoming QSRR/QSAR studies. Copyright © 2008 John Wiley & Sons, Ltd.     

TopoMS: Comprehensive topological exploration for molecular and condensed‐matter systems

We introduce Topo MS, a computational tool enabling detailed topological analysis of molecular and condensed‐matter systems, including the computation of atomic volumes and charges through the quantum theory of atoms in molecules, as well as the complete molecular graph. With roots in techniques from computational topology, and using a shared‐memory parallel approach, Topo MS provides scalable, numerically robust, and topologically consistent analysis. Topo MS can be used as a command‐line tool or with a GUI (graphical user interface), where the latter also enables an interactive exploration of the molecular graph. This paper presents algorithmic details of Topo MS and compares it with state‐of‐the‐art tools: Bader charge analysis v1.0 (Arnaldsson et al., 01/11/17) and molecular graph extraction using Critic2 (Otero‐de‐la‐Roza et al., Comput. Phys. Commun. 2014, 185, 1007). Topo MS not only combines the functionality of these individual codes but also demonstrates up to 4× performance gain on a standard laptop, faster convergence to fine‐grid solution, robustness against lattice bias, and topological consistency. Topo MS is released publicly under BSD License. © 2018 Wiley Periodicals, Inc.     

Quantum‐based models of charge‐dependent potential energy surfaces: Three‐state models

Quantum‐based models of how potential energies depend on charge are developed from a three‐state model, at the level of neglecting state‐to‐state overlap. The energy as a function of charge is defined as proposed previously (Valone and Atlas, J Chem Phys 2004, 120, 7262). With this definition, addition of a third state smooths the derivatives of the energy model with respect to charge at integer values of charge that are in the interior of the allowed charge range. These derivatives are related to the chemical potential. At the dissociation limit, this model converges to established limits. Another dependence is proposed that uses two different charges simultaneously. The concepts are illustrated, with calculations on an OH molecule. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Octane numbers (ONs) of hydrocarbons: a QSPR study using optimal topological indices for the topological equivalents of the ONs

A new method proposed for solving QSPR tasks is based on transition from numerical values to topological equivalents (TEs) of physicochemical properties of chemical compounds. The TEs are unambiguously related to corresponding properties; for n-alkanes, they are linear functions of the number, n, of carbon atoms. Since the TE depends only on the corresponding physicochemical parameter, it can be calculated for any hydrocarbon using the same relationships as those known for n-alkanes. The optimal topological index (OTI) constructed using the chemical structure matrix for TEs usually has a much smaller basis compared to the topological index obtained by analogous procedure for the physicochemical property. An algorithm for modeling of physicochemical properties using the TEs was developed and evaluated taking the octane numbers of alkanes and cycloalkanes as examples. Dedicated to Academician G. A. Abakumov on the occasion of his 70th birthday. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1619–1631, September, 2007.     

Prediction of branch on branch and topological characteristics of low‐density polyethylene polymerization by a novel stochastic approach

A novel approach using Monte Carlo method applied to simulation of low‐density polyethylene (LDPE) polymerization in tubular reactor showing topological characteristics, and the comprehensive kinetic mechanism has been taken into consideration. The results show the precise details of the structure of a chain in the three levels of the backbone, the main branches, and branches on branch. The chain types include dead polymer, dead polymer with unsaturated end, and live polymer with primary radical, secondary radical, and tertiary radical. In this work, the branches on branch were identified in terms of number, length, and position of the branch. Sixty percent of branches on branch are 1 to 5 carbons long, and the longest branch on branch is about 50 carbons. Thus, this study provides a tool for more accurately mapping the polymer chains architecture, superior to determine the number, and position of long‐ and short‐chain branches in past researches. Finally, this approach will advance the prediction of microstructure‐related properties of polymer one step further.     

Synthesis,crystal structure and topological analysis of a three‐dimensional polymeric network based on zinc(II), potassium and 5‐sulfobenzene‐1,3‐dicarboxylate (SIP)

Aromatic polycarboxylate linkers provide structural rigidity and strong interactions among the metal centre and the carboxylate O atoms. A new three‐dimensional coordination polymer namely, catena‐poly[potassium [tetraaqua(μ‐5‐sulfobenzene‐1,3‐dicarboxylato)zinc(II)]], {K[Zn(C₈H₃O₇S)(H₂O)₄]}_n or {K[Zn(SIP)(H₂O)₄]}_n, where SIP is 5‐sulfobenzene‐1,3‐dicarboxylate or 5‐sulfoisophthalate, was obtained and characterized by elemental analysis and IR vibrational spectroscopy, and the single‐crystal structure was determined by X‐ray diffraction analysis. The compound crystallizes in the monoclinic space group P2₁/n with Z = 4. Topological analysis revealed that K—O interactions form a two‐dimensional network, which is uninodal 4‐connected and can be described with a point symbol (4⁴.6²), and this plane network is classified as sql/Shubnikov . The layers are connected by Zn²⁺ ions coordinated to the SIP linker, forming a three‐dimensional network. This net is a trinodal (3,5,6)‐connected system with point symbol (3.4⁴.5².6².7³.8³).(3.4⁴.5².6².7).(3.7²).     

Development of a new highly efficient 17 X‐STR multiplex for forensic purposes

Currently, two of the most widely used X‐chromosome STR (X‐STR) multiplexes are composed by ten (GHEP‐ISFG decaplex) and 12 markers (Investigator Argus X‐12 Kit). The number of markers included is a drawback for complex relative testing cases, likewise the large size of some amplicons difficult their application to degraded samples. Here, we present a new multiplex of 17 X‐STRs with the aim of increasing both the resolution power and forensic applicability. This newly proposed set includes the X‐STRs of the GHEP‐ISFG decaplex, four X‐STRs from the Investigator Argus X‐12 Kit, three of them also included in the decaplex, and six additional more. In order to ensure the allele designation, an allelic ladder was developed. The validation of the present multiplex was carried out according to the revised guidelines by the SWGDAM (Scientific Working Group on DNA Analysis Methods). A total of 488 unrelated individuals from four different continents were analyzed. The forensic efficiency evaluation showed high values of combined power of discrimination in males (≥0.999999996) and females (≥0.999999999999995) as well as combined paternity exclusion probabilities in trios (≥0.99999998) and duos (≥0.999996). The results presented herein have demonstrated that the new 17 X‐STR set constitutes a high‐resolution alternative to the current X‐STR multiplexes.     

Observation of a Metastable P‐Heterocyclic Radical by Muonium Addition to a 1,3‐Diphosphacyclobutane‐2,4‐diyl

A 1,3‐diphosphacyclobutane‐2,4‐diyl contains a unique unsaturated cyclic unit, and the presence of radical‐type centers have been expected as a source of functionality. This study demonstrates that the P‐heterocyclic singlet biradical captures muonium (Mu=[μ⁺e^?]), the light isotope of a hydrogen radical, to generate an observable P‐heterocyclic paramagnetic species. Investigation of a powder sample of 2,4‐bis(2,4,6‐tri‐t‐butylphenyl)‐1‐t‐butyl‐3‐benzyl‐1,3‐diphosphacyclobutane‐2,4‐diyl using muon (avoided) level‐crossing resonance (μLCR) spectroscopy revealed that muonium adds to the cyclic P₂C₂ unit. The muon hyperfine coupling constant (A_μ) indicated that the phosphorus atom bearing the t‐butyl group trapped muonium to provide a metastable P‐heterocyclic radical involving the ylidic MuP(<)=C moiety. The observed regioselective muonium addition correlates the canonical formula of 1,3‐diphosphacyclobutane‐2,4‐diyl.     

Development of a highly sensitive and specific immunoassay for enrofloxacin based on heterologous coating haptens

In the paper, an enzyme-linked immunosorbent immunoassay (ELISA) for detection of enrofloxacin was described using one new derivative of enrofloxacin as coating hapten, resulting in surprisingly high sensitivity and specificity. Incorporation of aminobutyric acid (AA) in the new derivative of enrofloxacin had decreased the IC₅₀ of the ELISA for enrofloxacin from 1.3 μg L⁻¹ to as low as 0.07 μg L⁻¹. The assay showed neglect cross-reactivity for other fluoroquinolones but ofloxacin (8.23%), marbofloxacin (8.97%) and pefloxacin (7.29%). Analysis of enrofloxacin fortified chicken muscle showed average recoveries from 81 to 115%. The high sensitivity and specificity of the assay makes it a suitable screening method for the determination of low levels of enrofloxacin in chicken muscle without clean-up step.     

A co‐training algorithm for multi‐view data with applications in data fusion

In several scientific applications, data are generated from two or more diverse sources (views) with the goal of predicting an outcome of interest. Often it is the case that the outcome is not associated with any single view. However, the synergy of all measurements from each view may yield a more predictive classifier. For example, consider a drug discovery application in which individual molecules are described partially by several assay screens based on diverse profiles and partially by their chemical structural fingerprints. A common classification problem is to determine whether the molecule is associated with a particular disease. In this paper, a co‐training algorithm is developed to utilize data from diverse sources to predict the common class variable. Novel enhancements for variable importance, robustness to a mislabeled class variable, and a technique to handle unbalanced classes are applied to the motivating data set, highlighting that the approach attains strong performance and provides useful diagnostics for data analytic purposes. In addition, comparisons to a framework with data fusion using partial least squares (PLS) are also assessed on real data. An R package for performing the proposed approach is provided as Supporting information. Copyright © 2003 John Wiley & Sons, Ltd.