Medium-size Gaussian basis sets for hydrogen through argon

Summary Medium-sized Gaussian basis sets are reoptimized for the ground states of the atoms from hydrogen through argon. The composition of these basis sets is (4s), (5s), and (6s) for H and He, (9s5p) and (12s7p) for the atoms Li to Ne, and (12s8p) and (12s9p) for the atoms Na to Ar. Basis sets for the² P states of Li and Na, and the³ P states of Be and Mg are also constructed since they are useful in molecular calculations. In all cases, our energies are lower than those obtained previously with Gaussian basis sets of the same size.     

On molecular topological properties of hex‐derived networks

Topological indices are numerical parameters of a molecular graph, which characterize its topology and are usually graph invariant. In quantitative structure–activity relationship/quantitative structure–property relationship study, physico‐chemical properties and topological indices such as Randić, atom–bond connectivity (ABC), and geometric–arithmetic (GA) index are used to predict the bioactivity of chemical compounds. Graph theory has found a considerable use in this area of research. In this paper, we study hex‐derived networks HDN1(n) and HDN2(n), which are generated by hexagonal network of dimension n and derive analytical closed results of general Randić index R_α(G) for different values of α, for these networks of dimension n. We also compute the general first Zagreb, ABC, GA, ABC₄, and GA₅ indices for these hex‐derived networks for the first time and give closed formulae of these degree‐based indices for hex‐derived networks. Copyright © 2016 John Wiley & Sons, Ltd.     

Quantum chemical study of the host-guest inclusion complexes of the local anaesthetic drugs, procaine hydrochloride and butacaine hydrochloride, with α- and β-cyclodextrins

Quantum mechanical (QM) calculations were carried out in order to study the host-guest inclusion complexes of procaine hydrochloride (Pro-H) and butacaine hydrochloride (But-H) with α- and β-cyclodextrins (α- and β-CDs) by PM3 and AM1 methods. The systems were studied by a 1:1 (α-CD/Pro-H, α-CD/But-H, β-CD/Pro-H, and β-CD/But-H) stoichiometric ratio. In this work we calculated the energy of complex formation in vacuo, and this investigation was carried out on the basis of the host-guest approach. The stabilization energy results for the 1:1 host-guest inclusion complexes indicate that the β-CD/Pro-H complex is more stable than the α-CD/Pro-H complex. Furthermore, stabilization energy for the 1:1 inclusion complex of α-CD with But-H is lower than that for the 1:1 inclusion complex of β-CD with But-H. The calculation results show that all complexation processes for the four complexes are exothermic. Enthalpy changes for the α-CD/But-H and β-CD/Pro-H host-guest inclusion complexes are more negative than those for the other ones. ΔG ^o values for both the β-CD/Pro-H and α-CD/But-H complexes are negative. Correspondence: S. M. Hashemianzadeh, Department of Physical Chemistry, College of Chemistry, Iran University of Science and Technology, Tehran, Iran.     

Theory of Fast Capillary Gas Chromatography – Part 3: Column Performance vs. Gas Flow Rate

At the high pressure drop required for the fast analysis of complex mixtures, the equations for the column plate height, H, and plate duration, Q, as functions of the carrier gas velocity, u, differ substantially from the equations for the same quantities expressed via the carrier gas flow rate, F. While u as an independent pneumatic variable is more convenient for the theoretical studies, F is a more convenient as a control parameter in practical applications. Equations for H vs. u and for Q vs. u from Parts 1 and 2 are transformed here into expressions for H vs. F and Q vs. F. An efficiency-optimized flow rate (EOF) and a speed-optimized flow rate (SOF) are found. Expressions for these two quantities are considerably simpler than their velocity-based counterparts. In particular, SOF does not depend on column length, film thickness, and pressure drop.     

Comparison and prediction of the retention in micellar electrokinetic chromatography and microemulsion electrokinetic chromatography for disubstituted benzenes

Retention index (I), rather than retention factor (k), was found to be a more reasonable parameter for comparison of the relative affinity of disubstituted benzenes in MEEKC and MEKC, due to independent of I with the SDS surfactant concentration. MEKC and MEEKC may give similar or different I values, depending on types of moieties. With known I and K_ow for alkylbenzenes as references in MEKC and MEEKC, the values of K_ow for disubstituted benzenes can be estimated from the observed I values, where K_ow is the octanol–water distribution constant. In addition, a group additive approach can be used to predict I for disubstituted benzenes with different moieties from the average observed I for the disubstituted benzenes with same moieties. However, electronic effects and/or intramolecular interaction may result in the different observed I from prediction.     

Simultaneous determination of three dipeptides (JBP485, Gly–Sar and JBP923) in the cell lysates by liquid chromatography‐tandem mass spectrometry: application to identify the function of the PEPT1 transfected cell

A simple and rapid liquid chromatography–tandem mass spectrometry (LC‐MS/MS) method for the simultaneous determination of JBP485, Gly–Sar and JBP923 in the cell lysates using methanol as a deproteinization solvent was developed and validated. Detection was performed by turbo ionspray ionization in multiple reaction monitoring mode using the transitions of m/z 147.1 → m/z 90.1 for Gly–Sar, m/z 201.1 → m/z 86.1 for JBP485, m/z 219.1 → m/z 86.1 for JBP923 and m/z 152.0 → m/z 110.0 for paracetamol (internal standard). The analytes were separated on a Hypersil ODS C₁₈ HPLC column using isocratic elution mode with a mobile phase containing 0.1% formic acid in water–methanol (97:3, v/v) at a flow rate of 0.2 mL/min. The calibration curves were demonstrated to be linear over the concentration range of 5.00?5000 nm with coefficient of 0.9968 for Gly–Sar, 0.9975 for JBP485 and 0.9952 for JBP923. The intra‐ and inter‐day precisions were <10.2% for each quality contro; level, and the accuracy was within ±5.6% for each analyte. The matrix effect, the extraction recovery and stabilities of LC‐MS/MS analysis were also investigated. This validated method was successfully applied to the simultaneous determination of JBP485, Gly–Sar and JBP923 in the cell lysates for identification of stably transfected HeLa cells with human PEPT1. Copyright © 2014 John Wiley & Sons, Ltd.     

Metabolic profiles and pharmacokinetics of goitrin in rats through liquid chromatography combined with electrospray ionization–tandem mass spectrometry

Several chemical and biological studies have revealed R,S‐goitrin as the main bioactive constituent of Isatis indigotica Fort., responsible for antiviral antiendotoxin activity; however, few pharmacokinetic studies have been conducted. To comprehend the kinetics of R,S‐goitrin and promote its curative application, a rapid and sensitive UHPLC–MS/MS method was developed. The selected reaction monitoring transitions were m/z 130.0 → 70.0 for R,S‐goitrin and m/z 181.1 → 124.0 for the internal standard in a positive‐ion mode. The established UHPLC–MS/MS method achieved good linearity for R,S‐goitrin at 10–2000 ng/mL. The intra‐ and interday accuracy levels were within ±9.7%, whereas the intraday and interday precision levels were <11.3%. The extraction recovery, stability and matrix effect were within acceptable limits. The validated method was successfully applied for the pharmacokinetic analysis of R,S‐goitrin in rats after oral administration. Moreover, a total of six metabolites were structurally identified through UHPLC–Q/TOF–MS. The proposed metabolic pathways of R,S‐goitrin in rats involve demethylation, acetylation, glutathionylation and oxygenation.     

Mass cultivation of various algal species and their evaluation as a potential candidate for lipid production

Microalgae have been proposed as a promising source for biodiesel production. Focusing on algal strains for biodiesel production, efforts should be made to search new strains. Experiments were carried out to investigate the effects of growth parameters (nutrients, pH, light, aeration and temperature) and the oil percentage of eight algal strains (Chlorella sp., Cladophora sp., Hydrodictylium sp., Oedogonium sp., Oscillatoria sp., Spirogyra sp., Stigeocolonium sp., Ulothrix sp.). Results show that 6.5–7.5 is the optimum pH for the growth of all algal species. Temperature showed a greater variation (25°40°C). Ulothrix sp. gave more biomass productivity and is the most suitable strain for biodiesel production due to higher oil percentage (62%). Least biomass production was observed for Stigeocolonium sp. and least oil content was obtained from Hydrodictylium sp. It was observed that among these eight algal strains for biodiesel production, Ulothrix and Chlorella are the most promising algae species.     

Theoretical Study of the Interactions between Isolated <Emphasis Type="Italic">DNA</Emphasis> Bases and Various Groups IA and IIA Metal Ions by <Emphasis Type="Italic">Ab Initio</Emphasis> Calculations

Summary. Interactions of the DNA bases adenine (A), guanine (G), cytosine (C), and thymine (T) with various metal ions (M) of groups IA and IIA of the periodic table of the elements were studied at the HF, MP2, and DFT levels of theory. The structures and thermodynamic stabilities of these species were studied at the gas phase. The calculations uphold that there exist two active sites in G and one in A, C, and T. The calculations also show that the O² atom in T is a more active site for metal ion bindings than that in C. The stability energies for G … M complexes are larger than those for A … M complexes and the stability energies for T … M complexes are larger than those for C … M complexes. As z/r ratio for the metal ion increases, the interaction energy for the complex increases systematically. Thermodynamic quantities such as ΔH, ΔG, ΔS, and ln K were determined for each complexation reaction, [Base+M ⁿ⁺ →(Base … M) ⁿ⁺]. A, G, and C complexation reactions except for C … Rb⁺ are exothermic. The situation is quite different for T complexation reactions and all except for T … Be²⁺ and T … Mg²⁺ are endothermic.     

Separation of Xylene Isomers in the Anion-Pillared Square Grid Material SIFSIX-1-Cu

Xylene isomer separation is considered one of the seven separation challenges that changed the world. In addition, the high-energy demand of xylene separation highlights the need for efficient novel adsorbents. Herein, the liquid-phase separation potential of the anion-pillared hybrid material SIFSIX-1-Cu was studied for preferential adsorption of o-xylene and m-xylene over p-xylene, which was inspired by a previous complexation crystallization method for separating m-xylene. We report detailed experimental liquid-phase adsorption experiments, yielding selectivities of 3.0 for o-xylene versus p-xylene and 2.6 for m-xylene versus p-xylene. Our theoretical calculations thus provide a reasonable explanation that the xylene adsorption selectivity is attributed to the C−H⋅⋅⋅F interaction, and the host–guest interaction order agrees with the adsorption priority: o-xylene > m-xylene > p-xylene.     

New algorithms for the computation of column dynamics of multicomponent liquid phase adsorption

New and efficient numerical algorithms were developed for simulating column dynamics of multicomponent liquid phase adsorption. Simple and realistic models are used for the simulation. Langmuir form of isotherm and linear driving force rate expressions are employed in the model equations. Algorithms were formulated for three different rate control mechanisms, namely, film diffusion control, particle diffusion control and combined film and particle diffusion control. The algorithms derived are explicit with the exception of the requirement of solving a nonlinear equation in one single variable which is the concentration of a reference species. Thus the tedious iterative calculation procedure for solving simultaneous nonlinear equations in a multicomponent fixed bed system is avoided. Example calculations indicated very good numerical accuracy as verified from an independent check by means of an overall mass balance.Nomenclature C Concentration of speciesi in the solution. mol/l - h _i Dimensionless length variable for speciesi - H _i Dimensionless total length parameter for speciesi. - k _li Liquid phase mass transfer coefficient for speciesi, l/sec - K _li Overall liquid phase mass transfer coefficient for speciesi. l/sec - k _si Solid phase mass transfer coefficient for speciesi, l/sec - K _si Overall solid phase mass transfer coefficient for speciesi. l/sec - L Total bed height, m - Q _i Concentration of speciesi in the adsorbent. mol/g solid - t Absolute time, second - V Linear superficial flow rate, m/see - X _i Normalized liquid phase i species concentration - Y _i Normalized liquid phasei species concentration - Z Axial distance of the bed, m     

Tune-out and magic wavelengths for hydrogenlike and screened-hydrogenlike atoms

The tune-out and magic wavelengths (TMWs) for the hydrogenlike and screened-hydrogenlike atoms (Z = 1-8) are calculated using a variational method. The first three tune-out wavelengths for each of the nS (n = 1, 2, 3) states and the first three magic wavelengths for each of the 1S-nS (n = 2, 3) transitions of the hydrogenlike atoms in terms of nuclear charge Z, and the first TMWs for the above mentioned states or transitions of the screened-hydrogenlike atoms in terms of the screening parameter μ and Z are presented. All the results for the TMWs are reported for the first time in the literature except the magic wavelengths for the hydrogen atom. The magic wavelengths for hydrogen atom are in agreement with the available data. The precise estimation of the TMWs would be helpful for the design of the ion-trapping experiment of the hydrogenic systems. Our study is expected to be useful for the measurements of the hydrogenic 1S-2S and 1S-3S transitions spectroscopy for the improved accuracy.     

Calculation of j and jm symbols for arbitrary compact groups. III. Application to SO3 ⊃ T ⊃ C3 ⊃ C1

The methodology developed in earlier papers is used to compute the 6j symbols and 3jm factors that arise in the group chain SO₃ ? T ? C₁. The relevant character theory is given and the 2j and 3j symbols calculated. Selection rules are used to predict which j symbols or jm factors are necessarily zero, and then a set of 6j fundamentals computed for T. The complete set of primitive 6j symbols are then computed by application of the orthogonality and Racah backcoupling relations. Primitive 3jm factors are calculated for SO₃ ? T and T ? C₃ and, from these, all the 3jm factors for T ? C₃ and some of those for SO₃ ? T computed. A complete table of non-equivalent 6j symbols for T and 3jm factors for T ? C₃ is given, together with a table for SO₃ ? T of all 3jm factors with j ≤ 2.     

Development of classification models for predicting chronic toxicity of chemicals to Daphnia magna and Pseudokirchneriella subcapitata

Both the acute toxicity and chronic toxicity data on aquatic organisms are indispensable parameters in the ecological risk assessment priority chemical screening process (e.g. persistent, bioaccumulative and toxic chemicals). However, most of the present modelling actions are focused on developing predictive models for the acute toxicity of chemicals to aquatic organisms. As regards chronic aquatic toxicity, considerable work is needed. The major objective of the present study was to construct in silico models for predicting chronic toxicity data for Daphnia magna and Pseudokirchneriella subcapitata. In the modelling, a set of chronic toxicity data was collected for D. magna (21 days no observed effect concentration (NOEC)) and P. subcapitata (72 h NOEC), respectively. Then, binary classification models were developed for D. magna and P. subcapitata by employing the k-nearest neighbour method (k-NN). The model assessment results indicated that the obtained optimum models had high accuracy, sensitivity and specificity. The model application domain was characterized by the Euclidean distance-based method. In the future, the data gap for other chemicals within the application domain on their chronic toxicity for D. magna and P. subcapitata could be filled using the models developed here.     

Resolution of α-cyclohexyl-mandelic acid enantiomers by two-phase (O/W) recognition chiral extraction

This paper presents a new chiral separation technology: two-phase (O/W) recognition chiral extraction. Distribution behavior of α-cyclohexyl-mandelic acid enantiomers was studied in the extraction system with D(L)-isobutyl tartrate in 1,2-dichloroethane organic phase and β-CD derivatives in aqueous phase, and the influence of the kind and concentration of extractant and pH on extraction performance was investigated. The experimental results indicate that two-phase (O/W) recognition chiral extraction is of strong chiral separation ability. HP-β-CD, HE-β-CD and Me-β-CD have higher recognition ability for S-CHMA than that for R-CHMA, among which HP-β-CD has the strongest ability; whereas, D-isobutyl tartrate has reversed recognition ability for them. In the extraction system containing HP-β-CD and D-isobutyl tartrate, e.e.% of S-CHMA in aqueous phase reached 27.6% by one stage extraction, and the distribution ratio for R-CHMA(k _R ) and for S-CHMA(k _s ) and separation factor (α) are 2.44, 0.89 and 2.49, respectively. Meanwhile, pH and concentration of extractant have great effects on chiral separation ability. Two-phase (O/W) recognition chiral extraction has great significance for preparative separation of racemic compounds.     

Simultaneous Quantification of Seven Caffeoylquinic Acids in Ecotypes of Blumea balsamifera at Various Life Stages by High-Performance Liquid Chromatography

Blumea balsamifera is a traditional Chinese medicine containing various bioactive caffeoylquinic acids and usually used for the treatment of rheumatism, eczema, and dermatitis. An accurate and reliable high-performance liquid chromatography method was established for simultaneous determination of 5-O-caffeoylquinic acid, 3-O-caffeoylquinic acid, 4-O-caffeoylquinic acid, 1,3-di-O-caffeoylquinic acid, 3,4-di-O-caffeoylquinic acid, 3,5-di-O-caffeoylquinic acid, and 4,5-di-O-caffeoylquinic acid in B. balsamifera. The method was rigorously verified and was successfully applied to simultaneous quantification of seven caffeoylquinic acids in four ecotypes of B. balsamifera at five life stages. The results showed that the highest concentrations of seven compounds were present in September, October, and November, indicating that the optimal harvest time of B. balsamifera is in the autumn. Therefore, this method is suitable for the quantification of the seven compounds and quality control for B. balsamifera.     

Segmentation of Heteropolymer Sequences Specifying Subsequences with Different Composition and Statistical Properties

We have studied the segmentation of two‐letter AB heterosequences composed of subsequences with different composition and distribution of A and B monomer units along the chain. Our approach is based on the segmentation function S(k) introduced in the present work and on the Jensen–Shannon divergence measure determined with respect to the probabilities of the lengths of uniform blocks of A and B monomer units. It is shown that the function S(k) is extremely sensitive to the sequence statistics. Even visual analysis of S(k) allows judgment on some features of sequence statistics. In particular, function S(k) is constant for random copolymers, it is an oscillating function for random block copolymers and shows monotonic growth up to some constant value for proteinlike copolymers. However, due to significant fluctuations observed for short sequences, the function S(k) can be effectively used only for segmentation of a heterosequence composed of very long subsequences. On the other hand, we find that the Jensen–Shannon divergence measure does not allow one to judge the type of statistics, but is extremely efficient for segmentation of a heterosequence. Therefore, the two introduced functions, being mutually complementary, provide an effective approach for recognizing and segmentation of heterosequences. As an example, the methods developed are applied for concatenating sequences of different proteins.

Segmentation function S(k, l, x) as a function of parameter k and starting number x of “window” for a sequence composed of elastin and ribonuclease sequences.