Partition coefficients for the SAMPL5 challenge using transfer free energies

SAMPL challenges (Mobley et al. in J Comput Aided Mol Des 28:135–150, 2014; Skillman in J Comput Aided Mol Des 26:473–474, 2012; Geballe in J Comput Aided Mol Des 24:259–279, 2010; Guthrie in J Phys Chem B 113:4501–4507, 2009) provide excellent opportunities to assess theoretical approaches on new data sets with a goal of gaining greater insight towards protein and ligand modeling. In the SAMPL5 experiment, cyclohexane–water partition coefficients were determined using a vertical solvation scheme in conjunction with the SMD continuum solvent model. Several DFT functionals partnered with correlation consistent basis sets were evaluated for the prediction of the partition coefficients. The approach chosen for the competition, a B3PW91 vertical solvation scheme, yields a mean absolute deviation of 1.9 logP units and performs well at estimating the correct hydrophilicity and hydrophobicity for the full SAMPL5 molecule set.     

Expected distance based on random walks

By considering a graph as a network of resistances, Klein and Randi? (J Math Chem 12(1):81–95, 1993) proposed the definition of a distance measure. Indeed, if each edge of the graph represents a resistance of \(1 \varOmega \), the equivalent resistance of the graph between each pair of vertices may be used as a distance. Based upon random walks in graphs, Stephenson and Zelen (Soc Netw 11(1):1–37, 1989) built a computational model to find the probability that each edge is used. From a mathematical point of view, both articles are based upon exactly the same model and the link between random walks and the electrical representation was established by Newman (Soc Netw 27(1):39–54, 2005) when defining an alternative to Freeman’s (Sociometry 40:35–41, 1977, Soc Netw 1(3):215–239, 1979) betweenness centrality based upon random walks. In the present paper, the similitude between these two processes is exploited to propose a new random walks based distance measure that may be defined as the expected length of a walk between any pair of vertices. We call it the expected distance and we prove that it is actually a distance. From this new definition, the RW Index is proposed that sums the expected walks lengths between pairs of vertices exactly in the same way as the Wiener index sums the shortest paths distances or the Kirchhoff index sums the equivalent resistances. We compare the three indices and establish the vertex and the edge decompositions for both. We compute some value of the RW index for some families of graphs and conjecture the upper and lower bounds of the RW index.     

Synthesis,characterization, thermal,antimicrobial and antioxidant studies of some transition metal dithiocarbamates

Metal dithiocarbamate complexes of Co(II) [1], Cu(II) [2], Mn(II) [3], Cr(III) [4], and Pd(II) [5] have been synthesized using sodium N-ethyl-N-phenyldithiocarbamate (NaL). The complexes were characterized by elemental analyses, FTIR and UV–vis spectroscopic techniques, magnetic moment, molar conductance and thermal analyses (TGA and DSC). The infrared spectra indicated the coordination of dithiocarbamate through the two sulphur atoms in a symmetrical bidentate fashion. The thermal behavior of these complexes showed that the hydrated complexes lost water molecules in the first step, followed by decomposition of the ligand molecules in the final steps. Mass loss considerations at these final decomposition steps indicate conversion of the complexes to sulphides. The antimicrobial potentials of the complexes were evaluated against some selected bacteria strains (Escherichia coli, Pseudomonas aureginosa, Salmonella typhi and Staphylococcus aureus) and fungi organisms (Aspergillus flavus and Fasiparium oxysporium). The compounds showed a broad spectrum of fungicidal and bactericidal activities which exceeds that of the control drugs at a 100 μg/mL concentration. The antioxidant properties of the ligand and its Cu(II) complex were evaluated in vitro using DPPH assay, and the complex was found to exhibit better radical scavenging ability than the free ligand.     

The complexity of the Clar number problem and an exact algorithm

The Clar number of a (hydro)carbon molecule, introduced by Clar (The aromatic sextet, 1972), is the maximum number of mutually disjoint resonant hexagons in the molecule. Calculating the Clar number can be formulated as an optimization problem on 2-connected plane graphs. Namely, it is the maximum number of mutually disjoint even faces a perfect matching can simultaneously alternate on. It was proved by Abeledo and Atkinson (Linear Algebra Appl 420(2):441–448, 2007) that the Clar number can be computed in polynomial time if the plane graph has even faces only. We prove that calculating the Clar number in general 2-connected plane graphs is \(\mathsf {NP}\)-hard. We also prove \(\mathsf {NP}\)-hardness of the maximum independent set problem for 2-connected plane graphs with odd faces only, which may be of independent interest. Finally, we give an exact algorithm that determines the Clar number of a given 2-connected plane graph. The algorithm has a polynomial running time if the length of the shortest odd join in the planar dual graph is fixed, which gives an efficient algorithm for some fullerene classes, such as carbon nanotubes.     

On the determinant evaluation of quasi penta-diagonal matrices and quasi penta-diagonal Toeplitz matrices

Recently, three computational algorithms for evaluating the determinant of quasi penta-diagonal matrices have been proposed by El-Mikkawy and Rahmo (Comput Math Appl 59:1386–1396, 2010), by Neossi Nguetchue and Abelman (Appl Math Comput 203:629–634, 2008), and by Jia et al. (Int J Comput Math 89:851–860, 2013), respectively. In the current paper, two novel algorithms with less computational costs are proposed for the determinant evaluation of general quasi penta-diagonal matrices and quasi penta-diagonal Toeplitz matrices. Furthermore, three numerical experiments are given to show the performance of our algorithms. All of the numerical computations were performed on a computer with aid of programs written in MATLAB.     

Effect of solid-like nitrogen contact layers on graphite: anisotropy of tangential pressure and orientational order

Molecular simulation has provided a significant progress in understanding behavior of two-dimensional molecular layers of various gases deposited on a solid surface. Substantial efforts have been made to describe the state of noble gases, nitrogen, methane, carbon dioxide etc. on the graphite surface. As a result, mechanism of solidification and melting of molecular layers, formation of structures commensurate with substrate, orientational ordering of non-spherical molecules and other distinctive features of 2D layers are mainly clear for at least 2 decades. Some quantitative refinements in modeling of such systems and adjusting parameters basing on experimental data are still continuing, but the activity in fundamental study in this area has been weakened. In part, this is due to difficulties in reliable evaluating of thermodynamic functions of 2D systems, especially in the crystalline form, which hinders exact evaluation of the 2D liquid–solid transition parameters. Recently new possibilities were demonstrated in the framework of a methodology based on kinetic Monte Carlo and explicit accounting for the 2D gas–solid and gas–liquid interface with an adjustable external potential imposed on the gas phase (Ustinov and Do in J Colloid Interface Sci 366:216–223, 2012; Ustinov in J Chem Phys 140: 074706, 2014a, in J Chem Phys 141:134706, 2014b, in J Chem Phys 142: 074701, 2015). This study aims at an extension of the approach to adsorption of nitrogen on the graphite surface. A special attention is paid to effect of commensurate nitrogen monolayer on graphite, manifesting itself as the appearance of a significant tangential pressure directly in the graphite layer. This pressure has to be accounted for in all thermodynamic equations such as the Gibbs–Duhem equation and involved into simulation schemes realizing the NPT ensemble. In the case of nitrogen at low temperatures the herringbone structure of the crystalline layer has proved to result in a significant anisotropy of that pressure. The developed approach can be extended to 3D systems and various fluids confined in nanoporous materials.     

On the derivative of the associated Legendre function of the first kind of integer order with respect to its degree (with applications to the construction of the associated Legendre function of the second kind of integer degree and order)

In our recent works (R. Szmytkowski, J. Phys. A 39:15147, 2006; corrigendum: 40:7819, 2007; addendum: 40:14887, 2007), we have investigated the derivative of the Legendre function of the first kind, P _ν(z), with respect to its degree ν. In the present work, we extend these studies and construct several representations of the derivative of the associated Legendre function of the first kind, \({P_{\nu}^{\pm m}(z)}\), with respect to the degree ν, for \({m \in \mathbb{N}}\). At first, we establish several contour-integral representations of \({\partial P_{\nu}^{\pm m}(z)/\partial\nu}\). They are then used to derive Rodrigues-type formulas for \({[\partial P_{\nu}^{\pm m}(z)/\partial\nu]_{\nu=n}}\) with \({n \in \mathbb{N}}\). Next, some closed-form expressions for \({[\partial P_{\nu}^{\pm m}(z)/\partial\nu]_{\nu=n}}\) are obtained. These results are applied to find several representations, both explicit and of the Rodrigues type, for the associated Legendre function of the second kind of integer degree and order, \({Q_{n}^{\pm m}(z)}\); the explicit representations are suitable for use for numerical purposes in various regions of the complex z-plane. Finally, the derivatives \({[\partial^{2}P_{\nu}^{m}(z)/\partial\nu^{2}]_{\nu=n}, [\partial Q_{\nu}^{m}(z)/\partial\nu]_{\nu=n}}\) and \({[\partial Q_{\nu}^{m}(z)/\partial\nu]_{\nu=-n-1}}\), all with m > n, are evaluated in terms of \({[\partial P_{\nu}^{-m}(\pm z)/\partial\nu]_{\nu=n}}\). The present paper is a complementary to a recent one (R. Szmytkowski, J. Math. Chem 46:231, 2009), in which the derivative \({\partial P_{n}^{\mu}(z)/\partial\mu}\) has been investigated.     

Thermal evolution of ladder-like silsesquioxanes during formation of black glasses

Heat capacity of single-crystal samples of five chalcogenides (LiInS₂, LiInSe₂, LiGaS₂, LiGaSe₂, and LiGaTe₂) was measured with DSC in a temperature range from 180 to 460 K. The data for LiInS₂ and LiInSe₂ were compared with the literature data and shown to agree with the results of adiabatic calorimetry (Gmelin and Hönle in Thermochimica Acta 269: 575–590, 1995) better than with other DSC data (Kühn et al. in Cryst Res Technol 22: 265–269, 1987). Besides, the high-temperature fitting polynomial for C _P(T) published about 30 years ago for LiInS₂ is wrong. LiGaS₂, LiGaSe₂, and LiGaTe₂ were measured for the first time.     

Second derivative free sixth order continuation method for solving nonlinear equations with applications

In this paper, we deal with the study of convergence analysis of modified parameter based family of second derivative free continuation method for solving nonlinear equations. We obtain the order of convergence is at least five and especially, for parameter \(\alpha =2\) sixth order convergence. Some application such as Max Planck’s conservative law, multi-factor effect are discussed and demonstrate the efficiency and performance of the new method (for \(\alpha =2\)). We compare the absolutely value of function at each iteration \(|f(x_n)|\) and \(|x_n-\xi |\) with our method and Potra and Pták method [1], Kou et al. method [2]. We observed that our method is more efficient than existing methods. Also, the Dynamics of the method are studied for a special case of the parameter in convergence.     

An iterative perturbation theory with a Hamiltonian modifier

The aim of this paper is to show that the so-called Autoadjusting Perturbation Theory presented years ago [E. Besalú and R. Carbó-Dorca, J. Math. Chem., 22, 85 (1997)] can be modified and expressed in terms of operators, opening the possibility to define diverse variants with better convergence properties. This methodology is called here modified autoadjusting perturbation theory which is superior, at least numerically, to Rayleigh Schrödinger perturbation theory and the superconvergent perturbation theory [W. Scherer, Phys. Rev. Lett., 74, 1495 (1995)] applied to the one-dimensional quartic anharmonic oscillator. The new feature of this method is the Hamiltonian modifier which can be chosen in a proper way in order to improve the calculations and to obtain convergent energy series and wavefunction when Rayleigh Schrödinger perturbation theory gives divergent ones. Resummation techniques are used to check whether the correction terms of modified autoadjusting perturbation theory series resums similarly to the Rayleigh Schrödinger perturbation one. The iterative nature of the proposed method allows for a linear time scaling and for memory economization when it is numerically implemented.     

On the mechanism of the unwanted acetylation of polysaccharides by 1,3-dialkylimidazolium acetate ionic liquids: part 2—the impact of lignin on the kinetics of cellulose acetylation

Cellulose acetylation has been reported as a side reaction of cellulose treatment with the ionic liquid 1-ethyl-3-methylimidazolium acetate ([EMIm][OAc]) (Karatzos et al. in Cellulose 19:307–312, 2012) and other 1,3-dialkylimidazolium acetate ionic liquids. 1-Acetylimidazole (AcIm), an [EMIm][OAc] impurity, has been found to be the actual acetylating agent (Zweckmair et al. in Cellulose 22:3583–3596, 2015), and the degree of acetylation was relatively low, below a DS of approx. 0.1%. Higher degrees of cellulose acetylation (DS > 10%) have been observed when the entire wood was mixed with [EMIm][OAc] instead of cellulosic pulp only (Abushammala et al. in Carbohydr Polym 134:609–616, 2015). In this paper, we explore the impact of wood constituents, mainly lignin, on cellulose acetylation using AcIm. The results demonstrate that lignin itself can be readily acetylated upon mixing with AcIm, and—noteworthy—that lignin presence significantly accelerates cellulose acetylation. The initial rate of cellulose acetylation by AcIm increased from 1.8 to 4.7%/h when only 1% of lignin, based on cellulose mass, was added. A mechanistic study employing cellulose and lignin model compounds showed lignin to be more susceptible to acetylation than cellulose and to act as an intermediate acetyl group source for further cellulose acetylation in a catalytic scenario.     

Single-Run Mass Spectrometry Analysis Provides Deep Insight into <Emphasis Type="Italic">E. coli</Emphasis> Proteome

Single-run mass spectrometry has enabled the detection and quantifications of E. coli proteins. A total of 2068 proteins quantified by intensity-based absolute quantification (iBAQ) Schwanhäusser et al.: (Nature. 473, 337–342, 2011) procedure were obtained with single enzyme-trypsin, without pre-fractionation, by quadruplicate long liquid chromatography runs coupled with high-resolution linear trap quadrupole (LTQ)-Orbitrap Velos mass spectrometry. The single-run of 12 h has ability to cover almost 98% of the quadruplicate LC-MS/MS runs of E. coli proteome and is therefore almost equivalent to quadruplicate LC-MS/MS runs. These quantified proteins are about 52% of the total proteins present in E. coli genome according to Uniprot database. The quantified proteins covered almost all of the proteins in folate biosynthesis. Remarkably greater part of Gene Ontology (GO) Barrell et al.: (Nucleic Acids Res. 37, D396–D403, 2009), Ashburner et al.: (Nat. Genet. 25, 25–29, 2000) annotations, signaling pathways along with protein-protein interactions were covered. Some of the important biological processes-cell cycle, DNA repair, ion transport, ubiquinone biosynthetic process, pseudouridine synthesis, peptidoglycan biosynthetic process, RNA processing, and translation-revealed protein-protein interaction network generated by Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) Jensen, et al.:(Nucleic Acids Res 37, D412-D126, 2009) database. Therefore, to achieve the saturation point of detection of maximum number of proteins in single LC-MS/MS run, 12-h liquid chromatography gradient is appropriate.

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A novel algorithm for solving quasi penta-diagonal linear systems

In this paper, a novel numerical algorithm for solving quasi penta-diagonal linear systems is presented. The computational costs of the algorithm is less than those of three successful algorithms given by El-Mikkawy and Rahmo (Comput Math Appl 59:1386–1396, 2010), by Lv and Le (Appl Math Comput 204:707–712, 2008), and by Jia et al. (Int J Comput Math 89:851–860, 2012). In addition, a new recursive method for inverting the quasi penta-diagonal matrices is also discussed. The implementation of the algorithm using Computer Algebra Systems (CASs) such as MATLAB and MAPLE is straightforward. Two numerical examples are given in order to demonstrate the performance and efficiency of our algorithm.     

Using Sr Resin with mixed acid matrices

The quantification of radioactive material dispersed following the release of ⁹⁰Sr, whether accidental or intentional, would be of high importance. Depending on the circumstances, it is possible that the contaminated materials would need to be completely digested prior to quantification. Many sample matrices require a mixture of different acids be employed to achieve total dissolution. Unfortunately, one the most common approaches for the separation of strontium, extraction chromatography with Sr Resin, has only been fully characterized in pure mineral acid solutions (Filosofov et al. in Solv Extr Ion Exch 33(5): 496–509, 2015; Horwitz et al. in Solv Extr Ion Exch 10(2): 313–336, 1992). This work shows that Sr Resin can be used effectively with high concentration mixtures of nitric and hydrochloric acids in the presence or absence of hydrofluoric acid, thereby potentially negating the need for conversion to a pure mineral acid matrix.     

Compatibility of Spatially Coded Apertures with a Miniature Mattauch-Herzog Mass Spectrograph

In order to minimize losses in signal intensity often present in mass spectrometry miniaturization efforts, we recently applied the principles of spatially coded apertures to magnetic sector mass spectrometry, thereby achieving increases in signal intensity of greater than 10× with no loss in mass resolution Chen et al. (J. Am. Soc. Mass Spectrom. 26, 1633–1640, 2015), Russell et al. (J. Am. Soc. Mass Spectrom. 26, 248–256, 2015). In this work, we simulate theoretical compatibility and demonstrate preliminary experimental compatibility of the Mattauch-Herzog mass spectrograph geometry with spatial coding. For the simulation-based theoretical assessment, COMSOL Multiphysics finite element solvers were used to simulate electric and magnetic fields, and a custom particle tracing routine was written in C# that allowed for calculations of more than 15 million particle trajectory time steps per second. Preliminary experimental results demonstrating compatibility of spatial coding with the Mattauch-Herzog geometry were obtained using a commercial miniature mass spectrograph from OI Analytical/Xylem.

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Comments on “An experimental investigation on heating rate effect in the thermal behavior of perhydrous bituminous coal during pyrolysis”

This paper has the intension of discussing about the published paper by Wu et al. (J Therm Anal Calorim 119:2195–2203, 2015). The original paper has shown some errors in quoting and using the Coats–Redfern integral kinetic equation. This discussion is focused on the employment of this model, and some arguments and clarifications are also given.     

Comment on: ‘‘The effect of pressure on morphological features and quality of synthesized graphene’’ [Res Chem Intermed journal DOI 10.1007/s11164-016-2594-8]

In their recent article, Alipour et al. (Res Chem Intermed, 1. doi: 10.1007/s11164-016-2594-8) studied the effect of pressure on the morphological characteristics and quality of synthesized graphene from SEM data. Here, the basics of fractal calculations and depth histogram will be explained to avoid such egregious mistakes between using AFM, SEM and stereo SEM images by authors.     

Study of phase transformation temperatures of alloys based on Fe–C–Cr in high-temperature area

Three alloys based on Fe–C–Cr were studied. These alloys contained carbon in a range of 0.308–0.380 mass% and chromium 1.058–4.990 mass%. Temperatures of solidus (onward used as T_S), liquidus (onward used as T_L) and peritectic transformation (onward used as T_P) were studied in the high-temperature region. These temperatures were obtained using two thermal analysis methods: differential thermal analysis (onward used as DTA) and simple thermal analysis (onward used as TA). The Setaram Setsys 18_TM was used for experiments with employment of the DTA method. All measurements were taken in an inert atmosphere of pure argon at heating rate of 10 °C min^?1, and simple TA method was used for the experiments with the use of the Netzsch STA 449 F3 Jupiter. Measurements were taken in inert atmosphere of pure argon at a heating and cooling rate of 5 °C min^?1. Phase transformation temperatures were obtained by heating and cooling process and were approximated to “equilibrium conditions” (DTA method: zero heating rate and sample mass, standard, TA method: only standard) (?aludová et al. in J Therm Anal Calorim 112:465–471, 2013a. doi: https://doi.org/10.1007/s10973-012-2847-8; J Therm Anal Calorim 111:1203–1210, 2013b. doi: https://doi.org/10.1007/s10973-012-2346-y). The experimental data were compared and discussed with the calculation results using IDS (solidification analysis package) software (onward used as SW) Thermo-Calc and the TCFE8 (Thermo-Calc Fe-based alloys) database. The results of the two alloys were compared with those published for similar steels. The experimentally obtained transition temperatures were close to the calculated values. The solidus, liquidus and peritectic transformation temperatures were lowered with increasing carbon (range 0.308–0.380 mass%) and chromium content (range 1.058–4.990 mass%). The smallest difference between the experimental results and theoretical calculations was observed at the liquidus temperature for all alloys. Nonetheless, the difference measured for the solidus temperatures was much greater.