On the centrality of vertices of molecular graphs

For acyclic systems the center of a graph has been known to be either a single vertex of two adjacent vertices, that is, an edge. It has not been quite clear how to extend the concept of graph center to polycyclic systems. Several approaches to the graph center of molecular graphs of polycyclic graphs have been proposed in the literature. In most cases alternative approaches, however, while being apparently equally plausible, gave the same results for many molecules, but occasionally they differ in their characterization of molecular center. In order to reduce the number of vertices that would qualify as forming the center of the graph, a hierarchy of rules have been considered in the search for graph centers. We reconsidered the problem of “the center of a graph” by using a novel concept of graph theory, the vertex “weights,” defined by counting the number of pairs of vertices at the same distance from the vertex considered. This approach gives often the same results for graph centers of acyclic graphs as the standard definition of graph center based on vertex eccentricities. However, in some cases when two nonequivalent vertices have been found as graph center, the novel approach can discriminate between the two. The same approach applies to cyclic graphs without additional rules to locate the vertex or vertices forming the center of polycyclic graphs, vertices referred to as central vertices of a graph. In addition, the novel vertex “weights,” in the case of acyclic, cyclic, and polycyclic graphs can be interpreted as vertex centralities, a measure for how close or distant vertices are from the center or central vertices of the graph. Besides illustrating the centralities of a number of smaller polycyclic graphs, we also report on several acyclic graphs showing the same centrality values of their vertices. © 2013 Wiley Periodicals, Inc.     

CENCALC: A computational tool for conformational entropy calculations from molecular simulations

We present the CENCALC software that has been designed to estimate the conformational entropy of single molecules from extended Molecular Dynamics (MD) simulations in the gas‐phase or in solution. CENCALC uses both trajectory coordinates and topology information in order to characterize the conformational states of the molecule of interest by discretizing the time evolution of internal rotations. The implemented entropy methods are based on the mutual information expansion, which is built upon the converged probability density functions of the individual torsion angles, pairs of torsions, triads, and so on. Particularly, the correlation‐corrected multibody local approximation selects an optimum cutoff in order to retrieve the maximum amount of genuine correlation from a given MD trajectory. We illustrate these capabilities by carrying out conformational entropy calculations for a decapeptide molecule either in its unbound form or in complex with a metalloprotease enzyme. CENCALC is distributed under the GNU public license at http://sourceforge.net/projects/cencalc/ .     

Implicit and explicit solvent models for modeling a bifunctional arene ruthenium hydrogen‐storage catalyst: A classical and ab initio molecular simulation study

Classical and ab initio, density functional theory‐ and semiempirical‐based molecular simulation, including molecular dynamics, have been carried out to compare and contrast the effect of explicit and implicit solvation representation of tetrahydrofuran (THF) solvent on the structural, energetic, and dynamical properties of a novel bifunctional arene ruthenium catalyst embedded therein. Particular scrutiny was afforded to hydrogen‐bonding and energetic interactions with the THF liquid. It was found that the presence of explicit THF solvent molecules is required to capture an accurate picture of the catalyst's structural properties, particularly in view of the importance of hydrogen bonding with the surrounding THF molecules. This has implications for accurate modeling of the reactivity of the catalyst. © 2014 Wiley Periodicals, Inc.     

Grcarma: A fully automated task‐oriented interface for the analysis of molecular dynamics trajectories

We report the availability of grcarma, a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories of biological macromolecules. It is a cross‐platform, Perl/Tk‐based front‐end to the program carma and is designed to facilitate the needs of the novice as well as those of the expert user, while at the same time maintaining a user‐friendly and intuitive design. Particular emphasis was given to the automation of several tedious tasks, such as extraction of clusters of structures based on dihedral and Cartesian principal component analysis, secondary structure analysis, calculation and display of root‐mean‐square deviation (RMSD) matrices, calculation of entropy, calculation and analysis of variance–covariance matrices, calculation of the fraction of native contacts, etc. The program is free‐open source software available immediately for download. © 2013 Wiley Periodicals, Inc.     

LIBEFP: A new parallel implementation of the effective fragment potential method as a portable software library

A new high performance parallel implementation of the general Effective Fragment Potential (EFP) method in a form of a portable software library called libefp is presented. The libefp library was designed to provide developers of various quantum chemistry software packages with an easy way to add EFP functionality to the program of their choice. The general overview of the library is presented and various aspects of interfacing the library with third party quantum chemistry packages are considered. The reference implementation of common methods of computational chemistry such as geometry optimization and molecular dynamics on top of libefp is delivered in the form of efpmd program. Results of molecular dynamics simulation of liquid water using the developed software are described. © 2013 Wiley Periodicals, Inc.     

LEAP: Highly accurate prediction of protein loop conformations by integrating coarse‐grained sampling and optimized energy scores with all‐atom refinement of backbone and side chains

Prediction of protein loop conformations without any prior knowledge (ab initio prediction) is an unsolved problem. Its solution will significantly impact protein homology and template‐based modeling as well as ab initio protein‐structure prediction. Here, we developed a coarse‐grained, optimized scoring function for initial sampling and ranking of loop decoys. The resulting decoys are then further optimized in backbone and side‐chain conformations and ranked by all‐atom energy scoring functions. The final integrated technique called loop prediction by energy‐assisted protocol achieved a median value of 2.1 Å root mean square deviation (RMSD) for 325 12‐residue test loops and 2.0 Å RMSD for 45 12‐residue loops from critical assessment of structure‐prediction techniques (CASP) 10 target proteins with native core structures (backbone and side chains). If all side‐chain conformations in protein cores were predicted in the absence of the target loop, loop‐prediction accuracy only reduces slightly (0.2 Å difference in RMSD for 12‐residue loops in the CASP target proteins). The accuracy obtained is about 1 Å RMSD or more improvement over other methods we tested. The executable file for a Linux system is freely available for academic users at http://sparks‐lab.org . © 2013 Wiley Periodicals, Inc.     

A novel,simple and sensitive ligand affinity capture method for detecting molecular interactions by MALDI mass spectrometry

A simple and sensitive ligand affinity capture method (LAC) was developed to detect biotinylated biomolecules bound to a biotin–avidin base by matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry (MALDI ToF MS). Glass slides covered with a metal film for MALDI MS applications were treated with amino‐silane and derivatized with biotin followed by binding of avidin. Washing buffers with high ionic strength increased the specificity of the subsequent binding of biotinylated biomolecules to the avidin layer. A combined thin layer‐dried droplet method using α‐cyano‐4‐hydroxycinnamic acid (CHCA) in acetone or ethyl acetate resulted in the most intense ions of biotinylated polymyxin B, whereas the matrix conditions did not influence the detection of angiotensin II. Addition of biotinylated biomolecules in the low femtomole to low picomole range resulted in sufficient ion intensity for detection by the LAC method. The LAC concept was extended by binding of biotinylated lipopolysaccharide to the biotin–avidin base followed by preferential capture and specific detection of the binding antagonist polymyxin B. Copyright © 2008 John Wiley & Sons, Ltd.     

A novel approach to the characterization of end groups in styrene–methyl methacrylate copolymers by pyrolysis–gas chromatography

The end groups of styrene–methyl methacrylate (St‐MMA) copolymers polymerized radically with 2,2′‐azobisisobutyronitrile (AIBN) as an initiator, which are difficult to characterize even by NMR, were investigated by pyrolysis–gas chromatography. On the resulting pyrograms, characteristic products that formed from the end‐group moiety due to AIBN, such as 2‐cyanopropane, 2‐cyanopropen, and various compounds consisting of an isobutyronitrile group and a monomer unit, were observed together with those from the main chain, such as St and MMA monomers and various dimeric and trimeric products. The relative abundance between the recombination and disproportionation termination reactions in the copolymerization process was estimated from the relative intensities between the characteristic peaks of the end group and those of the main chain. Thus, the estimated abundance for the termination reactions suggested that the polymerization process for this particular copolymer system terminated preferentially by recombination rather than by disproportionation. Furthermore, the relative abundance between the monomer units adjacent to the chain‐end AIBN residues was estimated on the basis of the peak intensities of the products consisting of an isobutyronitrile group and either monomer unit, which reflected the penultimate neighboring structure of the end group in the polymer chain. Thus, the observed results suggested that the isobutyronitrile radical formed by the dissociation of AIBN in the initiation reaction was predominantly adjoined by St monomer rather than by MMA monomer. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 1880–1888, 2000     

Flying onto global minima on potential energy surfaces: A swarm intelligence guided route to molecular electronic structure

A novel quantum‐classical recipe for locating the global minimum on the potential energy surface of a large molecule and simultaneously predicting the associated electronic charge distribution is developed by interfacing the classical particle swarm optimization with a near optimal unitary evolution scheme for the trial one electron density matrix. The unitary transformation is generated by an antihermitian matrix linked to the molecular electronic Hamiltonian at the instantaneous nuclear configurations discovered by the swarm as it flies. The algorithm is used to predict the extensive reorganization of electronic charge distribution and bond lengths in polythiophene oligomers on doping at various levels.     

Poly(L‐lysine) and clay nanocomposite with desired matrix secondary structure: Effects of polypeptide molecular weight

Nanocomposites (NC) were formed using cationic poly(L ‐lysine) (PLL), a semicrystalline polypeptide, that was reinforced by sodium montmorillonite (MMT) clay via solution intercalation technique. By varying solution conditions such as pH, temperature, and polypeptide concentration in the presence of clay platelets, the secondary structure of PLL was controllably altered into α‐helical, β‐sheet, and random coil. The high molecular weight polypeptide shows a strong propensity to fold into the β‐sheet structure when cast as films, irrespective of the initial secondary structure in solution. Nanocomposite local morphology confirms intercalated MMT platelets with PLL over a wide range of compositions. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 239–252, 2007.     

A series of novel 2,6-bis(imino)pyridyl iron catalysts: synthesis, characterization and ethylene oligomerization

A series of novel 2,6-bis(imino)pyridyl iron complexes {2,6-(2-X-4-Y-5-ZC₆H₂NCCH₃)₂C₅H₃N}FeCl₂ (X = Cl, Y = CH₃, Z = H (2); X = Br, Y = CH₃, Z = H (3); X = F, Y = H, Z = CH₃ (4); X = Cl, Y = H, Z = CH₃ (5); X = Cl, Y = F (7)) have been synthesized and characterized with elemental analysis and IR. These iron coordinative complexes, activated with methylaluminoxane (MAO), lead to highly active ethylene oligomerization (>10⁷ g/mol Fe h) and the products are mostly linear α-olefins (>90%). The catalytic activities and product properties depend on the substituents on aryl rings and the reaction conditions. As reaction temperature increases, the catalytic activities decrease rapidly and more low-molar-mass products are produced. The product distributions are almost independent of the Al/Fe molar ratio, but the catalytic activities change in different trends when the ortho-substituents on the aryl rings are different. The other three complexes have also been synthesized for comparison to investigate the steric hindrance and electronic effect on the properties of complexes. The complex with adaptable steric hindrance and electronic properties exhibits the highest catalytic activities.     

The intermolecular interaction in the charge-transfer complexes between amines and halogens: A theoretical characterization of the trends in halogen bonding

The trends in the properties of prereactive or charge-transfer complexes formed between the simple amines NH₃, CH₃NH₂, (CH₃)₂NH, and (CH₃)₃N and the halogens F₂, ClF, Cl₂, BrF, BrCl, and Br₂ were investigated by the ab initio restricted Hartree–Fock approach, the Møller–Plesset second-order method, and with several density functional theory variants using extended polarized basis sets. The most important structural parameters, the stabilization energies, the dipole moments, and other quantities characterizing the intermolecular halogen bond in these complexes are monitored, discussed, and compared. A wide range of interaction strengths is spanned in these series. Successive methyl substitution of the amine as well as increasing polarities and polarizabilities of the halogen molecules both systematically enhance the signature of charge-transfer interaction. These trends in halogen bonds of varying strength, in many aspects, parallel the features of hydrogen bonding.     

A novel type of optically active helical polymers: Synthesis and characterization of poly(α,β‐unsaturated ketone)

New α,β‐unsaturated ketone monomers, menthyl vinyl ketone (MVK), and 1‐menthylbut‐3‐en‐2‐one (MBEK) were synthesized. The monomers were polymerized using butyllithium as an initiator. The polymer derived from MVK (poly‐MVK) had a tremendous specific optical rotation [α], which was as 32 times large as that of its monomer MVK. Poly‐MVK was confirmed to keep a prevailing helicity of backbone in solution by means of comparing the specific optical rotation and the CD spectra with that of MVK and the model compound such as ethyl menthyl ketone (EMK) and n‐hexyl menthyl ketone (n‐HMK). This conclusion was also confirmed by the fact that the specific optical rotation and the CD signal intensity of poly‐MBEK were not enough large due to backbone flexibility caused by the effective isolation of the main chain from the bulky menthyl. The excess value of one‐handed helicity of poly‐MVK decreased with the increase of polymerization temperature. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 1441–1448, 2010     

Synthesis of a “molecular rope curtain”: Preparation and characterization of a sliding graft copolymer with grafted poly(ethylene glycol) side chains by the “grafting onto” strategy

A sliding graft copolymer (SGC) with poly(ethylene glycol) (PEG) side chains was prepared by ester formation between terminal carboxyl groups of oxidized PEG methyl ether with molecular weight of 2000 (mPEG2000‐COOH) and hydroxyl groups of a polyrotaxane consisting of PEG and cyclodextrins (CDs). Formation of the SGC structure was confirmed by ¹H NMR, attenuated total reflectance Fourier‐transformed infrared, and gel permeation chromatography. The SGC was soluble in good solvents of PEG and insoluble in poor solvents of PEG. Estimation of the number of grafted mPEG chains suggested a “rope‐curtain” like structure, in which an mPEG chain is connected to each CD ring. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

A novel polyaddition of bifunctional acetylenes containing electron-withdrawing groups. III. Synthesis of polymers having β-alkoxyenoate moieties by the reaction of internal diynes with diols

Tri-n-butylphosphine-catalyzed polyadditions of activated internal diynes (bifunctional β-substituted propiolate, 1B and 1C ) with diols are described. Although a terminal bispropiolate ( 1A ) could not produce soluble polymers, with secondary diols, the polyaddition of 1B or 1C with primary as well as secondary diols gave corresponding polymers ( 3 , only composed of E isomeric units) in high yield. The rate of the present polyaddition was estimated by a model reaction of benzyl alcohol with methyl 2-heptynoate ( 4 ), from which the introduction of alkyl groups at the β-position of propiolate moieties was found to decrease the rate of the reaction by 80 times. Furthermore, the rate-determining step on this polymerization system was speculated to be a protonation step of zwitterionic intermediates with protons from diols. © 1996 John Wiley & Sons, Inc.     

Estimation of interaction energies by the critical molecular weight method: 1. Blends with polycarbonates

The interaction energies between PS, Pα-MS, and PMMA with several bisphenol-A-based polycarbonates were quantitatively determined from oligomer/oligomer, oligomer/homopolymer, and homopolymer/copolymer blends. Interaction energies were calculated from the Flory-Huggins theory and the Sanchez-Lacombe equation of state theory using experimental cloud points or miscibility boundaries. Alkyl addition to the phenyl rings of polycarbonate is favorable for miscibility with polystyrene whereas halogenation of the bisphenol connector unit is favorable for miscibility with poly(methyl methacrylate). Interaction energies are quantitatively ranked and described qualitatively in terms of changes in the electronic charge distribution of the polymer repeat units as calculated by SYBYL software. © 1994 John Wiley & Sons, Inc.     

Estimation of interaction energies by the critical molecular weight method: 2. Blends with polysulfones

The interaction energies between PS, Pα-MS, and PMMA, as well as acrylonitrile and maleic anhydride units, with a series of polysulfones were quantitatively determined from oligomer/oligomer, oligomer/homopolymer, and homopolymer/copolymer blends. Interaction energies were calculated from the Flory-Huggins theory and the Sanchez-Lacombe equation of state theory using experimental cloud points or miscibility boundaries. Alkyl addition to the phenyl rings of polysulfone is favorable for miscibility with polystyrene whereas halogenation of the bisphenol connector unit favors miscibility with poly(methyl methacrylate). Interaction energies are quantitatively ranked and described qualitatively in terms of changes in the electronic charge distribution of the polymer repeat units as calculated by SYBYL software. © 1994 John Wiley & Sons, Inc.     

Prebiotic Potential of Oligosaccharides Obtained by Acid Hydrolysis of α-(1→3)-Glucan from Laetiporus sulphureus: A Pilot Study

Increasing knowledge of the role of the intestinal microbiome in human health and well-being has resulted in increased interest in prebiotics, mainly oligosaccharides of various origins. To date, there are no reports in the literature on the prebiotic properties of oligosaccharides produced by the hydrolysis of pure fungal α-(1→3)-glucan. The aim of this study was to prepare α-(1→3)-glucooligosaccharides (α-(1→3)-GOS) and to perform initial evaluation of their prebiotic potential. The oligosaccharides were obtained by acid hydrolysis of α-(1→3)-glucan isolated from the fruiting bodies of Laetiporus sulphureus and then, characterized by HPLC. Fermentation of α-(1→3)-GOS and reference prebiotics was compared in in vitro pure cultures of Lactobacillus, Bifidobacterium, and enteric bacterial strains. A mixture of α-(1→3)-GOS, notably with a degree of polymerization of 2 to 9, was obtained. The hydrolysate was utilized for growth by most of the Lactobacillus strains tested and showed a strong bifidogenic effect, but did not promote the growth of Escherichia coli and Enterococcus faecalis. α-(1→3)-GOS proved to be effective in the selective stimulation of beneficial bacteria and can be further tested to determine their prebiotic functionality.