Sample records for macrocyclic molecular systems

  1. Bending rigid molecular rods: formation of oligoproline macrocycles.

    Scully, Conor C G; Rai, Vishal; Poda, Gennadiy; Zaretsky, Serge; Burns, Darcy C; Houliston, R Scott; Lou, Tiantong; Yudin, Andrei K


    Bent but not broken: cyclic oligoprolines are accessed in a reaction that effectively bends rigid oligoproline peptides (see scheme; TBDMS=tert-butyldimethylsilyl). The stitching is accomplished during macrocyclization enabled by aziridine aldehydes and isocyanides. Molecular modeling studies suggest that electrostatic attraction between the termini of the linear peptide is pivotal for macrocyclization. The macrocycles were studied by circular dichroism with a polyproline II structure being observed in larger macrocycles.

  2. Macrocycles

    Raymond, Kenneth N.; Xu, Jide; Pham, Tiffany A.


    The invention provides macrocycles useful in chelating metal ions, particularly radionuclides, to provide metal ion complexes. The invention also provides methods of using the compounds and complexes of the invention, such as in therapeutic and diagnostic applications.

  3. Creating molecular macrocycles for anion recognition

    Amar H. Flood


    Full Text Available The creation and functionality of new classes of macrocycles that are shape persistent and can bind anions is described. The genesis of triazolophane macrocycles emerges out of activity surrounding 1,2,3-triazoles made using click chemistry; and the same triazoles are responsible for anion capture. Mistakes made and lessons learnt in anion recognition provide deeper understanding that, together with theory, now provides for computer-aided receptor design. The lessons are acted upon in the creation of two new macrocycles. First, cyanostars are larger and like to capture large anions. Second is tricarb, which also favors large anions but shows a propensity to self-assemble in an orderly and stable manner, laying a foundation for future designs of hierarchical nanostructures.

  4. Dynamic covalent chemistry approaches toward macrocycles, molecular cages, and polymers.

    Jin, Yinghua; Wang, Qi; Taynton, Philip; Zhang, Wei


    The current research in the field of dynamic covalent chemistry includes the study of dynamic covalent reactions, catalysts, and their applications. Unlike noncovalent interactions utilized in supramolecular chemistry, the formation/breakage of covalent bonding has slower kinetics and usually requires the aid of a catalyst. Catalytic systems that enable efficient thermodynamic equilibrium are thus essential. In this Account, we describe the development of efficient catalysts for alkyne metathesis, and discuss the application of dynamic covalent reactions (mainly imine, olefin, and alkyne metathesis) in the development of organic functional materials. Alkyne metathesis is an emerging dynamic covalent reaction that offers robust and linear acetylene linkages. By introducing a podand motif into the catalyst ligand design, we have developed a series of highly active and robust alkyne metathesis catalysts, which, for the first time, enabled the one-step covalent assembly of ethynylene-linked functional molecular cages. Imine chemistry and olefin metathesis are among the most well-established reversible reactions, and have also been our main synthetic tools. Various shape-persistent macrocycles and covalent organic polyhedrons have been efficiently constructed in one-step through dynamic imine chemistry and olefin metathesis. The geometrical features and solubilizing groups of the building blocks as well as the reaction kinetics have significant effect on the outcome of a covalent assembly process. More recently, we explored the orthogonality of imine and olefin metatheses, and successfully synthesized heterosequenced macrocycles and molecular cages through one-pot orthogonal dynamic covalent chemistry. In addition to discrete molecular architectures, functional polymeric materials can also be accessed through dynamic covalent reactions. Defect-free solution-processable conjugated polyaryleneethynylenes and polydiacetylenes have been prepared through alkyne metathesis

  5. Molecular Rearrangement of an Aza-Scorpiand Macrocycle Induced by pH: A Computational Study

    Jesus Vicente De Julián-Ortiz


    Full Text Available Rearrangements and their control are a hot topic in supramolecular chemistry due to the possibilities that these phenomena open in the design of synthetic receptors and molecular machines. Macrocycle aza-scorpiands constitute an interesting system that can reorganize their spatial structure depending on pH variations or the presence of metal cations. In this study, the relative stabilities of these conformations were predicted computationally by semi-empirical and density functional theory approximations, and the reorganization from closed to open conformations was simulated by using the Monte Carlo multiple minimum method.

  6. Molecular Assemblies of Porphyrins and Macrocyclic Receptors: Recent Developments in Their Synthesis and Applications

    Abdirahman A. Mohamod


    Full Text Available Metalloporphyrins which form the core of many bioenzymes and natural light harvesting or electron transport systems, exhibit a variety of selective functional properties depending on the state and surroundings with which they exist in biological systems. The specificity and ease with which they function in each of their bio-functions appear to be largely governed by the nature and disposition of the protein globule around the porphyrin reaction center. Synthetic porphyrin frameworks confined within or around a pre-organized molecular entity like the protein network in natural systems have attracted considerable attraction, especially in the field of biomimetic reactions. At the same time a large number of macrocyclic oligomers such as calixarenes, resorcinarenes, spherands, cyclodextrins and crown ethers have been investigated in detail as efficient molecular receptors. These molecular receptors are synthetic host molecules with enclosed interiors, which are designed three dimensionally to ensure strong and precise molecular encapsulation/recognition. Due to their complex structures, enclosed guest molecules reside in an environment isolated from the outside and as a consequence, physical properties and chemical reactions specific to that environment in these guest species can be identified. The facile incorporation of such molecular receptors into the highly photoactive and catalytically efficient porphyrin framework allows for convenient design of useful molecular systems with unique structural and functional properties. Such systems have provided over the years attractive model systems for the study of various biological and chemical processes, and the design of new materials and molecular devices. This review focuses on the recent developments in the synthesis of porphyrin assemblies associated with cyclodextrins, calixarenes and resorcinarenes and their potential applications in the fields of molecular encapsulation/recognition, and

  7. Molecular recognition by multiple metal coordination inside wavy-stacked macrocycles.

    Nakamura, Takashi; Kaneko, Yuya; Nishibori, Eiji; Nabeshima, Tatsuya


    Most biological and synthetic receptors for small organic molecules employ a combination of relatively weak intermolecular interactions such as hydrogen bonds. A host compound that utilizes stronger yet reversible bonding in a synergistic manner could realize precise recognition, but the regulation and spatial arrangement of such reactive interaction moieties have been a challenge. Here, we show a multinuclear zinc complex synthesized from a macrocyclic ligand hexapap, which inwardly arranges labile metal coordination sites for external molecules. The metallomacrocycle forms a unique wavy-stacked structure upon binding a suitable length of dicarboxylic acids via multipoint coordination bonding. The saddle-shaped deformation and dimerization realize the differentiation of the interaction moieties, and change of guest-binding modes at specific metal coordination sites among the many present have been achieved utilizing acid/base as external stimuli.Synergistic use of coordination bonds that are strong and reversible realizes unique molecular recognition in artificial systems. Here, the authors show that a zinc-based metallomacrocyle can bind dicarboxylic acids of suitable length at specific metal sites by shape deformation and dimerization.

  8. Supramolecular polymers constructed from macrocycle-based host-guest molecular recognition motifs.

    Dong, Shengyi; Zheng, Bo; Wang, Feng; Huang, Feihe


    /physical properties, including stimuli responsiveness, self-healing, and environmental adaptation. It has been reported that macrocycle-based supramolecular polymers can respond to pH change, photoirradition, anions, cations, temperature, and solvent. Macrocycle-based supramolecular polymers have been prepared in solution, in gel, and in the solid state. Furthermore, the solvent has a very important influence on the formation of these supramolecular polymers. Crown ether- and pillararene-based supramolecular polymers have mainly formed in organic solvents, such as chloroform, acetone, and acetonitrile, while cyclodextrin- and cucurbituril-based supramolecular polymerizations have been usually observed in aqueous solutions. For calixarenes, both organic solvents and water have been used as suitable media for supramolecular polymerization. With the development of supramolecular chemistry and polymer science, various methods, such as nuclear magnetic resonance spectroscopy, X-ray techniques, electron microscopies, and theoretical calculation and computer simulation, have been applied for characterizing supramolecular polymers. The fabrication of macrocycle-based supramolecular polymers has become a currently hot research topic. In this Account, we summarize recent results in the investigation of supramolecular polymers constructed from macrocycle-based host-guest molecular recognition motifs. These supramolecular polymers are classified based on the different macrocycles used in them. Their monomer design, structure control, stimuli-responsiveness, and applications in various areas are discussed, and future research directions are proposed. It is expected that the development of supramolecular polymers will not only change the way we live and work but also exert significant influence on scientific research.

  9. Molecular mechanics approach for design and conformational studies of macrocyclic ligands

    Rohini,; Akbar, Rifat; Kanungo, B. K., E-mail: [Department of Chemistry, Sant Longowal Institute of Engineering & Technology, Longowal-148106 (India)


    Computational Chemistry has revolutionized way of viewing molecules at the quantum mechanical scale by allowing simulating various chemical scenarios that are not possible to study in a laboratory. The remarkable applications of computational chemistry have promoted to design and test of the effectiveness of various methods for searching the conformational space of highly flexible molecules. In this context, we conducted a series of optimization and conformational searches on macrocyclic based ligands, 9N3Me5Ox, (1,4,7-tris(5-methyl-8-hydroxyquinoline)-1,4,7-triazacyclononane) and 12N3Me5Ox, (1,5,9-tris(5-methyl-8-hydroxyquinoline)-1,5,9-triazacyclododecane) and studied their selectivity and coordination behavior with some lanthanide metal ions in molecular mechanics and semiempirical methods. The methods include both systematic and random conformational searches for dihedral angles, torsion angles and Cartesian coordinates. Structural studies were carried out by using geometry optimization, coordination scans and electronic properties were evaluated. The results clearly show that chair-boat conformational isomer of 9N3Me5Ox ligand is more stable due to lower eclipsing ethane interaction and form stronger adduct complexes with lanthanide metal ion. This is because of the fact that, in a central unit of 9N3 of the ligand form six endo type bonds out of nine. The rest of bonds have trans conformation. In contrast, for the adduct of 12N3Me5Ox, two C-C bonds have on eclipsed conformation, and others have synclinal and antiperiplanar confirmations. The distortion of the two eclipsed conformations may affect the yields and the stability of the complexes.

  10. The Crystal and Molecular Structure of a New Macrocyclic Ligand, (H6BDBPH)Br6·4H2O


    The hexahydro-bromide salt of a new 24-membered hexaaza diphenol macrocyclic ligand, (H6BDBPH)Br6·4H2O (C26H56N6O6Br6, M, = 1028.23), crystallizes in the monoclinic system, space group P21/c, with cell parameters: a = 14. 441(5), b=11.482(4), c=12.090(6)A, β=96.92°, V= 1990 (1)A3, Z=2, Dc=1. 716 g/cm3; F(000) = 1024. MoKa radiation, λ= 0. 71013A ), R = 0.0643 and wR = 0. 1356 for 3507 independent reflections with I > 2σ (I). The macrocyclic ligand adapts chair form, and the crystallographic inversion center is located in the macrocyclic cavity, and the six bromide ions and four water molecules are situated symmetrically outside the macrocyclic cavity.

  11. Co-conformational Exchange Triggered by Molecular Recognition in a Di(acylamino)pyridine-Based Molecular Shuttle Containing Two Pyridine Rings at the Macrocycle.

    Martinez-Cuezva, Alberto; Carro-Guillen, Fernando; Pastor, Aurelia; Marin-Luna, Marta; Orenes, Raul-Angel; Alajarin, Mateo; Berna, Jose


    We describe the incorporation of endo-pyridine units into the tetralactam ring of di(acylamino)pyridine-based rotaxanes. This macrocycle strongly associates with the linear interlocked component as confirmed by X-ray diffraction studies of rotaxane 2 b. Dynamic NMR studies of 2 b in solution revealed a rotational energy barrier that was higher than that of the related rotaxane 2 a, which lacks of pyridine rings in the macrocycle. The macrocycle distribution of the molecular shuttle 4 b, containing two endo-pyridine rings, shows that the major co-conformer is that with the cyclic component sitting over the di(acylamino)pyridine station. DFT calculations also support the marked preference of the ring for occupying the heterocyclic binding site. The association of N-hexylthymine with the di(acylamino)pyridine binding site of 4 b led to the formation of a rare 'S'-shaped co-conformer in which the tetralactam ring interacts simultaneously with both stations of the thread.

  12. [2+2+2] Cycloaddition Reactions of Macrocyclic Systems Catalyzed by Transition Metals. A Review

    Anna Roglans


    Full Text Available Polyalkyne and enediyne azamacrocycles are prepared from arenesulfonamides and various alkyne and alkene derivatives either under basic or neutral conditions. The new family of macrocyclic substrates is tested in the [2+2+2] cycloaddition reaction. Several catalysts are used for the cycloisomerization reaction, and their enantioinduction is evaluated as appropriate. The effect of the structural features of the macrocycles, namely the ring size, substituents in precise positions and the number and type of unsaturations, on the [2+2+2] cycloaddition reaction has also been studied.

  13. 常见大环自组装构建分子胶囊%Molecular Capsules Based on Common Macrocycles Self-Assembly

    郑睿; 梁丹霞; 于雪涛; 陈仁尔; 蒋华江; 周其忠


    Molecular capsules are amazing and fascinating because of their unusual structure and nanospaces. These unique microenvironments and nano-structures ultimately ensure their potential for applications in materials science, biological science, drug delivery and catalysis. Molecular capsules could be constructed by covalent bonds or non-covalent bonds with many kinds of different components. This article describes the syntheses and properties of a library of diverse molecular capsules by non-covalent bonds with common macrocycles, which covers (i) cyclodextrins based systems, (ii) calix[n]arenes based systems, (iii) calic[n]pyrroles based systems, (iv) porphyrins based systems, (v) cyclotriveratrylene (CTV) based systems, and finally (vi) cucurbit[n]urils based systems. These building blocks afford molecular capsules based on the self-assembly of several units, which is primarily driven by the interplay of weak attractions that act over short distances between molecules, including hydrogen bonds, electrostatic interaction, aromatic π-stacking, van der Waal's interactions, etc. These versatile molecular capsules providing different nanospaces, some of which are controllable and adjustable, could encapsulate different kinds of interesting guests in solution or solid states.%分子胶囊以其独特的分子结构在控制药物释放、催化、材料科学和生物医药等领域具有潜在的应用价值.分子胶囊可由不同的分子模块通过共价键或非共价键构建.着重描述了由常见的大环主体(环糊精、杯芳烃、杯吡咯、卟啉、环三藜芦烯和葫芦脲)通过自组装形成的分子胶囊.这些分子胶囊通过非共价键(氢键、静电作用、疏水作用及范德华力等)连接,使得分子胶囊具有可控的可调节的分子结构.通过这些独特的分子结构,分子胶囊可在溶液或固相中包裹各种各样的有趣的客体.

  14. Crossed and Linked Histories of Tetrapyrrolic Macrocycles and Their Use for Engineering Pores within Sol-Gel Matrices

    Miguel A. García-Sánchez


    Full Text Available The crossed and linked histories of tetrapyrrolic macrocycles, interwoven with new research discoveries, suggest that Nature has found in these structures a way to ensure the continuity of life. For diverse applications porphyrins or phthalocyanines must be trapped inside solid networks, but due to their nature, these compounds cannot be introduced by thermal diffusion; the sol-gel method makes possible this insertion through a soft chemical process. The methodologies for trapping or bonding macrocycles inside pristine or organo-modified silica or inside ZrO2 xerogels were developed by using phthalocyanines and porphyrins as molecular probes. The sizes of the pores formed depend on the structure, the cation nature, and the identities and positions of peripheral substituents of the macrocycle. The interactions of the macrocyclic molecule and surface Si-OH groups inhibit the efficient displaying of the macrocycle properties and to avoid this undesirable event, strategies such as situating the macrocycle far from the pore walls or to exchange the Si-OH species by alkyl or aryl groups have been proposed. Spectroscopic properties are better preserved when long unions are established between the macrocycle and the pore walls, or when oligomeric macrocyclic species are trapped inside each pore. When macrocycles are trapped inside organo-modified silica, their properties result similar to those displayed in solution and their intensities depend on the length of the alkyl chain attached to the matrix. These results support the prospect of tuning up the pore size, surface area, and polarity inside the pore cavities in order to prepare efficient catalytic, optical, sensoring, and medical systems. The most important feature is that research would confirm again that tetrapyrrolic macrocycles can help in the development of the authentic pore engineering in materials science.

  15. Macrocyclic fragrance materials

    Salvito, Daniel; Lapczynski, Aurelia; Sachse-Vasquez, Christen


    A screening-level aquatic environmental risk assessment for macrocyclic fragrance materials using a “group approach” is presented using data for 30 macrocyclic fragrance ingredients. In this group approach, conservative estimates of environmental exposure and ecotoxicological effects thresholds...... for compounds within two subgroups (15 macrocyclic ketones and 15 macrocyclic lactones/lactides) were used to estimate the aquatic ecological risk potential for these subgroups. It is reasonable to separate these fragrance materials into the two subgroups based on the likely metabolic pathway required...... for both regions is materials, and minimal in stream dilution (3:1), the conservatively predicted exposure concentrations for macrocyclic ketones would range from

  16. Solar Thermal Energy Storage in a Photochromic Macrocycle.

    Vlasceanu, Alexandru; Broman, Søren L; Hansen, Anne S; Skov, Anders B; Cacciarini, Martina; Kadziola, Anders; Kjaergaard, Henrik G; Mikkelsen, Kurt V; Nielsen, Mogens Brøndsted


    The conversion and efficient storage of solar energy is recognized to hold significant potential with regard to future energy solutions. Molecular solar thermal batteries based on photochromic systems exemplify one possible technology able to harness and apply this potential. Herein is described the synthesis of a macrocycle based on a dimer of the dihydroazulene/vinylheptafulvene (DHA/VHF) photo/thermal couple. By taking advantage of conformational strain, this DHA-DHA macrocycle presents an improved ability to absorb and store incident light energy in chemical bonds (VHF-VHF). A stepwise energy release over two sequential ring-closing reactions (VHF→DHA) combines the advantages of an initially fast discharge, hypothetically addressing immediate energy consumption needs, followed by a slow process for consistent, long-term use. This exemplifies another step forward in the molecular engineering and design of functional organic materials towards solar thermal energy storage and release.

  17. Giant vesicles from 72-membered macrocyclic archaeal phospholipid analogues: initiation of vesicle formation by molecular recognition between membrane components

    Eguchi; Arakawa; Kakinuma; Rapp; Ghosh; Nakatani; Ourisson


    Stereochemically pure archeal acyclic bola-amphiphilic diphosphates 4 and 5, with the basic structure of the phospholipids found in Sulfolobus, have been synthesized for the first time. The self-assembly properties have been compared with those of the nearly identical 72-membered macrocyclic tetraether phosphates 3a and 3b, analogues of the major phospholipid components of Sulfolobus, Thermoplasma, and methanogenic Archea, which were also synthesized. Phase contrast and fluorescence microscopies have shown that the dipolar lipids 1 and 2 spontaneously formed vesicles. Whereas the macrocyclic dipolar phosphates 3 spontaneously formed vesicles (phase contrast and fluorescence microscopies), the bolaform phosphate 4 gave only a lamellar structure (synchrotron diffraction pattern: repeat distance of about 4.25 nm but with only a few layers). However, upon addition of the unphosphorylated precursors phytanol, phytol, or geranylgeraniol to the acyclic lipids 4 and 5, giant vesicles were rapidly formed. Addition of n-hexadecanol or cholesterol did not lead to vesicle formation. Therefore it was concluded that this vesicle formation occurs only when the added molecule is closely compatible with the constituents of the lipid layer and can be inserted into the double layer. A slight mismatch (cholesterol or n-hexadecanol/polyprenyl chains) is therefore enough to block the insertion process presumably required for vesicle formation.

  18. Synthesis of macrocyclic polyazomethines

    Elizbarashvili,Elizbar; Matitaishvili,Tea; Topuria,Khatuna


    The synthesis of 20-membered macrocyclic polyazomethine dyes 3a and 3b from 4,4'-dihydroxybiphenyl-3,3'-dicarbaldehyde (2a) and 5,5'-diamino-4,4'-dihydroxybiphenyl-3,3'-dicarbaldehyde (2b) and macrocyclic polyazomethine pigments 4 and 5 from 3a is described.

  19. Observations on the Influence of Precursor Conformations on Macrocyclization Reactions

    Hammershøj, Peter; Beldring, Klavs; Nielsen, Anders R.


    macrocyclization to afford a mixture of diastereomeric sulfites, subjection of the other precursor to identical reaction conditions resulted in the isolation of the linear dichloride. We hypothesize that there is a difference in the ability of the two molecules to adopt a conformation that is germane...... to macrocyclization, a proposition that is supported by conformational analyses using molecular mechanics....

  20. Engineering macrocyclic figure-eight motif

    V Haridas; Harinder Singh; Yogesh K Sharma; Kashmiri Lal


    The design and synthesis of figure-eight macrocycles are very scarce owing to the intricacies and lack of predictability from first principles. This review emphasizes on discrete macrocyclic systems both synthetic and natural with a defined figure eight knotted topology. In almost all the helical macrocycles, the helical arrangement is held by intramolecular hydrogen bonding or as a backbone requirement, but in all cases, a planar graph can be drawn and so these compounds are trivial from the topological stand point. Nature presents great deal of complexity in terms of structures in macromolecules like DNA and proteins and also displays intriguing topology in simple natural products. Patellamide, tawicyclamides, nosiheptide and thiostrepton are natural products with figure eight topology which shows interesting biological activity. Expanded porphyrins, Cu(II) complexes of thiomacrocycles, cyclic peptides and oligoesters are synthetic macrocycles showing intriguing topology. Analysis of structure and folding behaviour will enable chemists to design molecules with intriguing topology.

  1. Features of use of modular training system armsportsmens 16–17 year olds in the annual macrocycle

    Dmytro Bezkorovainyi


    Full Text Available Purpose: to determine the most effective ratio of different means and methods of training 16–17 year olds armsportsmens the application of the block training system in the annual macrocycle. Material and Methods: 30 armsportsmens investigated 16–17 years to 15 in the control and experimental groups, analyzed and summarized the data of scientific and methodical literature, conducted teacher testing, pedagogical experiment, methods of research used functional state of cardio-respiratory. Results: it was found that the block system of training 16–17 year olds armsportsmens allows significantly increase the level of morphological and functional training base, improves functional indices of the cardiovascular system. Conclusions: the experimental training program for 16–17 year olds armsportsmens based modular training system allowed the athletes to create the experimental group was significantly higher level of morphofunctional sports training base, significantly improve the functionality of the body athletes, contributed to a high level of fitness and sports is recommended to practice the preparation armsportsmens

  2. Supramolecular networking of macrocycles based on exo-coordination: from discrete to continuous frameworks.

    Park, Sunhong; Lee, So Young; Park, Ki-Min; Lee, Shim Sung


    achieve in these networked macrocycles are one to three dimensional coordination polymers based on homo- and heteronuclear metal systems. Using crystal engineering methods, we have also investigated variation in the donors, interdonor distances, ligand isomer structures, and the effect of counter anions on the chemical and physical properties of the products. Understanding the relationship between structure and function in these exo-coordination products is an important step in the design of these new supramolecules for practical applications. We investigated the photophysical properties of the exocyclic complexes and a chromogenic macrocycle, which exhibited cation-selective and anion-controlled color change depending on an exo- or endo- ligand binding mode. Overall, we suggest that the exocyclic coordination behavior provides a versatile strategy for the preparation of new molecular networks and materials.

  3. Synthesis, Structure, and Molecular Recognition of S6 - and (SO2 )6 -Corona[6](het)arenes: Control of Macrocyclic Conformation and Properties by the Oxidation State of the Bridging Heteroatoms.

    Guo, Qing-Hui; Zhao, Liang; Wang, Mei-Xiang


    We report herein the synthesis, structure, and molecular recognition of S6 - and (SO2 )6 -corona[6](het)arenes, and demonstrate a unique and efficient strategy of regulating macrocyclic conformation and properties by adjusting the oxidation state of the heteroatom linkages. The one-pot nucleophilic aromatic substitution reaction of 1,4-benzenedithiol derivatives, biphenyl-4,4'-dithiol and 9,9-dipropyl-9H-fluorene-2,7-dithiol with 3,6-dichlorotetrazine afforded S6 -corona[3]arene[3]tetrazines. These compounds underwent inverse-electron-demand Diels-Alder reaction with enamines and norbornadiene to produce S6 -corona[3]arene[3]pyridazines. Facile oxidation of sulfide linkages yielded (SO2 )6 -corona[3]arene[3]pyridazines. All corona[6](het)arenes adopted generally hexagonal macrocyclic ring structures; however, their electronic properties and conformation could be fine-tuned by altering the oxidation state of the sulfur linkages. Whereas (SO2 )6 -corona[3]arene[3]pyridazines were electron-deficient, S6 -corona[3]arene[3]pyridazines acted as electron-rich macrocyclic hosts that recognized various organic cations in both aqueous and organic solutions.

  4. Efficient macrocyclization of U-turn preorganized peptidomimetics: the role of intramolecular H-bond and solvophobic effects.

    Becerril, Jorge; Bolte, Michael; Burguete, M Isabel; Galindo, Francisco; García-España, Enrique; Luis, Santiago V; Miravet, Juan F


    Simple peptidomimetic molecules derived from amino acids were reacted with meta- and para-bis(bromomethyl)benzene in acetonitrile to very efficiently yield macrocyclic structures. The cyclization reaction does not require high dilution techniques and seems to be insensitive to the size of the formed macrocycle. The analysis of data obtained by (1)H NMR, single-crystal X-ray diffraction, fluorescence measurements, and molecular mechanics indicate that folded conformations can preorganize the system for an efficient cyclization. The role played by intramolecular hydrogen-bonding and solvophobic effects in the presence of folded conformations is analyzed.

  5. Luminescent macrocyclic lanthanide complexes

    Raymond, Kenneth N [Berkeley, CA; Corneillie, Todd M [Campbell, CA; Xu, Jide [Berkeley, CA


    The present invention provides a novel class of macrocyclic compounds as well as complexes formed between a metal (e.g., lanthanide) ion and the compounds of the invention. Preferred complexes exhibit high stability as well as high quantum yields of lanthanide ion luminescence in aqueous media without the need for secondary activating agents. Preferred compounds incorporate hydroxy-isophthalamide moieties within their macrocyclic structure and are characterized by surprisingly low, non-specific binding to a variety of polypeptides such as antibodies and proteins as well as high kinetic stability. These characteristics distinguish them from known, open-structured ligands.

  6. Photoswitchable Dihydroazulene Macrocycles for Solar Energy Storage: The Effects of Ring Strain.

    Vlasceanu, Alexandru; Frandsen, Benjamin N; Skov, Anders B; Hansen, Anne Schou; Rasmussen, Mads Georg; Kjaergaard, Henrik G; Mikkelsen, Kurt V; Nielsen, Mogens Brøndsted


    Efficient energy storage and release are two major challenges of solar energy harvesting technologies. The development of molecular solar thermal systems presents one approach to address these issues by tuning the isomerization reactions of photo/thermoswitches. Here we show that the incorporation of photoswitches into macrocyclic structures is a particularly attractive solution for increasing the storage time. We present the synthesis and properties of a series of macrocycles incorporating two dihydroazulene (DHA) photoswitching subunits, bridged by linkers of varying chain length. Independent of ring size, all macrocycles exhibit stepwise, light-induced, ring-opening reactions (DHA-DHA to DHA-VHF to VHF-VHF; VHF = vinylheptafulvene) with the first DHA undergoing isomerization with a similar efficiency as the uncyclized parent system while the second (DHA-VHF to VHF-VHF) is significantly slower. The energy-releasing, VHF-to-DHA, ring closures also occur in a stepwise manner and are systematically found to proceed slower in the more strained (smaller) cycles, but in all cases with a remarkably slow conversion of the second VHF to DHA. We managed to increase the half-life of the second VHF-to-DHA conversion from 65 to 202 h at room temperature by simply decreasing the ring size. A computational study reveals the smallest macrocycle to have the most energetic VHF-VHF state and hence highest energy density.

  7. A diversity-oriented synthesis strategy enabling the combinatorial-type variation of macrocyclic peptidomimetic scaffolds.

    Isidro-Llobet, Albert; Hadje Georgiou, Kathy; Galloway, Warren R J D; Giacomini, Elisa; Hansen, Mette R; Méndez-Abt, Gabriela; Tan, Yaw Sing; Carro, Laura; Sore, Hannah F; Spring, David R


    Macrocyclic peptidomimetics are associated with a broad range of biological activities. However, despite such potentially valuable properties, the macrocyclic peptidomimetic structural class is generally considered as being poorly explored within drug discovery. This has been attributed to the lack of general methods for producing collections of macrocyclic peptidomimetics with high levels of structural, and thus shape, diversity. In particular, there is a lack of scaffold diversity in current macrocyclic peptidomimetic libraries; indeed, the efficient construction of diverse molecular scaffolds presents a formidable general challenge to the synthetic chemist. Herein we describe a new, advanced strategy for the diversity-oriented synthesis (DOS) of macrocyclic peptidomimetics that enables the combinatorial variation of molecular scaffolds (core macrocyclic ring architectures). The generality and robustness of this DOS strategy is demonstrated by the step-efficient synthesis of a structurally diverse library of over 200 macrocyclic peptidomimetic compounds, each based around a distinct molecular scaffold and isolated in milligram quantities, from readily available building-blocks. To the best of our knowledge this represents an unprecedented level of scaffold diversity in a synthetically derived library of macrocyclic peptidomimetics. Cheminformatic analysis indicated that the library compounds access regions of chemical space that are distinct from those addressed by top-selling brand-name drugs and macrocyclic natural products, illustrating the value of our DOS approach to sample regions of chemical space underexploited in current drug discovery efforts. An analysis of three-dimensional molecular shapes illustrated that the DOS library has a relatively high level of shape diversity.

  8. Push-pull macrocycles: donor-acceptor compounds with paired linearly conjugated or cross-conjugated pathways.

    Leu, Wade C W; Fritz, Amanda E; Digianantonio, Katherine M; Hartley, C Scott


    Two-dimensional π-systems are of current interest in the design of functional organic molecules, exhibiting unique behavior for applications in organic electronics, single-molecule devices, and sensing. Here we describe the synthesis and characterization of "push-pull macrocycles": electron-rich and electron-poor moieties linked by a pair of (matched) conjugated bridges. We have developed a two-component macrocyclization strategy that allows these structures to be synthesized with efficiencies comparable to acyclic donor-bridge-acceptor systems. Compounds with both cross-conjugated (m-phenylene) and linearly conjugated (2,5-thiophene) bridges have been prepared. As expected, the compounds undergo excitation to locally excited states followed by fluorescence from charge-transfer states. The m-phenylene-based systems exhibit slower charge-recombination rates presumably due to reduced electronic coupling through the cross-conjugated bridges. Interestingly, pairing the linearly conjugated 2,5-thiophene bridges also slows charge recombination. DFT calculations of frontier molecular orbitals show that the direct HOMO-LUMO transition is polarized orthogonal to the axis of charge transfer for these symmetrical macrocyclic architectures, reducing the electronic coupling. We believe the push-pull macrocycle design may be useful in engineering functional frontier molecular orbital symmetries.

  9. Predicting bioactive conformations and binding modes of macrocycles

    Anighoro, Andrew; de la Vega de León, Antonio; Bajorath, Jürgen


    Macrocyclic compounds experience increasing interest in drug discovery. It is often thought that these large and chemically complex molecules provide promising candidates to address difficult targets and interfere with protein-protein interactions. From a computational viewpoint, these molecules are difficult to treat. For example, flexible docking of macrocyclic compounds is hindered by the limited ability of current docking approaches to optimize conformations of extended ring systems for pose prediction. Herein, we report predictions of bioactive conformations of macrocycles using conformational search and binding modes using docking. Conformational ensembles generated using specialized search technique of about 70 % of the tested macrocycles contained accurate bioactive conformations. However, these conformations were difficult to identify on the basis of conformational energies. Moreover, docking calculations with limited ligand flexibility starting from individual low energy conformations rarely yielded highly accurate binding modes. In about 40 % of the test cases, binding modes were approximated with reasonable accuracy. However, when conformational ensembles were subjected to rigid body docking, an increase in meaningful binding mode predictions to more than 50 % of the test cases was observed. Electrostatic effects did not contribute to these predictions in a positive or negative manner. Rather, achieving shape complementarity at macrocycle-target interfaces was a decisive factor. In summary, a combined computational protocol using pre-computed conformational ensembles of macrocycles as a starting point for docking shows promise in modeling binding modes of macrocyclic compounds.

  10. Pyrazine motif containing hexagonal macrocycles: synthesis, characterization, and host-guest chemistry with nitro aromatics.

    Bhowmick, Sourav; Chakraborty, Sourav; Das, Atanu; Nallapeta, Sivaramaiah; Das, Neeladri


    The synthesis and characterization of cationic two-dimensional metallamacrocycles having a hexagonal shape and cavity are described. Both macrocycles utilize a pyrazine motif containing an organometallic acceptor tecton with platinum(II) centers along with different donor ligands. While one macrocycle is a relatively larger [6 + 6], the other is a relatively smaller [2 + 2] polygon. A unique feature of the smaller ensemble is that it is an irregular polygon in which all six edges are not of equal length. Molecular modeling of these macrocycles confirmed the presence of hexagonal cavities. The ability of these π-electron rich macrocycles to act as potential hosts for relatively electron deficient nitroaromatics (DNT = 2,4-dinitrotoluene and PA = picric acid) has been studied using isothermal titration calorimetry (ITC) as a tool. Molecular dynamics simulation studies were subsequently performed to gain critical insight into the binding interactions between the nitroaromatic guest molecules (PA/DNT) and the ionic macrocycles reported herein.

  11. Synergetics of molecular systems

    Lupichev, Lev N; Kadantsev, Vasiliy N


    Synergetics is the quantitative study of multicomponent systems that exhibit nonlinear dynamics and cooperativity. This book specifically considers basic models of the nonlinear dynamics of molecular systems and discusses relevant applications in biological physics and the polymer sciences.Emphasis is placed on specific solutions to the dynamical equations that correspond to the coherent formation of spatial-temporal structures, such as solitons, kinks and breathers, in particular. The emergence of these patterns in molecular structures provides a variety of information on their structural pro

  12. Fourth symposium on macrocyclic compounds

    Christensen, J. J.; Izatt, R. M.


    Both theoretical and experimental aspects of the properties and behavior of synthetic and naturally occurring macrocyclic compounds are covered in this symposium. This document contains abstracts of the papers. (DLC)

  13. Surface enhanced second harmonic generation from macrocycle, catenane, and rotaxane thin films : Experiments and theory

    Arfaoui, [No Value; Bermudez, [No Value; Bottari, G; De Nadai, C; Jalkanen, JP; Kajzar, F; Leigh, DA; Lubomska, M; Mendoza, SM; Niziol, J; Rudolf, P; Zerbetto, F; Arfaoui, Imad; Bermúdez, Verónica; Jalkanen, Jukka-Pekka


    Surface enhanced second harmonic generation (SE SHG) experiments on molecular structures, macrocycles, catenanes, and rotaxanes, deposited as monolayers and multilayers by vacuum sublimation on silver, are reported. The measurements show that the molecules form ordered thin films, where the highest

  14. Rigid, Conjugated Macrocycles for High Performance Organic Photodetectors.

    Zhang, Boyuan; Trinh, M Tuan; Fowler, Brandon; Ball, Melissa; Xu, Qizhi; Ng, Fay; Steigerwald, Michael L; Zhu, X-Y; Nuckolls, Colin; Zhong, Yu


    Organic photodetectors (OPDs) are attractive for their high optical absorption coefficient, broad wavelength tunability, and compatibility with lightweight and flexible devices. Here we describe a new molecular design that enables high performance organic photodetectors. We use a rigid, conjugated macrocycle as the electron acceptor in devices to obtain high photocurrent and low dark current. We make a direct comparison between the devices made with the macrocyclic acceptor and an acyclic control molecule; we find that the superior performance of the macrocycle originates from its rigid, conjugated, and cyclic structure. The macrocycle's rigid structure reduces the number of charged defects originating from deformed sp(2) carbons and covalent defects from photo/thermoactivation. With this molecular design, we are able to suppress dark current density while retaining high responsivity in an ultrasensitive nonfullerene OPD. Importantly, we achieve a detectivity of ∼10(14) Jones at near zero bias voltage. This is without the need for extra carrier blocking layers commonly employed in fullerene-based devices. Our devices are comparable to the best fullerene-based photodetectors, and the sensitivity at low working voltages (<0.1 V) is a record for nonfullerene OPDs.

  15. Synthesis, structure and ring-opening polymerization of macrocyclic arylates containing phthalic unit

    姜洪焱; 陈天禄; 邢彦; 林永华; 徐纪平


    A series of maerocyclic arylate diraers have been selectively synthesized by an interfacial polyconden-sation of o-phthaloyldichloride with bisphenols A combination of GPC,FAB-MS,1H and 13C NMR unambiguously confirmed the cyclic nature Although single-crystal X-ray analysis of two such macrocycles reveals no severe strain on the cyclic structures,these macrocycles can undergo facile melt polymerization to give high molecular weight polyary-lates.

  16. Schiff base oligopyrrolic macrocycles as ligands for lanthanides and actinides

    Sessler, Jonathan L. [Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, 1 University Station A5300, University of Texas at Austin, Austin, TX 78712-0165 (United States)]. E-mail:; Melfi, Patricia J. [Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, 1 University Station A5300, University of Texas at Austin, Austin, TX 78712-0165 (United States); Tomat, Elisa [Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, 1 University Station A5300, University of Texas at Austin, Austin, TX 78712-0165 (United States); Callaway, Wyeth [Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, 1 University Station A5300, University of Texas at Austin, Austin, TX 78712-0165 (United States); Huggins, Michael T. [Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, 1 University Station A5300, University of Texas at Austin, Austin, TX 78712-0165 (United States); Gordon, Pamela L. [C-Chemistry and NMT-Nuclear Materials Technology Divisions, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Webster Keogh, D. [C-Chemistry and NMT-Nuclear Materials Technology Divisions, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Date, Richard W. [Department of Chemistry, University of Exeter, Stocker Road, Exeter EX4 4QD (United Kingdom); Bruce, Duncan W. [Department of Chemistry, University of Exeter, Stocker Road, Exeter EX4 4QD (United Kingdom); Department of Chemistry, University of York, Heslington, YORK YO10 5DD (United Kingdom); Donnio, Bertrand [Institut de Physique et Chimie des Materiaux de Strasbourg (IPCMS), Groupe des Materiaux Organiques (GMO), CNRS-ULP - UMR 7504, 23 rue du Loess BP 43, F-67034 Strasbourg Cedex 2 (France)


    The coordination of f-block cations with Schiff base oligopyrrolic macrocycles is discussed. Analysis of the mesophase of a uranyl 2,5-diformylpyrrole-derived expanded porphyrin complex through temperature-dependent X-ray diffraction (XRD) methods has provided evidence for liquid-crystalline properties, and for molecular stacking into columns, arranged in a 2D hexagonal lattice. In separate studies, UV-vis spectral analysis has indicated the formation of three new f-block oligopyrrolic complexes. Addition of neptunyl ([NpO{sub 2}]{sup 2+}) or plutonyl ([PuO{sub 2}]{sup 2+}) chloride salts to the free base of a dipyrromethane-derived Schiff base macrocycle induces an immediate spectral change, namely the growth of a Q-like band at 630 nm. Such changes in the absorption spectra cause a dramatic color change from pale yellow to blue. It is postulated that oxidation of this macrocycle, stimulated by reduction of the metal center, leads to the observed spectral changes. An immediate visible and spectral change is also observed with the reaction of lutetium silylamide (Lu[N(Si(CH{sub 3}){sub 3}){sub 2}]{sub 3}), with a different, tetrapyrrole-containing Schiff base macrocycle. In this case, the formation of a complex with 1:1 metal-to-ligand binding stoichiometry is further supported by MALDI-TOF mass spectrometry.

  17. Correlation between oxygen adsorption energy and electronic structure of transition metal macrocyclic complexes.

    Liu, Kexi; Lei, Yinkai; Wang, Guofeng


    Oxygen adsorption energy is directly relevant to the catalytic activity of electrocatalysts for oxygen reduction reaction (ORR). In this study, we established the correlation between the O2 adsorption energy and the electronic structure of transition metal macrocyclic complexes which exhibit activity for ORR. To this end, we have predicted the molecular and electronic structures of a series of transition metal macrocyclic complexes with planar N4 chelation, as well as the molecular and electronic structures for the O2 adsorption on these macrocyclic molecules, using the density functional theory calculation method. We found that the calculated adsorption energy of O2 on the transition metal macrocyclic complexes was linearly related to the average position (relative to the lowest unoccupied molecular orbital of the macrocyclic complexes) of the non-bonding d orbitals (d(z(2)), d(xy), d(xz), and d(yz)) which belong to the central transition metal atom. Importantly, our results suggest that varying the energy level of the non-bonding d orbitals through changing the central transition metal atom and/or peripheral ligand groups could be an effective way to tuning their O2 adsorption energy for enhancing the ORR activity of transition metal macrocyclic complex catalysts.

  18. Functional materials from self-assembled bis-urea macrocycles.

    Shimizu, Linda S; Salpage, Sahan R; Korous, Arthur A


    CONSPECTUS: This Account highlights the work from our laboratories on bis-urea macrocycles constructed from two C-shaped spacers and two urea groups. These simple molecular units assembled with high fidelity into columnar structures guided by the three-centered urea hydrogen bonding motif and aryl stacking interactions. Individual columns are aligned and closely packed together to afford functional and homogeneous microporous crystals. This approach allows for precise and rational control over the dimensions of the columnar structure simply by changing the small molecular unit. When the macrocyclic unit lacks a cavity, columnar assembly gives strong pillars. Strong pillars with external functional groups such as basic lone pairs can expand like clays to accept guests between the pillars. Macrocycles that contain sizable interior cavities assemble into porous molecular crystals with aligned, well-defined columnar pores that are accessible to gases and guests. Herein, we examine the optimal design of the macrocyclic unit that leads to columnar assembly in high fidelity and probe the feasibility of incorporating a second functional group within the macrocycles. The porous molecular crystals prepared through the self-assembly of bis-urea macrocycles display surface areas similar to zeolites but lower than MOFs. Their simple one-dimensional channels are well-suited for studying binding, investigating transport, diffusion and exchange, and monitoring the effects of encapsulation on reaction mechanism and product distribution. Guests that complement the size, shape, and polarity of the channels can be absorbed into these porous crystals with repeatable stoichiometry to form solid host-guest complexes. Heating or extraction with an organic solvent enables desorption or removal of the guest and subsequent recovery of the solid host. Further, these porous crystals can be used as containers for the selective [2 + 2] cycloadditions of small enones such as 2-cyclohexenone or 3

  19. Effect of the chemical modification of a macrocycle and the acidity of a medium on the spectral properties and basicity of tetraphenylporphyrin in HCl- N, N-dimethylformamide system at 298 K

    Ivanova, Yu. B.; Razgonyaev, O. V.; Semeikin, A. S.; Mamardashvili, N. Zh.


    Spectrophotometric titration is used to study the basicity of tetraphenylporphine and its derivatives with electron-donor and electron-acceptor substituents in the 4-positions of meso-aryl fragments (5,10,15,20-tetra(4-R-phenyl)porphine, R:-OH,-NH2,-COOH,-Cl) in a system HCl- N, N-dimethylformamide at 298 K. An equation for calculating the dependence of the Hammett constant ( H 0) on the HCl concentration in a HCl- N, N-dimethylformamide system at 298 K is proposed. It is found that protonation of the intracycle nitrogen atoms of tetrapyrrole macrocycles of the indicated compounds occurs in two stages in this system. The corresponding ionization constants and concentration ranges of the existence of mono- and doubly-protonated dication forms of the indicated compounds are determined. It is found that both the introduction of strong substituents into the macrocycle of porphyrin and the properties of the medium facilitate the formation of mono- and doubly-protonated forms of porphyrins in solutions.

  20. A Redox-Controllable Molecular Switch Based on Weak Recognition of BPX26C6 at a Diphenylurea Station

    Jia-Cheng Chang


    Full Text Available The Na+ ion–assisted recognition of urea derivatives by BPX26C6 has allowed the construction of a redox-controllable [2]rotaxane-type molecular switch based on two originally very weakly interacting host/guest systems. Using NOBF4 to oxidize the triarylamine terminus into a corresponding radical cation attracted the macrocyclic component toward its adjacent carbamate station; subsequent addition of Zn powder moved the macrocyclic component back to its urea station.


    Title: Lanthanide Enhance Luminescence (LEL) with one and two photon excitation of Quantum Dyes? Lanthanide(III)-Macrocycles Principal Author:Robert C. Leif, Newport InstrumentsSecondary Authors:Margie C. Becker, Phoenix Flow Systems Al Bromm, Virginia Commonw...

  2. Convergent Synthesis of Rigid Macrocycles Containing One and Two Tetrathiafulvalene Units

    Simonsen, Klaus B.; Thorup, Niels; Becher, Jan


    The synthesis of rigid tetrathiafulvalenophanes containing one or two tetrathiafulvalene units is presented, together with a stepwise convergent synthesis of macrocyclic bis-tetrathiafulvalenes via several open dimeric tetrathiafulvalenes. These systems were investigated by cyclic voltammetry...


    Title: Lanthanide Enhance Luminescence (LEL) with one and two photon excitation of Quantum Dyes? Lanthanide(III)-Macrocycles Principal Author:Robert C. Leif, Newport InstrumentsSecondary Authors:Margie C. Becker, Phoenix Flow Systems Al Bromm, Virginia Commonw...

  4. Macrocyclic trichothecenes as antifungal and anticancer compounds.

    de Carvalho, Maira Peres; Weich, Herbert; Abraham, Wolf-Rainer


    Trichothecenes are sesquiterpenoid metabolites produced by fungi and species of the plant genus Baccharis, family Asteraceae. They comprise a tricyclic core with an epoxide at C-12 and C-13 and can be grouped into non-macrocyclic and macrocyclic compounds. While many of these compounds are of concern in agriculture, the macrocyclic metabolites have been evaluated as antiviral, anti-cancer, antimalarial and antifungal compounds. Some known cytotoxic responses on eukaryotic cells include inhibition of protein, DNA and RNA syntheses, interference with mitochondrial function, effects on cell division and membranes. These targets however have been elucidated essentially employing non-macrocyclic trichothecenes and only one or two closely related macrocyclic compounds. For several macrocyclic trichothecenes high selectivity against fungal species and against cancer cell lines have been reported suggesting that the macrocycle and its stereochemistry are of crucial importance regarding biological activity and selectivity. This review is focused on compounds belonging to the macrocyclic type, where a cyclic diester or triester ring binds to the trichothecane moiety at C-4 and C- 15 leading to natural products belonging to the groups of satratoxins, verrucarins, roridins, myrotoxins and baccharinoids. Their biological activities, cytotoxic mechanisms and structure-activity relationships (SAR) are discussed. From the reported data it becomes evident that even small changes in the molecules can lead to pronounced effects on biological activity or selectivity against cancer cells lines. Understanding the underlying mechanisms may help to design highly specific drugs for cancer therapy.

  5. Structural, electrochemical, and photophysical properties of a molecular shuttle attached to an acid-terminated self-assembled monolayer

    Cecchet, F; Rudolf, P; Rapino, S; Margotti, M; Paolucci, F; Baggerman, J; Kay, ER; Wong, JKY; Leigh, DA; Kay, Euan R.; Wong, Jenny K.Y.; Brouwer, A.M.


    A benzylic amide macrocycle containing a pyridine moiety (macrocycle 2) and a related benzylic amide macrocycle-based molecular shuttle (naphthalimide rotaxane) with two pyridine moieties on the macrocyclic unit were grafted onto a self-assembled monolayer (SAM) of 11-mercaptoundecanoic acid (11-MUA

  6. Smart macrocyclic molecules: induced fit and ultrafast self-sorting inclusion behavior through dynamic covalent chemistry.

    Han, Ji-Min; Pan, Jin-Long; Lei, Ting; Liu, Chenjiang; Pei, Jian


    A family of macrocycles with oligo(ethylene glycol) chains, 4O, 5O, and 6O, was developed to construct a series of new incorporated macrocycles through dynamic covalent chemistry. These flexible macrocycles exhibited excellent "self-sorting" abilities with diamine compounds, which depended on the "induced-fit" rule. For instance, the host macrocycles underwent conformational modulation to accommodate the diamine guests, affording [1+1] intramolecular addition compounds regardless of the flexibility of the diamine. These macrocycles folded themselves to fit various diamines with different chain length through modulation of the flexible polyether chain, and afforded intramolecular condensation products. However, if the chain of the diamine was too long and rigid, oligomers or polymers were obtained from the mixture of the macromolecule and the diamine. All results demonstrated that inclusion compounds involving conformationally suitable aromatic diamines were thermodynamically favorable candidates in the mixture due to the restriction of the macrocycle size. Furthermore, kinetic and thermodynamic studies of self-sorting behaviors of both mixed 4O-5O and 4O-6O systems were investigated in detail. Finally, theoretical calculations were also employed to further understand such self-sorting behavior, and indicated that the large enthalpy change of H(2)NArArNH(2)@4O is the driving force for the sorting behavior. Our system may provide a model to further understand the principle of biomolecules with high specificity due only to their conformational self-adjusting ability.

  7. Radical photocyclization route for macrocyclic lactone ring expansion and conversion to macrocyclic lactams and ketones.

    Nishikawa, Keisuke; Yoshimi, Yasuharu; Maeda, Kousuke; Morita, Toshio; Takahashi, Ichiro; Itou, Tatsuya; Inagaki, Sho; Hatanaka, Minoru


    A new method for the synthesis of macrocyclic lactones, lactams, and ketones, which utilizes photoinduced intramolecular radical cyclization reactions of substrates containing tethered carboxylic acids and α,β-unsaturated carbonyl moieties, has been uncovered. Photocyclization of the carboxylic acids tethered acrylate ester, which were prepared starting from the macrocyclic lactones, gave the two-carbon elongated macrocyclic lactones via decarboxylation. Similar photoreactions of carboxylic acid tethered acryl amide or α,β-unsaturated ketone moieties, which were also prepared starting from the macrocyclic lactones, produced macrocyclic lactams or ketones, respectively. The simple approach can be readily applied to the preparation of a variety of macrocyclic lactones, lactams, and ketones with tunable ring sizes.

  8. Templating irreversible covalent macrocyclization by using anions.

    Kataev, Evgeny A; Kolesnikov, Grigory V; Arnold, Rene; Lavrov, Herman V; Khrustalev, Victor N


    Inorganic anions were used as templates in the reaction between a diamine and an activated diacid to form macrocyclic amides. The reaction conditions were found to perform the macrocyclization sufficiently slow to observe a template effect. A number of analytical methods were used to clarify the reaction mechanisms and to show that the structure of the intermediate plays a decisive role in determining the product distribution. For the macrocyclization under kinetic control, it was shown that the amount of a template, the conformational rigidity of building blocks, and the anion affinities of reaction components and intermediates are important parameters that one should take into consideration to achieve high yields.

  9. Energy Dissipation in Molecular Systems

    Tramer, André; Lahmani, Fran oise


    Energy Dissipation in Molecular Systems analyzes experimental data on the redistribution and dissipation of energy injected into molecular systems by radiation or charged particles. These processes, competing with such practically important relaxation channels as chemical reaction or stimulated emission (laser action), are the primary focus in this monograph. Among other topics, the book treats vibrational redistribution and electronic relaxation in isolated molecules and the effects of inter-molecular interactions (collisions, complex formation, solvent effects) on the relaxation paths. Primary photo-chemical processes (such as isomerization, proton or hydrogen-atom transfer, electron transfer and ionization) are also treated as particular cases of vibrational or electronic relaxation. Only a basic knowledge of quantum mechanics and spectroscopy is assumed and calculations are kept to a strict minimum, making the book more accessible to students.

  10. Novel antibiotics: C-2 symmetrical macrocycles inhibiting Holliday junction DNA binding by E. coli RuvC.

    Pan, Po-Shen; Curtis, Fiona A; Carroll, Chris L; Medina, Irene; Liotta, Lisa A; Sharples, Gary J; McAlpine, Shelli R


    Holliday junctions (HJs) are formed as transient DNA intermediates during site-specific and homologous recombination. Both of these genetic exchange pathways are critical for normal DNA metabolism and repair. Trapping HJs leads to bacterial cell death by preventing proper segregation of the resulting interlinked chromosomes. Macrocyclic peptides designed to target this intermediate were synthesized with the goal of identifying compounds with specificity for this unique molecular target. We discovered ten macrocycles, both hexameric and octameric peptides, capable of trapping HJs in vitro. Those macrocycles containing tyrosine residues proved most effective. These data demonstrate that C-2 symmetrical macrocycles offer excellent synthetic targets for the development of novel antibiotic agents. Furthermore, the active compounds identified provide valuable tools for probing different pathways of recombinational exchange.

  11. 8th International Symposium on Supramolecular and Macrocyclic Chemistry

    Davis, Jeffery T. [Univ. of Maryland, College Park, MD (United States)


    This report summarizes the 8th International Conference on Supramolecular and Macrocyclic Chemistry (ISMSC-8). DOE funds were used to make it more affordable for students, post-docs and junior faculty to attend the conference by covering their registration costs. The conference was held in Crystal City, VA from July 7-11, 2013. See for the conference website. ISMSC-8 encompassed the broad scope and interdisciplinary nature of the field. We met our goal to bring together leading scientists in molecular recognition and supramolecular chemistry. New research directions and collaborations resulted this conference. The DOE funding was crucial for us achieving our primary goal.

  12. Light-powered, artificial molecular pumps: a minimalistic approach

    Giulio Ragazzon


    Full Text Available The realization of artificial molecular motors capable of converting energy into mechanical work is a fascinating challenge of nanotechnology and requires reactive systems that can operate away from chemical equilibrium. This article describes the design and construction of a simple, supramolecular ensemble in which light irradiation causes the directional transit of a macrocycle along a nonsymmetric molecular axle, thus forming the basis for the development of artificial molecular pumps.

  13. Information theory of molecular systems

    Nalewajski, Roman F


    As well as providing a unified outlook on physics, Information Theory (IT) has numerous applications in chemistry and biology owing to its ability to provide a measure of the entropy/information contained within probability distributions and criteria of their information ""distance"" (similarity) and independence. Information Theory of Molecular Systems applies standard IT to classical problems in the theory of electronic structure and chemical reactivity. The book starts by introducing the basic concepts of modern electronic structure/reactivity theory based upon the Density Functional Theory

  14. Systems biology in molecular psychiatry.

    Gebicke-Haerter, P J


    The last ten to fifteen years have seen a remarkable shift of research strategies from hypothesis-driven, reductionistic to data driven, hypothesis-free approaches. This tendency has become evident after completion of the sequencing of the human genome, when publications under the label systems biology have been skyrocketing. This shift marks a gradual revision of scientific understanding of biological systems. Whilst the former has been component-oriented, precluding elements that do not belong to the hypothesis, the latter try to extract information from the whole system in the first place. Only with this information at hand, data driven strategies develop hypotheses. Data driven strategies unearth the immense complexity of biological systems and, hence, necessitate computer-aided support. Mathematical tools derived from chaos theory appear to be applicable in biological systems, but require significant improvements. The combination of high throughput data collection with in silico modelling of molecular or higher order systems can markedly extend our understanding of onset and progression of diseases. Undoubtedly, systems thinking in brain research is the greatest challenge for the years to come.

  15. A comprehensive electronic structure description of a biscyanotetraazacobalt(III) macrocyclic complex.

    Ishiruji, Fabiana Hitomi Ono; Nunes, Fábio Souza


    Molecular modeling and a detailed spectroscopic characterization of the macrocyclic complex [Co(meso)(CN)(2)](+) (meso = 5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane) is herein presented. Structural, electronic and vibrational features are discussed and assignments were proposed on the basis of semi-empirical (molecular mechanics (MM+), ZINDO/S and PM3) quantum-mechanics calculations. The energy and the composition of the molecular orbitals of the complex were calculated and a quantitative diagram was constructed. The simulated UV-vis spectrum exhibited a reasonably good accordance with the experimental one and fully assignments of seven bands were made. An optimized configuration of the complex showed a strong cobalt-cyanide axial bond in agreement with the major contribution of the cyanide to the composition of the molecular orbitals in contrast to a discrete participation of the macrocyclic meso to the ground state of the complex.

  16. Molecular Spectroscopy of Living Systems

    Cheng, Ji-Xin


    Molecular spectroscopy has been a powerful tool in the study of molecules in gas phase, condensed phase, and at interfaces. The transition from in vitro spectroscopy to spectroscopic imaging of living systems is opening new opportunities to reveal cellular machinery and to enable molecule-based diagnosis (Science 2015, 350: 1054). Such a transition involves more than a simple combination of spectrometry and microscopy. In this presentation, I will discuss the most recent efforts that have pushed the physical limits of spectroscopic imaging in terms of spectral acquisition speed, detection sensitivity, spatial resolution and imaging depth. I will further highlight significant applications in functional analysis of single cells and in label-free detection of diseases.

  17. Enzymatic Macrocyclization of 1,2,3-Triazole Peptide Mimetics.

    Oueis, Emilia; Jaspars, Marcel; Westwood, Nicholas J; Naismith, James H


    The macrocyclization of linear peptides is very often accompanied by significant improvements in their stability and biological activity. Many strategies are available for their chemical macrocyclization, however, enzyme-mediated methods remain of great interest in terms of synthetic utility. To date, known macrocyclization enzymes have been shown to be active on both peptide and protein substrates. Here we show that the macrocyclization enzyme of the cyanobactin family, PatGmac, is capable of macrocyclizing substrates with one, two, or three 1,4-substituted 1,2,3-triazole moieties. The introduction of non-peptidic scaffolds into macrocycles is highly desirable in tuning the activity and physical properties of peptidic macrocycles. We have isolated and fully characterized nine non-natural triazole-containing cyclic peptides, a further ten molecules are also synthesized. PatGmac has now been shown to be an effective and versatile tool for the ring closure by peptide bond formation.

  18. Organic spin clusters: macrocyclic-macrocyclic polyarylmethyl polyradicals with very high spin S = 5-13.

    Rajca, Andrzej; Wongsriratanakul, Jirawat; Rajca, Suchada


    Synthesis and magnetic studies of a new class of organic spin clusters, possessing alternating connectivity of unequal spins, are described. Polyarylmethyl polyether precursors to the spin clusters, with linear and branched connectivity between calix[4]arene-based macrocycles, are prepared via modular, multistep syntheses. Their molecular connectivity and stereoisomerism are analyzed using NMR spectroscopy. The absolute masses (4-10 kDa) are determined by FABMS and GPC/MALS. Small angle neutron scattering (SANS) provides the radii of gyration of 1.2-1.8 nm. The corresponding polyradicals with 15, 22, and 36 triarylmethyls, which are prepared and studied as solutions in tetrahydrofuran-d(8), may be described as S' = 7/2, 1/2, 7/2 spin trimer (average S = 5-6), S' = 7/2, 1/2, 6/2, 1/2, 7/2 spin pentamer (average S = 7-9), and spin nonamer (average S = 11-13), respectively, as determined by SQUID magnetometry and numerical fits to linear combinations of the Brillouin functions. For spin trimer and pentamer, the quantitative magnetization data are fit to new percolation models, based upon random distributions of chemical defects and ferromagnetic vs antiferromagnetic couplings. The value of S = 13 is the highest for an organic molecule.

  19. Rapid synthesis of macrocycles from diol precursors

    Wingstrand, Magnus; Madsen, Charlotte Marie; Clausen, Mads Hartvig


    A method for the formation of synthetic macrocycles with different ring sizes from diols is presented. Reacting a simple diol precursor with electrophilic reagents leads to a cyclic carbonate, sulfite or phosphate in a single step in 25-60% yield. Converting the cyclization precursor to a bis-ele...

  20. Reactions of small molecular systems

    Wittig, C. [Univ. of Southern California, Los Angeles, CA (United States)


    This DOE program remains focused on small molecular systems relevant to combustion. Though a number of experimental approaches and machines are available for this research, the authors` activities are centered around the high-n Rydberg time-of-flight (HRTOF) apparatus in this laboratory. One student and one postdoc carry out experiments with this machine and also engage in small intra-group collaborations involving shared equipment. This past year was more productive than the previous two, due to the uninterrupted operation of the HRTOF apparatus. Results were obtained with CH{sub 3}OH, CH{sub 3}SH, Rg-HX complexes, HCOOH, and their deuterated analogs where appropriate. One paper is in print, three have been accepted for publication, and one is under review. Many preliminary results that augur well for the future were obtained with other systems such as HNO{sub 3}, HBr-HI complexes, toluene, etc. Highlights from the past year are presented below that display some of the features of this program.

  1. Synthesis, crystal structures and properties of two novel macrocyclic nickel(II) and copper(II) complexes

    Su, Yan-Hui; Liu, Jie; Li, Jia; Si, Xue-Zhi


    Two new 14-membered hexaaza macrocyclic complexes with the formulae [NiL](ClO 4) 2·CH 3COCH 3 ( 1) and [CuL](ClO 4) 2·CH 3COCH 3 ( 2), where L = 3,10-bis(2-thiophenemethyl)-1,3,5,8,10,12-hexaazacyclotetradecane, have been synthesized and characterized by elemental analyses, single-crystal X-ray diffraction analyses, electronic spectra, IR and TG-DTA. In 1, the nickel(II) ion is four-coordinated with four nitrogen atoms from the macrocycle and forms a square-planar coordination geometry. In 2, the copper(II) ion is six-coordinated with four nitrogen atoms from the macrocyclic ligand in the equatorial plane and two oxygen atoms from the perchlorate anions in the axial position exhibiting an elongated octahedron coordination geometry. The two complexes present two different molecular arrangements in which the [ML] 2+ (M = Ni, Cu) cation arrays in the manner of M(1)M(2)M(1)… in sequence. The pendant thiophene groups of the neighboring macrocycles have no π⋯π interactions. All the ClO4- anions and acetone molecules are involved in hydrogen-bonding interactions with the macrocyclic ligand.

  2. Synthesis and characterization of new azo containing Schiff base macrocycle

    Saeed Malek-Ahmadi; Amir Abdolmaleki


    Fully conjugated Schiff base macrocycle has been prepared through a simple and mild condition, a one-pot cyclization procedure of four-component without using a template. The condensation reaction of related bis (hydroxybenzaldehyde) with phenylenediamines to prepare a conjugated [2 + 2] Schiff base macrocycle has been investigated and fluorescent [2 + 2] Schiff base macrocycles with N2O2 binding pockets has been prepared and characterized by elemental analysis,' H NMR, IR, fluorescent, UV-visible and MALDI mass spectroscopies.

  3. Amide-based Fluorescent Macrocyclic Anion Receptors

    ZENG, Zhen-Ya(曾振亚); XU, Kuo-Xi(徐括喜); HE, Yong-Bing(何永炳); LIU, Shun-Ying(刘顺英); WU, Jin-Long(吴进龙); WEI, Lan-Hua(隗兰华); MENG, Ling-Zhi(孟令芝)


    Two fluorescent anion receptors (1 and 2) based on amide macrocycle were synthesized and corresponding fluorescence quenching induced by anion complexation was observed in different degree. Receptors form 1: 1 complexes with anions by hydrogen bonding interactions. Receptor 1 bound anions in the order of F->Cl->H2PO4->CH3COO->>Br-, I- and receptor 2 showed high selectivity to F- over other anions.

  4. Single-molecule phenyl-acetylene-macrocycle-based optoelectronic switch functioning as a quantum-interference-effect transistor.

    Hsu, Liang-Yan; Rabitz, Herschel


    This work proposes a new type of optoelectronic switch, the phenyl-acetylene-macrocycle-based single-molecule transistor, which utilizes photon-assisted tunneling and destructive quantum interference. The analysis uses single-particle Green's functions along with Floquet theory. Without the optical field, phenyl-acetylene-macrocycle exhibits a wide range of strong antiresonance between its frontier orbitals. The simulations show large on-off ratios (over 10(4)) and measurable currents (~10(-11) A) enabled by photon-assisted tunneling in a weak optical field (~2 × 10(5) V/cm) and at a small source-drain voltage (~0.05 V). Field amplitude power scaling laws and a range of field intensities are given for operating one- and two-photon assisted tunneling in phenyl-acetylene-macrocycle-based single-molecule transistors. This development opens up a new direction for creating molecular switches.

  5. A Macrocyclic 1,4-Diketone Enables the Synthesis of a p-Phenylene Ring That Is More Strained than a Monomer Unit of [4]Cycloparaphenylene.

    Mitra, Nirmal K; Corzo, Hector H; Merner, Bradley L


    The synthesis of a p-terphenyl-based macrocycle, containing a p-phenylene unit with 42.6 kcal/mol of strain energy (SE), is reported. The conversion of a macrocyclic 1,4-diketone to a highly strained arene system takes place over five synthetic steps, featuring iterative dehydrative reactions in the aromatization protocol. Spectroscopic data of the deformed benzenoid macrocycle are in excellent agreement with other homologues that have been reported, indicating that the central p-phenylene ring of 9 is aromatic.

  6. Molecular assembly in natural and engineered systems

    Howorka, Stefan


    This volume explores some of the most exciting recent advances in basic research on molecular assembly in natural and engineered systems and how this knowledge is leading to advances in the various fields.* This series provides a forum for discussion of new discoveries, approaches, and ideas * Contributions from leading scholars and industry experts * Reference guide for researchers involved in molecular biology and related fields

  7. Molecular motor assembly of a biomimetic system


    @@ Active biological molecules and functional structures can be fabricated into a bio-mimetic system by using molecular assembly method. Such materials can be used for the drug delivery, disease diagnosis and therapy, and new nanodevice construction.

  8. Orthogonal photoswitching in a multifunctional molecular system

    Lerch, Michael M.; Hansen, Mickel J.; Velema, Willem A.; Szymanski, Wiktor; Feringa, Ben L.


    The wavelength-selective, reversible photocontrol over various molecular processes in parallel remains an unsolved challenge. Overlapping ultraviolet-visible spectra of frequently employed photoswitches have prevented the development of orthogonally responsive systems, analogous to those that rely o

  9. Ring strain and total syntheses of modified macrocycles of the isoplagiochin type

    Andreas Speicher


    Full Text Available Macrocycles of the bisbibenzyl-type are natural products that are found exclusively in bryophytes (liverworts. The molecular framework of the subtype “isoplagiochin” is of substantial structural interest because of the chirality of the entire molecule, which arises from two biaryl axes in combination with two helical two-carbon units in a cyclic arrangement. From a structural as well as a synthetic point of view we report on the total synthesis of compounds which possess more rigid two-carbon biaryl bridges like stilbene (E or Z or even tolane moieties which were introduced starting with a Sonogashira protocol. The McMurry method proved to be a powerful tool for the cyclization to these considerably ring-strained macrocycles.

  10. New Copper and Oxomolybdate Robson-Type Polynuclear Macrocyclic Complexes: Structure, Spectroscopy, and Electrochemical Properties

    Marcelo Carpes Nunes


    Full Text Available The polynuclear complexes [Mo3O8(tidf]·dmso·2H2O (1 and [{Cu2(tidf}2(μ-Mo8O24] (2 (tidf2− is a symmetrical tetraiminodiphenolate Robson-type macrocyclic ligand were prepared from equimolar combinations of [Mg2(tidf](NO32·4H2O, [MoO2Cl2(dmso2] (for 1 and complex 1 and Cu(ClO42·4H2O (for 2 in acetonitrile. Molecular structures of both complexes were determined and showed atypical modes of coordination. A significant observation was the remarkable flexibility of the macrocycle ligand that effectively accommodated the steric demands of metal cations and the packing forces and showed a unique mode of coordination. Spectroscopic (UV-vis and FTIR and redox properties are discussed.

  11. The Click Reaction as an Efficient Tool for the Construction of Macrocyclic Structures

    Dario Pasini


    Full Text Available The Cu(I-catalyzed azide-alkyne cycloaddition (CuAAC, known as the click reaction is an established tool used for the construction of complex molecular architectures. Given its efficiency it has been widely applied for bioconjugation, polymer and dendrimer synthesis. More recently, this reaction has been utilized for the efficient formation of rigid or shape-persistent, preorganized macrocyclic species. This strategy also allows the installment of useful functionalities, in the form of polar and function-rich 1,2,3-triazole moieties, directly embedded in the macrocyclic structures. This review analyzes the state of the art in this context, and provides some elements of perspective for future applications.

  12. Synthesis of the macrocyclic core of (-)-pladienolide B

    Skaanderup, Philip Robert; Jensen, T.


    An efficient synthesis of the macrocyclic core of (-)-pladienolide B is disclosed. The concise route relies on a chiral auxiliary-mediated asymmetric aldol addition and an osmium-catalyzed asymmetric dihydroxylation to install the three oxygenated stereocenters of the macrocycle. This purely reag...

  13. Synthesis of New Macrocyclic Polyamides as Antimicrobial Agent Candidates

    Osama I. Abd El-Salam


    Full Text Available A series of macrocyclic imides and Schiff-bases have been prepared via the cyclocondensation of pyridine-2,6-dicarbonyl dichloride (1 with L-ornithine methyl ester to give the corresponding macrocyclic bisester 2. Treatment of 2 with hydrazine hydrate gave macrocyclic bisacid hydrazide 3, which was used as starting material. Condensation of bishydrazide 3 with diacid anhydrides or aromatic aldehydes in refluxing acetic acid or ethanol gave the corresponding macrocyclic bisimides 4, 5a,b and macrocyclic bis- hydrazones 6a–j, respectively. The structure assignments of the new compounds were based on chemical and spectroscopic evidence. The antimicrobial screening showed that many of these newly synthesized compounds have good antimicrobial activities, comparable to ampicillin and ketaconazole used as reference drugs.

  14. A Macrocyclic Peptide that Serves as a Cocrystallization Ligand and Inhibits the Function of a MATE Family Transporter

    Hiroaki Suga


    Full Text Available The random non-standard peptide integrated discovery (RaPID system has proven to be a powerful approach to discover de novo natural product-like macrocyclic peptides that inhibit protein functions. We have recently reported three macrocyclic peptides that bind to Pyrococcus furiosus multidrug and toxic compound extrusion (PfMATE transporter and inhibit the transport function. Moreover, these macrocyclic peptides were successfully employed as cocrystallization ligands of selenomethionine-labeled PfMATE. In this report, we disclose the details of the RaPID selection strategy that led to the identification of these three macrocyclic peptides as well as a fourth macrocyclic peptide, MaD8, which is exclusively discussed in this article. MaD8 was found to bind within the cleft of PfMATE’s extracellular side and blocked the path of organic small molecules being extruded. The results of an ethidium bromide efflux assay confirmed the efflux inhibitory activity of MaD8, whose behavior was similar to that of previously reported MaD5.

  15. Macrocyclic 2,7-Anthrylene Oligomers.

    Yamamoto, Yuta; Wakamatsu, Kan; Iwanaga, Tetsuo; Sato, Hiroyasu; Toyota, Shinji


    A macrocyclic compound consisting of six 2,7-anthrylene units was successfully synthesized by Ni-mediated coupling of the corresponding dibromo precursor as a novel π-conjugated compound. This compound was sufficiently stable and soluble in organic solvents due to the presence of mesityl groups. X-ray analysis showed that the molecule had a nonplanar and hexagonal wheel-shaped framework of approximately S6 symmetry. The dynamic process between two S6 structures was observed by using the dynamic NMR technique, the barrier being 58 kJ mol(-1) . The spectroscopic properties of the hexamer were compared with those of analogous linear oligomers.

  16. ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs

    Cleves, Ann E.; Jain, Ajay N.


    We introduce the ForceGen method for 3D structure generation and conformer elaboration of drug-like small molecules. ForceGen is novel, avoiding use of distance geometry, molecular templates, or simulation-oriented stochastic sampling. The method is primarily driven by the molecular force field, implemented using an extension of MMFF94s and a partial charge estimator based on electronegativity-equalization. The force field is coupled to algorithms for direct sampling of realistic physical movements made by small molecules. Results are presented on a standard benchmark from the Cambridge Crystallographic Database of 480 drug-like small molecules, including full structure generation from SMILES strings. Reproduction of protein-bound crystallographic ligand poses is demonstrated on four carefully curated data sets: the ConfGen Set (667 ligands), the PINC cross-docking benchmark (1062 ligands), a large set of macrocyclic ligands (182 total with typical ring sizes of 12-23 atoms), and a commonly used benchmark for evaluating macrocycle conformer generation (30 ligands total). Results compare favorably to alternative methods, and performance on macrocyclic compounds approaches that observed on non-macrocycles while yielding a roughly 100-fold speed improvement over alternative MD-based methods with comparable performance.

  17. How do the macrocyclic lactones kill filarial nematode larvae?

    Wolstenholme, Adrian J; Maclean, Mary J; Coates, Ruby; McCoy, Ciaran J; Reaves, Barbara J


    The macrocyclic lactones (MLs) are one of the few classes of drug used in the control of the human filarial infections, onchocerciasis and lymphatic filariasis, and the only one used to prevent heartworm disease in dogs and cats. Despite their importance in preventing filarial diseases, the way in which the MLs work against these parasites is unclear. In vitro measurements of nematode motility have revealed a large discrepancy between the maximum plasma concentrations achieved after drug administration and the amounts required to paralyze worms. Recent evidence has shed new light on the likely functions of the ML target, glutamate-gated chloride channels, in filarial nematodes and supports the hypothesis that the rapid clearance of microfilariae that follows treatment involves the host immune system.

  18. Characterizing Molecular Interactions in Chemical Systems.

    Günther, David; Boto, Roberto A; Contreras-Garcia, Juila; Piquemal, Jean-Philip; Tierny, Julien


    Interactions between atoms have a major influence on the chemical properties of molecular systems. While covalent interactions impose the structural integrity of molecules, noncovalent interactions govern more subtle phenomena such as protein folding, bonding or self assembly. The understanding of these types of interactions is necessary for the interpretation of many biological processes and chemical design tasks. While traditionally the electron density is analyzed to interpret the quantum chemistry of a molecular system, noncovalent interactions are characterized by low electron densities and only slight variations of them--challenging their extraction and characterization. Recently, the signed electron density and the reduced gradient, two scalar fields derived from the electron density, have drawn much attention in quantum chemistry since they enable a qualitative visualization of these interactions even in complex molecular systems and experimental measurements. In this work, we present the first combinatorial algorithm for the automated extraction and characterization of covalent and noncovalent interactions in molecular systems. The proposed algorithm is based on a joint topological analysis of the signed electron density and the reduced gradient. Combining the connectivity information of the critical points of these two scalar fields enables to visualize, enumerate, classify and investigate molecular interactions in a robust manner. Experiments on a variety of molecular systems, from simple dimers to proteins or DNA, demonstrate the ability of our technique to robustly extract these interactions and to reveal their structural relations to the atoms and bonds forming the molecules. For simple systems, our analysis corroborates the observations made by the chemists while it provides new visual and quantitative insights on chemical interactions for larger molecular systems.

  19. Applying Virtual Realitzy to Molecular Graphics System

    ChangNoYoon; MyungHwanChi; 等


    Mlecular graphics can be thought of as a window to the computer through which the chemist expresses ideas for computational evaluation and receives results in an understandable form.Furthermore,with beautiful graphic images it can give out the realistic molecular model like a real thing in real world.Molecule has various properties including volume,electronic,van der waals forces,etc.These properties are very important to understand the molecular world.So if the virtual reality tools are used,then the imaginary world can be studied intuitively by touching and feeling a tremendous amount of data.Computational chemistry generates such amount of molecular property data through supercomputing with molecular simulation experiment.One of the objects to investigate the molecular world is to understand the intermolecular interaction such as drug-receptor interaction.Another thing is to measure the geometrical data in molecular architecture.Virtual reality system provides the easiest way to meet these objects.This kind of simple system changes a numerical data set,which is very difficults to deal with,into a visible and understandable data set.Recently two functions of such a system were improved to get an insight into biomolecular interaction.The first one is a real time force generation during navigation in macromolecular environment.An cylindrical arrow shows the magnitude and direction of molecular force.The second one is to see a molecular vibration such as a concerted motion of the binding site in protein molecule.So one can understand th molecular shape change for drugreceptor docking procedure.But some problems which are difficult to solve still remain.

  20. Reaction dynamics in polyatomic molecular systems

    Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)


    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  1. Redox-Active Tetraruthenium Macrocycles Built from 1,4-Divinylphenylene-Bridged Diruthenium Complexes.

    Scheerer, Stefan; Linseis, Michael; Wuttke, Evelyn; Weickert, Sabrina; Drescher, Malte; Tröppner, Oliver; Ivanović-Burmazović, Ivana; Irmler, Andreas; Pauly, Fabian; Winter, Rainer F


    Metallamacrocylic tetraruthenium complexes were generated by treatment of 1,4-divinylphenylene-bridged diruthenium complexes with functionalized 1,3-benzene dicarboxylic acids and characterized by HR ESI-MS and multinuclear NMR spectroscopy. Every divinylphenylene diruthenium subunit is oxidized in two consecutive one-electron steps with half-wave potential splittings in the range of 250 to 330 mV. Additional, smaller redox-splittings between the +/2+ and 0/+ and the 3+/4+ and 2+/3+ redox processes, corresponding to the first and the second oxidations of every divinylphenylene diruthenium entity, are due to electrostatic effects. The lack of electronic coupling through bond or through space is explained by the nodal properties of the relevant molecular orbitals and the lateral side-by-side arrangement of the divinylphenylene linkers. The polyelectrochromic behavior of the divinylphenylene diruthenium precursors is retained and even amplified in these metallamacrocyclic structures. EPR studies down to T=4 K indicate that the dications 1-H(2+) and 1-OBu(2+) are paramagnetic. The dications and the tetracation of macrocycle 3-H display intense (dications) or weak (3-H(4+) ) EPR signals. Quantum chemical calculations indicate that the four most stable conformers of the macrocycles are largely devoid of strain. Bond parameters, energies as well as charge and spin density distributions of model macrocycle 5-H(Me) were calculated for the different charge and spin states.

  2. Heartworms, macrocyclic lactones, and the specter of resistance to prevention in the United States

    Bowman Dwight D


    Full Text Available Abstract In order to provide a background to current concerns relative to the possible resistance of heartworms to macrocyclic lactones, this review summarizes various studies in which lack of efficacies (LOEs have been observed in dogs on macrocyclic lactone preventives relative to the United States of America. Some of these studies have been published in the peer-reviewed literature, others have appeared in various reports to the Center for Veterinary Medicine (CVM of the Food and Drug Administration (FDA of the USA as New Animal Drug Application (NADA summaries, and one appeared as a letter to US veterinarians. This review also discusses reports relating to the potential problem of heartworm resistance in microfilariae and third-stage larvae, as well as molecular markers associated with resistance to macrocyclic lactones within Dirofilaria immitis. As more work is being done in this area of great concern relative to the protection of dogs from infection using this class of preventives, it seems timely to summarize what is known about heartworms, their potential resistance to treatment, and the means of selecting for resistance genes in populations of this helminth in the laboratory and in the field.

  3. Macrocyclic olefin metathesis at high concentrations by using a phase-separation strategy.

    Raymond, Michaël; Holtz-Mulholland, Michael; Collins, Shawn K


    Macrocyclic olefin metathesis has seen advances in the areas of stereochemistry, chemoselectivity, and catalyst stability, but strategies aimed at controlling dilution effects in macrocyclizations are rare. Herein, a protocol to promote macrocyclic olefin metathesis, one of the most common synthetic tools used to prepare macrocycles, at relatively high concentrations (up to 60 mM) is described by exploitation of a phase-separation strategy. A variety of macrocyclic skeletons could be prepared having either different alkyl, aryl, or amino acids spacers.

  4. Observations on the Influence of Precursor Conformations on Macrocyclization Reactions

    Hammershøj, Peter; Beldring, Klavs; Nielsen, Anders R.;


    Macrocycles hold great promise in drug discovery as an underutilized class of lead compounds. The low abundance of these molecules can, in part, be explained by the inherent difficulties in the synthesis of macrocycles and the lack of general methods for their rapid assembly. We have undertaken...... a research program aimed at developing methods for facile synthesis of macrocycles from simple precursors. The synthesis of two new cyclization precursors is described and the results of their reaction with thionyl chloride are presented and discussed. Whereas one acyclic diol smoothly underwent...

  5. Unsaturated macrocyclic dihydroxamic acid siderophores produced by Shewanella putrefaciens using precursor-directed biosynthesis.

    Soe, Cho Z; Codd, Rachel


    To acquire iron essential for growth, the bacterium Shewanella putrefaciens produces the macrocyclic dihydroxamic acid putrebactin (pbH2; [M + H(+)](+), m/zcalc 373.2) as its native siderophore. The assembly of pbH2 requires endogenous 1,4-diaminobutane (DB), which is produced from the ornithine decarboxylase (ODC)-catalyzed decarboxylation of l-ornithine. In this work, levels of endogenous DB were attenuated in S. putrefaciens cultures by augmenting the medium with the ODC inhibitor 1,4-diamino-2-butanone (DBO). The presence in the medium of DBO together with alternative exogenous non-native diamine substrates, (15)N2-1,4-diaminobutane ((15)N2-DB) or 1,4-diamino-2(E)-butene (E-DBE), resulted in the respective biosynthesis of (15)N-labeled pbH2 ((15)N4-pbH2; [M + H(+)](+), m/zcalc 377.2, m/zobs 377.2) or the unsaturated pbH2 variant, named here: E,E-putrebactene (E,E-pbeH2; [M + H(+)](+), m/zcalc 369.2, m/zobs 369.2). In the latter system, remaining endogenous DB resulted in the parallel biosynthesis of the monounsaturated DB-E-DBE hybrid, E-putrebactene (E-pbxH2; [M + H(+)](+), m/zcalc 371.2, m/zobs 371.2). These are the first identified unsaturated macrocyclic dihydroxamic acid siderophores. LC-MS measurements showed 1:1 complexes formed between Fe(III) and pbH2 ([Fe(pb)](+); [M](+), m/zcalc 426.1, m/zobs 426.2), (15)N4-pbH2 ([Fe((15)N4-pb)](+); [M](+), m/zcalc 430.1, m/zobs 430.1), E,E-pbeH2 ([Fe(E,E-pbe)](+); [M](+), m/zcalc 422.1, m/zobs 422.0), or E-pbxH2 ([Fe(E-pbx)](+); [M](+), m/zcalc 424.1, m/zobs 424.2). The order of the gain in siderophore-mediated Fe(III) solubility, as defined by the difference in retention time between the free ligand and the Fe(III)-loaded complex, was pbH2 (ΔtR = 8.77 min) > E-pbxH2 (ΔtR = 6.95 min) > E,E-pbeH2 (ΔtR = 6.16 min), which suggests one possible reason why nature has selected for saturated rather than unsaturated siderophores as Fe(III) solubilization agents. The potential to conduct multiple types of ex situ chemical

  6. A bambusuril macrocycle that binds anions in water with high affinity and selectivity.

    Yawer, Mirza Arfan; Havel, Vaclav; Sindelar, Vladimir


    Synthetic receptors that function in water are important for the qualitative and quantitative detection of anions, which may act as pollutants in the environment or play important roles in biological processes. Neutral receptors are particularly appealing because they are often more selective than positively charged receptors; however, their affinity towards anions in pure water is only in range of 1-10(3)  L mol(-1) . The anion-templated synthesis of a water-soluble bambusuril derivative is shown to be an outstanding receptor for various inorganic anions in pure water, with association constants of up to 10(7)  L mol(-1) . Furthermore, the macrocycle discriminates between anions with unprecedented selectivity (up to 500 000-fold). We anticipate that the combination of remarkable affinity and selectivity of this macrocycle will enable the efficient detection and isolation of diverse anions in aqueous solutions, which is not possible with current supramolecular systems.

  7. Relaxation time in disordered molecular systems

    Rocha, Rodrigo P. [Departamento de Física, Universidade Federal de Santa Catarina, 88040-900 Florianópolis-SC (Brazil); Freire, José A., E-mail: [Departamento de Física, Universidade Federal do Paraná, 81531-990 Curitiba-PR (Brazil)


    Relaxation time is the typical time it takes for a closed physical system to attain thermal equilibrium. The equilibrium is brought about by the action of a thermal reservoir inducing changes in the system micro-states. The relaxation time is intuitively expected to increase with system disorder. We derive a simple analytical expression for this dependence in the context of electronic equilibration in an amorphous molecular system model. We find that the disorder dramatically enhances the relaxation time but does not affect its independence of the nature of the initial state.

  8. Enantiocontrol in Macrocycle Formation from Catalytic MetalCarbene Transformations

    DOYLE, Michael P.; DOYLE, Michael P; HU, Wen-Hao(胡文浩); 胡文浩


    The development of catalytic metal carbene transformations for the construction of macrocyclic lactones has dramatically increased their synthetic advantages.This is the first review of this developing methodology.

  9. Structural basis for precursor protein-directed ribosomal peptide macrocyclization

    Li, Kunhua; Condurso, Heather L.; Li, Gengnan; Ding, Yousong; Bruner, Steven D. (Florida)


    Macrocyclization is a common feature of natural product biosynthetic pathways including the diverse family of ribosomal peptides. Microviridins are architecturally complex cyanobacterial ribosomal peptides that target proteases with potent reversible inhibition. The product structure is constructed via three macrocyclizations catalyzed sequentially by two members of the ATP-grasp family, a unique strategy for ribosomal peptide macrocyclization. Here we describe in detail the structural basis for the enzyme-catalyzed macrocyclizations in the microviridin J pathway of Microcystis aeruginosa. The macrocyclases MdnC and MdnB interact with a conserved α-helix of the precursor peptide using a novel precursor-peptide recognition mechanism. The results provide insight into the unique protein–protein interactions that are key to the chemistry, suggest an origin for the natural combinatorial synthesis of microviridin peptides, and provide a framework for future engineering efforts to generate designed compounds.

  10. Synthesis of novel symmetrical macrocycle via oxidative homocoupling of bisalkyne

    Kamalulazmy, Nurulain; Hassan, Nurul Izzaty [School of Chemical Sciences and Food Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan (Malaysia)


    A novel symmetrical macrocycle has been synthesised via oxidative homocoupling of bisalkyne, diprop-2-ynyl pyridine-2,6-dicarboxylate mediated by copper (I) iodide (CuI) and 4-dimethylaminopyridine (DMAP). The precursor compound was synthesised from 2,6-pyridine dicarbonyl dichloride and propargyl alcohol in the presence of triethylamine. The reaction mixture was stirred overnight and further purified via column chromatograpy with 76% yield. Single crystal for X-ray study was obtained by recrystallization from acetone. Subsequently, a symmetrical macrocycle was synthesised from oxidative homocoupling of precursor compound in open atmosphere. The crude product was purified by column chromatography to furnish macrocycle compound with 5% yield. Both compounds were characterised by IR, {sup 1}H and {sup 13}C NMR and mass spectral techniques. The unusual conformation of the bisalkyne and twisted conformation of designed macrocycle has influence the percentage yield. This has been studied thoroughly by X-ray crystallography and electronic structure calculations.

  11. Scalable Molecular Dynamics for Large Biomolecular Systems

    Robert K. Brunner


    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  12. Rules of Macrocycle Topology: A [13]-Macrodilactone Case Study.

    Magpusao, Anniefer N; Rutledge, Kelli; Hamlin, Trevor A; Lawrence, Jean-Marc; Mercado, Brandon Q; Leadbeater, Nicholas E; Peczuh, Mark W


    Shape is an inherent trait of a molecule that dictates how it interacts with other molecules, either in binding events or intermolecular reactions. Large-ring macrocyclic compounds in particular leverage their shape when they are selectively bound by biomolecules and also when they exhibit macrocyclic diastereoselectivity. Nonetheless, rules that link structural parameters to the conformation of a macrocycle are still rudimentary. Here we use a structural investigation of a family of [13]-macrodilactones as a case study to develop rules that can be applied generally to macrocycles of different sizes and with a variety of functionality. A characteristic "ribbon" shape is adopted by the [13]-macrodilactones in the absence of stereogenic centres, which exhibits planar chirality. When one stereogenic centre at key positions on the backbone is incorporated into the structure, the planar chirality is dictated by the configuration of the centre. In cases where two stereogenic centres are present, their relationships can either reinforce the characteristic ribbon shape or induce alternative shapes to be adopted. The rules established in the case study are then applied to the analysis of a structure of the natural product migrastatin. They lay the groundwork for the development of models to understand macrocycle-biomolecule interactions and for the preparation of macrocycles with designed properties and activities.

  13. Technologies for the Synthesis of mRNA-Encoding Libraries and Discovery of Bioactive Natural Product-Inspired Non-Traditional Macrocyclic Peptides

    Hiroaki Suga


    Full Text Available In this review, we discuss emerging technologies for drug discovery, which yields novel molecular scaffolds based on natural product-inspired non-traditional peptides expressed using the translation machinery. Unlike natural products, these technologies allow for constructing mRNA-encoding libraries of macrocyclic peptides containing non-canonical sidechains and N-methyl-modified backbones. The complexity of sequence space in such libraries reaches as high as a trillion (>1012, affording initial hits of high affinity ligands against protein targets. Although this article comprehensively covers several related technologies, we discuss in greater detail the technical development and advantages of the Random non-standard Peptide Integration Discovery (RaPID system, including the recent identification of inhibitors against various therapeutic targets.

  14. A flexible cyclophane: Design, synthesis, and structure of a multibridged tris-tetrathiafulvalene (TTF) macrocycle

    Takimiya, K.; Thorup, Niels; Becher, J.


    that the neutral molecules include two (3a) or one chloroform molecule (3b) as solvent of crystallization inside the cavity, whereas the I-3(-) salt of 3b, obtained by electrocrystallization, has a molecular structure which is different from that of the neutral molecule in that the cavity has completely collapsed.......The tris-tetrathiafulvalene (TTF) macrocycles 3 with a large end-cavity were effectively synthesized from the readily available tetrakis(cyanoethylthio)TTF by means of a selective deprotection/realkylation sequence followed by an intramolecular coupling reaction. Crystal structure analyses revealed...

  15. The role of macrocyclic ligands in the peroxo/superoxo nature of Ni-O2 biomimetic complexes.

    Zapata-Rivera, Jhon; Caballol, Rosa; Calzado, Carmen J


    The impact of the macrocyclic ligand on the electronic structure of two LNi-O2 biomimetic adducts, [Ni(12-TMC)O2](+) (12-TMC = 1,4,7,10-tetramethyl-1,4,7,10-tetraazacyclododecane) and [Ni(14-TMC)O2](+) (14-TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane), has been inspected by means of difference-dedicated configuration interaction calculations and a valence bond reading of the wavefunction. The system containing the 12-membered macrocyclic ligand has been experimentally described as a side-on nickel(III)-peroxo complex, whereas the 14-membered one has been characterized as an end-on nickel(II)-superoxide. Our results put in evidence the relationship between the steric effect of the macrocyclic ligand, the O2 coordination mode and the charge transfer extent between the Ni center and the O2 molecule. The 12-membered macrocyclic ligand favors a side-on coordination, a most efficient overlap between Ni 3d and O2 π* orbitals and, consequently, a larger charge transfer from LNi fragment to O2 molecule. The analysis of the ground-state electronic structure shows an enhancement of the peroxide nature of the Ni-O2 interaction for [Ni(12-TMC)O2](+), although a dominant superoxide character is found for both systems.

  16. Intelligent systems for the molecular biologist

    Brutlag, D.L.


    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. In this paper, one objective is to identify properties of DNA sequences that determine their function, by computer-aided statistical analysis and to accurately predict its function, given a new sequence. A related problem is to predict protein structure and function from the sequence.

  17. Optical antenna for photofunctional molecular systems.

    Ikeda, Katsuyoshi; Uosaki, Kohei


    Optical antennas can enhance the efficiency of photon-molecule interactions. To design efficient antenna structures, it is essential to consider physicochemical aspects in addition to electromagnetic considerations. Specifically, chemical interactions between optical antennas and molecules have to be controlled to enhance the overall efficiency. For this purpose, sphere-plane nanostructures are suitable optical antennas for molecular-modified functional electrode systems when a well-defined electrode is utilized as a platform.

  18. N-doped carbon networks: alternative materials tracing new routes for activating molecular hydrogen.

    Cortese, Remedios; Ferrante, Francesco; Roggan, Stefan; Duca, Dario


    The fragmentation of molecular hydrogen on N-doped carbon networks was investigated by using molecular (polyaromatic macrocycles) as well as truncated and periodic (carbon nanotubes) models. The computational study was focused on the ergonicity analysis of the reaction and on the properties of the transition states involved when constellations of three or four pyridinic nitrogen atom defects are present in the carbon network. Calculations show that whenever N-defects are embedded in species characterized by large conjugated π-systems, either in polyaromatic macrocycles or carbon nanotubes, the corresponding H2 bond cleavage is largely exergonic. The fragmentation Gibbs free energy is affected by the final arrangement of the hydrogen atoms on the defect and by the extension of the π-electron cloud, but it is not influenced by the curvature of the system.

  19. Accounting for intra-molecular vibrational modes in open quantum system description of molecular systems.

    Roden, Jan; Strunz, Walter T; Whaley, K Birgitta; Eisfeld, Alexander


    Electronic-vibrational dynamics in molecular systems that interact with an environment involve a large number of degrees of freedom and are therefore often described by means of open quantum system approaches. A popular approach is to include only the electronic degrees of freedom into the system part and to couple these to a non-Markovian bath of harmonic vibrational modes that is characterized by a spectral density. Since this bath represents both intra-molecular and external vibrations, it is important to understand how to construct a spectral density that accounts for intra-molecular vibrational modes that couple further to other modes. Here, we address this problem by explicitly incorporating an intra-molecular vibrational mode together with the electronic degrees of freedom into the system part and using the Fano theory for a resonance coupled to a continuum to derive an "effective" bath spectral density, which describes the contribution of intra-molecular modes. We compare this effective model for the intra-molecular mode with the method of pseudomodes, a widely used approach in simulation of non-Markovian dynamics. We clarify the difference between these two approaches and demonstrate that the respective resulting dynamics and optical spectra can be very different.




    A chemically modified field-effect transistor (CHEMFET) with satisfactory Ag+ selectivity is described. The potentiometric Ag+ selectivities of CHEMFETs with plasticized PVC membranes based on macrocyclic thioethers have been determined. All the macrocyclic thioethers tested showed silver response a

  1. Low-molecular-weight metabolite systems chemistry

    Franz eHadacek


    Full Text Available Low-molecular-weight metabolites (LMWMs comprise primary or central and a plethora of intermediary or secondary metabolites, all of which are characterized by a molecular weight below 900 Dalton. The latter are especially prominent in sessile higher organisms, such as plants, corals, sponges and fungi, but are produced by all types of microbial organisms too. Common to all of these carbon molecules are oxygen, nitrogen and, to a lesser extent, sulfur, as heteroatoms. The latter can contribute as electron donators or acceptors to cellular redox chemistry and define the potential of the molecule to enter charge-transfer complexes. Furthermore, they allow LMWMs to serve as organic ligands in coordination complexes of various inorganic metals as central atoms. Especially the transition metals Fe, Cu and Mn can catalyze one electron reduction of molecular oxygen, which results in formation of free radical species and reactive follow-up reaction products. As antioxidants LMWMs can scavenge free radicals. Depending on the chemical environment, the same LMWMs can act as pro-oxidants by reducing molecular oxygen. The cellular regulation of redox homeostasis, a balance between oxidation and reduction, is still far from being understood. Charge-transfer and coordination complex formation with metals shapes LMWMs into gel-like matrices in the cytosol. The quasi-polymer structure is lost usually during the isolation procedure. In the gel state, LMWMs possess semiconductor properties. Also proteins and membranes are semiconductors. Together they can represent biotransistor components that can be part of a chemoelectrical signaling system that coordinates systems chemistry by initiating cell differentiation or tissue homeostasis, the activated and the resting cell state, when it is required. This concept is not new and dates back to Albert Szent-Györgyi.

  2. Macrocyclic Assembly: A Dive into the Pecking Order and Applied Aspects of Multitalented Metallomacrocycles

    Ashu Chaudhary


    Full Text Available To aid in knowledge of macrocyclic complexes and biomedical scientists, we are presenting here a review article with compilation of work done so far along in relation to macrocyclic ligands and their metal complexes. The metal ion chemistry of macrocyclic ligands has now become a major subdivision of coordination chemistry. This overview focuses on developments in design, synthesis, and self-assembly of metal-based architectures and ligands related to macrocyclic chemistry.

  3. Molecular and Crystal Magnetic Engineering of Polymetallic Coupling System: From Magnetic Molecules to Molecular Magnets

    程鹏; 廖代正


    One of the main challenges in the field of molecular materials is the design of molecular ferromagnets. General design strategy includes two steps, that is molecular magnetic engineering and crystal magnetic engineering. The first step is the synthesis of ferromagnetically coupled polymetallic systems.Tne second step is the assembly of polymetallic systems with muti-dimensional structure and exhibiting a ferromagnetic transition.This paper summarized the strategies of molecular design and crystal engineering allowed to obtain such systems and our efforts in the fields of molecular magnetism and molecular-based magnets.

  4. Advances in molecular genetic systems in malaria.

    de Koning-Ward, Tania F; Gilson, Paul R; Crabb, Brendan S


    Robust tools for analysing gene function in Plasmodium parasites, which are the causative agents of malaria, are being developed at an accelerating rate. Two decades after genetic technologies for use in Plasmodium spp. were first described, a range of genetic tools are now available. These include conditional systems that can regulate gene expression at the genome, transcriptional or protein level, as well as more sophisticated tools for gene editing that use piggyBac transposases, integrases, zinc-finger nucleases or the CRISPR-Cas9 system. In this Review, we discuss the molecular genetic systems that are currently available for use in Plasmodium falciparum and Plasmodium berghei, and evaluate the advantages and limitations of these tools. We examine the insights that have been gained into the function of genes that are important during the blood stages of the parasites, which may help to guide the development and improvement of drug therapies and vaccines.

  5. Molecular ecology of anaerobic reactor systems

    Hofman-Bang, H. Jacob Peider; Zheng, D.; Westermann, Peter


    Anaerobic reactor systems are essential for the treatment of solid and liquid wastes and constitute a core facility in many waste treatment plants. Although much is known about the basic metabolism in different types of anaerobic reactors, little is known about the microbes responsible for these ...... specific nucleic acid probes are discussed and exemplified by studies of anaerobic granular sludge, biofilm and digester systems......Anaerobic reactor systems are essential for the treatment of solid and liquid wastes and constitute a core facility in many waste treatment plants. Although much is known about the basic metabolism in different types of anaerobic reactors, little is known about the microbes responsible...... and malfunctions of anaerobic digesters occasionally experienced, leading to sub-optimal methane production and wastewater treatment. Using a variety of molecular techniques, we are able to determine which microorganisms are active, where they are active, and when they are active, but we still need to determine...

  6. Molecular Imaging System for Monitoring Tumor Angiogenesis

    Aytac, Esra; Burcin Unlu, Mehmet


    In cancer, non-invasive imaging techniques that monitor molecular processes associated with the tumor angiogenesis could have a central role in the evaluation of novel antiangiogenic and proangiogenic therapies as well as early detection of the disease. Matrix metalloproteinases (MMP) can serve as specific biological targets for imaging of angiogenesis since expression of MMPs is required for angiogenesis and has been found to be upregulated in every type of human cancer and correlates with stage, invasive, metastatic properties and poor prognosis. However, for most cancers it is still unknown when, where and how MMPs are involved in the tumor angiogenesis [1]. Development of high-resolution, high sensitivity imaging techniques in parallel with the tumor models could prove invaluable for assessing the physical location and the time frame of MMP enzymatic acitivity. The goal of this study is to understand where, when and how MMPs are involved in the tumor angiogenesis. We will accomplish this goal by following two objectives: to develop a high sensitivity, high resolution molecular imaging system, to develop a virtual tumor simulator that can predict the physical location and the time frame of the MMP activity. In order to achieve our objectives, we will first develop a PAM system and develop a mathematical tumor model in which the quantitative data obtained from the PAM can be integrated. So, this work will develop a virtual tumor simulator and a molecular imaging system for monitoring tumor angiogenesis. 1.Kessenbrock, K., V. Plaks, and Z. Werb, MMP:regulators of the tumor microenvironment. Cell, 2010. 141(1)

  7. Microelectromechanical systems integrating molecular spin crossover actuators

    Manrique-Juarez, Maria D.; Rat, Sylvain; Mathieu, Fabrice; Saya, Daisuke; Séguy, Isabelle; Leïchlé, Thierry; Nicu, Liviu; Salmon, Lionel; Molnár, Gábor; Bousseksou, Azzedine


    Silicon MEMS cantilevers coated with a 200 nm thin layer of the molecular spin crossover complex [Fe(H2B(pz)2)2(phen)] (H2B(pz)2 = dihydrobis(pyrazolyl)borate and phen = 1,10-phenantroline) were actuated using an external magnetic field and their resonance frequency was tracked by means of integrated piezoresistive detection. The light-induced spin-state switching of the molecules from the ground low spin to the metastable high spin state at 10 K led to a well-reproducible shift of the cantilever's resonance frequency (Δfr = -0.52 Hz). Control experiments at different temperatures using coated as well as uncoated devices along with simple calculations support the assignment of this effect to the spin transition. This latter translates into changes in mechanical behavior of the cantilever due to the strong spin-state/lattice coupling. A guideline for the optimization of device parameters is proposed so as to efficiently harness molecular scale movements for large-scale mechanical work, thus paving the road for nanoelectromechanical systems (NEMS) actuators based on molecular materials.

  8. Control of olefin geometry in macrocyclic ring-closing metathesis using a removable silyl group.

    Wang, Yikai; Jimenez, Miguel; Hansen, Anders S; Raiber, Eun-Ang; Schreiber, Stuart L; Young, Damian W


    Introducing a silyl group at one of the internal olefin positions in diolefinic substrates results in E-selective olefin formation in macrocyclic ring-forming metathesis. The application of this method to a range of macrocyclic (E)-alkenylsiloxanes is described. Protodesilylation of alkenylsiloxane products yields novel Z-configured macrocycles.

  9. Molecular Mechanism of Macrocyclic Polyamines with Anti-HIV-1 Activity to Recognize RNA and Its Effect on Apoptosis%抗HIV-1活性的大环多胺类化合物与RNA的识别作用及其对细胞凋亡的影响

    郝美荣; 杨铭; 卜显和


    研究了具有抗HIV-1活性的大环多胺类化合物与RNA的识别作用,以及其对 cos-7细胞凋亡的影响,以进一步探讨其抗HIV-1的作用机理.实验采用琼脂糖凝胶电泳方法, 观察化合物与RNA的识别作用;通过流式细胞计数法探讨其对cos-7细胞凋亡的影响; 运用计算机分子模型, 从理论上Docking计算化合物与TAR RNA结合的可能性.结果表明, 大环多胺类化合物MP-1、MP-2和MP-3不仅具有断裂RNA的作用,并可抑制Tat-RNA的相互作用, 还可影响cos-7细胞亚二倍体的含量; 理论化学计算数据与实验结果基本一致.这一结果提示化合物的抗HIV-1活性可能通过作用于病毒基因组RNA而发挥作用,是多靶作用的结果.%The molecular recognition of macrocyclic polyamines (MP-1 ,MP-2 and MP-3) to RNA, and its effects on apoptosis of cos-7 cells were stu died in order to explore their mechanism of anti-HIV-1 activity. Cleavage of R NA was observed by agarose electrophoresis; and apoptosis was determined by flow cytometry assay. Computer modeling was used to investigate the theoretical poss ibility of compounds binding to TAR RNA. Results showed that: (1) Compounds MP -1,MP-2 and MP-3 could not only cleave the polyA *polyU and TAR RNA, but al so inhibit the interaction of Tat-RNA. (2) Compounds could affect the percentag e of hypodiploid cell. It is proposed that compounds MP-1,MP-2 and MP-3 cou ld recognize the polyA*polyU and TAR RNA molecules and cleave them, and affect the interaction of Tat-RNA. The compounds may affect the apoptosis of cos-7 ce lls.

  10. Systems Pharmacology in Small Molecular Drug Discovery.

    Zhou, Wei; Wang, Yonghua; Lu, Aiping; Zhang, Ge


    Drug discovery is a risky, costly and time-consuming process depending on multidisciplinary methods to create safe and effective medicines. Although considerable progress has been made by high-throughput screening methods in drug design, the cost of developing contemporary approved drugs did not match that in the past decade. The major reason is the late-stage clinical failures in Phases II and III because of the complicated interactions between drug-specific, human body and environmental aspects affecting the safety and efficacy of a drug. There is a growing hope that systems-level consideration may provide a new perspective to overcome such current difficulties of drug discovery and development. The systems pharmacology method emerged as a holistic approach and has attracted more and more attention recently. The applications of systems pharmacology not only provide the pharmacodynamic evaluation and target identification of drug molecules, but also give a systems-level of understanding the interaction mechanism between drugs and complex disease. Therefore, the present review is an attempt to introduce how holistic systems pharmacology that integrated in silico ADME/T (i.e., absorption, distribution, metabolism, excretion and toxicity), target fishing and network pharmacology facilitates the discovery of small molecular drugs at the system level.

  11. Systems Pharmacology in Small Molecular Drug Discovery

    Zhou, Wei; Wang, Yonghua; Lu, Aiping; Zhang, Ge


    Drug discovery is a risky, costly and time-consuming process depending on multidisciplinary methods to create safe and effective medicines. Although considerable progress has been made by high-throughput screening methods in drug design, the cost of developing contemporary approved drugs did not match that in the past decade. The major reason is the late-stage clinical failures in Phases II and III because of the complicated interactions between drug-specific, human body and environmental aspects affecting the safety and efficacy of a drug. There is a growing hope that systems-level consideration may provide a new perspective to overcome such current difficulties of drug discovery and development. The systems pharmacology method emerged as a holistic approach and has attracted more and more attention recently. The applications of systems pharmacology not only provide the pharmacodynamic evaluation and target identification of drug molecules, but also give a systems-level of understanding the interaction mechanism between drugs and complex disease. Therefore, the present review is an attempt to introduce how holistic systems pharmacology that integrated in silico ADME/T (i.e., absorption, distribution, metabolism, excretion and toxicity), target fishing and network pharmacology facilitates the discovery of small molecular drugs at the system level. PMID:26901192

  12. Systems Pharmacology in Small Molecular Drug Discovery

    Wei Zhou


    Full Text Available Drug discovery is a risky, costly and time-consuming process depending on multidisciplinary methods to create safe and effective medicines. Although considerable progress has been made by high-throughput screening methods in drug design, the cost of developing contemporary approved drugs did not match that in the past decade. The major reason is the late-stage clinical failures in Phases II and III because of the complicated interactions between drug-specific, human body and environmental aspects affecting the safety and efficacy of a drug. There is a growing hope that systems-level consideration may provide a new perspective to overcome such current difficulties of drug discovery and development. The systems pharmacology method emerged as a holistic approach and has attracted more and more attention recently. The applications of systems pharmacology not only provide the pharmacodynamic evaluation and target identification of drug molecules, but also give a systems-level of understanding the interaction mechanism between drugs and complex disease. Therefore, the present review is an attempt to introduce how holistic systems pharmacology that integrated in silico ADME/T (i.e., absorption, distribution, metabolism, excretion and toxicity, target fishing and network pharmacology facilitates the discovery of small molecular drugs at the system level.

  13. Molecular hydrogen absorption systems in SDSS

    Balashev, S A; Ivanchik, A V; Varshalovich, D A; Petitjean, P; Noterdaeme, P


    We present a systematic search for molecular hydrogen absorption systems at high redshift in quasar spectra from the Sloan Digital Sky Survey (SDSS) II Data Release 7 and SDSS-III Data Release 9. We have selected candidates using a modified profile fitting technique taking into account that the Ly$\\alpha$ forest can effectively mimic H$_2$ absorption systems at the resolution of SDSS data. To estimate the confidence level of the detections, we use two methods: a Monte-Carlo sampling and an analysis of control samples. The analysis of control samples allows us to define regions of the spectral quality parameter space where H$_2$ absorption systems can be confidently identified. We find that H$_2$ absorption systems with column densities $\\log {\\rm N_{H_2}} > 19$ can be detected in only less than 3% of SDSS quasar spectra. We estimate the upper limit on the detection rate of saturated H$_2$ absorption systems ($\\log {\\rm N_{H_2}} > 19$) in Damped Ly-$\\alpha$ (DLA) systems to be about 7%. We provide a sample of ...

  14. Macrocyclic Hepatitis C Virus NS3/4A Protease Inhibitors: An Overview of Medicinal Chemistry.

    Pillaiyar, Thanigaimalai; Namasivayam, Vigneshwaran; Manickam, Manoj


    Hepatitis C virus (HCV) is a causative agent of hepatitis C infectious disease that primarily affects the liver, ranging in severity from a mild illness lasting a few weeks to a lifelong illness. The 9.6 kb RNA genome of HCV encodes approximately 3000 amino acid polyprotein that must be processed by host and viral proteases into both structural (S) and non-structural (NS) proteins, respectively. Targeting the serine protease NS3 with an activating factor NS4A, i.e., NS3/4A has been considered as one of the most attractive targets for the development of anti-HCV therapy. Although there is no vaccine available, antiviral medicines cure approximately 90% of the persons with hepatitis C infection. On the other hand, efficacy of these medications can be hampered due to the rapid drug and cross resistances. To date, all developed HCV NS3/4A inhibitors are mainly peptide-based compounds derived from the cleavage products of substrate. Specifically macrocyclic peptidomimetics have rapidly emerged as a classical NS3/4A protease inhibitors for treating the HCV infection. This review highlights the development of macrocyclic anti-HCV NS3/4A protease, as well as clinically important inhibitors developed from linear peptides, discovered during the last 12 years (2003-2015) from all sources, including laboratory synthetic methods, virtual screening and structure-based molecular docking studies. We emphasize the rationale behind the design, study of structure-activity relationships, and mechanism of inhibitions and cellular effect of the macrocyclic inhibitors.

  15. A crystalline sponge based on dispersive forces suitable for X-ray structure determination of included molecular guests† †Electronic supplementary information (ESI) available: Synthesis of macrocycle 3 together with characterization data. TGA and DSC traces. CIF files of all structures. Computational details and additional calculations. CCDC 1012389–1012397 and 1063714. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc01838b Click here for additional data file. Click here for additional data file.

    Sanna, Elena; Escudero-Adán, Eduardo C.; Bauzá, Antonio; Ballester, Pablo; Frontera, Antonio; Rotger, Carmen


    A crystalline porous material showing one-dimensional (1-D) rectangular micropores (12 × 9 Å2) has been assembled from a semirigid macrocyclic tetraimine and EtOAc as the templating agent. The 1-D nature of the material is intrinsic to the conformationally rigid structure of a macrocyclic sub-unit bearing four cyclohexylidene residues. The multiple dispersive forces established among the aliphatic residues glutted the 1-D channels and provided thermal stability to the material at temperatures below 160 °C. Upon removal of the template, the structure of the empty solid exhibited permanent microporosity (S BET = 342 m2 g–1). Being a true molecular sponge, the channel framework of this material allowed the inclusion of a variety of molecular sample guests without compromising its crystalline nature. Remarkably, this crystalline material enabled the structure determination by X-ray diffraction of the included molecules. Theoretical studies demonstrated the vital role played by the dispersive forces in the overall stabilization of the crystal packing. PMID:28757946

  16. Molecular Imaging with Activatable Reporter Systems

    Gang Niu, Xiaoyuan Chen


    Full Text Available Molecular imaging is a newly emerged multiple disciplinary field that aims to visualize, characterize and quantitatively measure biological processes at cellular and molecular levels in humans and other living systems. A reporter gene is a piece of DNA encoding reporter protein, which presents as a readily measurable phenotype that can be distinguished easily from the background of endogenous protein. After being transferred into cells of organ systems (transgenes, the reporter gene can be utilized to visualize transcriptional and posttranscriptional regulation of gene expression, protein-protein interactions, or trafficking of proteins or cells in living subjects. Herein, we review previous classification of reporter genes and regroup the reporter gene based imaging as basic, inducible and activatable, based on the regulation of reporter gene transcription and post-translational modification of reporter proteins. We then focus on activatable reporters, in which the signal can be activated at the posttranslational level for visualizing protein-protein interactions, protein phosphorylation or tertiary structure changes. The applications of several types of activatable reporters will also be summarized. We conclude that activatable reporter imaging can benefit both basic biomedical research and drug development.

  17. [Novel bioconversion systems using a yeast molecular display system].

    Shibasaki, Seiji


    The budding yeast Saccharomyces cerevisiae has been used for the process of fermentation as well as for studies in biochemistry and molecular biology as a eukaryotic model cell or tool for the analysis of gene functions. Thus, yeast is essential in industries and researches. Yeast cells have a cell wall, which is one characteristic that helps distinguish yeast cells from other eukaryotic cells such as mammalian cells. We have developed a molecular display system using the protein of the yeast cell wall as an anchor for foreign proteins. Yeast cells have been designed for use in sensing and metal adsorption, and have been used in vaccines and for screening novel proteins. Currently, yeast is used not only as a tool for analyzing gene or protein function but also in molecular display technology. The phage display system, which is at the forefront of molecular display technologies, is a powerful tool for screening ligands bound to a target molecule and for analyzing protein-protein interactions; however, in some cases, eukaryotic proteins are not easily expressed by this system. On the other hand, yeast cells have the ability to express eukaryotic proteins and proliferate; thus, these cells display various proteins. Yeast cells are more appropriate for white biotechnology. In this review, displays of enzymes that are important in bioconversion, such as lipases and β-glucosidases, are going to be introduced.

  18. Macrocycle synthesis by trimerization of boronic acids around a hexaol template, and recognition of polyols by resulting macrocyclic oligoboronic acids.

    Stoltenberg, Dennis; Lüning, Ulrich


    2,6-Bis(alkenyloxy) substituted arylboronic acids can be cyclotrimerized with the help of a hexaol as a template. First, the boronic acids are assembled by boronic ester formation with hexahydroxy-bicyclo[2.2.2]octane. Next, the resulting triboronates are cyclized by ring-closing metathesis to yield trimacrocycles as diastereomeric E/Z mixtures. Catalytic hydrogenation yields a single saturated trimacrocycle. Cleavage of the boronic ester functions liberates the template and generates a macrocycle with three boronic acid functionalities in endo-orientation. Due to this preorganization, macrocycles with boronic acids in endo-positions are good receptors for polyols. The binding of carbohydrates such as fructose was compared with the uptake of the respective templates into macrocycles with two or three boronic acids in endo-orientation.

  19. Mono- and multilayers of molecular spoked carbazole wheels on graphite

    Stefan-S. Jester


    Full Text Available Self-assembled monolayers of a molecular spoked wheel (a shape-persistent macrocycle with an intraannular spoke/hub system and its synthetic precursor are investigated by scanning tunneling microscopy (STM at the liquid/solid interface of 1-octanoic acid and highly oriented pyrolytic graphite. The submolecularly resolved STM images reveal that the molecules indeed behave as more or less rigid objects of certain sizes and shapes – depending on their chemical structures. In addition, the images provide insight into the multilayer growth of the molecular spoked wheels (MSWs, where the first adlayer acts as a template for the commensurate adsorption of molecules in the second layer.

  20. Kinetic Analysis for Macrocyclizations Involving Anionic Template at the Transition State

    Vicente Martí-Centelles


    competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes.

  1. Biomechanical Assessment of the Strength of Volleyball Players in Different Stages of the Training Macrocycle

    Śliwa Marcin


    Full Text Available Introduction. In order to help volleyball players achieve superior results, their coaches are constantly seeking new training methods. One of the methods used to improve the effectiveness of the training that is being implemented is conducting tests which make it possible to assess the player’s locomotor system in terms of its motor and biomechanical functions. The aim of the study was to determine the torque of the knee flexor and extensor muscles of volleyball players in three stages of the annual macrocycle.

  2. Magnetism in (Semi)Conducting Macrocycles of pi conjugated Polymers


    estimation of the chain length or the number of repetitive thiophene units, which were for the four samples 18, 25, 33 and 42. The formyl moieties at...leading to radicals , which can associate together. Scheme 5: Synthetic pathway of fully thiophenic bridged macrocycle by oxidative

  3. Flexible macrocycles as versatile supports for catalytically active metal clusters

    Ryan, JD; Gagnon, KJ; Teat, SJ; McIntosh, RD


    Here we present three structurally diverse clusters stabilised by the same macrocyclic polyphenol; t-butylcalix[8]arene. This work demonstrates the range of conformations the flexible ligand is capable of adopting, highlighting its versatility in metal coordination. In addition, a Ti complex displays activity for the ring-opening polymerisation of lactide

  4. Synthesis of macrocyclic lactones with methoxysulfonyl side chain

    Chuan Jin Hou; Xiao Mei Liang; Jing Ping Wu; Dao Quan Wang


    Two representative macrocyclic lactones with methoxysulfonyl side chain (5a and 5b) were synthesized employing Michael addition with acrolein and ring enlargement as the key steps,starting from potassium a-oxocycloalkylsulfonates (1) in total yields of 45 and 57%,respectively.

  5. Synthesis of new diverse macrocycles from diol precursors

    Madsen, Charlotte Marie; Hansen, Martin; Thrane, Marie V.;


    The formation of a library of diverse macrocycles with different ring sizes from two easily accessible building blocks is presented. Reacting diol precursors with electrophilic reagents lead to 17-membered sulfites and 19-membered malonates in 34–79% yield. Double-reductive amination of dialdehyd...

  6. Computer modeling of properties of complex molecular systems

    Kulkova, E.Yu. [Moscow State University of Technology “STANKIN”, Vadkovsky per., 1, Moscow 101472 (Russian Federation); Khrenova, M.G.; Polyakov, I.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); Nemukhin, A.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow 119334 (Russian Federation)


    Large molecular aggregates present important examples of strongly nonhomogeneous systems. We apply combined quantum mechanics / molecular mechanics approaches that assume treatment of a part of the system by quantum-based methods and the rest of the system with conventional force fields. Herein we illustrate these computational approaches by two different examples: (1) large-scale molecular systems mimicking natural photosynthetic centers, and (2) components of prospective solar cells containing titan dioxide and organic dye molecules. We demonstrate that modern computational tools are capable to predict structures and spectra of such complex molecular aggregates.


    V. Lozan


    Full Text Available A series of novel tri-, tetra- and pentanuclear complexes composed of dinuclear LM units (M=Co, Ni, Zn; L=24-membered macrocyclic hexaaza-dithiophenolate ligand and ferrocenecarboxylate ([CpFeC5H4CO2]ˉ, 1,1’-ferrocenedicarboxy-late ([Fe(C5H4-CO22]2ˉ, acetylene-dicarboxylate, terephthalate, isophthalate, and naphthalene diimide dicarboxylate groups is reported. The complexes, have been synthesized and characterised by UV/Vis-, IR-, NMR-spectroscopy, Cyclovoltammetry, and X-ray crystallography. Each dicarboxylate dianion acts as a quadridentate bridging ligand linking two bioctahedral LM2 units via µ1,3-bridging carboxylate functions to generate discrete dications with a central LM2(O2C-R-CO2M2L core. The magnetic properties of these compounds reveal the presence of weak ferromagnetic exchange interactions between the NiII ions of the dinuclear subunits and negligible coupling across the dicarboxylate bridges.

  8. Molecular communications and nanonetworks from nature to practical systems

    Atakan, Barış


    In this book, the concepts of molecular communications and nanonetworks are introduced. Throughout the book, the existing molecular communication paradigms are categorized into two main groups. The first group includes the Passive Molecular Communication (PMC) paradigms in which molecules freely diffuse to transfer information from a transmitter to a receiver. The second group includes the Active Molecular Communication (AMC) paradigms in which molecules are carried or guided by some mediators such as molecular motors, gap junction channels and bacteria. In the book, after briefly discussing why molecular communication is needed for the sophisticated nano and biotechnology applications, the existing molecular communication systems are first presented. Then, the principles of diffusion phenomena and molecular reception with absorbers and the ligand-receptor binding mechanism are introduced. Based on these principles, the communication theories and techniques are given for the PMC. Then, the physical dynamics o...

  9. Tunable photophysical processes of porphyrin macrocycles on the surface of ZnO nanoparticles

    Parida, Manas R.


    We investigated the impact of the molecular structure of cationic porphyrins on the degree of electrostatic interactions with zinc oxide nanoparticles (ZnO NPs) using steady-state and time-resolved fluorescence and transient absorption spectroscopy. Our results demonstrate that the number of cationic pyridinium units has a crucial impact on the photophysics of the porphyrin macrocycle. Fluorescence enhancement, relative to initial free porphyrin fluorescence, was found to be tuned from 3.4 to 1.3 times higher by reducing the number of cationic substituents on the porphyrin from 4 to 2. The resulting enhancement of the intensity of the fluorescence is attributed to the decrease in the intramolecular charge transfer (ICT) character between the porphyrin cavity and its meso substituent. The novel findings reported in this work provide an understanding of the key variables involved in nanoassembly, paving the way toward optimizing the interfacial chemistry of porphyrin-ZnO NP assembly for photodynamic therapy and energy conversion.

  10. Five-State Molecular Shuttling of a Pair of [2]Rotaxanes: Distinct Outputs in Response to Acid and Base Stimuli.

    Ueda, Masahiro; Terazawa, Shoya; Deguchi, Yasuaki; Kimura, Masaki; Matsubara, Naoki; Miyagawa, Shinobu; Kawasaki, Tsuneomi; Tokunaga, Yuji


    In this study we synthesized two acid-/base-controllable [2]rotaxanes featuring aminodiazobenzene and aminocoumarin units, respectively, as chromophores and dibenzo[24]crown-8 and dibenzo[25]crown-8 units, respectively, as their macrocyclic components. Each [2]rotaxane contained N-alkylarylamine (ammonium) and N,N-dialkylamine (ammonium) centers as binding sites for their crown ether components. The absorption patterns of the chromophores were dependent on the position of the encircling macrocyclic component and the degree of protonation, with three distinct states (under acidic, neutral, and basic conditions) evident for each [2]rotaxane. The mixed [2]rotaxane system displayed stepwise and independent molecular shuttling behavior based on the degree of protonation of the amino groups in response to both the amount and strength of added acids or bases; as such, the system provided five different absorption signals as outputs that could be read using UV/Vis spectroscopy.

  11. Increasing the luminescence of lanthanide(III) macrocyclic complexes by the use of polymers and lanthanide enhanced luminescence

    Leif, Robert C.; Becker, Margie C.; Bromm, Alfred J., Jr.; Vallarino, Lidia M.; Williams, Steven A.; Yang, Sean


    A Eu (III)-macrocycle-isothiocyanate, Quantum DyeTM, has been reacted with lysine homo- and hetero-peptides to give polymers with multiple luminescent side chains. Contrary to the concentration quenching that occurs with conventional organic fluorophores, the attachment of multiple Quantum Dyes to a polymer results in a concomitant increase in luminescence. The emission intensity of the peptide-bound Quantum Dye units is approximately linearly related to their number. The attachment of peptides containing multiple lanthanide (III) macrocycles to analyte-binding species is facilitated by employing solid-phase technology. Bead-bound peptides are first labeled with multiple Quantum Dye units, then conjugated to an antibody, and finally released from the bead by specific cleavage with Proteinase K unedr physiological conditions. Since the luminescence of lanthanide(III) macrocycles is enhanced by the presence of GD(III) or Y(III) ions in a micellar system, a significant increase in signal can be achieved by attaching a polymer labeled with multiple Quantum Dye units to an analyte- binding species, such as a monoclonal antibody, or by taking advantage of the luminescence enhancing effects of Gd(III) or Y(III), or by both approaches concomitantly. A comparison between the integrated intensity and lifetime measurements of the Eu(III)-macrocycle under a variety of conditions show that the signal increase caused by Gd(III) can not be explained solely by the increase in lifetime, and must result in significant part from an energy transfer process invloving donors not directly bound to the Eu(III).

  12. Dynamical Systems and Control Theory Inspired by Molecular Biology


    in both bacterial and eukaryotic signaling pathways. A common theme in the systems biology literature is that certain systems whose output variables...AFRL-OSR-VA-TR-2014-0282 DYNAMICAL SYSTEMS AND CONTROL THEORY INSPIRED BY MOLECULAR BIOLOGY Eduardo Sontag RUTGERS THE STATE UNIVERSITY OF NEW JERSEY...Standard Form 298 (Re . 8-98) v Prescribed by ANSI Std. Z39.18 DYNAMICAL SYSTEMS AND CONTROL THEORY INSPIRED BY MOLECULAR BIOLOGY AFOSR FA9550-11-1-0247

  13. Synthesis and Crystal Structure of a New Dinuclear Manganese(Ⅱ) Manganese(Ⅲ) Complex of a Macrocyclic Ligand

    JIAN Fang-fang; XIAO Hai-lian; XU Liang-zhong; PANG Lei


    A mixed-valence dinuclear manganese complex, [MnⅡMnⅢL](ClO4)·1/2MeOH, where L is a macrocyclic ligand derived from the cyclocondensation of sodium 2,6-diformyl-4-methylphenolate with N,N-bis(2-aminoethyl)-2-hydroxybenzyl amine, was obtained and its structure was determined by X-ray diffraction. The orange crystal is a monoclinic system with space group P21/c and lattice parameters a=1.1617(4), b=1.4005(3), c=1.4641(3) nm, β=113.03(2)°, and Z=2. The crystal structure shows that each pendant-arm is bonded in a bidentate fashion to the adjacent metal atom and that both the arms are on the same side of the macrocycle. The two Mn atoms are bridged by two μ2-phenoxy oxygen atoms of the tetra-imine macrocycle, and each Mn atom, locating in a trigonal prismatic coordination environment(N3O3), is six-coordinated by the two imine nitrogen atoms, one tertiary nitrogen atom and a pendant phenol moiety apart from the two oxygen atoms.

  14. Gold-catalyzed Synthesis of Pyridine Containing Macrocycles, Related to Porphyrin

    DYKER,Gerald; LIU,Jian-Hui; MERZ,Klaus


    @@ Porphyrins are very important substances used in a wide range of model systems in many areas, such as biomimic chemistry and material science. This kind of macrocycle generally consists of 5-membered ring to form a cyclic extended aromatic network. Recently much work have been done concerning the modification of porphyrins core structures, and many kinds of analogues have been recorded. One of the important aspects was the research of the porphyrinogen ligand.These macrocycles bear functional resemblance to certain kind of polydentate ligand, and provide a variety of tri-dimensional binding cavities for metal ions. In addition, some other kinds of analogues have been recorded, involving the introduction of a CH unit to replace one of the nitrogen atoms. We also notice the fact that pyridine is a very effective ligand, and it can coordinate with many kinds of metals. Based on these observations, we would like to design and synthesize a new porphyrinogen (5) analogue containing a NNNN core, two of the N atoms from pyrrole and the other two N from pyridine. Such core modifications may alter the electronic structure of the ring and provide variable cavity for metal coordination.

  15. Potent macrocyclic inhibitors of insulin-regulated aminopeptidase (IRAP) by olefin ring-closing metathesis.

    Andersson, Hanna; Demaegdt, Heidi; Johnsson, Anders; Vauquelin, Georges; Lindeberg, Gunnar; Hallberg, Mathias; Erdelyi, Mate; Karlen, Anders; Hallberg, Anders


    Macrocyclic analogues of angiotensin IV (Ang IV, Val(1)-Tyr(2)-Ile(3)-His(4)-Pro(5)-Phe(6)) targeting the insulin-regulated aminopeptidase (IRAP) have been designed, synthesized, and evaluated biologically. Replacement of His(4)-Pro(5)-Phe(6) by a 2-(aminomethyl)phenylacetic acid (AMPAA) moiety and of Val(1) and Ile(3) by amino acids bearing olefinic side chains followed by macrocyclization provided potent IRAP inhibitors. The impact of the ring size and the type (saturated versus unsaturated), configuration, and position of the carbon-carbon bridge was assessed. The ring size generally affects the potency more than the carbon-carbon bond characteristics. Replacing Tyr(2) by β(3)hTyr or Phe is accepted, while N-methylation of Tyr(2) is deleterious for activity. Removal of the carboxyl group in the C-terminal slightly reduced the potency. Inhibitors 7 (K(i) = 4.1 nM) and 19 (K(i) = 1.8 nM), both encompassing 14-membered ring systems connected to AMPAA, are 10-fold more potent than Ang IV and are also more selective over aminopeptidase N (AP-N). Both compounds displayed high stability against proteolysis by metallopeptidases.

  16. Does a water-training macrocycle really create imbalances in swimmers' shoulder rotator muscles?

    Batalha, Nuno; Marmeleira, José; Garrido, Nuno; Silva, António J


    The continuous execution of swimming techniques may cause muscle imbalances in shoulder rotators leading to injury. However, there is a lack of published research studies on this topic. The aim of this study was to analyze the influence of a competitive swim period on the shoulder rotator-cuff balance in young swimmers. A randomized controlled pretest-posttest design was used, with two measurements performed during the first macrocycle of the swimming season (baseline and 16 weeks). Twenty-seven young male swimmers (experimental group) and 22 male students who were not involved in swim training (control group) with the same characteristics were evaluated. Peak torque of shoulder internal and external rotators was assessed. Concentric action at 1.04 rad s(-1) (3 repetitions) and 3.14 rad s(-1) (20 repetitions) was measured using an isokinetic dynamometer (Biodex System 3). External/internal rotators strength ratios were also obtained. For both protocols, there were significant training effects on internal rotator strength and external/internal rotator ratios (p ≤ .05). This trend was the same for both shoulders. Within-group analysis showed significant changes from baseline to 16 weeks for internal rotators strength and unilateral ratios of the experimental group. Swimmers' internal rotator strength levels increased significantly. In contrast, a significant decrease of the unilateral ratios was observed. Findings suggest that a competitive swim macrocycle leads to an increase in muscular imbalances in the shoulder rotators of young competitive swimmers. Swimming coaches should consider implementing a compensatory strength-training program.

  17. The ex vivo neurotoxic, myotoxic and cardiotoxic activity of cucurbituril-based macrocyclic drug delivery vehicles.

    Oun, Rabbab; Floriano, Rafael S; Isaacs, Lyle; Rowan, Edward G; Wheate, Nial J


    The cucurbituril family of drug delivery vehicles have been examined for their tissue specific toxicity using ex vivo models. Cucurbit[6]uril (CB[6]), cucurbit[7]uril (CB[7]) and the linear cucurbituril-derivative Motor2 were examined for their neuro-, myo- and cardiotoxic activity and compared with β-cyclodextrin. The protective effect of drug encapsulation by CB[7] was also examined on the platinum-based anticancer drug cisplatin. The results show that none of the cucurbiturils have statistically measurable neurotoxicity as measured using mouse sciatic nerve compound action potential. Cucurbituril myotoxicity was measured by nerve-muscle force of contraction through chemical and electrical stimulation. Motor2 was found to display no myotoxicity, whereas both CB[6] and CB[7] showed myotoxic activity via a presynaptic effect. Finally, cardiotoxicity, which was measured by changes in the rate and force of right and left atria contraction, was observed for all three cucurbiturils. Free cisplatin displays neuro-, myo- and cardiotoxic activity, consistent with the side-effects seen in the clinic. Whilst CB[7] had no effect on the level of cisplatin's neurotoxic activity, drug encapsulation within the macrocycle had a marked reduction in both the drug's myo- and cardiotoxic activity. Overall the results are consistent with the relative lack of toxicity displayed by these macrocycles in whole animal acute systemic toxicity studies and indicate continued potential of cucurbiturils as drug delivery vehicles for the reduction of the side effects associated with platinum-based chemotherapy.

  18. Synthesis of arylenealkyne conjugated macrocycles containing a long alkylene bridge

    Xiaohong CHENG; Sigurd HOEGER


    The synthesis of the first two arylenealkyne conjugated macrocycles containing a long alkylene bridge via Glaser coupling of template-directed tetra-acetylenes was reported. Tetraacetylene intermediates with complex structures were constructed rapidly via quadruple Hagihara coupling of monoprotected bisace-tylenes to appropriate tetraiodides and subsequent desilylation. The characterization of such compounds was carried out by NMR, GPC and UV-Vis spectra. Unfortunately, the two compounds were not liquid crystals and had no biaxial nematic mesophase character as expected,

  19. Studies of Flerovium and Element 115 Homologs with Macrocyclic Extractants

    Despotopulos, John D. [Univ. of Nevada, Las Vegas, NV (United States)


    Study of the chemistry of the heaviest elements, Z ≥ 104, poses a unique challenge due to their low production cross-sections and short half-lives. Chemistry also must be studied on the one-atom-at-a-time scale, requiring automated, fast, and very efficient chemical schemes. Recent studies of the chemical behavior of copernicium (Cn, element 112) and flerovium (Fl, element 114) together with the discovery of isotopes of these elements with half-lives suitable for chemical studies have spurred a renewed interest in the development of rapid systems designed to study the chemical properties of elements with Z ≥ 114. This dissertation explores both extraction chromatography and solvent extraction as methods for development of a rapid chemical separation scheme for the homologs of flerovium (Pb, Sn, Hg) and element 115 (Bi, Sb), with the goal of developing a chemical scheme that, in the future, can be applied to on-line chemistry of both Fl and element 115. Carrier-free radionuclides, used in these studies, of the homologs of Fl and element 115 were obtained by proton activation of high-purity metal foils at the Lawrence Livermore National Laboratory (LLNL) Center for Accelerator Mass Spectrometry (CAMS): natIn(p,n)113Sn, natSn(p,n)124Sb, and Au(p,n)197m,gHg. The carrier-free activity was separated from the foils by novel separation schemes based on ion exchange and extraction chromatography techniques. Carrier-free Pb and Bi isotopes were obtained from development of a novel generator based on cation exchange chromatography using the 232U parent to generate 212Pb and 212Bi. Macrocyclic extractants, specifically crown ethers and their derivatives, were chosen for these studies; crown ethers show high selectivity for metal ions. Finally. a potential chemical system for Fl was established based on the Eichrom Pb resin, and insight to an improved system based on thiacrown ethers is

  20. Logic circuits based on molecular spider systems.

    Mo, Dandan; Lakin, Matthew R; Stefanovic, Darko


    Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized reactions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi-spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  1. A pH-sensitive peptide-containing lasso molecular switch.

    Clavel, Caroline; Fournel-Marotte, Karine; Coutrot, Frédéric


    The synthesis of a peptide-containing lasso molecular switch by a self-entanglement strategy is described. The interlocked rotaxane molecular machine consists of a benzometaphenylene[25]crown-8 (BMP25C8) macrocycle surrounding a molecular axle. This molecular axle contains a tripeptidic sequence and two molecular stations: a N-benzyltriazolium and a pH-sensitive anilinium station. The tripeptide is located between the macrocycle and the triazolium station, so that its conformation can be tailored depending on the shuttling of the macrocycle from one station to the other. At acidic pH, the macrocycle resides around the anilinium moiety, whereas it shuttles around the triazolium station after deprotonation. This molecular machinery thus forces the lasso to adopt a tightened or a loosened conformation.

  2. Macrocyclic compound as ionophores in lead(Ⅱ)ion-selective electrodes with excellent response characteristics

    HUANG MeiRong; MA XiaoLi; LI XinGui


    Macrocyclic compounds, such as crown ethers, azacrown ethers, thiacrown ethers, calixarenes and porphyrins, which act as ionophores in lead(Ⅱ) ion-selective electrodes, are systematically summarized based on the latest literatures. The molecular structure characteristics of the ionophores are general-ized. The modification regulations for the substituted ionophores are elaborated with the purpose ofimproving the response features of the lead(Ⅱ) ion-selective electrodes assembled by them. It is pointed out that the introduction of pendant moieties which contain soft base coordination centers like N, S and P atoms is in favor of adjusting the cavity size and conformation of the macrocyclic com-pounds. Furthermore, there is synergic effect between the cavity and the donor sites of the ligand and thus the selective complexation of lead ions is easily realized, resulting in significant avoidance of the interference from other metal ions. The macrocyclic ionophore having the best response characteris-tics thus far was found to be N,N'-dimethylcyanodiaza-18-crown-6 with the detection limit of 7.0×10-8 (14.5 μg/L), which is one of the uncommon ionophores that can really eliminate the interference from silver and mercury ions. The selectivity coefficients of the ionophore for lead ions over other metal ions, such as alkali, alkaline earth and transition metal ions are in the order of 10-4 or smaller, where the se-lectivity coefficient of lead(Ⅱ) over mercury(Ⅱ) ions is much lower, down to 8.9×10-4. The structure de-sign idea for high-performance ionophore is proposed according to present results. The incorporation of nitrogen atom, especially cyano group or thiocyano group or amino/imino groups, rather than thio atom alone could result in new excellent lead ionophores. The aborative design for metacyclophanes containing aromatic nitrogen atoms with the aim of creating excellent ionophores would also become a potential research trend. The lead(Ⅱ) ion

  3. Kinetically E-selective macrocyclic ring-closing metathesis

    Shen, Xiao; Nguyen, Thach T.; Koh, Ming Joo; Xu, Dongmin; Speed, Alexander W. H.; Schrock, Richard R.; Hoveyda, Amir H.


    Macrocyclic compounds are central to the development of new drugs, but preparing them can be challenging because of the energy barrier that must be surmounted in order to bring together and fuse the two ends of an acyclic precursor such as an alkene (also known as an olefin). To this end, the catalytic process known as ring-closing metathesis (RCM) has allowed access to countless biologically active macrocyclic organic molecules, even for large-scale production. Stereoselectivity is often critical in such cases: the potency of a macrocyclic compound can depend on the stereochemistry of its alkene; alternatively, one isomer of the compound can be subjected to stereoselective modification (such as dihydroxylation). Kinetically controlled Z-selective RCM reactions have been reported, but the only available metathesis approach for accessing macrocyclic E-olefins entails selective removal of the Z-component of a stereoisomeric mixture by ethenolysis, sacrificing substantial quantities of material if E/Z ratios are near unity. Use of ethylene can also cause adventitious olefin isomerization—a particularly serious problem when the E-alkene is energetically less favoured. Here, we show that dienes containing an E-alkenyl–B(pinacolato) group, widely used in catalytic cross-coupling, possess the requisite electronic and steric attributes to allow them to be converted stereoselectively to E-macrocyclic alkenes. The reaction is promoted by a molybdenum monoaryloxide pyrrolide complex and affords products at a yield of up to 73 per cent and an E/Z ratio greater than 98/2. We highlight the utility of the approach by preparing recifeiolide (a 12-membered-ring antibiotic) and pacritinib (an 18-membered-ring enzyme inhibitor), the Z-isomer of which is less potent than the E-isomer. Notably, the 18-membered-ring moiety of pacritinib—a potent anti-cancer agent that is in advanced clinical trials for treating lymphoma and myelofibrosis—was prepared by RCM carried out at a

  4. Molecular Dynamics Studies of Energy Transfer Processes in Crystal Systems.


    Computer molecular dynamics studies have been carried out on the problem of attaining a fundamental understanding of shock-induced initiation of...intramolecular energy exchange in shock-loaded systems are presented. Originator-supplied keywords include: Molecular dynamics , Energy transfer, Shock front, Shock wave, Explosives, Shock structure.

  5. Open quantum system parameters from molecular dynamics

    Wang, Xiaoqing; Wüster, Sebastian; Eisfeld, Alexander


    We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different combinations of methods, we investigate the origin of quantitative differences regarding site energies and spectral densities obtained previously in the literature. We find that different forcefields for molecular dynamics and varying local energy minima found by the structure relaxation yield significantly different results. Nevertheless, a picture averaged over these variations is in good agreement with experiments and some other theory results. Throughout, we discuss how vibrations external- or internal to the pigment molecules enter the extracted quantities differently and can be distinguished. Our results offer some guidance to set up more computationally intensive calculations for a precise determination of spectral densities in the future. These are required to determ...

  6. Heterogeneous and Homogeneous Routes in Water Oxidation Catalysis Starting from Cu(II) Complexes with Tetraaza Macrocyclic Ligands.

    Prevedello, Andrea; Bazzan, Irene; Dalle Carbonare, Nicola; Giuliani, Angela; Bhardwaj, Sunil; Africh, Cristina; Cepek, Cinzia; Argazzi, Roberto; Bonchio, Marcella; Caramori, Stefano; Robert, Marc; Sartorel, Andrea


    Since the first report in 2012, molecular copper complexes have been proposed as efficient electrocatalysts for water oxidation reactions, carried out in alkaline/neutral aqueous media. However, in some cases the copper species have been recognized as precursors of an active copper oxide layer, electrodeposited onto the working electrode. Therefore, the question whether copper catalysis is molecular or not is particularly relevant in the field of water oxidation. In this study, we investigate the electrochemical activity of copper(II) complexes with two tetraaza macrocyclic ligands, distinguishing heterogeneous or homogeneous processes depending on the reaction media. In an alkaline aqueous solution, and upon application of an anodic bias to working electrodes, an active copper oxide layer is observed to electrodeposit at the electrode surface. Conversely, water oxidation in neutral aqueous buffers is not associated to formation of the copper oxide layer, and could be exploited to evaluate and optimize a molecular, homogeneous catalysis.

  7. Spectrophotometric study of the reaction of iodine and bromine with two new macrocycle diamides and di-ortho methoxybenzoyl thiourea in chloroform solution.

    Sharghi, H; Massah, A R; Abedi, M


    The complex formation reactions of iodine and bromine with two new macrocycle diamides (1 and 2) and di-ortho methoxybenzoyl thiourea (DOMBT) (3) have been studied spectrophotometrically at various temperatures in chloroform solution. In all cases the resulting 1:2 (macrocycle to halogen) or (DOMBT to halogen) molecular complexes were formulated as (macrocycle...X(+))X(3)(-) or (DOMBT.... X(+))X(3)(-). The formation constants of the resulting molecular complexes were evaluated from computer fitting of the absorbance-mole ratio data. For iodine complexes we found that the values of K(f) vary in the order of 1 approximately 2>3. In the case of bromine complexes the values of K(f) are larger (>10(8)) and vary in the order of 1>2>3. The enthalpy and entropy of complexation reactions of iodine with 1, 2 and 3 were determined from the temperature dependence of the formation constants. In all cases it was found that the complexation reactions are enthalpy stabilized, but entropy destabilized.

  8. pysimm: A python package for simulation of molecular systems

    Fortunato, Michael E.; Colina, Coray M.

    In this work, we present pysimm, a python package designed to facilitate structure generation, simulation, and modification of molecular systems. pysimm provides a collection of simulation tools and smooth integration with highly optimized third party software. Abstraction layers enable a standardized methodology to assign various force field models to molecular systems and perform simple simulations. These features have allowed pysimm to aid the rapid development of new applications specifically in the area of amorphous polymer simulations.

  9. Biologically Active Macrocyclic Compounds – from Natural Products to Diversity‐Oriented Synthesis

    Madsen, Charlotte Marie; Clausen, Mads Hartvig


    Macrocyclic compounds are attractive targets when searching for molecules with biological activity. The interest in this compound class is increasing, which has led to a variety of methods for tackling the difficult macrocyclization step in their synthesis. This microreview highlights some recent...

  10. Hydrogen bond templated 1:1 macrocyclization through an olefin metathesis/hydrogenation sequence.

    Trita, Andrada Stefania; Roisnel, Thierry; Mongin, Florence; Chevallier, Floris


    The construction of pyridine-containing macrocyclic architectures using a nonmetallic template is described. 4,6-Dichlororesorcinol was used as an exotemplate to self-organize two aza-heterocyclic units by OH···N hydrogen bonds. Subsequent sequential double olefin metathesis/hydrogenation reactions employing a single ruthenium-alkylidene precatalyst open access to macrocyclic molecules.

  11. A Molecular Communication System Model for Particulate Drug Delivery Systems.

    Chahibi, Youssef; Pierobon, Massimiliano; Song, Sang Ok; Akyildiz, Ian F


    The goal of a drug delivery system (DDS) is to convey a drug where the medication is needed, while, at the same time, preventing the drug from affecting other healthy parts of the body. Drugs composed of micro- or nano-sized particles (particulate DDS) that are able to cross barriers which prevent large particles from escaping the bloodstream are used in the most advanced solutions. Molecular communication (MC) is used as an abstraction of the propagation of drug particles in the body. MC is a new paradigm in communication research where the exchange of information is achieved through the propagation of molecules. Here, the transmitter is the drug injection, the receiver is the drug delivery, and the channel is realized by the transport of drug particles, thus enabling the analysis and design of a particulate DDS using communication tools. This is achieved by modeling the MC channel as two separate contributions, namely, the cardiovascular network model and the drug propagation network. The cardiovascular network model allows to analytically compute the blood velocity profile in every location of the cardiovascular system given the flow input by the heart. The drug propagation network model allows the analytical expression of the drug delivery rate at the targeted site given the drug injection rate. Numerical results are also presented to assess the flexibility and accuracy of the developed model. The study of novel optimization techniques for a more effective and less invasive drug delivery will be aided by this model, while paving the way for novel communication techniques for Intrabody communication networks.

  12. The mechanism of patellamide macrocyclization revealed by the characterization of the PatG macrocyclase domain.

    Koehnke, Jesko; Bent, Andrew; Houssen, Wael E; Zollman, David; Morawitz, Falk; Shirran, Sally; Vendome, Jeremie; Nneoyiegbe, Ada F; Trembleau, Laurent; Botting, Catherine H; Smith, Margaret C M; Jaspars, Marcel; Naismith, James H


    Peptide macrocycles are found in many biologically active natural products. Their versatility, resistance to proteolysis and ability to traverse membranes has made them desirable molecules. Although technologies exist to synthesize such compounds, the full extent of diversity found among natural macrocycles has yet to be achieved synthetically. Cyanobactins are ribosomal peptide macrocycles encompassing an extraordinarily diverse range of ring sizes, amino acids and chemical modifications. We report the structure, biochemical characterization and initial engineering of the PatG macrocyclase domain of Prochloron sp. from the patellamide pathway that catalyzes the macrocyclization of linear peptides. The enzyme contains insertions in the subtilisin fold to allow it to recognize a three-residue signature, bind substrate in a preorganized and unusual conformation, shield an acyl-enzyme intermediate from water and catalyze peptide bond formation. The ability to macrocyclize a broad range of nonactivated substrates has wide biotechnology applications.

  13. The mechanism of patellamide macrocyclization revealed by the characterization of the PatG macrocyclase domain

    Koehnke, Jesko; Bent, Andrew; Houssen, Wael E; Zollman, David; Morawitz, Falk; Shirran, Sally; Vendome, Jeremie; Nneoyiegbe, Ada F; Trembleau, Laurent; Botting, Catherine H; Smith, Margaret C M; Jaspars, Marcel; Naismith, James H


    Peptide macrocycles are found in many biologically active natural products. Their versatility, resistance to proteolysis and ability to traverse membranes has made them desirable molecules. Although technologies exist to synthesize such compounds, the full extent of diversity found among natural macrocycles has yet to be achieved synthetically. Cyanobactins are ribosomal peptide macrocycles encompassing an extraordinarily diverse range of ring sizes, amino acids and chemical modifications. We report the structure, biochemical characterization and initial engineering of the PatG macrocyclase domain of Prochloron sp. from the patellamide pathway that catalyzes the macrocyclization of linear peptides. The enzyme contains insertions in the subtilisin fold to allow it to recognize a three-residue signature, bind substrate in a preorganized and unusual conformation, shield an acyl-enzyme intermediate from water and catalyze peptide bond formation. The ability to macrocyclize a broad range of nonactivated substrates has wide biotechnology applications. PMID:22796963

  14. The posttranslational modification cascade to the thiopeptide berninamycin generates linear forms and altered macrocyclic scaffolds.

    Malcolmson, Steven J; Young, Travis S; Ruby, J Graham; Skewes-Cox, Peter; Walsh, Christopher T


    Berninamycin is a member of the pyridine-containing thiopeptide class of antibiotics that undergoes massive posttranslational modifications from ribosomally generated preproteins. Berninamycin has a 2-oxazolyl-3-thiazolyl-pyridine core embedded in a 35-atom macrocycle rather than typical trithiazolylpyridine cores embedded in 26-atom and 29-atom peptide macrocycles. We describe the cloning of an 11-gene berninamycin cluster from Streptomyces bernensis UC 5144, its heterologous expression in Streptomyces lividans TK24 and Streptomyces venezuelae ATCC 10712, and detection of variant and incompletely processed scaffolds. Posttranslational maturation in S. lividans of both the wild-type berninamycin prepeptide (BerA) and also a T3A mutant generates macrocyclic compounds as well as linear variants, which have failed to form the pyridine and the macrocycle. Expression of the gene cluster in S. venezuelae generates a variant of the 35-atom skeleton of berninamycin, containing a methyloxazoline in the place of a methyloxazole within the macrocyclic framework.

  15. Stokes Efficiency of Molecular Motor-Cargo Systems

    Hongyun Wang


    Full Text Available A molecular motor utilizes chemical free energy to generate a unidirectional motion through the viscous fluid. In many experimental settings and biological settings, a molecular motor is elastically linked to a cargo. The stochastic motion of a molecular motor-cargo system is governed by a set of Langevin equations, each corresponding to an individual chemical occupancy state. The change of chemical occupancy state is modeled by a continuous time discrete space Markov process. The probability density of a motor-cargo system is governed by a two-dimensional Fokker-Planck equation. The operation of a molecular motor is dominated by high viscous friction and large thermal fluctuations from surrounding fluid. The instantaneous velocity of a molecular motor is highly stochastic: the past velocity is quickly damped by the viscous friction and the new velocity is quickly excited by bombardments of surrounding fluid molecules. Thus, the theory for macroscopic motors should not be applied directly to molecular motors without close examination. In particular, a molecular motor behaves differently working against a viscous drag than working against a conservative force. The Stokes efficiency was introduced to measure how efficiently a motor uses chemical free energy to drive against viscous drag. For a motor without cargo, it was proved that the Stokes efficiency is bounded by 100% [H. Wang and G. Oster, (2002]. Here, we present a proof for the general motor-cargo system.


    Vasile Lozan


    Full Text Available The steric protection offered by the macrobinucleating hexaazaditiophenolate ligand (L allows for the preparation of the first stable dinuclear nickel(II borohydride bridged complex, which reacts rapidly with elemental sulphur producing a tetranuclear nickel(II complex [{(LNi2}2(μ-S6]2+ bearing a helical μ4-hexa- sulfide ligand. The [(LCoII 2]2+ fragment have been able to trap a monomethyl orthomolybdate in the binding pocket. Unusual coordination modes of substrate in dinuclear macrocyclic compounds was demonstrated.

  17. Natural and Synthetic Macrocyclic Inhibitors of the Histone Deacetylase Enzymes

    Maolanon, Alex; Kristensen, Helle; Leman, Luke


    Inhibition of histone deacetylase (HDAC) enzymes has emerged as a target for development of cancer chemotherapy. Four compounds have gained approval for clinical use by the Food and Drug Administration (FDA) in the US, and several are currently in clinical trials. However, none of these compounds...... HDAC enzymes may hold an advantage over traditional hydroxamic acid-containing inhibitors, which rely on chelation to the conserved active site zinc ion. Here, we review the literature on macrocyclic HDAC inhibitors obtained from natural sources and structure-activity relationship studies inspired...

  18. Probing Interactions in Complex Molecular Systems through Ordered Assembly

    De Yoreo, J J; Bartelt, M C; Orme, C A; Villacampa, A; Weeks, B L; Miller, A E


    Emerging from the machinery of epitaxial science and chemical synthesis, is a growing emphasis on development of self-organized systems of complex molecular species. The nature of self-organization in these systems spans the continuum from simple crystallization of large molecules such as dendrimers and proteins, to assembly into large organized networks of nanometer-scale structures such as quantum dots or nanoparticles. In truth, self-organization in complex molecular systems has always been a central feature of many scientific disciplines including fields as diverse as structural biology, polymer science and geochemistry. But over the past decade, changes in those fields have often been marked by the degree to which researchers are using molecular-scale approaches to understand the hierarchy of structures and processes driven by this ordered assembly. At the same time, physical scientists have begun to use their knowledge of simple atomic and molecular systems to fabricate synthetic self-organized systems. This increasing activity in the field of self-organization is testament to the success of the physical and chemical sciences in building a detailed understanding of crystallization and epitaxy in simple atomic and molecular systems, one that is soundly rooted in thermodynamics and chemical kinetics. One of the fundamental challenges of chemistry and materials science in the coming decades is to develop a similarly well-founded physical understanding of assembly processes in complex molecular systems. Over the past five years, we have successfully used in situ atomic force microscopy (AFM) to investigate the physical controls on single crystal epitaxy from solutions for a wide range of molecular species. More recently, we have combined this method with grazing incidence X-ray diffraction and kinetic Monte Carlo modeling in order to relate morphology to surface atomic structure and processes. The purpose of this proposal was to extend this approach to assemblies

  19. Enhanced sampling techniques in molecular dynamics simulations of biological systems.

    Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus


    Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Exciton Localization in Extended {\\pi}-electron Systems: Comparison of Linear and Cyclic Structures

    Thiessen, Alexander; Jester, Stefan-S; Aggarwal, A Vikas; Idelson, Alissa; Bange, Sebastian; Vogelsang, Jan; Höger, Sigurd; Lupton, John M


    We employ five {\\pi}-conjugated model materials of different molecular shape --- oligomers and cyclic structures --- to investigate the extent of exciton self-trapping and torsional motion of the molecular framework following optical excitation. Our studies combine steady-state and transient fluorescence spectroscopy in the ensemble with measurements of polarization anisotropy on single molecules, supported by Monte Carlo simulations. The dimer exhibits a significant spectral red-shift within $\\sim$ 100 ps after photoexcitation which is attributed to torsional relaxation. This relaxation mechanism is inhibited in the structurally rigid macrocyclic analogue. However, both systems show a high degree of exciton localization but with very different consequences: while in the macrocycle the exciton localizes randomly on different parts of the ring, scrambling polarization memory, in the dimer, localization leads to a deterministic exciton position with luminescence characteristics of a dipole. Monte Carlo simulati...

  1. Electromagnetically induced grating in a crystal of molecular magnets system

    Liu, Jibing; Liu, Na; Shan, Chuanjia; Liu, Tangkun; Li, Hong; Zheng, Anshou; Xie, Xiao-Tao


    We investigate the response of the molecular system to the magnetic field modulation. Molecular magnets are subjected to a strong standing ac magnetic field and a weak probe magnetic field. The transmission and absorption of the weak probe magnetic field can be changed due to quantum coherence and the spatially modulating of the standing field. And a electromagnetically induced grating is formed in the crystal of molecular magnets via electromagnetically induced transparency (EIT). The diffraction efficiency of the grating can be adjusted efficiently by tuning the intensity of the standing wave field and the single photon detuning.

  2. Synthesis, Characterization and Antitumor Activities of Co, Ni, Cu, Zn Complexes with 1,4,7,10- tetrakis (4- nitrobenzyl )- 1,4,7,10- tetraazacyclododecane Macrocyclic Ligand

    孔德源; 谢雨礼; 谢毓元; 黄小荧


    New tetraazamacrocyclic ligand with 1, 4, 7, 10-tetrakis (4-nitrobenzyl) pendent groups (C36H40N8O8, Mr= 712.76) crystallized in the monoclinic system, P21/n space group with unit cell parameters: a=7. 834(2), b=22. 902(6), c =10. 147(3)A, β=106.53(2)°, V=1745(1)A3, Z=2, Dc=1. 356 g/cm3, λ(MoKa)=0. 71069 A ; μ=0. 92cm-1, F(000)=752, T=296K. The final R and Rw values are 0.065 and 0.066, respectively. The Cu( Ⅱ ), Ni( Ⅱ ), Co( Ⅱ ), Zn( Ⅱ ) complexes with this new ligand have been synthesized and characterized by elemental analyses, IR, UV, ESI-MS and molar conductance. The macrocyclic ligand molecular structure is centrosymmetrical. All complexes are in accordance with the general forN8O8). The central metal ions coordinate to four nitrogen atoms of azamacrocycle and two oxygen atoms of one nitrate ion. Preliminary pharmacological tests against P-388and A-549 tumor cell lines showed that all these complexes had considerable activities in vitro.

  3. A molecular dynamics study of polymer/graphene interfacial systems

    Rissanou, Anastassia N.; Harmandaris, Vagelis [Department of Mathematics and Applied Mathematics, University of Crete, GR-71409, Heraklion, Crete, Greece and Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), GR-71110, Heraklion, Cret (Greece)


    Graphene based polymer nanocomposites are hybrid materials with a very broad range of technological applications. In this work, we study three hybrid polymer/graphene interfacial systems (polystyrene/graphene, poly(methyl methacrylate)/graphene and polyethylene/graphene) through detailed atomistic molecular dynamics (MD) simulations. Density profiles, structural characteristics and mobility aspects are being examined at the molecular level for all model systems. In addition, we compare the properties of the hybrid systems to the properties of the corresponding bulk ones, as well as to theoretical predictions.

  4. Nitrogen and oxygen bridged calixaromatics: synthesis, structure, functionalization, and molecular recognition.

    Wang, Mei-Xiang


    Pedersen, Lehn, and Cram established supramolecular chemistry through their pioneering work with crown ethers, cryptands, and spherands. Since then, the hallmark of supramolecular science has been an increasing sophistication in the design and construction of macrocyclic molecules, as manifested in cyclodextrin derivatives, calixarenes, resorcinarenes, cyclotriveratrylenes, cucurbiturils, calixpyrroles, cyclophanes, and many other examples. Indeed, macrocyclic compounds provide unique models for the study of noncovalent molecular interactions. They also constitute building blocks for constructing high-level molecular and supramolecular architectures and fabricating molecular devices and advanced materials. As a postgraduate in the Huang laboratory in the late 1980s, I became interested in the calix[n]arenes because of their unique conformational structures and versatile complexation properties. The notion of introducing heteroatoms, and particularly nitrogen, into the bridging position of conventional calixarenes was particularly intriguing. Nitrogen, unlike methylene, can adopt either an sp(2) or sp(3) electronic configuration, providing different conjugation systems with adjacent aromatic rings. Consequently, depending on the configuration and conjugation, a range of C-N bond lengths and C-N-C bond angles is possible. The conformation and cavity size in heteroatom-bridged calixarenes might thus be tuned through the bridging heteroatoms and the number of aromatic rings. Furthermore, because heteroatom linkages significantly affect the electron density and distribution on aromatic rings, the electronic features of macrocyclic cavities might be regulated by heteroatoms. Given the essentially limitless combinations possible, only synthetic hurdles would prevent access to numerous diverse heteracalixaromatics. We began a systematic study on nitrogen- and oxygen-bridged calixarenes in 2000, years later than originally envisioned. Before this study, very few

  5. Photoelectrochemical solar conversion systems molecular and electronic aspects

    Munoz, Andres G


    Providing new insights into the molecular and electronic processes involved in the conversion of sunlight into chemical products, Photoelectrochemical Solar Conversion Systems: Molecular and Electronic Aspects begins with an historical overview and a survey of recent developments in the electrochemistry of semiconductors and spectroscopic techniques. It then provides a comprehensive introduction to the science of conversion cells, reviews current issues and potential directions, and covers a wide range of materials from organic to inorganic cells.Employing a tutorial organization with balanced

  6. Energy conservation in molecular dynamics simulations of classical systems

    Toxværd, Søren; Heilmann, Ole; Dyre, J. C.


    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

  7. The 'Visualized' macrocycles: Chemistry and application of fluorophore tagged cyclodextrins.

    Benkovics, Gábor; Malanga, Milo; Fenyvesi, Éva


    Cyclodextrins are macrocyclic molecules able to form host-guest complexes due to their hydrophobic cavity. Because of their carbohydrate nature they do not absorb light in the UV-vis region (200-800nm), but they can be converted into spectroscopically active compounds via modification with a chromophore unit. Among the chromophores, the group of fluorophores can provide high sensitivity in analytical applications (chemosensing) and low detection limit in optical imaging methods (fluorescent microscopy). Fluorophore-tagged cyclodextrins therefore combine interesting spectroscopic properties with promising supramolecular features which make these conjugates widely applicable in various pharmaceutical fields. The aim of this work is to review the various types of fluorophores which have been used for cyclodextrin tagging, to discuss the synthetic strategies used for the conjugation and to summarize the pharmaceutical applications of these 'visualized' macrocycles including their use in photodynamic therapy. The recent achievements in studying how the fluorophore-appended cyclodextrin derivatives cross biological barriers are also reviewed. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Novel archaeal macrocyclic diether core membrane lipids in a methane-derived carbonate crust from a mud volcano in the Sorokin Trough, NE Black Sea

    Alina Stadnitskaia


    Full Text Available A methane-derived carbonate crust was collected from the recently discovered NIOZ mud volcano in the Sorokin Trough, NE Black Sea during the 11th Training-through-Research cruise of the R/V Professor Logachev. Among several specific bacterial and archaeal membrane lipids present in this crust, two novel macrocyclic diphytanyl glycerol diethers, containing one or two cyclopentane rings, were detected. Their structures were tentatively identified based on the interpretation of mass spectra, comparison with previously reported mass spectral data, and a hydrogenation experiment. This macrocyclic type of archaeal core membrane diether lipid has so far been identified only in the deep-sea hydrothermal vent methanogen Methanococcus jannaschii. Here, we provide the first evidence that these macrocyclic diethers can also contain internal cyclopentane rings. The molecular structure of the novel diethers resembles that of dibiphytanyl tetraethers in which biphytane chains, containing one and two pentacyclic rings, also occur. Such tetraethers were abundant in the crust. Compound-specific isotope measurements revealed δ13C values of –104 to –111‰ for these new archaeal lipids, indicating that they are derived from methanotrophic archaea acting within anaerobic methane-oxidizing consortia, which subsequently induce authigenic carbonate formation.

  9. ABO System: molecular mimicry of Ascaris lumbricoides

    Ponce de León Patricia


    Full Text Available A. lumbricoides has been associated to the ABO System by various authors. The objective was to detect ABO System epitopes in A. lumbricoides of groups O, A, B and AB patients. 28 adult parasites were obtained from children to be used as assay material. The patients ABO blood groups were determined. Extracts of A. lumbricoides [AE] were prepared by surgical remotion of the cuticle and refrigerated mechanical rupture. Agglutination Inhibition (AI and Hemoagglutination Kinetics (HK tests were used with the [AE]. Of the 28 [AE], eight belonged to O group patients, 15 to A group, three to B group and the remaining two to AB children. The AI Test showed A epitopes in two [AE] of group A patients and B epitopes in two [AE] of group B patients. The HK Test showed B antigenic determiners in two [AE] of group B patients and in two [AE] of group AB patients as well as A antigenic determiners in one [AE] of A group patient. Of the 28 [AE] studied in both tests B epitopes were detected in all [AE] from B and AB patients and A epitopes in three of the 15 [AE] of group A patients. The experiments carried out suggest that A. lumbricoides might absorb A and B antigens from the host, and/or modify the cuticular carbohydrates expression as a kind of antigenic mimicry.

  10. Continuous-terahertz-wave molecular imaging system for biomedical applications

    Zhang, Rui; Zhang, Liangliang; Wu, Tong; Wang, Ruixue; Zuo, Shasha; Wu, Dong; Zhang, Cunlin; Zhang, Jue; Fang, Jing


    Molecular imaging techniques are becoming increasingly important in biomedical research and potentially in clinical practice. We present a continuous-terahertz (THz)-wave molecular imaging system for biomedical applications, in which an infrared (IR) laser is integrated into a 0.2-THz reflection-mode continuous-THz-wave imaging system to induce surface plasmon polaritons on the nanoparticles and further improve the intensity of the reflected signal from the water around the nanoparticles. A strong and rapid increment of the reflected THz signal in the nanoparticle solution upon the IR laser irradiation is demonstrated, using either gold or silver nanoparticles. This low-cost, simple, and stable continuous-THz-wave molecular imaging system is suitable for miniaturization and practical imaging applications; in particular, it shows great promise for cancer diagnosis and nanoparticle drug-delivery monitoring.

  11. Giant Nuclear Systems of Molecular Type

    Zagrebaev, Valery; Greiner, Walter

    Low-energy dynamics of heavy nuclear systems is studied within the extended version of the two-center shell model and Langevin type equations of motion. The shell effects lead to the appearance of local minima and deep valleys on the multi-dimensional potential energy surface. It is shown that the local minima on the fission path of a heavy nucleus—so called isomeric states—are nothing else but the two-cluster configurations with magic or semi-magic cores surrounded with a certain number of shared nucleons. Clustering phenomena caused by the shell effects play an important role also in low-energy dynamics of heavy nuclear systems. Fission and quasi-fission are the well-known processes of such kind discussed in the paper. We found that in low-energy damped multi-nucleon transfer reactions the shell effects may significantly enhance the yield of new heavy neutron-rich nuclei located in the unexplored "north-east" area of the nuclear map which is important for astrophysical nucleosynthesis. A possibility for the production of long-living neutron-rich superheavy nuclei in collisions of actinide ions (such as 238U + 248Cm) is another important finding. In these reactions a large mass and charge transfer due to the inverse (anti-symmetrized) quasi-fission process is significantly enhanced by the clustering process with formation of closed shell nuclei around Z = 82 and N = 126. In many such collisions the lifetime of a composite system consisting of two touching actinide nuclei turns out to be rather long (> 10-20S). This time delay is sufficient for the observation of the line structure in spontaneous e + e - production from the supercritical electric field of a giant quasi-atom—a fundamental QED process not observed yet experimentally. In addition, this giant nuclear molecule might undergo to a three-body clusterization (ternary quasi-fission) with formation of two heavy lead-like fragments in the exit channel. The "true ternary fission" is also possible for

  12. A simplified electrophoretic system for determining molecular weights of proteins.

    Manwell, C


    Electrophoresis of 31 different proteins in commercially prepared polyacrylamide gradient gels, Gradipore, yields a linear relationship between a hypothetical limiting pore size (the reciprocal of a limiting gel concentration, GL) and the cube root of the mol.wt., over the range 13 500-9000 000. A regression analysis of these data reveals that 98.6% of all variability in 1/GL is explained by the molecular weight, and this degree of accuracy compares favourably with existing methods for the determination of molecular weight by retardation of mobility in polyacrylamide. This new procedure has the additional advantages that molecular-weight standards can be obtained from readily available body fluids or tissue extracts by localizing enzymes and other proteins by standard histochemical methods, and that the same electrophoretic system can be used in determining molecular weights as is used in routine surveys of populations for individual and species variation in protein heterogeneity.

  13. Double template effect in [4 + 4] Schiff base macrocycle formation; an ESI-MS study.

    Barreira-Fontecha, Julia; Kulmaczewski, Rafal; Ma, Xiaomei; McKee, Vickie


    The mechanism of self-assembly of a polynuclear complex of a [4 + 4] Schiff base iminomethylenediphenolate macrocycle [BaCu(4)(4 + 4)](2+) via a non-macrocyclic dialdehyde intermediate has been followed using ESI-MS of the reaction solutions. Both assembly of the intermediate and Schiff-base condensation with diamine give rise to single products; formation of the intermediate metallacycle is fast but Schiff-base condensation is much slower. Both intermediate complex and macrocyclic product have been structurally characterised.

  14. Ab initio centroid path integral molecular dynamics: Application to vibrational dynamics of diatomic molecular systems

    Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi


    An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.

  15. Multi-Scale Molecular Deconstruction of the Serotonin Neuron System.

    Okaty, Benjamin W; Freret, Morgan E; Rood, Benjamin D; Brust, Rachael D; Hennessy, Morgan L; deBairos, Danielle; Kim, Jun Chul; Cook, Melloni N; Dymecki, Susan M


    Serotonergic (5HT) neurons modulate diverse behaviors and physiology and are implicated in distinct clinical disorders. Corresponding diversity in 5HT neuronal phenotypes is becoming apparent and is likely rooted in molecular differences, yet a comprehensive approach characterizing molecular variation across the 5HT system is lacking, as is concomitant linkage to cellular phenotypes. Here we combine intersectional fate mapping, neuron sorting, and genome-wide RNA-seq to deconstruct the mouse 5HT system at multiple levels of granularity-from anatomy, to genetic sublineages, to single neurons. Our unbiased analyses reveal principles underlying system organization, 5HT neuron subtypes, constellations of differentially expressed genes distinguishing subtypes, and predictions of subtype-specific functions. Using electrophysiology, subtype-specific neuron silencing, and conditional gene knockout, we show that these molecularly defined 5HT neuron subtypes are functionally distinct. Collectively, this resource classifies molecular diversity across the 5HT system and discovers sertonergic subtypes, markers, organizing principles, and subtype-specific functions with potential disease relevance.

  16. Molecular biology of the renin-angiotensin system

    Dzau, V.J.; Burt, D.W.; Pratt, R.E. (Harvard Medical School, Boston, MA (USA))


    This paper reviews the molecular biology of the renin-angiotensin system. The renin gene structure is analyzed in detail, including an examination of the putative regulatory regions. The combined action of these regulatory sequences would result in the complex, tissue-specific expression and regulation observed in vivo. The expression of the tissue renin-angiotensin systems, which may have important physiological functions, is also described. In addition, the pathway of renin biosynthesis and secretion is reviewed. This includes speculation on the fate of circulating prorenin and the physiological role of multiple renin forms and secretory pathways. The molecular approaches described in this paper have greatly advanced our knowledge of the biology of the renin-angiotensin system. Future studies using these and other approaches should provide further insight into this complex system.

  17. Molecular clocks and the early evolution of metazoan nervous systems.

    Wray, Gregory A


    The timing of early animal evolution remains poorly resolved, yet remains critical for understanding nervous system evolution. Methods for estimating divergence times from sequence data have improved considerably, providing a more refined understanding of key divergences. The best molecular estimates point to the origin of metazoans and bilaterians tens to hundreds of millions of years earlier than their first appearances in the fossil record. Both the molecular and fossil records are compatible, however, with the possibility of tiny, unskeletonized, low energy budget animals during the Proterozoic that had planktonic, benthic, or meiofaunal lifestyles. Such animals would likely have had relatively simple nervous systems equipped primarily to detect food, avoid inhospitable environments and locate mates. The appearance of the first macropredators during the Cambrian would have changed the selective landscape dramatically, likely driving the evolution of complex sense organs, sophisticated sensory processing systems, and diverse effector systems involved in capturing prey and avoiding predation. © 2015 The Author(s).

  18. Quantum dynamics of bio-molecular systems in noisy environments

    Huelga S.F.; Plenio M.B.


    We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical descripti...

  19. Organic Electrofluorescent Materials Using Pyridine-Containing Macrocyclic Compounds

    Tingxi LI; Long FU; Wenwen YU; Renhe HUANG


    Novel pyridine-containing macrocyclic compounds, such as 6,12,19,25-tetramethyl-7,11,20,24-dinitrilo-dibenzo[b,m]l,4,12,15-tetra-azacyclodoc osine (TMCD), were synthesized and used as electron transport layer in organic electroluminescent devices. Devices with a structure of glass/indium-tin oxide/arylamine derivative/tris(quinolinolato)aluminum(Ⅲ) (AIq)/TMCD/LiF/AI exhibited green emission from the Alq layer with external quantum efficiency of 0.84% and luminous efficiency of 1.3 lm/W. The derivatives of TMCD were synthesized and characterized as well. These compounds were also found to be useful as the electron-transporting materials in organic electroluminescent devices.

  20. Molecular absorption cryogenic cooler for liquid hydrogen propulsion systems

    Klein, G. A.; Jones, J. A.


    A light weight, long life molecular absorption cryogenic cooler (MACC) system is described which can use low temperature waste heat to provide cooling for liquid hydrogen propellant tanks for interplanetary spacecraft. Detailed tradeoff studies were made to evaluate the refrigeration system component interactions in order to minimize the mass of the spacecraft cooler system. Based on this analysis a refrigerator system mass of 31 kg is required to provide the .48 watts of cooling required by a 2.3 meter diameter liquid hydrogen tank.

  1. Radical Polymerization of Vinyl Acetate and Methyl Methacrylate Using Organochromium Initiators Complexed with Macrocyclic Polyamines


    METHYL METHACRYLATE USING ORGANOCHROMIUM REA NTS COMPLEXED WITH MACROCYCLIC A• by Daniela Mardare, Scott Gaynor, Krzysztof Matyjaszewski DTIC Published... Daniela Mardare, Scott Gaynor, Krzysztof Matyjaszewski 7. PERFORMING ORGANIZATION NAME(S) AND ADORESS(ES) a. PERFORMING ORGANIZATION Carnegie Mellon

  2. Design, synthesis and biological evaluation of a macrocyclic discodermolide/dictyostatin hybrid.

    Paterson, Ian; Gardner, Nicola M


    A 22-membered macrocyclic discodermolide/dictyostatin hybrid has been designed and synthesised; biological evaluation against a range of human cancer cell lines revealed significant levels of growth inhibition.

  3. Selective Synthesis of [2+2] Macrocyclic Schiff Bases from Chiral 1,4-Diamines

    ZHU Hai-Bin; HU Da-Hua; DONG Hua-Ze; LI Gen-Xi; GOU Shao-Hua


    [2+2] macrocyclic Schiff bases of three kinds have been synthesized from chiral 1,4-diamines by use of different methods. Macrocyclic Schiff bases 1a-1c have been selectively obtained based on a non-templated dilution method from chiral 1,4-diamines a-c and dialdehyde DA1, whereas macrocycles 2a-2c have been selectively produced from reaction of diamines a-c and dialdehyde DA2 in the presence of boric acid as templates. Macrocyclic Schiff bases 3a-3c have been afforded in high selectivity from diamines a-c and dialdehyde DA3 by means of sodium-template. All the titled compounds have been confirmed by 1H NMR and ESI-MS analyses.

  4. Heartworms, macrocyclic lactones, and the specter of resistance to prevention in the United States

    Bowman, Dwight D


    In order to provide a background to current concerns relative to the possible resistance of heartworms to macrocyclic lactones, this review summarizes various studies in which lack of efficacies (LOEs...

  5. Assembly of macrocycles by zirconocene-mediated, reversible carbon-carbon bond formation.

    Gessner, Viktoria H; Tannaci, John F; Miller, Adam D; Tilley, T Don


    Macrocyclic compounds have attracted considerable attention in numerous applications, including host-guest chemistry, chemical sensing, catalysis, and materials science. A major obstacle, however, is the limited number of convenient, versatile, and high-yielding synthetic routes to functionalized macrocycles. Macrocyclic compounds have been typically synthesized by ring-closing or condensation reactions, but many of these procedures produce mixtures of oligomers and cyclic compounds. As a result, macrocycle syntheses are often associated with difficult separations and low yields. Some successful approaches that circumvent these problems are based on "self-assembly" processes utilizing reversible bond-forming reactions, but for many applications, it is essential that the resulting macrocycle be built with a strong covalent bond network. In this Account, we describe how zirconocene-mediated reductive couplings of alkynes can provide reversible carbon-carbon bond-forming reactions well-suited for this purpose. Zirconocene coupling of alkenes and alkynes has been used extensively as a source of novel, versatile pathways to functionalized organic compounds. Here, we describe the development of zirconocene-mediated reductive couplings as a highly efficient method for the preparation of macrocycles and cages with diverse compositions, sizes, and shapes. This methodology is based on the reversible, regioselective coupling of alkynes with bulky substituents. In particular, silyl substituents provide regioselective, reversible couplings that place them into the α-positions of the resulting zirconacyclopentadiene rings. According to density functional theory (DFT) calculations and kinetic studies, the mechanism of this coupling involves a stepwise process, whereby an insertion of the second alkyne influences regiochemistry through both steric and electronic factors. Zirconocene coupling of diynes that incorporate silyl substituents generates predictable macrocyclic products

  6. Molecular system generation with strong resonance optical pumping

    Kuntsevich, B.F.; Churakov, V.V.


    A study was made of molecular system generation modulated by three oscillating levels with a rotating structure with strong resonance optical pumping. Molecular behavior of the active medium is described by equations for the density matrix. The relationship between the amplification coefficient and pressure at various pumping intensities was examined. In approaching the assigned pumping field, an examination was made of how the generation field is affected by the volumetric density of the pumping energy, partial pressure of the buffer gas and frequency difference in the pumping channel.

  7. Macrocyclic effects upon isomeric CuIIMII and MIICuII cores. Formation with unsymmetric phenol-based macrocyclic ligands

    Masami Yonemura; Yuuki Nakamura; Naoki Usuki; Hisashi Okawa


    This paper discusses coordination-position isomeric MIICuII and CuIIMII complexes, using unsymmetric dinucleating macrocycles (Lm;n)2- ((L2;2)2-, (L2;3)2- and (L2;4)2- that comprise two 2-(N-methyl)-aminomethyl-6-iminomethyl-4-bromophenonate entities, combined through the ethylene chain ( = 2) between the two amine nitrogens and through the ethylene, trimethylene or tetramethylene chain ( = 2, 3 or 4) between the two imine nitrogens. The macrocycles have dissimilar N(amine)2O2 and N(imine)2O2 metal-binding sites sharing the phenolic oxygens. The reaction of the mononuclear CuII precursors, [Cu(L2;2)], [Cu(L2;2)] and [Cu(L2;2)], with a MII perchlorate and a MII acetate salt formed (acetato)MII CuII complexes:[CoCu(L2;2)(AcO)]ClO4 0 5H2O] (1), [NiCu(L2;2) (AcO)]ClO4 (2), [ZnCu(L2;2((AcO)]ClO4 (3), [CoCu(L2;3)(AcO)]ClO4 0 5H2O (4), [NiCu(L2;3)(AcO)]ClO4 (5), [ZnCu(L2;3)(AcO)]ClO4 0 5H2O (6), [CoCu(L2;4)(AcO)(DMF)]ClO4 (7), [NiCu(L2;4)(AcO)]ClO4 2DMF (8) and [ZnCu(L2;4)(AcO)]ClO4 (9) (the formulation [MM (Lm;n)]2+ means that M resides in the aminic site and M in the iminic site). The site selectivity of the metal ions is demonstrated by X-ray crystallographic studies for 2 MeOH, 3, 5, 7, and 9. An (acetato)CuIIZnII complex, [CuZn(L2;3)(AcO)]ClO4 (10), was obtained by the reaction of [PbCu(L2;3)]-(ClO4)2 with ZnSO4 4H2O, in the presence of sodium acetate. Other complexes of the CuIIMII type were thermodynamically unstable to cause a scrambling of metal ions. The Cu migration from the iminic site to the aminic site in the synthesis of 10 is explained by the `kinetic macrocyclic effect’. The coordination-position isomers, 6 and 10, are differentiated by physicochemical properties.

  8. A set of homologous hetarylenediyne macrocycles by oxidative acetylene-acetylene coupling.

    Opris, Dorina M; Ossenbach, Alexander; Lentz, Dieter; Schlüter, A Dieter


    The synthesis of a set of bipyridine-containing macrocycles by oxidative acetylene-acetylene dimerization is described. The cycles are separated by preparative GPC, and the smallest homologue is analyzed by single-crystal X-ray diffraction, which shows a layered structure with channels that are partially filled with parts of the flexible chains of adjacent macrocycles. The cyclic trimer has a D3h symmetry and is a possible candidate for the formation of metal organic supramolecular assemblies on surfaces.

  9. A mesoporous metal–organic framework based on a shape-persistent macrocycle

    Chen, Teng-Hao; Popov, Ilya; Chuang, Yu-Chun; Chen, Yu-Sheng; Miljani; #263; , Ognjen Š. (NSRRC); (UC); (Houston)


    A mesoporous Zn-based metal–organic framework (MOF) was prepared from a shape-persistent phenylene ethynylene macrocycle functionalized with three –COOH groups. The rigid ligand has a ~ 9 Å wide central cavity which serves as a predesigned pore. The macrocycles [ππ] stack into pairs, with their carboxylate groups connected via three Zn₃O₁₄C₆H₂ clusters. The resulting MOF has a void volume of 86%.

  10. Pulsed EPR and NMR spectroscopy of paramagnetic iron porphyrinates and related iron macrocycles: how to understand patterns of spin delocalization and recognize macrocycle radicals.

    Walker, F Ann


    Pulsed EPR spectroscopic techniques, including ESEEM (electron spin echo envelope modulation) and pulsed ENDOR (electron-nuclear double resonance), are extremely useful for determining the magnitudes of the hyperfine couplings of macrocycle and axial ligand nuclei to the unpaired electron(s) on the metal as a function of magnetic field orientation relative to the complex. These data can frequently be used to determine the orientation of the g-tensor and the distribution of spin density over the macrocycle, and to determine the metal orbital(s) containing unpaired electrons and the macrocycle orbital(s) involved in spin delocalization. However, these studies cannot be carried out on metal complexes that do not have resolved EPR signals, as in the case of paramagnetic even-electron metal complexes. In addition, the signs of the hyperfine couplings, which are not determined directly in either ESEEM or pulsed ENDOR experiments, are often needed in order to translate hyperfine couplings into spin densities. In these cases, NMR isotropic (hyperfine) shifts are extremely useful in determining the amount and sign of the spin density at each nucleus probed. For metal complexes of aromatic macrocycles such as porphyrins, chlorins, or corroles, simple rules allow prediction of whether spin delocalization occurs through sigma or pi bonds, and whether spin density on the ligands is of the same or opposite sign as that on the metal. In cases where the amount of spin density on the macrocycle and axial ligands is found to be too large for simple metal-ligand spin delocalization, a macrocycle radical may be suspected. Large spin density on the macrocycle that is of the same sign as that on the metal provides clear evidence of either no coupling or weak ferromagnetic coupling of a macrocycle radical to the unpaired electron(s) on the metal, while large spin density on the macrocycle that is of opposite sign to that on the metal provides clear evidence of antiferromagnetic coupling

  11. Meaningful timescales from Monte Carlo simulations of molecular systems

    Costa, Liborio I


    A new Markov Chain Monte Carlo method for simulating the dynamics of molecular systems with atomistic detail is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is associated with minima in the energy landscape, in the proposed method, the state of the system is associated with the set of paths traveled by the atoms and the transition probabilities for an atom to be displaced are proportional to the corresponding velocities. In this way, the number of possible state-to-state transitions is reduced to a discrete set, and a direct link between the Monte Carlo time step and true physical time is naturally established. The resulting rejection-free algorithm is validated against event-driven molecular dynamics: the equilibrium and non-equilibrium dynamics of hard disks converge to the exact results with decreasing displacement size.

  12. Rapid synthesis of cyclic oligomeric depsipeptides with positional, stereochemical, and macrocycle size distribution control.

    Batiste, Suzanne M; Johnston, Jeffrey N


    Macrocyclic small molecules are attractive tools in the development of sensors, new materials, and therapeutics. Within early-stage drug discovery, they are increasingly sought for their potential to interact with broad surfaces of peptidic receptors rather than within their narrow folds and pockets. Cyclization of linear small molecule precursors is a straightforward strategy to constrain conformationally mobile motifs, but forging a macrocycle bond typically becomes more difficult at larger ring sizes. We report the development of a general approach to discrete collections of oligomeric macrocyclic depsipeptides using an oligomerization/macrocyclization process governed by a series of Mitsunobu reactions of hydroxy acid monomers. Ring sizes of 18, 24, 30, and 36 are formed in a single reaction from a didepsipeptide, whereas sizes of 24, 36, and 60 result from a tetradepsipeptide. The ring-size selectivity inherent to the approach can be modulated by salt additives that enhance the formation of specific ring sizes. Use of chemical synthesis to prepare the monomers suggests broad access to functionally and stereochemically diverse collections of natural product-like oligodepsipeptide macrocycles. Two cyclodepsipeptide natural products were prepared along with numerous unnatural oligomeric congeners to provide rapid access to discrete collections of complex macrocyclic small molecules from medium (18) to large (60) ring sizes.

  13. Template Syntheses, Crystal Structures and Supramolecular Assembly of Hexaaza Macrocyclic Copper(II) Complexes

    Kim, Taehyung; Kim, Ju Chang [Pukyong National Univ., Busan (Korea, Republic of); Lough, Alan J. [Univ. of Toronto, Toronto (Canada)


    Two new hexaaza macrocyclic copper(II) complexes were prepared by a template method and structurally characterized. In the solid state, they were self-assembled by intermolecular interactions to form the corresponding supramolecules 1 and 2, respectively. In the structure of 1, the copper(II) macrocycles are bridged by a tp ligand to form a macrocyclic copper(II) dimer. The dimer extends its structure by intermolecular forces such as hydrogen bonds and C-H···π interactions, resulting in the formation of a double stranded 1D supramolecule. In 2, the basic structure is a monomeric copper(II) macrocycle with deprotonated imidazole pendants. An undulated 1D hydrogen bonded array is achieved through hydrogen bonds between imidazole pendants and secondary amines, where the imidazole pendants act as a hydrogen bond acceptor. The 1D hydrogen bonded supramolecular chain is supported by C-H···π interactions between the methyl groups of acetonitrile ligands and imidazole pendants of the copper(II) macrocycles. In both complexes, the introduction of imidazoles to the macrocycle as a pendant plays an important role for the formation of supramolecules, where they act as intermolecular hydrogen bond donors and/or acceptors, C-H···π and π-π interactions.

  14. Easy creation of polymeric systems for molecular dynamics with Assemble!

    Degiacomi, Matteo T.; Erastova, Valentina; Wilson, Mark R.


    We present Assemble!, a program greatly simplifying the preparation of molecular dynamics simulations of polymeric systems. The program is controlled either via command line or an intuitive Graphical User Interface, and runs on all major operating systems. Assemble! allows the creation of a desired system of polymer chains from constituent monomers, packs the chains into a box according to the required concentration and returns all the files needed for simulation with Gromacs. We illustrate the capabilities of Assemble! by demonstrating the easy preparation of a 300 monomers-long polyisoprene in hexane, and a heterogeneous mixture of polybutadiene.

  15. Tailoring approach for obtaining molecular orbitals of large systems

    Anuja P Rahalkar; Shridhar R Gadre


    Molecular orbitals (MO’s) within Hartree-Fock (HF) theory are of vital importance as they provide preliminary information of bonding and features such as electron localization and chemical reactivity. The contemporary literature treats the Kohn-Sham orbitals within density functional theory (DFT) equivalently to the MO's obtained within HF framework. The high scaling order of ab initio methods is the main hurdle in obtaining the MO's for large molecular systems. With this view, an attempt is made in the present work to employ molecular tailoring approach (MTA) for obtaining the complete set of MO's including occupied and virtual orbitals, for large molecules at HF and B3LYP levels of theory. The energies of highest occupied and lowest unoccupied molecular orbitals, and hence the band gaps, are accurately estimated by MTA for most of the test cases benchmarked in this study, which include -conjugated molecules. Typically, the root mean square errors of valence MO's are in range of 0.001 to 0.010 a.u. for all the test cases examined. MTA shows a time advantage factor of 2 to 3 over the corresponding actual calculation, for many of the systems reported.

  16. ANN expert system screening for illicit amphetamines using molecular descriptors

    Gosav, S.; Praisler, M.; Dorohoi, D. O.


    The goal of this study was to develop and an artificial neural network (ANN) based on computed descriptors, which would be able to classify the molecular structures of potential illicit amphetamines and to derive their biological activity according to the similarity of their molecular structure with amphetamines of known toxicity. The system is necessary for testing new molecular structures for epidemiological, clinical, and forensic purposes. It was built using a database formed by 146 compounds representing drugs of abuse (mainly central stimulants, hallucinogens, sympathomimetic amines, narcotics and other potent analgesics), precursors, or derivatized counterparts. Their molecular structures were characterized by computing three types of descriptors: 38 constitutional descriptors (CDs), 69 topological descriptors (TDs) and 160 3D-MoRSE descriptors (3DDs). An ANN system was built for each category of variables. All three networks (CD-NN, TD-NN and 3DD-NN) were trained to distinguish between stimulant amphetamines, hallucinogenic amphetamines, and nonamphetamines. A selection of variables was performed when necessary. The efficiency with which each network identifies the class identity of an unknown sample was evaluated by calculating several figures of merit. The results of the comparative analysis are presented.

  17. Macrocyclic polyamine-functionalized silica as a solid-phase extraction material coupled with ionic liquid dispersive liquid-liquid extraction for the enrichment of polycyclic aromatic hydrocarbons.

    Liu, Longhui; He, Lijun; Jiang, Xiuming; Zhao, Wenjie; Xiang, Guoqiang; Anderson, Jared L


    In this study, silica modified with a 30-membered macrocyclic polyamine was synthesized and first used as an adsorbent material in SPE. The SPE was further combined with ionic liquid (IL) dispersive liquid-liquid microextraction (DLLME). Five polycyclic aromatic hydrocarbons were employed as model analytes to evaluate the extraction procedure and were determined by HPLC combined with UV/Vis detection. Acetone was used as the elution solvent in SPE as well as the dispersive solvent in DLLME. The enrichment of analytes was achieved using the 1,3-dibutylimidazolium bis[(trifluoromethyl)sulfonyl]imide IL/acetone/water system. Experimental conditions for the overall macrocycle-SPE-IL-DLLME method, such as the amount of adsorbent, sample solution volume, sample solution pH, type of elution solvent as well as addition of salt, were studied and optimized. The developed method could be successfully applied to the analysis of four real water samples. The macrocyclic polyamine offered higher extraction efficiency for analytes compared with commercially available C18 cartridge, and the developed method provided higher enrichment factors (2768-5409) for model analytes compared with the single DLLME. Good linearity with the correlation coefficients ranging from 0.9983 to 0.9999 and LODs as low as 0.002 μg/L were obtained in the proposed method.

  18. Covalent lanthanide(III) macrocyclic complexes: the bonding nature and optical properties of a promising single antenna molecule.

    Rabanal-León, Walter A; Páez-Hernández, Dayán; Arratia-Pérez, Ramiro


    The present work is focused on the elucidation of the electronic structure, bonding nature and optical properties of a series of low symmetry (C2) coordination compounds of type [Ln(III)HAM](3+), where "Ln(III)" are the trivalent lanthanide ions: La(3+), Ce(3+), Eu(3+) and Lu(3+), while "HAM" is the neutral six-nitrogen donor macrocyclic ligand [C22N6H26]. This systematic study has been performed in the framework of the Relativistic Density Functional Theory (R-DFT) and also using a multi-reference approach via the Complete Active Space (CAS) wavefunction treatment with the aim of analyzing their ground state and excited state electronic structures as well as electronic correlation. Furthermore, the use of the energy decomposition scheme proposed by Morokuma-Ziegler and the electron localization function (ELF) allows us to characterize the bonding between the lanthanide ions and the macrocyclic ligand, obtaining as a result a dative-covalent interaction. Due to a great deal of lanthanide optical properties and their technological applications, the absorption spectra of this set of coordination compounds were calculated using the time-dependent density functional theory (TD-DFT), where the presence of the intense Ligand to Metal Charge Transfer (LMCT) bands in the ultraviolet and visible region and the inherent f-f electronic transitions in the Near-Infra Red (NIR) region for some lanthanide ions allow us to propose these systems as "single antenna molecules" with potential applications in NIR technologies.

  19. Complement system part I - molecular mechanisms of activation and regulation

    Nicolas eMerle


    Full Text Available Complement is a complex innate immune surveillance system, playing a key role in defense against pathogens and in host homeostasis. The complement system is initiated by conformational changes in recognition molecular complexes upon sensing danger signals. The subsequent cascade of enzymatic reactions is tightly regulated to assure that complement is activated only at specific locations requiring defense against pathogens, thus avoiding host tissue damage. Here we discuss the recent advances describing the molecular and structural basis of activation and regulation of the complement pathways and their implication on physiology and pathology. This article will review the mechanisms of activation of alternative, classical and lectin pathways, the formation of C3 and C5 convertases, the action of anaphylatoxins and the membrane attack complex. We will also discuss the importance of structure-function relationships using the example of atypical hemolytic uremic syndrome. Lastly we will discuss the development and benefits of therapies using complement inhibitors.

  20. Extending Molecular Theory to Steady-State Diffusing Systems



    Predicting the properties of nonequilibrium systems from molecular simulations is a growing area of interest. One important class of problems involves steady state diffusion. To study these cases, a grand canonical molecular dynamics approach has been developed by Heffelfinger and van Swol [J. Chem. Phys., 101, 5274 (1994)]. With this method, the flux of particles, the chemical potential gradients, and density gradients can all be measured in the simulation. In this paper, we present a complementary approach that couples a nonlocal density functional theory (DFT) with a transport equation describing steady-state flux of the particles. We compare transport-DFT predictions to GCMD results for a variety of ideal (color diffusion), and nonideal (uphill diffusion and convective transport) systems. In all cases excellent agreement between transport-DFT and GCMD calculations is obtained with diffusion coefficients that are invariant with respect to density and external fields.

  1. The system of molecular-genetic triggers as self--organizing computing system

    A. Profir


    Full Text Available In this paper is shown, that the system of molecular-genetic triggers can solve the SAT problem. The molecular-genetic trigger represents the self-organizing structure and has attractors. The signal from one attractor is transmitted to other attractor, from the first level to the second level of the system. Molecular-genetic triggers work separately. The system of molecular-genetic triggers represents an example of parallel computing system. Suppose, that the system can receive two types of signals. In the first case, the system switches with the help of signals of a molecular nature (concentration of activators x1, x>sub>2, x3, x4. In the second case, the signals of wave nature of a resonant frequency can be utilized. It is possible to show, that the molecular--genetic system, can recognize images encoded by 2-dimensional vectors. Thus, the cells can be considered as parallel self-organizing system producing, receiving and transmitting the information.

  2. Stokes Efficiency of Molecular Motor-Cargo Systems


    2655, 1994. 11 F. Reif , Fundamentals of Statistical and Thermal Physics, McGraw-Hill, New York, NY, USA, 1985. 12 H. Kleinert, Path Integrals in...Quantum Mechanics , Statistics , Polymer Physics, and Financial Markets, World Scientific, River Edge, NJ, USA, 3rd edition, 2004. 13 A. Einstein...Efficiency of Molecular Motor-Cargo Systems Hongyun Wang1 and Hong Zhou2 1Department of Applied Mathematics and Statistics , University of California

  3. Efficient construction of nonorthogonal localized molecular orbitals in large systems.

    Cui, Ganglong; Fang, Weihai; Yang, Weitao


    Localized molecular orbitals (LMOs) are much more compact representations of electronic degrees of freedom than canonical molecular orbitals (CMOs). The most compact representation is provided by nonorthogonal localized molecular orbitals (NOLMOs), which are linearly independent but are not orthogonal. Both LMOs and NOLMOs are thus useful for linear-scaling calculations of electronic structures for large systems. Recently, NOLMOs have been successfully applied to linear-scaling calculations with density functional theory (DFT) and to reformulating time-dependent density functional theory (TDDFT) for calculations of excited states and spectroscopy. However, a challenge remains as NOLMO construction from CMOs is still inefficient for large systems. In this work, we develop an efficient method to accelerate the NOLMO construction by using predefined centroids of the NOLMO and thereby removing the nonlinear equality constraints in the original method ( J. Chem. Phys. 2004 , 120 , 9458 and J. Chem. Phys. 2000 , 112 , 4 ). Thus, NOLMO construction becomes an unconstrained optimization. Its efficiency is demonstrated for the selected saturated and conjugated molecules. Our method for fast NOLMO construction should lead to efficient DFT and NOLMO-TDDFT applications to large systems.

  4. Electron transfer reactions of macrocyclic compounds of cobalt

    Heckman, R.A.


    The kinetics and mechanisms of reduction of H/sub 2/O/sub 2/, Br/sub 2/, and I/sub 2/ by various macrocyclic tetraaza complexes of cobalt(II), including Vitamin B/sub 12r/, were studied. The synthetic macrocycles studied were all 14-membered rings which varied in the degree of unsaturation,substitution of methyl groups on the periphery of the ring, and substitution within the ring itself. Scavenging experiments demonstrated that the reductions of H/sub 2/O/sub 2/ produce free hydroxyl radicals only in the case of Co((14)ane)/sup 2 +/ but with none of the others. In the latter instances apparently H/sub 2/O/sub 2/ simultaneously oxidizes the metal center and the ligand. The reductions of Br/sub 2/ and I/sub 2/ produce an aquohalocobalt(III) product for all reductants (except B/sub 12r/ + Br/sub 2/, which was complicated by bromination of the corrin ring). The mechanism of halogen reduction was found to involve rate-limiting inner-sphere electron transfer from cobalt to halogen to produce a dihalide anion coordinated to the cobalt center. This intermediate subsequently decomposes in rapid reactions to halocobalt(III) and halogen atom species or reacts with another cobalt(II) center to give two molecules of halocobalt(III). The reductions of halomethylcobaloximes and related compounds and diamminecobaloxime by Cr/sup 2 +/ were also studied. The reaction was found to be biphasic in all cases with the reaction products being halomethane (for the halomethylcobaloximes), Co/sup 2 +/ (in less than 100 percent yield), a Cr(III)-dimethylglyoxime species, a small amount of free dmgH/sub 2/, and a highly-charged species containing both cobalt and chromium. The first-stage reaction occurs with a stoichiometry of 1:1 producing an intermediate with an absorption maximum at 460 nm for all starting reagents. The results were interpreted in terms of inner-sphere coordination of the cobaloxime to the Cr(II) and electron transfer through the oxime N-O bond.

  5. [Tl(III)(dota)](-): An Extraordinarily Robust Macrocyclic Complex.

    Fodor, Tamás; Bányai, István; Bényei, Attila; Platas-Iglesias, Carlos; Purgel, Mihály; Horváth, Gábor L; Zékány, László; Tircsó, Gyula; Tóth, Imre


    The X-ray structure of {C(NH2)3}[Tl(dota)]·H2O shows that the Tl(3+) ion is deeply buried in the macrocyclic cavity of the dota(4-) ligand (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate) with average Tl-N and Tl-O distances of 2.464 and 2.365 Å, respectively. The metal ion is directly coordinated to the eight donor atoms of the ligand, which results in a twisted square antiprismatic (TSAP') coordination around Tl(3+). A multinuclear (1)H, (13)C, and (205)Tl NMR study combined with DFT calculations confirmed the TSAP' structure of the complex in aqueous solution, which exists as the Λ(λλλλ)/Δ(δδδδ) enantiomeric pair. (205)Tl NMR spectroscopy allowed the protonation constant associated with the protonation of the complex according to [Tl(dota)](-) + H(+) ⇆ [Tl(Hdota)] to be determined, which turned out to be pK(H)Tl(dota) = 1.4 ± 0.1. [Tl(dota)](-) does not react with Br(-), even when using an excess of the anion, but it forms a weak mixed complex with cyanide, [Tl(dota)](-) + CN(-) ⇆ [Tl(dota)(CN)](2-), with an equilibrium constant of Kmix = 6.0 ± 0.8. The dissociation of the [Tl(dota)](-) complex was determined by UV-vis spectrophotometry under acidic conditions using a large excess of Br(-), and it was found to follow proton-assisted kinetics and to take place very slowly (∼10 days), even in 1 M HClO4, with the estimated half-life of the process being in the 10(9) h range at neutral pH. The solution dynamics of [Tl(dota)](-) were investigated using (13)C NMR spectroscopy and DFT calculations. The (13)C NMR spectra recorded at low temperature (272 K) point to C4 symmetry of the complex in solution, which averages to C4v as the temperature increases. This dynamic behavior was attributed to the Λ(λλλλ) ↔ Δ(δδδδ) enantiomerization process, which involves both the inversion of the macrocyclic unit and the rotation of the pendant arms. According to our calculations, the arm-rotation process limits the Λ(λλλλ) ↔

  6. High-order-harmonic generation in atomic and molecular systems

    Suárez, Noslen; Chacón, Alexis; Pérez-Hernández, Jose A.; Biegert, Jens; Lewenstein, Maciej; Ciappina, Marcelo F.


    High-order-harmonic generation (HHG) results from the interaction of ultrashort laser pulses with matter. It configures an invaluable tool to produce attosecond pulses, moreover, to extract electron structural and dynamical information of the target, i.e., atoms, molecules, and solids. In this contribution, we introduce an analytical description of atomic and molecular HHG, that extends the well-established theoretical strong-field approximation (SFA). Our approach involves two innovative aspects: (i) First, the bound-continuum and rescattering matrix elements can be analytically computed for both atomic and multicenter molecular systems, using a nonlocal short range model, but separable, potential. When compared with the standard models, these analytical derivations make possible to directly examine how the HHG spectra depend on the driven media and laser-pulse features. Furthermore, we can turn on and off contributions having distinct physical origins or corresponding to different mechanisms. This allows us to quantify their importance in the various regions of the HHG spectra. (ii) Second, as reported recently [N. Suárez et al., Phys. Rev. A 94, 043423 (2016), 10.1103/PhysRevA.94.043423], the multicenter matrix elements in our theory are free from nonphysical gauge- and coordinate-system-dependent terms; this is accomplished by adapting the coordinate system to the center from which the corresponding time-dependent wave function originates. Our SFA results are contrasted, when possible, with the direct numerical integration of the time-dependent Schrödinger equation in reduced and full dimensionality. Very good agreement is found for single and multielectronic atomic systems, modeled under the single active electron approximation, and for simple diatomic molecular systems. Interference features, ubiquitously present in every strong-field phenomenon involving a multicenter target, are also captured by our model.

  7. The System of Molecular Clouds in the Gould Belt

    Bobylev, V V


    Based on high-latitude molecular clouds with highly accurate distance estimates taken from the literature, we have redetermined the parameters of their spatial orientation. This system can be approximated by a 350x235x140 pc ellipsoid inclined by the angle i=17+/-2 degrees to the Galactic plane with the longitude of the ascending node l{\\Omega}=337+/-1 degrees. Based on the radial velocities of the clouds, we have found their group velocity relative to the Sun to be (u0,v0,w0) = (10.6,18.2,6.8)+/-(0.9,1.7,1.5) km/s. The trajectory of the center of the molecular cloud system in the past in a time interval of ~60 Myr has been constructed. Using data on masers associated with low-mass protostars, we have calculated the space velocities of the molecular complexes in Orion, Taurus, Perseus, and Ophiuchus. Their motion in the past is shown to be not random.

  8. Review and application of group theory to molecular systems biology

    Rietman Edward A


    Full Text Available Abstract In this paper we provide a review of selected mathematical ideas that can help us better understand the boundary between living and non-living systems. We focus on group theory and abstract algebra applied to molecular systems biology. Throughout this paper we briefly describe possible open problems. In connection with the genetic code we propose that it may be possible to use perturbation theory to explore the adjacent possibilities in the 64-dimensional space-time manifold of the evolving genome. With regards to algebraic graph theory, there are several minor open problems we discuss. In relation to network dynamics and groupoid formalism we suggest that the network graph might not be the main focus for understanding the phenotype but rather the phase space of the network dynamics. We show a simple case of a C6 network and its phase space network. We envision that the molecular network of a cell is actually a complex network of hypercycles and feedback circuits that could be better represented in a higher-dimensional space. We conjecture that targeting nodes in the molecular network that have key roles in the phase space, as revealed by analysis of the automorphism decomposition, might be a better way to drug discovery and treatment of cancer.

  9. Review and application of group theory to molecular systems biology.

    Rietman, Edward A; Karp, Robert L; Tuszynski, Jack A


    In this paper we provide a review of selected mathematical ideas that can help us better understand the boundary between living and non-living systems. We focus on group theory and abstract algebra applied to molecular systems biology. Throughout this paper we briefly describe possible open problems. In connection with the genetic code we propose that it may be possible to use perturbation theory to explore the adjacent possibilities in the 64-dimensional space-time manifold of the evolving genome. With regards to algebraic graph theory, there are several minor open problems we discuss. In relation to network dynamics and groupoid formalism we suggest that the network graph might not be the main focus for understanding the phenotype but rather the phase space of the network dynamics. We show a simple case of a C6 network and its phase space network. We envision that the molecular network of a cell is actually a complex network of hypercycles and feedback circuits that could be better represented in a higher-dimensional space. We conjecture that targeting nodes in the molecular network that have key roles in the phase space, as revealed by analysis of the automorphism decomposition, might be a better way to drug discovery and treatment of cancer.

  10. Light scattering from macromolecular systems: Molecular crystals and polymers

    Bernstein, E. R.


    The research objectives were to: (1) characterize phase transitions theoretically and experimentally in molecular crystal systems; (2) use the above understanding gained by light scattering studies and theoretical interpretation to apply to the more complex system of lyotropic liquid crystals; and (3) then apply knowledge gained on the model systems of increasing complexity to polymer liquid crystals and solid polymers as observed by laser light scattering techniques. Systems experimentally and theoretically discussed are: trioxane, triazine, benzil, and chloranil. Studies of lyotropic liquid crystals (sodium decyl sulfate, sodium sulfate, decanol, water) have progressed. The major findings are: a number of phase transitions occur between 20 and 60 C; these transitions evidence strong critical behavior and long correlation times for fluctuations; and liquid crystals can be studied by light scattering. Spectra of solid powders, ribbons, and liquid crystals of PBT and solid PBO were obtained.

  11. Quantum dynamics of bio-molecular systems in noisy environments

    Plenio, M B


    We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical description of system-environment interaction in the non-perturbative regime and present a promising new method that can overcome some limitations of existing methods. Thirdly, we present an approach towards deciding and quantifying the non-classicality of the action of the environment and the observed system-dynamics. We stress the relevance of these tools for strengthening the interplay between theoretical and experimental research in this field.

  12. Subtle Monte Carlo Updates in Dense Molecular Systems

    Bottaro, Sandro; Boomsma, Wouter; Johansson, Kristoffer E.;


    Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as the native state of globular proteins. Here, we introduce...... as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater efficiency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results...... a kinetic algorithm, CRISP, that greatly enhances the sampling efficiency in all-atom MC simulations of dense systems. The algorithm is based on an exact analytical solution to the classic chain-closure problem, making it possible to express the interdependencies among degrees of freedom in the molecule...

  13. Nucleocytoplasmic Transport: A Paradigm for Molecular Logistics in Artificial Systems.

    Vujica, Suncica; Zelmer, Christina; Panatala, Radhakrishnan; Lim, Roderick Y H


    Artificial organelles, molecular factories and nanoreactors are membrane-bound systems envisaged to exhibit cell-like functionality. These constitute liposomes, polymersomes or hybrid lipo-polymersomes that display different membrane-spanning channels and/or enclose molecular modules. To achieve more complex functionality, an artificial organelle should ideally sustain a continuous influx of essential macromolecular modules (i.e. cargoes) and metabolites against an outflow of reaction products. This would benefit from the incorporation of selective nanopores as well as specific trafficking factors that facilitate cargo selectivity, translocation efficiency, and directionality. Towards this goal, we describe how proteinaceous cargoes are transported between the nucleus and cytoplasm by nuclear pore complexes and the biological trafficking machinery in living cells (i.e. nucleocytoplasmic transport). On this basis, we discuss how biomimetic control may be implemented to selectively import, compartmentalize and accumulate diverse macromolecular modules against concentration gradients in artificial organelles.

  14. Radiative Corrections and Quantum Gates in Molecular Systems

    Reina, John H.; Beausoleil, Ray G.; Spiller, Tim P.; Munro, William J.


    We propose a method for quantum information processing using molecules coupled to an external laser field. This utilizes molecular interactions, control of the external field, and an effective energy shift of the doubly excited state of two coupled molecules. Such a level shift has been seen in the two-photon resonance experiments recently reported by Hettich etal. Here we show that this can be explained in terms of the QED Lamb shift. We quantify the performance of the proposed quantum logic gates in the presence of dissipative mechanisms. The unitary transformations required for performing one- and two-qubit operations can be implemented with present day molecular technology. The proposed techniques can also be applied to coupled quantum dot and biomolecular systems.

  15. A New Class of Macrocyclic Chiral Selectors for Stereochemical Analysis



    This report summarizes the work accomplished in the authors laboratories over the previous three years. During the funding period they have had 23 monographs published or in press, 1 book chapter, 1 patent issued and have delivered 28 invited seminars or plenary lectures on DOE sponsored research. This report covers the work that has been published (or accepted). The most notable aspect of this work involves the successful development and understanding of a new class of fused macrocyclic compounds as pseudophases and selectors in high performance separations (including high performance liquid chromatography, HPLC; capillary electrophoresis, CE; and thin layer chromatography, TLC). They have considerably extended their chiral biomarker work from amber to crude oil and coal. In the process of doing this we've developed several novel separation approaches. They finished their work on the new GSC-PLOT column which is now being used by researchers world-wide for the analysis of gases, light hydrocarbons and halocarbons. Finally, we completed basic studies on immobilizing a cyclodextrin/oligosiloxane hybrid on the wall of fused silica, as well as a basic study on the separation behavior of buckminster fullerene and higher fullerenes.

  16. Short communication: Macrocyclic lactone residues in butter from Brazilian markets.

    Macedo, Fabio; Marsico, Eliane Teixeira; Conte-Júnior, Carlos Adam; de Almeida Furtado, Leonardo; Brasil, Taila Figueredo; Pereira Netto, Annibal Duarte


    Macrocyclic lactones (ML) are commonly used in drug formulations for the treatment of parasites in cattle. In Brazil, except for drugs (or formulations) with long-term (half-life) effects, ML are registered for use in bovines. Indiscriminate use of ML may result in the presence of residues in milk and dairy products due to their lipophilic properties and thermal stability. This study applied a method of liquid chromatography with fluorimetric detection, recently developed and validated for the determination of residues of abamectin, doramectin, ivermectin, and moxidectin in butter. The method was applied to 38 samples of commercial butter purchased in the metropolitan area of Rio de Janeiro, Brazil, between June and September 2013, analyzed in triplicate. Ivermectin was detected in 89.5% of the samples, with concentrations between 0.3 and 119.4 µg/kg; 76.3% of the samples contained doramectin (0.6 to 64.7 µg/kg) and 55.2% contained abamectin (0.7 to 4.5 µg/kg). Most butter samples (76.3%) contained residues of more than 1 ML; however, no residues of moxidectin were detected. The results showed a high incidence of the presence of avermectins in butter samples. Butter is not included in the Brazilian National Plan for Control of Residues and Contaminants in Animal Products. As ML residues concentrate in lipophilic compounds, butter and other fatty dairy products should be screened for the presence of ML residues.

  17. Dermatobia hominis: Potencial risk of resistance to macrocyclic lactones.

    das Neves, José Henrique; Carvalho, Nadino; Amarante, Alessandro F T


    Dermatobia hominis is an ectoparasite that infests various species of mammals, including cattle, impairing the quality of cowhides and leather. After observing natural infestation with D. hominis larvae in cattle on two farms in the state of São Paulo, Brazil, we evaluated the efficacy of two macrocyclic lactones, ivermectin and moxidectin, against this parasite. The drugs were administered to 10 animals in each group, following the manufacturer's instructions. The groups were: Group 1-treated with ivermectin (0.2mg/kg of body weight (BW)); Group 2-treated with moxidectin (0.2mg/kg BW); and Group 3-control (untreated). On the farm in Pardinho, a total of 12 and 16 live larvae were found in 6 and in 8 animals 10 days after the treatment with ivermectin and moxidectin, respectively, while in the control group 4 bovines had a total of 7 live larvae. On the farm in Anhembi, 2, 4 and 6 live larvae were extracted from ivermectin, moxidectin and control groups, respectively, after the treatment. This is the first report of the presence of live D. hominis larvae after the treatment of cattle with ivermectin and moxidectin in Brazil. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. A photochemically driven molecular-level abacus

    Ashton; Ballardini; Balzani; Credi; Dress; Ishow; Kleverlaan; Kocian; Preece; Spencer; Stoddart; Venturi; Wenger


    A molecular-level abacus-like system driven by light inputs has been designed in the form of a [2]rotaxane, comprising the pi-electron-donating macrocyclic polyether bis-p-phenylene-34-crown-10 (BPP34C10) and a dumbbell-shaped component that contains 1) a Ru(II) polypyridine complex as one of its stoppers in the form of a photoactive unit, 2) a p-terphenyl-type ring system as a rigid spacer, 3) a 4,4'-bipyridinium unit and a 3,3'-dimethyl-4,4'-bipyridinium unit as pi-electron-accepting stations, and 4) a tetraarylmethane group as the second stopper. The synthesis of the [2]rotaxane was accomplished in four successive stages. First of all, the dumbbell-shaped component of the [2]rotaxane was constructed by using conventional synthetic methodology to make 1) the so-called "west-side" comprised of the Ru(II) polypyridine complex linked by a bismethylene spacer to the p-terphenyl-type ring system terminated by a benzylic bromomethyl function and 2) the so-called "east-side" comprised of the tetraarylmethane group, attached by a polyether linkage to the bipyridinium unit, itself joined in turn by a trismethylene spacer to an incipient 3,3'-dimethyl-4,4'-bipyridinium unit. Next, 3) the "west-side" and "east-side" were fused together by means of an alkylation to give the dumbbell-shaped compound, which was 4) finally subjected to a thermodynamically driven slippage reaction, with BPP34C10 as the ring, to afford the [2]rotaxane. The structure of this interlocked molecular compound was characterized by mass spectrometry and NMR spectroscopy, which also established, along with cyclic voltammetry, the co-conformational behavior of the molecular shuttle. The stable translational isomer is the one in which the BPP34C10 component encircles the 4,4'-bipyridinium unit, in keeping with the fact that this station is a better pi-electron acceptor than the other station. This observation raises the question- can the BPP34C10 macrocycle be made to shuttle between the two stations by a

  19. Sequence-defined bioactive macrocycles via an acid-catalysed cascade reaction

    Porel, Mintu; Thornlow, Dana N.; Phan, Ngoc N.; Alabi, Christopher A.


    Synthetic macrocycles derived from sequence-defined oligomers are a unique structural class whose ring size, sequence and structure can be tuned via precise organization of the primary sequence. Similar to peptides and other peptidomimetics, these well-defined synthetic macromolecules become pharmacologically relevant when bioactive side chains are incorporated into their primary sequence. In this article, we report the synthesis of oligothioetheramide (oligoTEA) macrocycles via a one-pot acid-catalysed cascade reaction. The versatility of the cyclization chemistry and modularity of the assembly process was demonstrated via the synthesis of >20 diverse oligoTEA macrocycles. Structural characterization via NMR spectroscopy revealed the presence of conformational isomers, which enabled the determination of local chain dynamics within the macromolecular structure. Finally, we demonstrate the biological activity of oligoTEA macrocycles designed to mimic facially amphiphilic antimicrobial peptides. The preliminary results indicate that macrocyclic oligoTEAs with just two-to-three cationic charge centres can elicit potent antibacterial activity against Gram-positive and Gram-negative bacteria.

  20. Unsaturated 15 and 16 Membered Appended Naphthalene Macrocyclic Molecules for The Development of Fluorometric Chemosensors

    Hasan, S.; Salleh, S.; Hamdan, S.; Yamin, B.


    Unsaturated macrocyclic molecules have got an interest due to their potential in catalysis, ion exchange and electron transfer. Salicaldehyde derivatives macrocyclic molecules have a broad range in synthesis. In this study, two unsaturated macrocyclic molecules (L1 and L2) have been synthesized. The preparation of unsaturated macrocyclic ligands involve two steps; the reaction of salicylaldehyde with 1,2-dibromoethane or 1,4-dibromobutane to produce precursor, then cyclisation were completed using schiff base technique by adding diamines (naphthalene diamine). The ligands were characterized spectroscopically. In FT-IR spectrums, the form of the ligands mainly can be observed on the disappearance of the carbonyl group of aldehyde at approximately 1650cm-1 that was readily assigned to C=O group of salicylaldehyde with the replacement of C=N peak at 1684.13cm-1. The success in producing macrocyclic ligands have been further characterized using fluorescence emission spectroscopy (FES) and revealed the typical emission of naphthalene at ∼430nm. Fluorescence changes of L1 and L2 showed high selectivity for Fe3+ and Cu2+ respectively in the presence of other common metal ions, such as Zn2+, Ni2+ and Co2+. Besides, the ligand was sensitive enough to detect the concentration of ferric ion with the detection limit down to 1.08 x 10-6 M and fluorescence change that was unaffected by the presence of other common coexisting metal ions. Complexation with Co(II) was also attempted.

  1. Molecular physiology of vesicular glutamate transporters in the digestive system

    Tao Li; Fayez K. Ghishan; Liqun Bai


    Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system (CNS). Packaging and storage of glutamate into glutamatergic neuronal vesicles require ATP-dependent vesicular glutamate uptake systems, which utilize the electrochemical proton gradient as a driving force. Three vesicular glutamate transporters (VGLUT1-3) have been recently identified from neuronal tissue where they play a key role to maintain the vesicular glutamate level. Recently, it has been demonstrated that glutamate signaling is also functional in peripheral neuronal and non-neuronal tissues, and occurs in sites of pituitary, adrenal, pineal glands, bone, GI tract, pancreas,skin, and testis. The glutamate receptors and VGLUTs in digestivesystem have been found in both neuronal and endocrinal cells. The glutamate signaling in the digestive system may have significant relevance to diabetes and GI tract motility disorders. This review will focus on the most recent update of molecular physiology of digestive VGLUTs.

  2. Microscale Symmetrical Electroporator Array as a Versatile Molecular Delivery System

    Ouyang, Mengxing; Hill, Winfield; Lee, Jung Hyun; Hur, Soojung Claire


    Successful developments of new therapeutic strategies often rely on the ability to deliver exogenous molecules into cytosol. We have developed a versatile on-chip vortex-assisted electroporation system, engineered to conduct sequential intracellular delivery of multiple molecules into various cell types at low voltage in a dosage-controlled manner. Micro-patterned planar electrodes permit substantial reduction in operational voltages and seamless integration with an existing microfluidic technology. Equipped with real-time process visualization functionality, the system enables on-chip optimization of electroporation parameters for cells with varying properties. Moreover, the system’s dosage control and multi-molecular delivery capabilities facilitate intracellular delivery of various molecules as a single agent or in combination and its utility in biological research has been demonstrated by conducting RNA interference assays. We envision the system to be a powerful tool, aiding a wide range of applications, requiring single-cell level co-administrations of multiple molecules with controlled dosages.

  3. Subtle Monte Carlo Updates in Dense Molecular Systems.

    Bottaro, Sandro; Boomsma, Wouter; E Johansson, Kristoffer; Andreetta, Christian; Hamelryck, Thomas; Ferkinghoff-Borg, Jesper


    Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as the native state of globular proteins. Here, we introduce a kinetic algorithm, CRISP, that greatly enhances the sampling efficiency in all-atom MC simulations of dense systems. The algorithm is based on an exact analytical solution to the classic chain-closure problem, making it possible to express the interdependencies among degrees of freedom in the molecule as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater efficiency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results suggest our method as a valuable tool in the study of molecules in atomic detail, offering a potential alternative to molecular dynamics for probing long time-scale conformational transitions.

  4. A 3D visualization system for molecular structures

    Green, Terry J.


    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  5. New hybrid method for reactive systems from integrating molecular orbital or molecular mechanics methods with analytical potential energy surfaces.

    Espinosa-Garciá, Joaquín; Rangel, Cipriano; Navarrete, Marta; Corchado, José C


    A computational approach to calculating potential energy surfaces for reactive systems is presented and tested. This hybrid approach is based on integrated methods where calculations for a small model system are performed by using analytical potential energy surfaces, and for the real system by using molecular orbital or molecular mechanics methods. The method is tested on a hydrogen abstraction reaction by using the variational transition-state theory with multidimensional tunneling corrections. The agreement between the calculated and experimental information depends on the quality of the method chosen for the real system. When the real system is treated by accurate quantum mechanics methods, the rate constants are in excellent agreement with the experimental measurements over a wide temperature range. When the real system is treated by molecular mechanics methods, the results are still good, which is very encouraging since molecular mechanics itself is not at all capable of describing this reactive system. Since no experimental information or additional fits are required to apply this method, it can be used to improve the accuracy of molecular orbital methods or to extend the molecular mechanics method to treat any reactive system with the single constraint of the availability of an analytical potential energy surface that describes the model system.

  6. High-pressure Brillouin scattering in a simple molecular system

    Shimizu, H


    Recent developments in high-pressure in situ Brillouin spectroscopy of a simple molecular system are reviewed by demonstrating experimental and analytical methods for the study of acoustic velocities in any direction, adiabatic elastic constants, and elastic anisotropy. Detailed applications to solid argon (Ar) are presented, at pressures up to 70 GPa in a diamond anvil cell, using recently developed approaches that combine the method of in situ Brillouin spectroscopy, for a single crystal of Ar up to 4 GPa, and the envelope method applied to both longitudinal acoustic and transverse acoustic modes, for recrystallized Ar between 4 and 70 GPa.

  7. An attempt to understand the observed plateau of the magnetization in tetranuclear iron(II) complexes of thiacalixarene macrocycles

    Ali Bayri; H Gokhan Bakir; Mustafa Sulu; Mustafa Karakaplan


    The next-nearest-neighbour (NNN) effect in tetranuclear iron(II) complexes of thiacalixarene macrocycles using the isotropic Heisenberg model has been investigated in order to understand its effects on the observed plateau of magnetization. Although NNN effect is generally very weak in these kinds of systems, it was calculated that its response is quite significant to the external perturbations in certain temperature regions. Using the isotropic Heisenberg exchange Hamiltonian, zero-field energy spectra have been calculated for this particular tetranuclear system. The average magnetic moments with and without next-nearest-neighbour interactions were also calculated. In order to verify the calculations, the results were compared with experimental data taken from the literature, whence, it is suggested that observed magnetic behaviour can be improved by taking into account the NNN effect.

  8. Rigid Organization of Fluorescence-Active Ligands by Artificial Macrocyclic Receptor to Achieve the Thioflavin T-Amyloid Fibril Level Association.

    Zhang, Ying-Ming; Zhang, Xu-Jie; Xu, Xiufang; Fu, Xiao-Ning; Hou, Hong-Biao; Liu, Yu


    The push-pull molecules with an intramolecular charge transfer from donor to acceptor sides upon excitation exhibit a wide variety of biological and electronic activities, as exemplified by the in vivo fluorescence imaging probes for amyloid fibrils in the diagnosis and treatment of amyloid diseases. Interestingly, the structurally much simpler bis(4,8-disulfonato-1,5-naphtho)-32-crown-8 (DNC), in keen contrast to the conventional macrocyclic receptors, was found to dramatically enhance the fluorescence of twisted intramolecular charge-transfer molecules possessing various benzothiazolium and stilbazolium fluorophores upon complexation. Spectroscopic and microcalorimetric titrations jointly demonstrated the complex structures and the interactions that promote the extremely strong complexation, revealing that the binding affinity in these artificial host-guest pairs could reach up to a nearly 10(7) M(-1) order of magnitude in water, and the sandwich-type complexation is driven by electrostatic, hydrophobic, π-stacking, and hydrogen-bonding interactions. Quantum chemical calculations on free molecules and their DNC-bound species in both the ground and excited states elucidated that the encapsulation by DNC could greatly deter the central single and double chemical bonds from free intramolecular rotation in the singlet excited state, thus leading to the unique and unprecedented fluorescence enhancement upon sandwich-type complexation. This complexation-induced structural reorganization mechanism may also apply to the binding of other small-molecule ligands by functional receptors and contribute to the molecular-level understanding of the receptor-ligand interactions in many biology-related systems.

  9. Synthesis of azomethine macrocycles by condensation of dicarbonyl compounds with diamines without using metal ions as template agents

    Borisova, Natalia E; Reshetova, Marina D; Ustynyuk, Yuri A [Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow (Russian Federation)


    Different strategies for the synthesis of symmetrical and unsymmetrical macrocyclic Schiff bases in the absence of metal ions are considered. General methods for performing macrocyclisation under thermodynamic or kinetic control are analysed. The key factors influencing the structure of macrocyclic azomethines are discussed.

  10. Self-assembled benzophenone bis-urea macrocycles facilitate selective oxidations by singlet oxygen.

    Geer, Michael F; Walla, Michael D; Solntsev, Kyril M; Strassert, Cristian A; Shimizu, Linda S


    This manuscript investigates how incorporation of benzophenone, a well-known triplet sensitizer, within a bis-urea macrocycle, which self-assembles into a columnar host, influences its photophysical properties and affects the reactivity of bound guest molecules. We further report the generation of a remarkably stable organic radical. As expected, UV irradiation of the host suspended in oxygenated solvents efficiently generates singlet oxygen similar to the parent benzophenone. In addition, this host can bind guests such as 2-methyl-2-butene and cumene to form stable solid host-guest complexes. Subsequent UV irradiation of these complexes facilitated the selective oxidation of 2-methyl-2-butene into the allylic alcohol, 3-methyl-2-buten-1-ol, at 90% selectivity as well as the selective reaction of cumene to the tertiary alcohol, α,α'-dimethyl benzyl alcohol, at 63% selectivity. However, these products usually arise through radical pathways and are not observed in the presence of benzophenone in solution. In contrast, typical reactions with benzophenone result in the formation of the reactive singlet oxygen that reacts with alkenes to form endoperoxides, diooxetanes, or hydroperoxides, which are not observed in our system. Our results suggest that the confinement, the formation of a stable radical species, and the singlet oxygen photoproduction are responsible for the selective oxidation processes. A greater understanding of the mechanism of this selective oxidation could lead to development of greener oxidants.

  11. Molecular Evolution of Freshwater Snails with Contrasting Mating Systems.

    Burgarella, Concetta; Gayral, Philippe; Ballenghien, Marion; Bernard, Aurélien; David, Patrice; Jarne, Philippe; Correa, Ana; Hurtrez-Boussès, Sylvie; Escobar, Juan; Galtier, Nicolas; Glémin, Sylvain


    Because mating systems affect population genetics and ecology, they are expected to impact the molecular evolution of species. Self-fertilizing species experience reduced effective population size, recombination rates, and heterozygosity, which in turn should decrease the efficacy of natural selection, both adaptive and purifying, and the strength of meiotic drive processes such as GC-biased gene conversion. The empirical evidence is only partly congruent with these predictions, depending on the analyzed species, some, but not all, of the expected effects have been observed. One possible reason is that self-fertilization is an evolutionary dead-end, so that most current selfers recently evolved self-fertilization, and their genome has not yet been strongly impacted by selfing. Here, we investigate the molecular evolution of two groups of freshwater snails in which mating systems have likely been stable for several millions of years. Analyzing coding sequence polymorphism, divergence, and expression levels, we report a strongly reduced genetic diversity, decreased efficacy of purifying selection, slower rate of adaptive evolution, and weakened codon usage bias/GC-biased gene conversion in the selfer Galba compared with the outcrosser Physa, in full agreement with theoretical expectations. Our results demonstrate that self-fertilization, when effective in the long run, is a major driver of population genomic and molecular evolutionary processes. Despite the genomic effects of selfing, Galba truncatula seems to escape the demographic consequences of the genetic load. We suggest that the particular ecology of the species may buffer the negative consequences of selfing, shedding new light on the dead-end hypothesis.

  12. Nitrogen-Phosphorus(III)-Chalcogen Macrocycles for the Synthesis of Polynuclear Silver(I) Sandwich Complexes.

    Yogendra, Sivathmeehan; Hennersdorf, Felix; Weigand, Jan J


    The synthesis of inorganic N-P(III)-Ch-based macrocycles [-PhP-NMe-PPh-Ch-]2 (8Ch; Ch = S, Se) is presented by incorporating two nitrogen, two chalcogen, and four phosphorus atoms. The macrocycles are conveniently obtained via the cyclocondensation reaction of Na2Ch (Ch = S, Se) with the acyclic dichlorodiphosphazane ClPhP-NMe-PClPh (9). Treatment with elemental sulfur (S8) or gray selenium (Segray) results in an oxidative ring contraction to give 1,3,2,4-thiazadiphosphetidine 2,4-disulfide (10S) and 1,3,2,4-selenazadiphosphetidine 2,4-diselenide (10Se), respectively. Macrocycles 8Ch are excellent multidentate ligands for transition metal complexation, as demonstrated by the isolation of mono-, di- tri-, and tetranuclear silver sandwich complexes. The polynuclear silver complexes are comprehensively characterized, including detailed NMR and X-ray analysis.

  13. Self-assembled monolayers of shape-persistent macrocycles on graphite: interior design and conformational polymorphism.

    Vollmeyer, Joscha; Eberhagen, Friederike; Höger, Sigurd; Jester, Stefan-S


    Three shape-persistent naphthylene-phenylene-acetylene macrocycles of identical backbone structures and extraannular substitution patterns but different (empty, apolar, polar) nanopore fillings are self-assembled at the solid/liquid interface of highly oriented pyrolytic graphite and 1,2,4-trichlorobenzene. Submolecularly resolved images of the resulting two-dimensional (2D) crystalline monolayer patterns are obtained by in situ scanning tunneling microscopy. A concentration-dependent conformational polymorphism is found, and open and more dense packing motifs are observed. For all three compounds alike lattice parameters are found, therefore the intermolecular macrocycle distances are mainly determined by their size and symmetry. This is an excellent example that the graphite acts as a template for the macrocycle organization independent from their specific interior.

  14. Theoretical prediction of some novel nanotubes composed of macrocyclic structures: A DFT study

    Masoodi, Hamid Reza; Bagheri, Sotoodeh; Ranjbar-Karimi, Reza


    Our interests in this paper are the elucidation of structural and electronic properties of some π-conjugated macrocycles composed of borazine and alumazene rings as well as the investigation of their potential utility for the creation of new nanotubes. Here, the calculations are performed at B3LYP/6-31+G(d) and M06-2X/6-31+G(d)//B3LYP/6-31+G(d) levels of theory. The results suggest that the self-assembly of the macrocyclic compounds can be considered to form new nanotubes through π-π stacking. Also, meaningful correlations are found between the stability and photoconductivity applications of the nanotubes and the number of stacked π-conjugated macrocycles.

  15. Self-assembled monolayers of shape-persistent macrocycles on graphite: interior design and conformational polymorphism

    Joscha Vollmeyer


    Full Text Available Three shape-persistent naphthylene–phenylene–acetylene macrocycles of identical backbone structures and extraannular substitution patterns but different (empty, apolar, polar nanopore fillings are self-assembled at the solid/liquid interface of highly oriented pyrolytic graphite and 1,2,4-trichlorobenzene. Submolecularly resolved images of the resulting two-dimensional (2D crystalline monolayer patterns are obtained by in situ scanning tunneling microscopy. A concentration-dependent conformational polymorphism is found, and open and more dense packing motifs are observed. For all three compounds alike lattice parameters are found, therefore the intermolecular macrocycle distances are mainly determined by their size and symmetry. This is an excellent example that the graphite acts as a template for the macrocycle organization independent from their specific interior.

  16. DNA-enabled integrated molecular systems for computation and sensing.

    LaBoda, Craig; Duschl, Heather; Dwyer, Chris L


    CONSPECTUS: Nucleic acids have become powerful building blocks for creating supramolecular nanostructures with a variety of new and interesting behaviors. The predictable and guided folding of DNA, inspired by nature, allows designs to manipulate molecular-scale processes unlike any other material system. Thus, DNA can be co-opted for engineered and purposeful ends. This Account details a small portion of what can be engineered using DNA within the context of computer architectures and systems. Over a decade of work at the intersection of DNA nanotechnology and computer system design has shown several key elements and properties of how to harness the massive parallelism created by DNA self-assembly. This work is presented, naturally, from the bottom-up beginning with early work on strand sequence design for deterministic, finite DNA nanostructure synthesis. The key features of DNA nanostructures are explored, including how the use of small DNA motifs assembled in a hierarchical manner enables full-addressability of the final nanostructure, an important property for building dense and complicated systems. A full computer system also requires devices that are compatible with DNA self-assembly and cooperate at a higher level as circuits patterned over many, many replicated units. Described here is some work in this area investigating nanowire and nanoparticle devices, as well as chromophore-based circuits called resonance energy transfer (RET) logic. The former is an example of a new way to bring traditional silicon transistor technology to the nanoscale, which is increasingly problematic with current fabrication methods. RET logic, on the other hand, introduces a framework for optical computing at the molecular level. This Account also highlights several architectural system studies that demonstrate that even with low-level devices that are inferior to their silicon counterparts and a substrate that harbors abundant defects, self-assembled systems can still

  17. Optimal methyl labeling for studies of supra-molecular systems

    Religa, Tomasz L.; Kay, Lewis E., E-mail: [The University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada)


    Selective methyl labeling combined with HMQC spectroscopy that exploits a TROSY effect in {sup 13}CH{sub 3} spin systems has significantly extended the utility of solution NMR spectroscopy in studies of high molecular weight particles. Herein we compare the utility of {sup 13}CH{sub 3}- versus {sup 13}CHD{sub 2}-labeling of Ile, Leu, Val probes in supra-molecular systems through quantification of relative signal-to-noise ratios in optimized spectra of highly deuterated, {sup 13}CH{sub 3}- and {sup 13}CHD{sub 2}-labeled samples of the half proteasome ({alpha}{sub 7}{alpha}{sub 7}, 360 kDa). It is shown that the sensitivity of spectra recorded on Ile, Leu, Val {sup 13}CH{sub 3}-labeled samples is between 1.5 and 2 fold higher than the corresponding data sets obtained on {alpha}{sub 7}{alpha}{sub 7} with {sup 13}CHD{sub 2} probes. Thus, labeling of supra-molecules with {sup 13}CH{sub 3} isotopomers remains the method of choice, but in applications where {sup 13}CHD{sub 2} moieties are required, sensitivity will in general not be limiting.

  18. International Conference on Intelligent Systems for Molecular Biology (ISMB)

    Goldberg, Debra; Hibbs, Matthew; Kall, Lukas; Komandurglayavilli, Ravikumar; Mahony, Shaun; Marinescu, Voichita; Mayrose, Itay; Minin, Vladimir; Neeman, Yossef; Nimrod, Guy; Novotny, Marian; Opiyo, Stephen; Portugaly, Elon; Sadka, Tali; Sakabe, Noboru; Sarkar, Indra; Schaub, Marc; Shafer, Paul; Shmygelska, Olena; Singer, Gregory; Song, Yun; Soumyaroop, Bhattacharya; Stadler, Michael; Strope, Pooja; Su, Rong; Tabach, Yuval; Tae, Hongseok; Taylor, Todd; Terribilini, Michael; Thomas, Asha; Tran, Nam; Tseng, Tsai-Tien; Vashist, Akshay; Vijaya, Parthiban; Wang, Kai; Wang, Ting; Wei, Lai; Woo, Yong; Wu, Chunlei; Yamanishi, Yoshihiro; Yan, Changhui; Yang, Jack; Yang, Mary; Ye, Ping; Zhang, Miao


    The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 13 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on "intelligent systems" and actual biological data makes ISMB a unique and highly important meeting, and 13 years of experience in holding the conference has resulted in a consistently well organized, well attended, and highly respected annual conference. The ISMB 2005 meeting was held June 25-29, 2005 at the Renaissance Center in Detroit, Michigan. The meeting attracted over 1,730 attendees. The science presented was exceptional, and in the course of the five-day meeting, 56 scientific papers, 710 posters, 47 Oral Abstracts, 76 Software demonstrations, and 14 tutorials were presented. The attendees represented a broad spectrum of backgrounds with 7% from commercial companies, over 28% qualifying for student registration, and 41 countries were represented at the conference, emphasizing its important international aspect. The ISMB conference is especially important because the cultures of computer science and biology are so disparate. ISMB, as a full-scale technical conference with refereed proceedings that have been indexed by both MEDLINE and Current Contents since 1996, bridges this cultural gap.

  19. Pipe Phantoms With Applications in Molecular Imaging and System Characterization.

    Wang, Shiying; Herbst, Elizabeth B; Pye, Stephen D; Moran, Carmel M; Hossack, John A


    Pipe (vessel) phantoms mimicking human tissue and blood flow are widely used for cardiovascular related research in medical ultrasound. Pipe phantom studies require the development of materials and liquids that match the acoustic properties of soft tissue, blood vessel wall, and blood. Over recent years, pipe phantoms have been developed to mimic the molecular properties of the simulated blood vessels. In this paper, the design, construction, and functionalization of pipe phantoms are introduced and validated for applications in molecular imaging and ultrasound imaging system characterization. There are three major types of pipe phantoms introduced: 1) a gelatin-based pipe phantom; 2) a polydimethylsiloxane-based pipe phantom; and 3) the "Edinburgh pipe phantom." These phantoms may be used in the validation and assessment of the dynamics of microbubble-based contrast agents and, in the case of a small diameter tube phantom, for assessing imaging system spatial resolution/contrast performance. The materials and procedures required to address each of the phantoms are described.

  20. The generation of meaningful information in molecular systems.

    Wills, Peter R


    The physico-chemical processes occurring inside cells are under the computational control of genetic (DNA) and epigenetic (internal structural) programming. The origin and evolution of genetic information (nucleic acid sequences) is reasonably well understood, but scant attention has been paid to the origin and evolution of the molecular biological interpreters that give phenotypic meaning to the sequence information that is quite faithfully replicated during cellular reproduction. The near universality and age of the mapping from nucleotide triplets to amino acids embedded in the functionality of the protein synthetic machinery speaks to the early development of a system of coding which is still extant in every living organism. We take the origin of genetic coding as a paradigm of the emergence of computation in natural systems, focusing on the requirement that the molecular components of an interpreter be synthesized autocatalytically. Within this context, it is seen that interpreters of increasing complexity are generated by series of transitions through stepped dynamic instabilities (non-equilibrium phase transitions). The early phylogeny of the amino acyl-tRNA synthetase enzymes is discussed in such terms, leading to the conclusion that the observed optimality of the genetic code is a natural outcome of the processes of self-organization that produced it.


    Debra Goldberg; Matthew Hibbs; Lukas Kall; Ravikumar Komandurglayavilli; Shaun Mahony; Voichita Marinescu; Itay Mayrose; Vladimir Minin; Yossef Neeman; Guy Nimrod; Marian Novotny; Stephen Opiyo; Elon Portugaly; Tali Sadka; Noboru Sakabe; Indra Sarkar; Marc Schaub; Paul Shafer; Olena Shmygelska; Gregory Singer; Yun Song; Bhattacharya Soumyaroop; Michael Stadler; Pooja Strope; Rong Su; Yuval Tabach; Hongseok Tae; Todd Taylor; Michael Terribilini; Asha Thomas; Nam Tran; Tsai-Tien Tseng; Akshay Vashist; Parthiban Vijaya; Kai Wang; Ting Wang; Lai Wei; Yong Woo; Chunlei Wu; Yoshihiro Yamanishi; Changhui Yan; Jack Yang; Mary Yang; Ping Ye; Miao Zhang


    The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 13 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on “intelligent systems” and actual biological data makes ISMB a unique and highly important meeting, and 13 years of experience in holding the conference has resulted in a consistently well organized, well attended, and highly respected annual conference. The ISMB 2005 meeting was held June 25-29, 2005 at the Renaissance Center in Detroit, Michigan. The meeting attracted over 1,730 attendees. The science presented was exceptional, and in the course of the five-day meeting, 56 scientific papers, 710 posters, 47 Oral Abstracts, 76 Software demonstrations, and 14 tutorials were presented. The attendees represented a broad spectrum of backgrounds with 7% from commercial companies, over 28% qualifying for student registration, and 41 countries were represented at the conference, emphasizing its important international aspect. The ISMB conference is especially important because the cultures of computer science and biology are so disparate. ISMB, as a full-scale technical conference with refereed proceedings that have been indexed by both MEDLINE and Current Contents since 1996, bridges this cultural gap.

  2. Characterization of ionic, dipolar and molecular mobility in polymer systems

    Guo, Zhenrong

    Changes in the ionic and dipolar molecular mobility in a polymer system are the basis for the changes in the dielectric mechanical properties of polymer materials. Frequency Dependent Dielectric Measurements (FDEMS) and Ion Time-of-Flight (ITOF) are two important techniques to investigate ionic and dipolar molecular mobility in polymer systems. The results can be related to the macro- and molecular dielectric, electrical and dynamic properties of polymeric materials. The combination of these two methods provides a full view of electric, dielectric and dynamic behavior for the systems as they undergo chemical and/or physical changes during polymerization crystallization, vitrification, and/or phase separation. The research on microscopic mass mobility in polymer systems was done on three aspects: (1) ion mobility in an epoxy-amine reaction system; (2) dipolar mobility and relaxation during dimethacrylate resin cure and (3) dye molecule migration and diffusion in polymer films. In the ion mobility study, we separately monitor the changes in the ion mobility and the number of charge carriers during the epoxy-amine polymerization with FDEMS and ITOF measurements. The isolation of the number of carriers and their mobility allows significant improvement in monitoring changes in the state and structure of a material as it cures. For the dipolar mobility and relaxation study, FDEMS measurements were used to detect structural evolution and spatial heterogeneity formation during the polymerization process of dimethacrylate resins. The dielectric spectra, glass transition (Tg) profiles and dynamic mechanical measurements were used to investigate the existence of two cooperative regions of sufficient size to create two alpha-relaxation processes representing oligomer rich and polymer microgel regions during the polymerization. For the dye migration research, we tried to develop a visually color changing paper (VCP) due to dye molecule migration in polymer films. The mobility

  3. Nonlinear Absorption and Refraction in Multilevel Organic Molecular System

    LI Chun-Fei; DENG Xiao-Xu; WANG Yu-Xiao


    The nonlinear absorption and refraction in a multilevel organic molecular system is described by using the density matrix theory. The total absorptive coefficient of the system in the low-density case is equal to a linear sum of contributions from each energy level. Similarly, the total refractive index is equal to a linear sum of contributions from each energy level plus the refractive index of the vacuum. The absorption coefficient or refractive index due to each level is proportional to the population of that level, where the constant of proportionality is called the absorption cross-section or the refraction volume, respectively. The relation between the absorption cross-section and the refraction volume for each level is also given.

  4. Macrocyclic ligands for uranium complexation. Final report, August 1, 1986--March 31, 1993

    Potts, K.T.


    Macrocycles, designed for complexation of the uranyl ion by computer modeling studies and utilizing six ligating atoms in the equatorial plane of the uranyl ions, have been prepared and their complexation of the uranyl ions evaluated. The ligating atoms, either oxygen or sulfur, were part of acylurea, biuret or thiobiuret subunits with alkane chains or pyridine units completing the macrocyclic periphery. These macrocycles with only partial preorganization formed uranyl complexes in solution but no crystalline complexes were isolated. Refinement of the cavity diameter by variation of the peripheral functional groups is currently studied to achieve an optimized cavity diameter of 4.7--5.2 {angstrom}. Acyclic ligands containing the same ligating atoms in equivalent functional entities were found to form a crystalline 1:1 uranyl-ligand complex (stability constant log K = 10.7) whose structure was established by X-ray data. This complex underwent a facile, DMSO-induced rearrangement to a 2:1 uranyl-ligand complex whose structure was also established by X-ray data. The intermediates to the macrocycles all behaved as excellent ligands for the complexation of transition metals. Acylthiourea complexes of copper and nickel as well as intermolecular, binuclear copper and nickel complexes of bidentate carbonyl thioureas formed readily and their structures were established in several representative instances by X-ray structural determinations. Tetradentate bis(carbonylthioureas) were found to be very efficient selective reagents for the complexation of copper in the presence of nickel ions. Several preorganized macrocycles were also prepared but in most instances these macrocycles underwent ring-opening under complexation conditions.

  5. The Porphobilinogen Conundrum in Prebiotic Routes to Tetrapyrrole Macrocycles

    Taniguchi, Masahiko; Ptaszek, Marcin; Chandrashaker, Vanampally; Lindsey, Jonathan S.


    Attempts to develop a credible prebiotic route to tetrapyrroles have relied on enzyme-free recapitulation of the extant biosynthesis, but this process has foundered from the inability to form the pyrrole porphobilinogen ( PBG) in good yield by self-condensation of the precursor δ-aminolevulinic acid ( ALA). PBG undergoes robust oligomerization in aqueous solution to give uroporphyrinogen (4 isomers) in good yield. ALA, PBG, and uroporphyrinogen III are universal precursors to all known tetrapyrrole macrocycles. The enzymic formation of PBG entails carbon-carbon bond formation between the less stable enolate/enamine of one ALA molecule (3-position) and the carbonyl/imine (4-position) of the second ALA molecule; without enzymes, the first ALA reacts at the more stable enolate/enamine (5-position) and gives the pyrrole pseudo-PBG. pseudo-PBG cannot self-condense, yet has one open α-pyrrole position and is proposed to be a terminator of oligopyrromethane chain-growth from PBG. Here, 23 analogues of ALA have been subjected to density functional theoretical (DFT) calculations, but no motif has been identified that directs reaction at the 3-position. Deuteriation experiments suggested 5-(phosphonooxy)levulinic acid would react preferentially at the 3- versus 5-position, but a hybrid condensation with ALA gave no observable uroporphyrin. The results suggest efforts toward a biomimetic, enzyme-free route to tetrapyrroles from ALA should turn away from structure-directed reactions and focus on catalysts that orient the two aminoketones to form PBG in a kinetically controlled process, thereby avoiding formation of pseudo-PBG.

  6. BINOL Macrocycle Derivatives: Synthesis of New Dinaphthyl Sulfide Aza Oxa Thia Crowns (Lariats

    Abbas Shockravi


    Full Text Available In this research work, dinaphthyl sulfide diester was prepared from the reaction of 1,1′-thiobis (2-hydroxy naphthalene and methylchloroacetate. Its aza-macrocyclic derivative was synthesized from the reaction of dinaphthyl sulfide diester and diethylenetriamine. Lariats were prepared from the reaction of chloroamides (four derivatives and initial macrocycle. Chloroamides were synthesized from the reaction of amines (aniline, benzylamine, 8-amino quinoline and 4-amino azobenzene and chloroacetyl chloride. All the materials were identified by IR, 1H NMR, 13C NMR, and mass spectroscopies, and elemental analysis.

  7. Synthesis and electrochemical studies of phenylazo substituted tetraaza macrocyclic complexes of Ni(II)

    Randhir Singh; Suresh Kumar; Amarendra Bhattacharya


    Synthesis and characterization of some phenyl azo substituted tetraaza macrocyclic complexes of Ni(II) are reported. Electrochemical behaviour of these macrocyclic complexes has been examined using polarographic, voltammetric and spectroscopic techniques. These studies show that both the ligand and the metal are electrochemically active. The electrochemical behaviour of the azo function has been shown to occur through a single four-electron process. When a nitro group is also present, the nitro function of the azo moiety is reduced in a six-electron cathodic wave.

  8. Synthesis and extended activity of triazole-containing macrocyclic protease inhibitors

    Pehere, A.D.; Pietsch, M.; Gütschow, M.;


    Peptide-derived protease inhibitors are an important class of compounds with the potential to treat a wide range of diseases. Herein, we describe the synthesis of a series of triazole- containing macrocyclic protease inhibitors pre-organized into a b-strand conformation and an evaluation...... of their activity against a panel of proteases. Acyclic azidoalkyne-based aldehydes are also evaluated for comparison. The macrocyclic peptidomimetics showed considerable activity towards calpain II, cathepsin L and S, and the 20S proteasome chymotrypsin-like activity. Some of the first examples of highly potent...

  9. Macrocyclic prolinyl acyl guanidines as inhibitors of β-secretase (BACE).

    Boy, Kenneth M; Guernon, Jason M; Wu, Yong-Jin; Zhang, Yunhui; Shi, Joe; Zhai, Weixu; Zhu, Shirong; Gerritz, Samuel W; Toyn, Jeremy H; Meredith, Jere E; Barten, Donna M; Burton, Catherine R; Albright, Charles F; Good, Andrew C; Grace, James E; Lentz, Kimberley A; Olson, Richard E; Macor, John E; Thompson, Lorin A


    The synthesis, evaluation, and structure-activity relationships of a class of acyl guanidines which inhibit the BACE-1 enzyme are presented. The prolinyl acyl guanidine chemotype (7c), unlike compounds of the parent isothiazole chemotype (1), yielded compounds with good agreement between their enzymatic and cellular potency as well as a reduced susceptibility to P-gp efflux. Further improvements in potency and P-gp ratio were realized via a macrocyclization strategy. The in vivo profile in wild-type mice and P-gp effects for the macrocyclic analog 21c is presented.

  10. Chemomechanics with Molecular Force Probes


    probe should have [25,26]: (1) a size that is small enough to allow high-level quantum -chemical calcu- lations of geometries and energies of...macrocycles makes them amenable to high-level quantum -chemical calculations, which yield restoring forces without the ambi- guities intrinsic to...reactions to be measured and in- terpreted structurally and mechanistically by integrating molecular design, synthesis, kinetic/ mechanis - tic studies and

  11. Structure-Activity Relationship Studies on a Macrocyclic Agouti-Related Protein (AGRP) Scaffold Reveal Agouti Signaling Protein (ASP) Residue Substitutions Maintain Melanocortin-4 Receptor Antagonist Potency and Result in Inverse Agonist Pharmacology at the Melanocortin-5 Receptor.

    Ericson, Mark D; Freeman, Katie T; Schnell, Sathya M; Fleming, Katlyn A; Haskell-Luevano, Carrie


    The melanocortin system consists of five reported receptors, agonists from the proopiomelanocortin gene transcript, and two antagonists, agouti-signaling protein (ASP) and agouti-related protein (AGRP). For both ASP and AGRP, the hypothesized Arg-Phe-Phe pharmacophores are on exposed β-hairpin loops. In this study, the Asn and Ala positions of a reported AGRP macrocyclic scaffold (c[Pro-Arg-Phe-Phe-Asn-Ala-Phe-DPro]) were explored with 14-compound and 8-compound libraries, respectively, to generate more potent, selective melanocortin receptor antagonists. Substituting diaminopropionic acid (Dap), DDap, and His at the Asn position yielded potent MC4R ligands, while replacing Ala with Ser maintained MC4R potency. Since these substitutions correlate to ASP loop residues, an additional Phe to Ala substitution was synthesized and observed to maintain MC4R potency. Seventeen compounds also possessed inverse agonist activity at the MC5R, the first report of this pharmacology. These findings are useful in developing molecular probes to study negative energy balance conditions and unidentified functions of the MC5R.

  12. Pancreatic Cancer Gene Therapy: From Molecular Targets to Delivery Systems

    Fillat, Cristina, E-mail:; Jose, Anabel; Ros, Xavier Bofill-De; Mato-Berciano, Ana; Maliandi, Maria Victoria; Sobrevals, Luciano [Programa Gens i Malaltia, Centre de Regulació Genòmica-CRG, UPF, Parc de Recerca Biomedica de Barcelona-PRBB and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona (Spain)


    The continuous identification of molecular changes deregulating critical pathways in pancreatic tumor cells provides us with a large number of novel candidates to engineer gene-targeted approaches for pancreatic cancer treatment. Targets—both protein coding and non-coding—are being exploited in gene therapy to influence the deregulated pathways to facilitate cytotoxicity, enhance the immune response or sensitize to current treatments. Delivery vehicles based on viral or non-viral systems as well as cellular vectors with tumor homing characteristics are a critical part of the design of gene therapy strategies. The different behavior of tumoral versus non-tumoral cells inspires vector engineering with the generation of tumor selective products that can prevent potential toxic-associated effects. In the current review, a detailed analysis of the different targets, the delivery vectors, the preclinical approaches and a descriptive update on the conducted clinical trials are presented. Moreover, future possibilities in pancreatic cancer treatment by gene therapy strategies are discussed.

  13. Degree of molecular self-sorting in multicomponent systems.

    Saha, Manik Lal; Schmittel, Michael


    Self-sorting represents the spontaneous and high fidelity self and/or non-self-recognition of two or more related components within a complex mixture. While the effective management of self-sorting principles perceptibly requires some key expertise in molecular programming, at a higher stage of operation it is of supreme interest to guide the process to increasingly higher degrees of self-sorting. In this article, we present the emerging principles of how to guide several components toward formation of self-sorted multicomponent architectures. To provide further guidance in denominating such systems, we suggest to utilise a systematic classification as well as a formula to evaluate their degree of self-sorting (M).

  14. The large system of molecular clouds in Orion and Monoceros

    Maddalena, R. J.; Moscowitz, J.; Thaddeus, P.; Morris, M.


    Emission is noted over about one-eighth of an 850-sq deg region centered on Orion and Monoceros that has been surveyed in the J = 1 to 0 line of CO; most of the emission arises from giant molecular clouds associated with Orion A and B, and Mon R2. A much smaller area was surveyed for C-13O emission. A comparison of cloud masses obtained by three independent methods indicates that CO luminosity is as accurate a measure of cloud mass as other indicators. The possible relationships among clouds in the survey are discussed, including the conjecture that the overall Orion complex of clouds is a much larger system than previously considered, incorporating most of the clouds in the present survey.

  15. Molecular dynamic simulations of the sputtering of multilayer organic systems

    Postawa, Z; Piaskowy, J; Krantzman, K; Winograd, N; Garrison, B J


    Sputtering of organic overlayers has been modeled using molecular dynamics computer simulations. The investigated systems are composed of benzene molecules condensed into one, two and three layers on an Ag left brace 1 1 1 right brace surface. The formed organic overlayers were bombarded with 4 keV Ar projectiles at normal incidence. The development of the collision cascade in the organic overlayer was investigated. The sputtering yield, mass, internal and kinetic energy distributions of ejected particles have been analyzed as a function of the thickness of the organic layer. The results show that all emission characteristics are sensitive to the variation of layer thickness. Although most of the ejected intact benzene molecules originate from the topmost layer, the emission of particles located initially in second and third layers is significant. The analysis indicates that the metallic substrate plays a dominant role in the ejection of intact organic molecules.

  16. Molecular dynamic simulations of the sputtering of multilayer organic systems

    Postawa, Z. E-mail:; Ludwig, K.; Piaskowy, J.; Krantzman, K.; Winograd, N.; Garrison, B.J


    Sputtering of organic overlayers has been modeled using molecular dynamics computer simulations. The investigated systems are composed of benzene molecules condensed into one, two and three layers on an Ag{l_brace}1 1 1{r_brace} surface. The formed organic overlayers were bombarded with 4 keV Ar projectiles at normal incidence. The development of the collision cascade in the organic overlayer was investigated. The sputtering yield, mass, internal and kinetic energy distributions of ejected particles have been analyzed as a function of the thickness of the organic layer. The results show that all emission characteristics are sensitive to the variation of layer thickness. Although most of the ejected intact benzene molecules originate from the topmost layer, the emission of particles located initially in second and third layers is significant. The analysis indicates that the metallic substrate plays a dominant role in the ejection of intact organic molecules.

  17. Minor changes in the macrocyclic ligands but major consequences on the efficiency of gold nanoparticles designed for radiosensitization

    Laurent, G.; Bernhard, C.; Dufort, S.; Jiménez Sánchez, G.; Bazzi, R.; Boschetti, F.; Moreau, M.; Vu, T. H.; Collin, B.; Oudot, A.; Herath, N.; Requardt, H.; Laurent, S.; Vander Elst, L.; Muller, R.; Dutreix, M.; Meyer, M.; Brunotte, F.; Perriat, P.; Lux, F.; Tillement, O.; Le Duc, G.; Denat, F.; Roux, S.


    Many studies have been devoted to adapting the design of gold nanoparticles to efficiently exploit their promising capability to enhance the effects of radiotherapy. In particular, the addition of magnetic resonance imaging modality constitutes an attractive strategy for enhancing the selectivity of radiotherapy since it allows the determination of the most suited delay between the injection of nanoparticles and irradiation. This requires the functionalization of the gold core by an organic shell composed of thiolated gadolinium chelates. The risk of nephrogenic systemic fibrosis induced by the release of gadolinium ions should encourage the use of macrocyclic chelators which form highly stable and inert complexes with gadolinium ions. In this context, three types of gold nanoparticles (Au@DTDOTA, Au@TADOTA and Au@TADOTAGA) combining MRI, nuclear imaging and radiosensitization have been developed with different macrocyclic ligands anchored onto the gold cores. Despite similarities in size and organic shell composition, the distribution of gadolinium chelate-coated gold nanoparticles (Au@TADOTA-Gd and Au@TADOTAGA-Gd) in the tumor zone is clearly different. As a result, the intravenous injection of Au@TADOTAGA-Gd prior to the irradiation of 9L gliosarcoma bearing rats leads to the highest increase in lifespan whereas the radiophysical effects of Au@TADOTAGA-Gd and Au@TADOTA-Gd are very similar.Many studies have been devoted to adapting the design of gold nanoparticles to efficiently exploit their promising capability to enhance the effects of radiotherapy. In particular, the addition of magnetic resonance imaging modality constitutes an attractive strategy for enhancing the selectivity of radiotherapy since it allows the determination of the most suited delay between the injection of nanoparticles and irradiation. This requires the functionalization of the gold core by an organic shell composed of thiolated gadolinium chelates. The risk of nephrogenic systemic

  18. Parametrizing coarse grained models for molecular systems at equilibrium

    Kalligiannaki, E.


    Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

  19. The Role of the Environment in Molecular Systems

    Kilin, D S


    The work is devoted to the investigation of the influence of a heat bath on the physical processes in a quantum system. We use the density matrix theory as one of the most powerfool tool for investigation of quantum relaxation. In the beginning of the work (chapter 2) we mention and recall the most important steps of derivation of the equation of motion for the reduced density matrix (master equation) for an arbitrary quantum system in diabatic representation interacting with the environment modeled by a set of independent harmonic oscillators. Chapter 3 deals with the question of the border between classical and quantum effects and reports on a study of the environmental influence on the time evolution of a coherent state or the superposition of two coherent states of a harmonic oscillator as a simple system displaying the peculiarities of the transition from quantum to classical regime. Chapters 4 and 5 concern the electron transfer (ET) problem, namely the mathematical description of the ET in molecular zi...

  20. Parametrizing coarse grained models for molecular systems at equilibrium

    Kalligiannaki, E.; Chazirakis, A.; Tsourtis, A.; Katsoulakis, M. A.; Plecháč, P.; Harmandaris, V.


    Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

  1. PathSys: integrating molecular interaction graphs for systems biology

    Raval Alpan


    Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at

  2. Energy conservation in molecular dynamics simulations of classical systems.

    Toxvaerd, Søren; Heilmann, Ole J; Dyre, Jeppe C


    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete "Verlet" algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence of a "shadow Hamiltonian" H [S. Toxvaerd, Phys. Rev. E 50, 2271 (1994)], i.e., a Hamiltonian close to the original H with the property that the discrete positions of the Verlet algorithm for H lie on the analytic trajectories of H. The shadow Hamiltonian can be obtained from H by an asymptotic expansion in the time step length. Here we use the first non-trivial term in this expansion to obtain an improved estimate of the discrete values of the energy. The investigation is performed for a representative system with Lennard-Jones pair interactions. The simulations show that inclusion of this term reduces the standard deviation of the energy fluctuations by a factor of 100 for typical values of the time step length. Simulations further show that the energy is conserved for at least one hundred million time steps provided the potential and its first four derivatives are continuous at the cutoff. Finally, we show analytically as well as numerically that energy conservation is not sensitive to round-off errors.

  3. Bicanonical ab Initio Molecular Dynamics for Open Systems.

    Frenzel, Johannes; Meyer, Bernd; Marx, Dominik


    Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

  4. Aromatic Lateral Substituents Influence the Excitation Energies of Hexaaza Lanthanide Macrocyclic Complexes: A Wave Function Theory and Density Functional Study.

    Rabanal-León, Walter A; Murillo-López, Juliana A; Páez-Hernández, Dayán; Arratia-Pérez, Ramiro


    The high interest in lanthanide chemistry, and particularly in their luminescence, has been encouraged by the need of understanding the lanthanide chemical coordination and how the design of new luminescent materials can be affected by this. This work is focused on the understanding of the electronic structure, bonding nature, and optical properties of a set of lanthanide hexaaza macrocyclic complexes, which can lead to potential optical applications. Here we found that the DFT ground state of the open-shell complexes are mainly characterized by the manifold of low lying f states, having small HOMO-LUMO energy gaps. The results obtained from the wave function theory calculations (SO-RASSI) put on evidence the multiconfigurational character of their ground state and it is observed that the large spin-orbit coupling and the weak crystal field produce a strong mix of the ground and the excited states. The electron localization function (ELF) and the energy decomposition analysis (EDA) support the idea of a dative interaction between the macrocyclic ligand and the lanthanide center for all the studied systems; noting that, this interaction has a covalent character, where the d-orbital participation is evidenced from NBO analysis, leaving the f shell completely noninteracting in the chemical bonding. From the optical part we observed in all cases the characteristic intraligand (IL) (π-π*) and ligand to metal charge-transfer (LMCT) bands that are present in the ultraviolet and visible regions, and for the open-shell complexes we found the inherent f-f electronic transitions on the visible and near-infrared region.

  5. Comparative Study of the Optical and Textural Properties of Tetrapyrrole Macrocycles Trapped Within ZrO2, TiO2, and SiO2 Translucent Xerogels

    Eduardo Salas-Bañales


    Full Text Available The entrapping of physicochemical active molecules inside mesoporous networks is an appealing field of research due to the myriad of potential applications in optics, photocatalysis, chemical sensing, and medicine. One of the most important reasons for this success is the possibility of optimizing the properties that a free active species displays in solution but now trapped inside a solid substrate. Additionally it is possible to modulate the textural characteristics of substrates, such as pore size, specific surface area, polarity and chemical affinity of the surface, toward the physical or chemical adhesion of a variety of adsorbates. In the present document, two kinds of non-silicon metal alkoxides, Zr and Ti, are employed to prepare xerogels containing entrapped tetrapyrrolic species that could be inserted beforehand in analogue silica systems. The main goal is to develop efficient methods for trapping or binding tetrapyrrole macrocycles inside TiO2 and ZrO2 xerogels, while comparing the properties of these systems against those of the SiO2 analogues. Once the optimal synthesis conditions for obtaining translucent monolithic xerogels of ZrO2 and TiO2 networks were determined, it was confirmed that these substrates allowed the entrapment, in monomeric form, of macrocycles that commonly appear as aggregates within the SiO2 network. From these experiments, it could be determined that the average pore diameters, specific surface areas, and water sorption capacities depicted by each one of these substrates, are a consequence of their own nature combined with the particular structure of the entrapped tetrapyrrole macrocycle. Furthermore, the establishment of covalent bonds between the intruding species and the pore walls leads to the obtainment of very similar pore sizes in the three different metal oxide (Ti, Zr, and Si substrates as a consequence of the templating effect of the encapsulated species.

  6. Template Synthesis of a Tetraaza Macrocycle Which Involves Benzaldehyde Rather Than Formaldehyde as a Building Block. Isolation and Structure Determination of the Open-Chain Schiff Base Intermediate Complex.

    Fabbrizzi, Luigi; Licchelli, Maurizio; Manotti Lanfredi, Anna Maria; Vassalli, Omar; Ugozzoli, Franco


    The classical formaldehyde building block has been replaced by the bulkier benzaldehyde in the Cu(II) template synthesis of the cyclam-like tetraaza macrocycle of type 1, in which nitroethane operated as locking fragment. The synthetic pathway involves three distinct steps: (i) Schiff base condensation of the metal-free open-chain tetramine; (ii) Cu(II) coordination and preorientation of the Schiff base; (iii) nucleophilic attack by the deprotonated nitroethane fragment and formation of the macrocyclic complex. Both the Schiff base Cu(II) complex and the Cu(II) macrocyclic complex were isolated in a crystalline form and their molecular structures were determined: {N-[2-((E)-benzylideneamino)ethyl]-N'-[2-((Z)-benzylideneamino)ethyl]propane-1,3-diamine}copper(II) nitrate: triclinic, space group P&onemacr;, with a = 12.296(5) Å, b = 10.787(6) Å, c = 10.547(7) Å, V = 1161(1) Å(3), and Z = 2 (R = 0.055, R(w) = 0.061); [(5R,6S,7S)-6-methyl-6-nitro-5,7-diphenyl-1,4,8,11-tetraazacyclotetradecane]copper(II) perchlorate: monoclinic, space group P2(1)/n, with a = 15.246(5) Å, b = 23240(7) Å, c = 8.540(4) Å, V = 2980(2) Å(3), and Z = 4 (R = 0.095, R(w) = 0.095). This allowed us to define mechanistic details of the macrocyclization process. It is suggested that the same three-step pathway takes place in the much easier and faster one-pot template syntheses of cyclam-like macrocyles, which involve formaldehyde as a building block.

  7. Molecular tailoring of interfaces for thin film on substrate systems

    Grady, Martha Elizabeth

    Thin film on substrate systems appear most prevalently within the microelectronics industry, which demands that devices operate in smaller and smaller packages with greater reliability. The reliability of these multilayer film systems is strongly influenced by the adhesion of each of the bimaterial interfaces. During use, microelectronic components undergo thermo-mechanical cycling, which induces interfacial delaminations leading to failure of the overall device. The ability to tailor interfacial properties at the molecular level provides a mechanism to improve thin film adhesion, reliability and performance. This dissertation presents the investigation of molecular level control of interface properties in three thin film-substrate systems: photodefinable polyimide films on passivated silicon substrates, self-assembled monolayers at the interface of Au films and dielectric substrates, and mechanochemically active materials on rigid substrates. For all three materials systems, the effect of interfacial modifications on adhesion is assessed using a laser-spallation technique. Laser-induced stress waves are chosen because they dynamically load the thin film interface in a precise, noncontacting manner at high strain rates and are suitable for both weak and strong interfaces. Photodefinable polyimide films are used as dielectrics in flip chip integrated circuit packages to reduce the stress between silicon passivation layers and mold compound. The influence of processing parameters on adhesion is examined for photodefinable polyimide films on silicon (Si) substrates with three different passivation layers: silicon nitride (SiNx), silicon oxynitride (SiOxNy), and the native silicon oxide (SiO2). Interfacial strength increases when films are processed with an exposure step as well as a longer cure cycle. Additionally, the interfacial fracture energy is assessed using a dynamic delamination protocol. The high toughness of this interface (ca. 100 J/m2) makes it difficult

  8. Sceliphrolactam, a polyene macrocyclic lactam from a wasp-associated Streptomyces sp

    Oh, Dong-Chan; Poulsen, Michael; Currie, Cameron R


    A previously unreported 26-membered polyene macrocyclic lactam, sceliphrolactam, was isolated from an actinomycete, Streptomyces sp., associated with the mud dauber, Sceliphron caementarium. Sceliphrolactam's structure was determined by 1D- and 2D-NMR, MS, UV, and IR spectral analysis. Sceliphrol...

  9. New macrocycles with potent antituberculosis activity accessed by one-pot multicomponent reactions

    Kim, D.; Huang, Y.; Wang, K.; Doemling, A.

    Based on modeling studies, we hypothesized that tylosin derivatives without formyl group should rather adopt an erythromycin-like binding mode to the ribosome. Twenty four 16-membered macrocyclic compounds were accessed by multicomponent reactions (Gewald, Ugi) of tylosin and investigated for their

  10. Haemonchus contortus P-glycoprotein-2: in situ localisation and characterisation of macrocyclic lactone transport.

    Godoy, Pablo; Lian, Jing; Beech, Robin N; Prichard, Roger K


    Haemonchus contortus is a veterinary nematode that infects small ruminants, causing serious decreases in animal production worldwide. Effective control through anthelmintic treatment has been compromised by the development of resistance to these drugs, including the macrocyclic lactones. The mechanisms of resistance in H. contortus have yet to be established but may involve efflux of the macrocyclic lactones by nematode ATP-binding-cassette transporters such as P-glycoproteins. Here we report the expression and functional activity of H. contortus P-glycoprotein 2 expressed in mammalian cells and characterise its interaction with the macrocyclic lactones, ivermectin, abamectin and moxidectin. The ability of H. contortus P-glycoprotein 2 to transport different fluorophore substrates was markedly inhibited by ivermectin and abamectin in a dose-dependent and saturable way. The profile of transport inhibition by moxidectin was markedly different. H. contortus P-glycoprotein 2 was expressed in the pharynx, the first portion of the worm's intestine and perhaps in adjacent nervous tissue, suggesting a role for this gene in regulating the uptake of avermectins and in protecting nematode tissues from the effects of macrocyclic lactone anthelmintic drugs. H. contortus P-glycoprotein 2 may thus contribute to resistance to these drugs in H. contortus.

  11. Synthesis of Tetra-Schiff Base Macrocyclic Compound Containing Benzo-12-crown-4


    Tetra-Schiff base macrocyclic compound containing benzo-12-crown-4 was synthesized via condensation of 2, 6-diformyl-4-methyl-phenol with 4(, 5(- diaminobenzo-12-C- 4 promoted by proton. The compound was characterized by MS, IR 1HNMR spectroscopy and elemental analysis.

  12. New Cleft-like Molecules and Macrocycles from Phosphonate Substituted Spirobisindanol

    Paolo Finocchiaro


    Full Text Available We have synthetized medium-sized cyclophanes and macrocycles containingphosphonic groups, directly linked to the aromatic rings of the phanes or as pendant arms,for use as specific receptors for the selective complexation of neutral guests or forcomplexing lanthanides, as luminescent sensors and for diagnostic bioassays in medicine.Furthermore, because it would be of great interest for biochemistry as well as forpharmacological studies to dispose of preorganized rigid chiral hosts for biorelevantmolecules we designed inter alia, some new chiral macrocycles capable of a triple bindingmode and we used them for constructing macrocycles that could also be of interest forchiral recognition and chiral separations. Thus, in this paper we shall review the salientaspects of some macrocycles synthetized in our laboratory, all possessing the phosphonatemoiety and a spirobisindanol scaffold and able to act as complexing agents for cations andorganic substrates. In particular, we shall describe their NMR characterization, theirstereochemistry in solution and in the solid state, and their use as chiral receptors forbiorelevant molecules. Chiral HPLC resolution of some of them is also reported.

  13. Short and diverse route toward complex natural product-like macrocycles.

    Beck, Barbara; Larbig, Gregor; Mejat, Beatrice; Magnin-Lachaux, Marina; Picard, Anne; Herdtweck, Eberhardt; Dömling, Alexander


    [reaction: see text] A general strategy toward macrocyclic compounds using multicomponent reaction (MCR) chemistry, e.g., Passerini and Ugi variants, and ring-closing metathesis (RCM) is introduced. The corresponding bifunctional isocyanides carboxylic acids bearing a terminal olefin are easy to pre

  14. Structural and Biochemical Basis for Intracellular Kinase Inhibition by Src-specific Peptidic Macrocycles.

    Aleem, Saadat; Georghiou, George; Kleiner, Ralph E; Guja, Kip; Craddock, Barbara P; Lyczek, Agatha; Chan, Alix I; Garcia-Diaz, Miguel; Miller, W Todd; Liu, David R; Seeliger, Markus A


    Protein kinases are attractive therapeutic targets because their dysregulation underlies many diseases, including cancer. The high conservation of the kinase domain and the evolution of drug resistance, however, pose major challenges to the development of specific kinase inhibitors. We recently discovered selective Src kinase inhibitors from a DNA-templated macrocycle library. Here, we reveal the structural basis for how these inhibitors retain activity against a disease-relevant, drug-resistant kinase mutant, while maintaining Src specificity. We find that these macrocycles display a degree of modularity: two of their three variable groups interact with sites on the kinase that confer selectivity, while the third group interacts with the universally conserved catalytic lysine and thereby retains the ability to inhibit the "gatekeeper" kinase mutant. We also show that these macrocycles inhibit migration of MDA-MB-231 breast tumor cells. Our findings establish intracellular kinase inhibition by peptidic macrocycles, and inform the development of potent and specific kinase inhibitors. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. New macrocycles with potent antituberculosis activity accessed by one-pot multicomponent reactions

    Kim, D.; Huang, Y.; Wang, K.; Doemling, A.


    Based on modeling studies, we hypothesized that tylosin derivatives without formyl group should rather adopt an erythromycin-like binding mode to the ribosome. Twenty four 16-membered macrocyclic compounds were accessed by multicomponent reactions (Gewald, Ugi) of tylosin and investigated for their

  16. Macrocyclic Peptoid–Peptide Hybrids as Inhibitors of Class I Histone Deacetylases

    Olsen, Christian Adam; Montero, Ana; Leman, Luke J.;


    We report the design, synthesis, and biological evaluation of the first macrocyclic peptoid-containing histone deacetylase (HDAC) inhibitors. The compounds selectively inhibit human class I HDAC isoforms in vitro, with no inhibition of the tubulin deacetylase activity associated with class IIb HD...

  17. Neurodevelopmental and neuropsychiatric disorders represent an interconnected molecular system.

    Cristino, A S; Williams, S M; Hawi, Z; An, J-Y; Bellgrove, M A; Schwartz, C E; Costa, L da F; Claudianos, C


    Many putative genetic factors that confer risk to neurodevelopmental disorders such as autism spectrum disorders (ASDs) and X-linked intellectual disability (XLID), and to neuropsychiatric disorders including attention deficit hyperactivity disorder (ADHD) and schizophrenia (SZ) have been identified in individuals from diverse human populations. Although there is significant aetiological heterogeneity within and between these conditions, recent data show that genetic factors contribute to their comorbidity. Many studies have identified candidate gene associations for these mental health disorders, albeit this is often done in a piecemeal fashion with little regard to the inherent molecular complexity. Here, we sought to abstract relationships from our knowledge of systems level biology to help understand the unique and common genetic drivers of these conditions. We undertook a global and systematic approach to build and integrate available data in gene networks associated with ASDs, XLID, ADHD and SZ. Complex network concepts and computational methods were used to investigate whether candidate genes associated with these conditions were related through mechanisms of gene regulation, functional protein-protein interactions, transcription factor (TF) and microRNA (miRNA) binding sites. Although our analyses show that genetic variations associated with the four disorders can occur in the same molecular pathways and functional domains, including synaptic transmission, there are patterns of variation that define significant differences between disorders. Of particular interest is DNA variations located in intergenic regions that comprise regulatory sites for TFs or miRNA. Our approach provides a hypothetical framework, which will help discovery and analysis of candidate genes associated with neurodevelopmental and neuropsychiatric disorders.

  18. Reaction Ensemble Monte Carlo Simulation of Complex Molecular Systems.

    Rosch, Thomas W; Maginn, Edward J


    Acceptance rules for reaction ensemble Monte Carlo (RxMC) simulations containing classically modeled atomistic degrees of freedom are derived for complex molecular systems where insertions and deletions are achieved gradually by utilizing the continuous fractional component (CFC) method. A self-consistent manner in which to utilize statistical mechanical data contained in ideal gas free energy parameters during RxMC moves is presented. The method is tested by applying it to two previously studied systems containing intramolecular degrees of freedom: the propene metathesis reaction and methyl-tert-butyl-ether (MTBE) synthesis. Quantitative agreement is found between the current results and those of Keil et al. (J. Chem. Phys. 2005, 122, 164705) for the propene metathesis reaction. Differences are observed between the equilibrium concentrations of the present study and those of Lísal et al. (AIChE J. 2000, 46, 866-875) for the MTBE reaction. It is shown that most of this difference can be attributed to an incorrect formulation of the Monte Carlo acceptance rule. Efficiency gains using CFC MC as opposed to single stage molecule insertions are presented.

  19. Tren centered tris-macrocycles as polytopic ligands for Cu(II) and Ni(II).

    Siegfried, Liselotte; McMahon, C Niamh; Kaden, Thomas A; Palivan, Cornelia; Gescheidt, Georg


    Two novel symmetric polytopic ligands L(1) and L(2) have been synthesized. They are composed of three 1,4,8,11-tetraazacyclotetradecane macrocycles which are connected to a central tren moiety via an ethylene and a trimethylene bridge, respectively. The complexation potential and the speciation diagrams of L(1) and L(2) towards Cu(2+) and Ni(2+) were determined by spectrophotometric and potentiometric titrations. Insight into the geometry of the Cu(2+) complexes is provided by UV-VIS and EPR spectroscopy. The simplified ligands L(3) and L(4) are utilized as references for an aminoethyl- and a tren-substituted tetraaza macrocycle to help assign the EPR spectra of the polytopic ligands L(1) and L(2). At a metal-to-ligand ratio of 3 : 1, the metal cations are preferentially bound to the tetraaza macrocycles of L(1) and L(2) in a square planar geometry. At high pH values, a nitrogen atom of the tren moiety in L(1) serves as an additional ligand in an axial position leading to a square pyramidal coordination around Cu(2+), whereas in L(2) no such geometry change is observed. At a metal-to-ligand ratio of 4 : 1, the additional metal cation resides in the central tren moiety of L(1) and L(2). However, in contrast to the typical trigonal bipyramidal geometry found in the [Cutren](2+) complex, the fourth Cu(2+) has a square pyramidal coordination caused by the interaction with the Cu(2+) cations in the macrocycles (as evidenced by EPR spectra). Since the sequence of metal complexation is such that the first three metal ions always bind to the three macrocycles of L(1) and L(2) and the fourth to the tren unit, it is possible to prepare heteronuclear complexes such as [Cu(3)NiL](8+) or [Ni(3)CuL](8+), which can be unambiguously identified by their spectral properties.

  20. Carbon nanotubes as nanodelivery systems an insight through molecular dynamics simulations

    Lim, Melvin Choon Giap


    This book showcases the application of carbon nanotubes as nanodelivery systems for copper atoms, using molecular dynamics simulations as a means of investigation. The nanodelivery system of the carbon nanotube presents the possible usage of the carbon structure in many areas in the future. This book is comprehensive and informative, and serves as a guide for any reader who wishes to perform a molecular dynamics simulation of his own and to conduct an analytical study of a molecular system.

  1. Design of optimal collimation for dedicated molecular breast imaging systems

    Weinmann, Amanda L.; Hruska, Carrie B.; O' Connor, Michael K. [Department of Radiology, Division of Nuclear Medicine, Mayo Clinic, Rochester, Minnesota 55905 (United States)


    Molecular breast imaging (MBI) is a functional imaging technique that uses specialized small field-of-view gamma cameras to detect the preferential uptake of a radiotracer in breast lesions. MBI has potential to be a useful adjunct method to screening mammography for the detection of occult breast cancer. However, a current limitation of MBI is the high radiation dose (a factor of 7-10 times that of screening mammography) associated with current technology. The purpose of this study was to optimize the gamma camera collimation with the aim of improving sensitivity while retaining adequate resolution for the detection of sub-10-mm lesions. Square-hole collimators with holes matched to the pixilated cadmium zinc telluride detector elements of the MBI system were designed. Data from MBI patient studies and parameters of existing dual-head MBI systems were used to guide the range of desired collimator resolutions, source-to-collimator distances, pixel sizes, and collimator materials that were examined. General equations describing collimator performance for a conventional gamma camera were used in the design process along with several important adjustments to account for the specialized imaging geometry of the MBI system. Both theoretical calculations and a Monte Carlo model were used to measure the geometric efficiency (or sensitivity) and resolution of each designed collimator. Results showed that through optimal collimation, collimator sensitivity could be improved by factors of 1.5-3.2, while maintaining a collimator resolution of either {<=}5 or {<=}7.5 mm at a distance of 3 cm from the collimator face. These gains in collimator sensitivity permit an inversely proportional drop in the required dose to perform MBI.

  2. Theoretical Studies of the Relaxation Matrix for Molecular Systems

    Ma, Qiancheng; Boulet, C.


    The phenomenon of collisional transfer of intensity due to line mixing has an increasing importance for atmospheric monitoring. From a theoretical point of view, all relevant information about the collisional processes is contained in the relaxation matrix where the diagonal elements give half-widths and shifts, and the off-diagonal elements correspond to line interferences. For simple systems such as those consisting of diatom-atom or diatom-diatom, accurate fully quantum calculations based on interaction potentials are feasible. However, fully quantum calculations become unrealistic for more complex systems. On the other hand, the semi-classical Robert-Bonamy formalism, which has been widely used to calculate half-widths and shifts for decades, fails in calculating the off-diagonal matrix elements resulting from applying the isolated line approximation. As a result, in order to simulate atmospheric spectra where the effects from line mixing are important, semi-empirical fitting or scaling laws such as the energy corrected sudden (ECS) and the infinite order sudden (IOS) models are commonly used. Recently, we have found that in developing this semi-classical line shape theory, to rely on the isolated line approximation is not necessary. By eliminating this unjustified assumption, and accurately evaluating matrix elements of the exponential operators, we have developed a more capable formalism that enables one not only to reduce uncertainties for calculated half-widths and shifts, but also to calculate the whole relaxation matrix. This implies that we can address the line mixing with the semi-classical theory based on interaction potentials between molecular absorber and molecular perturber. We have applied this formalism for Raman and infrared spectra of linear and asymmetric-top molecules. Recently, the method has been extended into symmetric-tops with inverse symmetry such as the NH3 molecule. Our calculated half-widths of NH3 lines in the νb{1} and the pure

  3. Spectroscopic Studies of Molecular Systems relevant in Astrobiology

    Fornaro, Teresa


    In the Astrobiology context, the study of the physico-chemical interactions involving "building blocks of life" in plausible prebiotic and space-like conditions is fundamental to shed light on the processes that led to emergence of life on Earth as well as to molecular chemical evolution in space. In this PhD Thesis, such issues have been addressed both experimentally and computationally by employing vibrational spectroscopy, which has shown to be an effective tool to investigate the variety of intermolecular interactions that play a key role in self-assembling mechanisms of nucleic acid components and their binding to mineral surfaces. In particular, in order to dissect the contributions of the different interactions to the overall spectroscopic signals and shed light on the intricate experimental data, feasible computational protocols have been developed for the characterization of the spectroscopic properties of such complex systems. This study has been carried out through a multi-step strategy, starting the investigation from the spectroscopic properties of the isolated nucleobases, then studying the perturbation induced by the interaction with another molecule (molecular dimers), towards condensed phases like the molecular solid, up to the case of nucleic acid components adsorbed on minerals. A proper modeling of these weakly bound molecular systems has required, firstly, a validation of dispersion-corrected Density Functional Theory methods for simulating anharmonic vibrational properties. The isolated nucleobases and some of their dimers have been used as benchmark set for identifying a general, reliable and effective computational procedure based on fully anharmonic quantum mechanical computations of the vibrational wavenumbers and infrared intensities within the generalized second order vibrational perturbation theory (GVPT2) approach, combined with the cost-effective dispersion-corrected density functional B3LYP-D3, in conjunction with basis sets of

  4. Anti-influenza activity of marchantins, macrocyclic bisbibenzyls contained in liverworts.

    Yuma Iwai

    Full Text Available The H1N1 influenza A virus of swine-origin caused pandemics throughout the world in 2009 and the highly pathogenic H5N1 avian influenza virus has also caused epidemics in Southeast Asia in recent years. The threat of influenza A thus remains a serious global health issue and novel drugs that target these viruses are highly desirable. Influenza A possesses an endonuclease within its RNA polymerase which comprises PA, PB1 and PB2 subunits. To identify potential new anti-influenza compounds in our current study, we screened 33 different types of phytochemicals using a PA endonuclease inhibition assay in vitro and an anti-influenza A virus assay. The marchantins are macrocyclic bisbibenzyls found in liverworts, and plagiochin A and perrottetin F are marchantin-related phytochemicals. We found from our screen that marchantin A, B, E, plagiochin A and perrottetin F inhibit influenza PA endonuclease activity in vitro. These compounds have a 3,4-dihydroxyphenethyl group in common, indicating the importance of this moiety for the inhibition of PA endonuclease. Docking simulations of marchantin E with PA endonuclease suggest a putative "fitting and chelating model" as the mechanism underlying PA endonuclease inhibition. The docking amino acids are well conserved between influenza A and B. In a cultured cell system, marchantin E was further found to inhibit the growth of both H3N2 and H1N1 influenza A viruses, and marchantin A, E and perrotein F showed inhibitory properties towards the growth of influenza B. These marchantins also decreased the viral infectivity titer, with marchantin E showing the strongest activity in this assay. We additionally identified a chemical group that is conserved among different anti-influenza chemicals including marchantins, green tea catechins and dihydroxy phenethylphenylphthalimides. Our present results indicate that marchantins are candidate anti-influenza drugs and demonstrate the utility of the PA endonuclease assay in

  5. From 2 + 2 to 8 + 8 Condensation Products of Diamine and Dialdehyde: Giant Container-Shaped Macrocycles for Multiple Anion Binding.

    Gregoliński, Janusz; Ślepokura, Katarzyna; Paćkowski, Tomasz; Panek, Jarosław; Stefanowicz, Piotr; Lisowski, Jerzy


    The combination of 2,6-diformylpyridine and trans-1,2-diaminocyclopentane fragments results in 2 + 2, 3 + 3, 4 + 4, 6 + 6, and 8 + 8 macrocyclic imine condensation products. These imines can be reduced to the corresponding 2 + 2, 3 + 3, 4 + 4, 6 + 6, and 8 + 8 macrocyclic amines. The X-ray crystal structures of their protonated derivatives show a rich variety of macrocycle conformations ranging from a stepped 2 + 2 macrocycle to a multiply folded 8 + 8 macrocycle of globular shape. These compounds bind anions via hydrogen bonds: two chloride anions are bound above and below the macrocyclic ring of the 2 + 2 amine, one chloride anion is bound approximately in the center of the 3 + 3 macrocycle, and two chloride anions are deeply buried inside a folded container-shaped 4 + 4 macrocycle, while in the case of the previously reported 6 + 6 amine four chloride anions and two solvent molecules are buried inside a container-shaped macrocycle. Yet another situation was observed for a multiply folded protonated 8 + 8 macrocycle which binds six sulfate anions; two of them are deeply buried inside the container structure while four anions interact with the clefts at the surface of the container.

  6. The roles of integration in molecular systems biology.

    O'Malley, Maureen A; Soyer, Orkun S


    A common way to think about scientific practice involves classifying it as hypothesis- or data-driven. We argue that although such distinctions might illuminate scientific practice very generally, they are not sufficient to understand the day-to-day dynamics of scientific activity and the development of programmes of research. One aspect of everyday scientific practice that is beginning to gain more attention is integration. This paper outlines what is meant by this term and how it has been discussed from scientific and philosophical points of view. We focus on methodological, data and explanatory integration, and show how they are connected. Then, using some examples from molecular systems biology, we will show how integration works in a range of inquiries to generate surprising insights and even new fields of research. From these examples we try to gain a broader perspective on integration in relation to the contexts of inquiry in which it is implemented. In today's environment of data-intensive large-scale science, integration has become both a practical and normative requirement with corresponding implications for meta-methodological accounts of scientific practice. We conclude with a discussion of why an understanding of integration and its dynamics is useful for philosophy of science and scientific practice in general.

  7. Pancreatic Cancer Gene Therapy: From Molecular Targets to Delivery Systems

    Fillat, Cristina; Jose, Anabel; Ros, Xavier Bofill-De; Mato-Berciano, Ana; Maliandi, Maria Victoria; Sobrevals, Luciano


    The continuous identification of molecular changes deregulating critical pathways in pancreatic tumor cells provides us with a large number of novel candidates to engineer gene-targeted approaches for pancreatic cancer treatment. Targets—both protein coding and non-coding—are being exploited in gene therapy to influence the deregulated pathways to facilitate cytotoxicity, enhance the immune response or sensitize to current treatments. Delivery vehicles based on viral or non-viral systems as well as cellular vectors with tumor homing characteristics are a critical part of the design of gene therapy strategies. The different behavior of tumoral versus non-tumoral cells inspires vector engineering with the generation of tumor selective products that can prevent potential toxic-associated effects. In the current review, a detailed analysis of the different targets, the delivery vectors, the preclinical approaches and a descriptive update on the conducted clinical trials are presented. Moreover, future possibilities in pancreatic cancer treatment by gene therapy strategies are discussed. PMID:24212620

  8. Inducibility of a molecular bioreporter system by heavy metals

    Klimowski, L.; Rayms-Keller, A.; Olson, K.E.; Yang, R.S.H.; Tessari, J.; Carlson, J.; Beaty, B. [Colorado State Univ., Fort Collins, CO (United States)


    The authors have developed a molecular bioreporter model for detecting an invertebrate response to heavy metals in streams. The bioreporter system, pMt2-luc, utilizes a Drosophila melanogaster metallothionein promoter to regulate luciferase expression in stably transformed mosquito cells.The LucC5 clone, which was isolated from pMt2-luc transformed, hygromycin-resistant C6/36 (Aedes albopictus) cells, demonstrated a 12-fold increase in luciferase-specific activity 48 h after exposure to 13 ppm copper (Cu). In addition to Cu, exposure of LucC5 cells to 19 ppm lead (Pb) or 3 ppm mercury (Hg) for 48 h induced luciferase expression threefold and fourfold, respectively. Exposures of up to 30 ppm arsenic (As), 8 ppm cadmium (Cd), 7 ppm chromium (Cr), or 5 ppm nickel (Ni) had no effect on luciferase induction. LucC5 cells exposed to metal mixtures of 13 ppm Cu and 19 ppm Pb yielded an additive response with a 14-fold increase in luciferase expression. When organic chemicals such as phenol (3 ppm) were mixed with 13 ppm Cu, 19 ppm Pb, or 3 ppm Hg a significant reduction in luciferase activity was noted. Additionally, atomic absorption spectroscopy suggested that two of the metals, Cu and Pb, show marked differences in accumulation within the LucC5 cell line.

  9. Development of a Molecular System for Studying Microbial Arsenate Respiration

    Saltikov, C. W.; Newman, D. K.


    The toxic element arsenic is a major contaminant of many groundwaters and surface waters throughout the world. Arsenic enrichment is primarily of geological origin resulting from weathering processes and geothermal activity. Not surprisingly, microorganisms inhabiting anoxic arsenic-contaminated environments have evolved to exploit arsenate during respiration. Numerous bacteria have been isolated that use arsenate as a terminal electron acceptor for respiratory growth. The diversity of this metabolism appears to be widespread throughout the microbial tree of life, suggesting respiratory arsenate reduction is ancient in origin. Yet little is known about the molecular mechanisms for how these organisms respire arsenate. We have developed a model system in Shewanella trabarsenatis, strain ANA-3, a facultative anaerobe that respires arsenate and tolerates high concentrations of arsenite (10 mM). Through loss-of-function studies, we have identified genes involved in both arsenic resistance and arsenate respiration. The genes that confer resistance to arsenic are homologous to the well-characterized ars operon of E. coli. However, the respiratory arsenate reductase is predicted to encode a novel protein that shares homologous regions (~ 40 % similarity) to molybdopterin anaerobic reductases specific for DMSO, thiosulfate, nitrate, and polysulfide. I will discuss our emerging model for how strain ANA-3 respires arsenate and the relationship between arsenite resistance and arsenate respiration. I will also highlight the relevance of this type of analysis for biogeochemical studies.

  10. Plant systems for recognition of pathogen-associated molecular patterns.

    Postel, Sandra; Kemmerling, Birgit


    Research of the last decade has revealed that plant immunity consists of different layers of defense that have evolved by the co-evolutional battle of plants with its pathogens. Particular light has been shed on PAMP- (pathogen-associated molecular pattern) triggered immunity (PTI) mediated by pattern recognition receptors. Striking similarities exist between the plant and animal innate immune system that point for a common optimized mechanism that has evolved independently in both kingdoms. Pattern recognition receptors (PRRs) from both kingdoms consist of leucine-rich repeat receptor complexes that allow recognition of invading pathogens at the cell surface. In plants, PRRs like FLS2 and EFR are controlled by a co-receptor SERK3/BAK1, also a leucine-rich repeat receptor that dimerizes with the PRRs to support their function. Pathogens can inject effector proteins into the plant cells to suppress the immune responses initiated after perception of PAMPs by PRRs via inhibition or degradation of the receptors. Plants have acquired the ability to recognize the presence of some of these effector proteins which leads to a quick and hypersensitive response to arrest and terminate pathogen growth.

  11. Pancreatic Cancer Gene Therapy: From Molecular Targets to Delivery Systems

    Maria Victoria Maliandi


    Full Text Available The continuous identification of molecular changes deregulating critical pathways in pancreatic tumor cells provides us with a large number of novel candidates to engineer gene-targeted approaches for pancreatic cancer treatment. Targets—both protein coding and non-coding—are being exploited in gene therapy to influence the deregulated pathways to facilitate cytotoxicity, enhance the immune response or sensitize to current treatments. Delivery vehicles based on viral or non-viral systems as well as cellular vectors with tumor homing characteristics are a critical part of the design of gene therapy strategies. The different behavior of tumoral versus non-tumoral cells inspires vector engineering with the generation of tumor selective products that can prevent potential toxic-associated effects. In the current review, a detailed analysis of the different targets, the delivery vectors, the preclinical approaches and a descriptive update on the conducted clinical trials are presented. Moreover, future possibilities in pancreatic cancer treatment by gene therapy strategies are discussed.

  12. Ring-closing metathesis for the synthesis of a highly G-quadruplex selective macrocyclic hexaoxazole having enhanced cytotoxic potency.

    Satyanarayana, Mavurapu; Rzuczek, Suzanne G; Lavoie, Edmond J; Pilch, Daniel S; Liu, Angela; Liu, Leroy F; Rice, Joseph E


    The synthesis of a 24-membered macrocyclic hexaoxazole via ring-closing metathesis is described. The target compound selectively stabilizes G-quadruplex DNA with no detectable stabilization of duplex DNA. An MTT cytotoxicity assay indicated that this unsaturated macrocyclic hexaoxazole exhibits significant cytotoxicity toward P388, RPMI 8402, and KB3-1 cell lines with IC50 values of 45, 25, and 38 nM, respectively.

  13. Molecular photoionization studies of nucleobases and correlated systems

    Poliakoff, Erwin D. [Louisiana State Univ., Baton Rouge, LA (United States)


    We proposed molecular photoionization studies in order to probe correlated events in fundamental scattering phenomena. In particular, we suggested that joint theoretical-experimental studies would provide a window into the microscopic aspects that are of central importance in AMO and chemical physics generally, and would generate useful data for wide array of important DOE topics, such as ultrafast dynamics, high harmonic generation, and probes of nonadiabatic processes. The unifying theme is that correlations between electron scattering dynamics and molecular geometry highlight inherently molecular aspects of the photoelectron behavior.

  14. Modern spectroscopic technique in the characterization of biosensitive macrocyclic Schiff base ligand and its complexes: Inhibitory activity against plantpathogenic fungi

    Tyagi, Monika; Chandra, Sulekh; Akhtar, Jameel; Chand, Dinesh


    Complexes of the type [M(L)Cl2], where M = Co(II), Ni(II) and Cu(II) have been synthesized with a macrocyclic Schiff base ligand (1,4,5,7,10,11,12,15-octaaza,5,11,16,18-tetraphenyl, 3,4,12,13-tetramethyl cyclo-octadecane) derived from Schiff base (obtained by the condensation of 4-aminoantipyrine and dibenzoyl methane) and ethylenediamine. The ligand was characterized on the basis of elemental analysis, IR, 1H NMR, EI Mass and molecular modeling studies while the complexes were characterized by elemental analysis, molar conductance measurements, magnetic susceptibility measurements, IR, electronic and EPR spectral studies. All the complexes are non-electrolyte in nature. The covalency factor (β) and coefficient factor (α) suggest the covalent nature of the complexes. The ligand and its metal complexes have shown antifungal activity with their LD50 values determined by probit analysis against two economically important fungal plant pathogens i.e. Macrophomina phaseolina and Fusarium solani.

  15. The addition of a second lanthanide ion to increase the luminescence of europium(III) macrocyclic complexes

    Bromm, A.J. Jr.; Vallarino, L.M. [Virginia Commonwealth Univ., Richmond, VA (United States). Dept. of Chemistry; Leif, R.C. [Newport Instruments, San Diego, CA (United States); Quagliano, J.R. [Los Alamos National Lab., NM (United States)


    At present, the microscopic visualization of luminescent labels containing lanthanide(III) ions, primarily europium(III), as light-emitting centers is best performed with time-gated instrumentation, which by virtually eliminating the background fluorescence results in an improved signal to noise ratio. However, the use of the europium(III) macrocycle, Quantum Dye{trademark}, in conjunction with the strong luminescence enhancing effect (cofluorescence) of yttrium(III) or gadolinium(III), can eliminate the need for such specialized instrumentation. In the presence of Gd(III), the luminescence of the Eu(III)-macrocycles can be conveniently observed with conventional fluorescence instrumentation at previously unattainable low levels. The Eu(III) {sup 5}D{sub 0} {r_arrow} {sup 7}F{sub 2} emission of the Eu(III)-macrocycles was observed as an extremely sharp band with a maximum at 619 nm and a clearly resolved characteristic pattern. At very low Eu(III)-macrocycle concentrations, another sharp emission was detected at 614 nm, arising from traces of Eu(III) present in even the purest commercially available gadolinium products. Discrimination of the resolved emissions of the Eu(III)-macrocycle and Eu(III) contaminant should provide a means to further lower the limit of detection of the Eu(III)-macrocycle.

  16. Experimental and theoretical study for corrosion inhibition of mild steel in normal hydrochloric acid solution by some new macrocyclic polyether compounds

    Lebrini, M. [Unite de Catalyse et de Chimie du Solide, CNRS UMR 8181, ENSCL, BP 90108, F-59652 Villeneuve d' Ascq Cedex (France); Lagrenee, M. [Unite de Catalyse et de Chimie du Solide, CNRS UMR 8181, ENSCL, BP 90108, F-59652 Villeneuve d' Ascq Cedex (France); Vezin, H. [Laboratoire de Chimie Organique et Macromoleculaire, CNRS UMR 8009, USTL Bat C4, F-59655 Villeneuve d' Ascq Cedex (France); Traisnel, M. [Laboratoire des Procedes d' Elaboration des Revetements Fonctionnels, PERF UMR 8008, ENSCL, BP 90108, F-59652 Villeneuve d' Ascq Cedex (France); Bentiss, F. [Laboratoire de Chimie de Coordination et d' Analytique, Faculte des Sciences, Universite Chouaib Doukkali, BP 20, M-24000 El Jadida (Morocco)]. E-mail:


    New macrocyclic polyether compounds containing a 1,3,4-thiadiazole moiety have been prepared to study the corrosion inhibitive effect of mild steel in normal hydrochloric acid solutions. The salient features obtained from weight loss and electrochemical impedance spectroscopy (EIS) have been discussed. The results of these investigations have shown enhancement in inhibition efficiencies with the extent of the polyethylene glycol unit that forms a cavity. Data obtained from EIS show a frequency distribution and therefore a modelling element with frequency dispersion behaviour, a constant phase element (CPE) has been used. Display Omitted Adsorption of n-MCTH was found to follow the Langmuir's adsorption isotherm. The thermodynamic functions of adsorption process were calculated from experimental ac impedance data and the interpretation of the results are given. Molecular modelling has been conducted in an attempt to correlate the corrosion inhibition properties with the calculated quantum chemical parameters.

  17. Planning and periodization in swimming: An example of a macrocycle for an adapted swimming group

    A. Querido


    Full Text Available The planning of the training process in is commonly recognized as a fundamental aspect for the correct and harmonious development of the capacities and to improve sports results. The aim of this paper was to present an example of a macrocyle of training in a group of adapted swimmers. The group includes 5 swimmers, being 4 male and 1 female: three swimmers with Down syndrome, one swimmer with intellectual disability and one swimmer with autism. The macrocycle of training was subdivided in 23 weeks: 15 belonging to the General Preparation Period, 4 to the Specific Preparation Period, 2 to the Competitive Period, culminating with the Winter National Championships, and 2 to the Transition Period trying. At the Winter National Championships, the most important competition of this macrocycle, these swimmers obtained 7 national titles, 4 national vice-champions titles and 2 third places. These results gave the swimmers an important incentive to keep up the good work.

  18. Planning and periodization in swimming: An example of a macrocycle for an adapted swimming group

    A. Querido


    Full Text Available The planning of the training process in is commonly recognized as a fundamental aspect for the correct and harmonious development of the capacities and to improve sports results. The aim of this paper was to present an example of a macrocyle of training in a group of adapted swimmers. The group includes 5 swimmers, being 4 male and 1 female: three swimmers with Down syndrome, one swimmer with intellectual disability and one swimmer with autism. The macrocycle of training was subdivided in 23 weeks: 15 belonging to the General Preparation Period, 4 to the Specific Preparation Period, 2 to the Competitive Period, culminating with the Winter National Championships, and 2 to the Transition Period trying. At the Winter National Championships, the most important competition of this macrocycle, these swimmers obtained 7 national titles, 4 national vice-champions titles and 2 third places. These results gave the swimmers an important incentive to keep up the good work.

  19. Uranyl-selective PVC membrane electrodes based on some recently synthesized benzo-substituted macrocyclic diamides.

    Shamsipur, Mojtaba; Soleymanpour, Ahmad; Akhond, Morteza; Sharghi, Hashem; Massah, Ahmad Reza


    Four different recently synthesized macrocyclic diamides were studied to characterize their abilities as uranyl ion carriers in PVC membrane electrodes. The electrodes based on macrocycle 1,18-diaza-3,4;15,16-dibenzo-5,8,11,14,21,24-hexaoxacyclohexaeicosane-2,17-dione resulted in a Nernstian response for UO(2)(2+) ion over wide concentration ranges. The linear concentration range for the polymeric membrane electrode (PME) is 3.0x10(-6)-8.2x10(-3) M with a detection limit of 2.2x10(-6) and that for the coated graphite electrode (CGE) is 5.0x10(-7)-1.5x10(-3) M with a detection limit of 3.5x10(-7) M. The electrodes manifest advantages of low resistance, very fast response and, most importantly, good selectivities relative to a wide variety of other cations.

  20. Synthesis and anion recognition properties of shape-persistent binaphthyl-containing chiral macrocyclic amides

    Marco Caricato


    Full Text Available We report on the synthesis and characterization of novel shape-persistent, optically active arylamide macrocycles, which can be obtained using a one-pot methodology. Resolved, axially chiral binol scaffolds, which incorporate either methoxy or acetoxy functionalities in the 2,2' positions and carboxylic functionalities in the external 3,3' positions, were used as the source of chirality. Two of these binaphthyls are joined through amidation reactions using rigid diaryl amines of differing shapes, to give homochiral tetraamidic macrocycles. The recognition properties of these supramolecular receptors have been analyzed, and the results indicate a modulation of binding affinities towards dicarboxylate anions, with a drastic change of binding mode depending on the steric and electronic features of the functional groups in the 2,2' positions.

  1. STM visualisation of counterions and the effect of charges on self-assembled monolayers of macrocycles.

    Kudernac, Tibor; Shabelina, Natalia; Mamdouh, Wael; Höger, Sigurd; De Feyter, Steven


    Despite their importance in self-assembly processes, the influence of charged counterions on the geometry of self-assembled organic monolayers and their direct localisation within the monolayers has been given little attention. Recently, various examples of self-assembled monolayers composed of charged molecules on surfaces have been reported, but no effort has been made to prove the presence of counterions within the monolayer. Here we show that visualisation and exact localisation of counterions within self-assembled monolayers can be achieved with scanning tunnelling microscopy (STM). The presence of charges on the studied shape-persistent macrocycles is shown to have a profound effect on the self-assembly process at the liquid-solid interface. Furthermore, preferential adsorption was observed for the uncharged analogue of the macrocycle on a surface.

  2. A Novel Cobalt(Ⅲ) Complex with Macrocyclic Triamine Ligand for High Capacity Hydrogen Adsorption

    ZHU Hai-Yan; GUO Hui; LI Sai


    The coordination complex of Co(Ⅲ) based on a macrocyclic triamine ligand 1,4-diacetate-1,4,7-triazacyclodecane (L) has been synthesized and characterized. The metal cation is bonded with three nitrogen atoms and two oxygen atoms of L and one chloride ion to form a distorted octahedral geometry. This complex coordinated with macrocyclic ligand possesses large pore volume that will be contributed to observe high H2 adsorption. With respect to the first-principles electronic structure calculations, the feasibility to store hydrogen in the complex is explored. Indeed, the complex has shown a very high total H2 adsorption of 7.2 wt% (wt% = (weight of adsorbed H2)/(weight of host material)), with a binding energy of 0.03 eV/H2

  3. mRNA display: from basic principles to macrocycle drug discovery.

    Josephson, Kristopher; Ricardo, Alonso; Szostak, Jack W


    We describe a new discovery technology that uses mRNA-display to rapidly synthesize and screen macrocyclic peptide libraries to explore a valuable region of chemical space typified by natural products. This technology allows high-affinity peptidic macrocycles containing modified backbones and unnatural side chains to be readily selected based on target binding. Success stories covering the first examples of these libraries suggest that they could be used for the discovery of intracellular protein-protein interaction inhibitors, highly selective enzyme inhibitors or synthetic replacements for monoclonal antibodies. The review concludes with a look to the future regarding how this technology might be improved with respect to library design for cell permeability and bioavailability.

  4. Biodegradable polyester-based eco-composites containing hemp fibers modified with macrocyclic oligomers

    Conzatti, Lucia; Utzeri, Roberto; Hodge, Philip; Stagnaro, Paola


    An original compatibilizing pathway for hemp fibers/poly(1,4-butylene adipate-co-terephtalate) (PBAT) eco-composites was explored exploiting the capability of macrocyclic oligomers (MCOs), obtained by cyclodepolymerization (CDP) of PBAT at high dilution, of being re-converted into linear chains by entropically-driven ring-opening polymerization (ED-ROP) that occurs simply heating the MCOS in the bulk. CDP reaction of PBAT was carried out varying solvent, catalyst and reaction time. Selected MCOs were used to adjust the conditions of the ED-ROP reaction. The best experimental conditions were then adopted to modify hemp fibers. Eco-composites based on PBAT and hemp fibers as obtained or modified with PBAT macrocyclics or oligomers were prepared by different process strategies. The best fiber-PBAT compatibility was observed when the fibers were modified with PBAT oligomers before incorporation in the polyester matrix.

  5. Template synthesis of macrocyclic complexes and their spectroscopic and antibacterial studies.

    Singh, D P; Grover, Vidhi; Kumar, Ramesh; Jain, Kiran


    A new series of macrocyclic complexes of type [M(TML)X]X(2), where M = Cr(III), Fe(III), TML is tetradentate macrocyclic ligand, and X = Cl(-), NO(3)(-), CH(3)COO(-), have been synthesized by condensation of isatin and ethylenediamine in the presence of metal salt. The complexes were synthesized by both conventional and microwave methods. The complexes have been characterized with the help of elemental analysis, conductance measurement, magnetic measurement, and infrared, far infrared, and electronic spectral studies. Molar conductance values indicate them to be 1:2 electrolytes. Electronic spectra along with magnetic moments suggest five-coordinate square pyramidal geometry for these complexes. The complexes were also tested for their in vitro antibacterial activity. Some of the complexes showed satisfactory antibacterial activitiy.

  6. Induction of a type I interferon signature in normal human monocytes by gadolinium-based contrast agents: comparison of linear and macrocyclic agents.

    Wermuth, P J; Jimenez, S A


    The gadolinium-based contrast agent (GdBCA) Omniscan activates human macrophages through Toll-like receptor (TLR)-4 and TLR-7 signalling. To explore the mechanisms responsible we compared the ability of linear and macrocyclic GdBCA to induce a type I interferon signature and a proinflammatory/profibrotic phenotype in normal human monocytes in vitro. Expression of genes associated with type I interferon signalling and inflammation and production of their corresponding proteins were determined. Both linear and macrocyclic GdBCA stimulated expression of multiple type I interferon-regulated genes and the expression of numerous chemokines, cytokines and growth factors in normal human peripheral blood monocytes. There was no correlation between the magnitude of the measured response and the Gd chelate used. To explore the mechanisms responsible for GdBCA induction of fibrosis in nephrogenic systemic fibrosis (NSF) in vitro, normal human dermal fibroblasts were incubated with GdBCA-treated monocyte culture supernatants and the effects on profibrotic gene expression were examined. Supernatants from monocytes exposed to all GdBCA stimulated types I and III collagen, fibronectin and α-smooth muscle actin (α-SMA) expression in normal dermal fibroblasts. The results indicate that the monocyte activation induced by GdBCA may be the initial step in the development of GdBCA associated fibrosis in NSF.

  7. Environmental Molecular Sciences Laboratory Operations System: Version 4.0 - system requirements specification

    Kashporenko, D.


    This document is intended to provide an operations standard for the Environmental Molecular Sciences Laboratory OPerations System (EMSL OPS). It is directed toward three primary audiences: (1) Environmental Molecular Sciences Laboratory (EMSL) facility and operations personnel; (2) laboratory line managers and staff; and (3) researchers, equipment operators, and laboratory users. It is also a statement of system requirements for software developers of EMSL OPS. The need for a finely tuned, superior research environment as provided by the US Department of Energy`s (DOE) Environmental Molecular Sciences Laboratory has never been greater. The abrupt end of the Cold War and the realignment of national priorities caused major US and competing overseas laboratories to reposition themselves in a highly competitive research marketplace. For a new laboratory such as the EMSL, this means coming into existence in a rapidly changing external environment. For any major laboratory, these changes create funding uncertainties and increasing global competition along with concomitant demands for higher standards of research product quality and innovation. While more laboratories are chasing fewer funding dollars, research ideas and proposals, especially for molecular-level research in the materials and biological sciences, are burgeoning. In such an economically constrained atmosphere, reduced costs, improved productivity, and strategic research project portfolio building become essential to establish and maintain any distinct competitive advantage. For EMSL, this environment and these demands require clear operational objectives, specific goals, and a well-crafted strategy. Specific goals will evolve and change with the evolution of the nature and definition of DOE`s environmental research needs. Hence, EMSL OPS is designed to facilitate migration of these changes with ease into every pertinent job function, creating a facile {open_quotes}learning organization.{close_quotes}

  8. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

    De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda


    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

  9. Variational path integral molecular dynamics and hybrid Monte Carlo algorithms using a fourth order propagator with applications to molecular systems

    Kamibayashi, Yuki; Miura, Shinichi


    In the present study, variational path integral molecular dynamics and associated hybrid Monte Carlo (HMC) methods have been developed on the basis of a fourth order approximation of a density operator. To reveal various parameter dependence of physical quantities, we analytically solve one dimensional harmonic oscillators by the variational path integral; as a byproduct, we obtain the analytical expression of the discretized density matrix using the fourth order approximation for the oscillators. Then, we apply our methods to realistic systems like a water molecule and a para-hydrogen cluster. In the HMC, we adopt two level description to avoid the time consuming Hessian evaluation. For the systems examined in this paper, the HMC method is found to be about three times more efficient than the molecular dynamics method if appropriate HMC parameters are adopted; the advantage of the HMC method is suggested to be more evident for systems described by many body interaction.

  10. Special physical preparation of skilled wrestlers during a macrocycle in the conditions of higher educational establishment.

    Ogar' G.O.


    Full Text Available It is developed and experimentally grounded efficiency and methods of improvement of the special physical preparedness of skilled fighters. It is certain that a method parts on a few stages of preparation of training macrocycle and optimized for sportsmen which parallel study in higher educational establishment. It is set that the educational training process of skilled fighters must take into account the specific of organization of educational process of educational establishment and answer the calendar of competitions on a CY.

  11. Lead Diversification through a Prins-Driven Macrocyclization Strategy: Application to C13-Diversified Bryostatin Analogues.

    Wender, Paul A; Billingsley, Kelvin L


    The design, synthesis, and biological evaluation of a novel class of C13-diversified bryostatin analogues are described. An innovative and general strategy based on a Prins macrocyclization-nucleophilic trapping cascade was used to achieve late-stage diversification. In vitro analysis of selected library members revealed that modification at the C13 position of the bryostatin scaffold can be used as a diversification handle to regulate biological activity.

  12. Ligand and Metalloligand Design for Macrocycles, Multimetallic Arrays, Coordination Polymers and Assemblies

    E. C. Constable; Housecroft, C. E.


    This overview of ligand design focuses on three areas: (i) principles of ligand binding, the formation of complexes, and popular strategies for ligand synthesis; (ii) ligand design in macrocyclic complexes, coordination polymers and networks and metallopolygons, and assembly strategies based upon the use of metalloligand building blocks; (iii) ligand design for the extraction and transport of metals. This area of coordination chemistry is too large to permit a comprehensive survey in the spac...

  13. Syntheses of Macrocyclic Amides from L-Amino Acid Esters by RCM


    A series of succinate-derived macrocyclic amides( 1 ) was synthesized via ring-closing metathesis (RCM) as the key step. The substrate included 12 to 15 members. The metathesis precursors were obtained from the amide coupling of tert-butyl 3-carboxyhex-5-enoate(2) with numerous side-chain alkenylated amino acid esters of general type(3)derived from L-lysine and L-ornithine.

  14. Macrocyclic hexaoxazoles: Influence of aminoalkyl substituents on RNA and DNA G-quadruplex stabilization and cytotoxicity.

    Satyanarayana, Mavurapu; Kim, Young-Ah; Rzuczek, Suzanne G; Pilch, Daniel S; Liu, Angela A; Liu, Leroy F; Rice, Joseph E; LaVoie, Edmond J


    A series of 24-membered macrocyclic hexaoxazoles containing one or two aminoalkyl substituents was synthesized and evaluated for cytotoxicity and for their ability to selectively stabilize G-quadruplex DNA and RNA. The most cytotoxic analog 4a, with IC(50) values of 25 and 130 nM using KB3-1 and RPMI 8402 cells, is efficacious in vivo in athymic nude mice with a human tumor xenograft from the breast cancer cell line MDA-MB-435.

  15. Synthesis, spectral and extended spectrum beta-lactamase studies of transition metal tetraaza macrocyclic complexes.

    Kumar, Dinesh; Sharma, Nutan; Nair, Manjula


    Urinary tract infections commonly occur in humans due to microbial pathogens invading the urinary tract, which can bring about a range of clinical symptoms and potentially fatal sequelae. The present study is aimed at addressing the development of a new antimicrobial agent against extended spectrum beta lactamase (ESBL) producing E. coli bacteria. We have synthesised some biologically potent (NNNN) donor macrocycles (L 1  = dibenzo[f,n]dipyrido[3,4-b:4',3'-j][1,4,9,12]tetraazacyclohexadecine-6,11,18,23(5H,12H, 7H, 24H)-tetraone, and L 2  = 6,12,19,25-tetraoxo-4,6,11,12,16,18,23,24-octahydrotetrabenzo [b,g,k,p][1,5,10,14]tetra azacyclooctadecine-2,13-dicarboxylic acid) and their Ti and Zr metal complexes in alcoholic media using microwave protocol. Macrocyclic ligands were synthesised by incorporating of 3,5-diaminobenzoic acid, phthalic acid and 3,4-diaminopyridine in 1:1:1 molar ratio. The macrocyclic ligands and their metal complexes have been characterised by elemental analysis, conductance measurement, magnetic measurement and their structure configurations have been determined by various spectroscopic (FTIR, (1)H/(13)C NMR, UV-Vis, LC-MS mass, XRD and TGA) techniques. [ZrL2Cl2]Cl2 metal complex shows excellent antibacterial activity against ESBLs. A zone of inhibition and minimum inhibitory concentration was determined by McFarland and the dilution method, respectively. The spectral studies confirm the binding sites of the nitrogen atom of the macrocycles. An octahedral geometry has been assigned to the metal complexes based on the findings.

  16. Phthalocyanine-nanocarbon ensembles: From discrete molecular and supramolecular systems to hybrid nanomaterials

    Bottari, Giovanni; De La Torre, Gema; Torres, Tomas


    This document is the Accepted Manuscript version of a Published Work that appeared in final form in Accounts of Chemical Research, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see Conspectus Phthalocyanines (Pcs) are macrocyclic and aromatic compounds that present unique electronic features such as high molar absorption coefficients, rich redox chemistry, and...

  17. Alternating 2,6-/3,5-substituted pyridine-acetylene macrocycles: π-stacking self-assemblies enhanced by intermolecular dipole-dipole interaction.

    Abe, Hajime; Ohtani, Kohei; Suzuki, Daiki; Chida, Yusuke; Shimada, Yuta; Matsumoto, Shinya; Inouye, Masahiko


    Macrocyclic compounds consisting of three 2,6-pyridylene and three 3,5-pyridylene units linked by acetylene bonds were synthesized by a Sonogashira reaction. The X-ray structures showed π-stacked pairs of two macrocycles, in which a 2,6-pyridylene unit of the one molecule overlaps a 3,5-pyridylene of the other molecule because of dipole-dipole interaction. Atomic force microscope (AFM) measurements revealed fibril structures indicating the stacking of the rigid planar macrocycles. Hydrogen-bonding ability of the macrocyclic inside was demonstrated by the addition of octyl β-D-glucopyranoside.

  18. Transport diffusion in one dimensional molecular systems: Power law and validity of Fick's law

    Xu, Zhi-cheng; Zheng, Dong-qin; Ai, Bao-quan; Hu, Bambi; Zhong, Wei-rong


    The transport diffusion in one-dimensional molecular systems is investigated through non-equilibrium molecular dynamics and Monte Carlo methods. We have proposed the power law relationship of the transport diffusion coefficient with the temperature, the mass and the transport length, D* ∝ T*m*-1L*β, where β equals to 0.8 for small systems and zero for large systems. It is found that Fick's law is valid in long transport length but invalid in short transport length. Our results can provide a new perspective for understanding the microscopic mechanism of the molecular transport phenomena in low-dimensional systems.

  19. Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases

    Yu, Hao; Dranchak, Patricia; Li, Zhiru; MacArthur, Ryan; Munson, Matthew S.; Mehzabeen, Nurjahan; Baird, Nathan J.; Battalie, Kevin P.; Ross, David; Lovell, Scott; Carlow, Clotilde K.S.; Suga, Hiroaki; Inglese, James (U of Tokyo); (NEB); (Kansas); (NIH); (NIST); (HHMI)


    Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >1012 members. Functional analysis of the ligands, named ipglycermides, demonstrates sub-nanomolar inhibition of iPGM with complete selectivity over dPGM. The crystal structure of an iPGM macrocyclic peptide complex illuminated an allosteric, locked-open inhibition mechanism placing the cyclic peptide at the bi-domain interface. This binding mode aligns the pendant lariat cysteine thiolate for coordination with the iPGM transition metal ion cluster. The extended charged, hydrophilic binding surface interaction rationalizes the persistent challenges these enzymes have presented to small-molecule screening efforts highlighting the important roles of macrocyclic peptides in expanding chemical diversity for ligand discovery.

  20. History of avermectin and ivermectin, with notes on the history of other macrocyclic lactone antiparasitic agents.

    Campbell, William C


    The macrocyclic lactones enjoy a position of prominence in the control of parasites, and their history may be of interest, and even of use, in an age in which the search for chemotherapeutic agents has been transformed by modern technology. Much of their history has been recorded piecemeal in a wide variety of publications. The present review provides additional detail, and offers a personal perspective on the history of ivermectin and related avermectins. Brief notes are included on the subsequent development of other macrocyclic lactones. Milbemycin preceded the avermectins as a macrocyclic lactone of agricultural importance, but was used for a different purpose. Development of the avermectins arose from the isolation, in the laboratories of the Kitasato Institute, of a novel soil-dwelling bacterium and its transmittal (in 1974) to the laboratories of Merck & Co., Inc. There it was found (in 1975) to produce a potent anthelmintic substance, which was then identified and transmuted by interdisciplinary research into an antiparasitic product. Initially the focus was on its applicability to veterinary science and animal husbandry; and after developmental research by many scientific teams, the product was introduced commercially (in 1981) for the control of endoparasitic nematodes and ectoparasitic arthropods in livestock. Subsequently, special applications in human medicine were developed, and were successfully implemented in partnership with World Health Organization and several non-governmental organizations (NGOs).

  1. Increasing AIP Macrocycle Size Reveals Key Features of agr Activation in Staphylococcus aureus.

    Johnson, Jeffrey G; Wang, Boyuan; Debelouchina, Galia T; Novick, Richard P; Muir, Tom W


    The agr locus in the commensal human pathogen, Staphylococcus aureus, is a two-promoter regulon with allelic variability that produces a quorum-sensing circuit involved in regulating virulence within the bacterium. Secretion of unique autoinducing peptides (AIPs) and detection of their concentrations by AgrC, a transmembrane receptor histidine kinase, coordinates local bacterial population density with global changes in gene expression. The finding that staphylococcal virulence can be inhibited through antagonism of this quorum-sensing pathway has fueled tremendous interest in understanding the structure-activity relationships underlying the AIP-AgrC interaction. The defining structural feature of the AIP is a 16-membered, thiolactone-containing macrocycle. Surprisingly, the importance of ring size on agr activation or inhibition has not been explored. In this study, we address this deficiency through the synthesis and functional analysis of AIP analogues featuring enlarged and reduced macrocycles. Notably, this study is the first to interrogate AIP function by using both established cell-based reporter gene assays and newly developed in vitro AgrC-I binding and autophosphorylation activity assays. Based on our data, we present a model for robust agr activation involving a cooperative, three-points-of-contact interaction between the AIP macrocycle and AgrC.

  2. Dethreading of Tetraalkylsuccinamide-Based [2]Rotaxanes for Preparing Benzylic Amide Macrocycles.

    Martinez-Cuezva, Alberto; Rodrigues, Leticia V; Navarro, Cristian; Carro-Guillen, Fernando; Buriol, Lilian; Frizzo, Clarissa P; Martins, Marcos A P; Alajarin, Mateo; Berna, Jose


    The dethreading of a series of succinamide-based [2]rotaxanes bearing benzylic amide macrocycles is reported herein. These transformations proceeded quantitatively either under flash vacuum pyrolysis, conventional heating, or microwave irradiation. Studying the size complementarity of the stoppers at the ends of the thread and the cavity of the macrocycle allowed us to set up the best substituents for implementing the extrusion of the thread from the interlocked precursors. A variety of (1)H NMR kinetic experiments were carried out in order to evaluate the rate constants of the dethreading process, the half-life times of the rotaxanes, and the influence of temperature and solvents on these processes. The use of dibutylamino groups as stoppers yielded the rotaxane precursor in a reasonable yield and allowed the quantitative deslipping of the rotaxane. The overall process, including the rotaxane formation and its further dethreading, has been exploited for preparing benzylic amide macrocycles enhancing, in most cases, the results of the classical (2 + 2) condensation and other reported stepwise syntheses. The kinetics of the dethreading process is fairly sensitive to the electronic effects of the substituents on the isophthalamide unit or to the electronic nature of the pyridine rings through a conformational equilibrium expanding or contracting the cavity of the interlocked precursor.

  3. Preface - From molecules to molecular materials, biological molecular systems and nanostructures: A collection of contributions presented at the XIIIth International Conference on Molecular Spectroscopy

    Ratajczak, Henryk; Drozd, Marek; Fausto, Rui


    This volume contains a series of selected contributions presented at the XIIIth International Conference on Molecular Spectroscopy (ICMS): "From Molecules to Molecular Materials, Biological Molecular Systems and Nanostructures" held in Wrocław, Poland, 9-12 September 2015, under the auspices of the Mayor of Wrocław and the European Academy of Sciences, Arts and Humanities. Wrocław was chosen not accidentally as venue for the conference. With more than a thousand years of history, Wrocław is the location of one of the oldest universities in Central Europe. Being a place where education and science play major roles in the daily life of its inhabitants, Wrocław is also a privileged center for spectroscopy in Poland.

  4. Charge and Energy Transfer Dynamics in Molecular Systems

    May, Volkhard


    This second edition is based on the successful concept of the first edition in presenting a unified perspective on molecular charge and energy transfer processes. The authors bridge the regimes of coherent and dissipative dynamics, thus establishing the connection between classic rate theories and modern treatments of ultrafast phenomena. The book serves as an introduction for graduate students and researchers. Among the new topics of this second edition are. - semiclassical and quantum-classical hybrid formulations of molecular dynamics. - the basics of femtosecond nonlinear spectroscopy. - e

  5. Molecular materials and devices: developing new functional systems based on the coordination chemistry approach

    Toma Henrique E.


    Full Text Available At the onset of the nanotechnology age, molecular designing of materials and single molecule studies are opening wide possibilities of using molecular systems in electronic and photonic devices, as well as in technological applications based on molecular switching or molecular recognition. In this sense, inorganic chemists are privileged by the possibility of using the basic strategies of coordination chemistry to build up functional supramolecular materials, conveying the remarkable chemical properties of the metal centers and the characteristics of the ancillary ligands. Coordination chemistry also provides effective self-assembly strategies based on specific metal-ligand affinity and stereochemistry. Several molecular based materials, derived from inorganic and metal-organic compounds are focused on this article, with emphasis on new supramolecular porphyrins and porphyrazines, metal-clusters and metal-polyimine complexes. Such systems are also discussed in terms of their applications in catalysis, sensors and molecular devices.

  6. Molecular Engineering of Nonplanar Porphyrin and Carbon Nanotube Assemblies: A Linear and Nonlinear Spectroscopic and Modeling Study

    Éimhín M. Ní Mhuircheartaigh


    Full Text Available The importance of molecular conformation to the nature and strength of noncovalent interactions existing between a series of increasingly nonplanar tetraphenylporphyrin (TPP derivatives and carbon nanotubes was systematically investigated experimentally in solution using a range of linear and nonlinear optical techniques. Additional complementary molecular dynamics studies were found to support the experimental observations. Convincing evidence of binding between single walled nanotubes (SWNTs and some of these porphyrins was discovered, and a nonplanar macrocycle conformation was found to increase the likelihood of noncovalent binding onto nanotubes. Nonlinear optical studies showed that the optical limiting behavior of the TPP derivatives deteriorated with increasing porphyrin nonplanarity, but that formation of nanotube composites dramatically improved the optical limiting properties of all molecules studied. It was also found that the significant photoluminescence quenching behavior reported in the literature for such porphyrin/SWNT composites is at least partly caused by photoluminescence and excitation self-absorption and is, therefore, an artifact of the system.

  7. Photoproduction of molecular hydrogen by a plant-algal symbiotic system

    Newton, J.W.


    The rapidly growing water fern Azolla, which contains a nitrogen-fixing blue-green algal symbiont, has been studied as a possible system for photoproduction of molecular hydrogen. When this plant is grown on a combined nitrogen supply, photochemically generated hydrogen can be diverted through the algal nitrogenase system, which serves as a source of molecular hydrogen generated from water. This symbiosis has several advantages as a possible biological energy conversion system. (auth)

  8. Parallel β-sheet vibrational couplings revealed by 2D IR spectroscopy of an isotopically labeled macrocycle: quantitative benchmark for the interpretation of amyloid and protein infrared spectra.

    Woys, Ann Marie; Almeida, Aaron M; Wang, Lu; Chiu, Chi-Cheng; McGovern, Michael; de Pablo, Juan J; Skinner, James L; Gellman, Samuel H; Zanni, Martin T


    Infrared spectroscopy is playing an important role in the elucidation of amyloid fiber formation, but the coupling models that link spectra to structure are not well tested for parallel β-sheets. Using a synthetic macrocycle that enforces a two stranded parallel β-sheet conformation, we measured the lifetimes and frequency for six combinations of doubly (13)C═(18)O labeled amide I modes using 2D IR spectroscopy. The average vibrational lifetime of the isotope labeled residues was 550 fs. The frequencies of the labels ranged from 1585 to 1595 cm(-1), with the largest frequency shift occurring for in-register amino acids. The 2D IR spectra of the coupled isotope labels were calculated from molecular dynamics simulations of a series of macrocycle structures generated from replica exchange dynamics to fully sample the conformational distribution. The models used to simulate the spectra include through-space coupling, through-bond coupling, and local frequency shifts caused by environment electrostatics and hydrogen bonding. The calculated spectra predict the line widths and frequencies nearly quantitatively. Historically, the characteristic features of β-sheet infrared spectra have been attributed to through-space couplings such as transition dipole coupling. We find that frequency shifts of the local carbonyl groups due to nearest neighbor couplings and environmental factors are more important, while the through-space couplings dictate the spectral intensities. As a result, the characteristic absorption spectra empirically used for decades to assign parallel β-sheet secondary structure arises because of a redistribution of oscillator strength, but the through-space couplings do not themselves dramatically alter the frequency distribution of eigenstates much more than already exists in random coil structures. Moreover, solvent exposed residues have amide I bands with >20 cm(-1) line width. Narrower line widths indicate that the amide I backbone is solvent

  9. Incorporation of trinuclear lanthanide(III) hydroxo bridged clusters in macrocyclic frameworks.

    Kobyłka, Michał J; Ślepokura, Katarzyna; Acebrón Rodicio, Maria; Paluch, Marta; Lisowski, Jerzy


    A cluster of lanthanide(III) or yttrium(III) ions, Ln3(μ3-OH)2, (Ln(III) = Nd(III), Sm(III), Eu(III), Gd(III), Tb(III), Dy(III), Yb(III), or Y(III)) can be bound in the center of a chiral macrocyclic amines H3L1(R), H3L1(S), and H3L2(S) obtained in a reduction of a 3 + 3 condensation product of (1R,2R)- or (1S,2S)-1,2-diaminocyclohexane and 2,6-diformyl-4-methylphenol or 2,6-diformyl-4-tertbutylphenol. X-ray crystal structures of the Nd(III), Sm(III), Gd(III), Dy(III), and Y(III) complexes reveal trinuclear complexes with Ln(III) ions bridged by the phenolate oxygen atoms of the macrocycle as well as by μ3-hydroxo bridges. In the case of the Nd(III) ion, another complex form can be obtained, whose X-ray crystal structure reveals two trinuclear macrocyclic units additionally bridged by hydroxide anions, corresponding to a [Ln3(μ3-OH)]2(μ2-OH)2 cluster encapsulated by two macrocycles. The formation of trinuclear complexes is confirmed additionally by (1)H NMR, electrospray ionization mass spectrometry (ESI MS), and elemental analyses. Titrations of free macrocycles with Sm(III) or Y(III) salts and KOH also indicate that a trinuclear complex is formed in solution. On the other hand, analogous titrations with La(III) salt indicate that this kind of complex is not formed even with the excess of La(III) salt. The magnetic data for the trinuclear Gd(III) indicate weak antiferromagnetic coupling (J = -0.17 cm(-1)) between the Gd(III) ions. For the trinuclear Dy(III) and Tb(III) complexes the χ(M)T vs T plots indicate a more complicated dependence, resulting from the combination of thermal depopulation of mJ sublevels, magnetic anisotropy, and possibly weak antiferromagnetic and ferromagnetic interactions.

  10. Enantiomeric self-recognition in homo- and heterodinuclear macrocyclic lanthanide(III) complexes.

    Lisowski, Jerzy


    The controlled formation of lanthanide(III) dinuclear μ-hydroxo-bridged [Ln(2)L(2)(μ-OH)(2)X(2)](n+) complexes (where X = H(2)O, NO(3)(-), or Cl(-)) of the enantiopure chiral macrocycle L is reported. The (1)H and (13)C NMR resonances of these complexes have been assigned on the basis of COSY, NOESY, TOCSY, and HMQC spectra. The observed NOE connectivities confirm that the dimeric solid-state structure is retained in solution. The enantiomeric nature of the obtained chiral complexes and binding of hydroxide anions are reflected in their CD spectra. The formation of the dimeric complexes is accompanied by a complete enantiomeric self-recognition of the chiral macrocyclic units. The reaction of NaOH with a mixture of two different mononuclear lanthanide(III) complexes, [Ln(1)L](3+) and [Ln(2)L](3+), results in formation of the heterodinuclear [Ln(1)Ln(2)L(2)(μ-OH)(2)X(2)](n+) complexes as well as the corresponding homodinuclear complexes. The formation of the heterodinuclear complex is directly confirmed by the NOESY spectra of [EuLuL(2)(μ-OH)(2)(H(2)O)(2)](4+), which reveal close contacts between the macrocyclic unit containing the Eu(III) ion and the macrocyclic unit containing the Lu(III) ion. While the relative amounts of homo- and heterodinuclear complexes are statistical for the two lanthanide(III) ions of similar radii, a clear preference for the formation of heterodinuclear species is observed when the two mononuclear complexes contain lanthanide(III) ions of markedly different sizes, e.g., La(III) and Yb(III). The formation of heterodinuclear complexes is accompanied by the self-sorting of the chiral macrocyclic units based on their chirality. The reactions of NaOH with a pair of homochiral or racemic mononuclear complexes, [Ln(1)L(RRRR)](3+)/[Ln(2)L(RRRR)](3+), [Ln(1)L(SSSS)](3+)/[Ln(2)L(SSSS)](3+), or [Ln(1)L(rac)](3+)/[Ln(2)L(rac)](3+), results in mixtures of homochiral, homodinuclear and homochiral, heterodinuclear complexes. On the contrary, no

  11. Novel Potent Hepatitis C Virus NS3 Serine Protease Inhibitors Derived from Proline-Based Macrocycles

    Chen, Kevin X.; Njoroge, F. George; Arasappan, Ashok; Venkatraman, Srikanth; Vibulbhan, Bancha; Yang, Weiying; Parekh, Tejal N.; Pichardo, John; Prongay, Andrew; Cheng, Kuo-Chi; Butkiewicz, Nancy; Yao, Nanhua; Madison, Vincent; Girijavallabhan, Viyyoor (SPRI)


    The hepatitis C virus (HCV) NS3 protease is essential for viral replication. It has been a target of choice for intensive drug discovery research. On the basis of an active pentapeptide inhibitor, 1, we envisioned that macrocyclization from the P2 proline to P3 capping could enhance binding to the backbone Ala156 residue and the S4 pocket. Thus, a number of P2 proline-based macrocyclic {alpha}-ketoamide inhibitors were prepared and investigated in an HCV NS3 serine protease continuous assay (K*{sub i}). The biological activity varied substantially depending on factors such as the ring size, number of amino acid residues, number of methyl substituents, type of heteroatom in the linker, P3 residue, and configuration at the proline C-4 center. The pentapeptide inhibitors were very potent, with the C-terminal acids and amides being the most active ones (24, K*{sub i} = 8 nM). The tetrapeptides and tripeptides were less potent. Sixteen- and seventeen-membered macrocyclic compounds were equally potent, while fifteen-membered analogues were slightly less active. gem-Dimethyl substituents at the linker improved the potency of all inhibitors (the best compound was 45, K*{sub i} = 6 nM). The combination of tert-leucine at P3 and dimethyl substituents at the linker in compound 47 realized a selectivity of 307 against human neutrophil elastase. Compound 45 had an IC{sub 50} of 130 nM in a cellular replicon assay, while IC{sub 50} for 24 was 400 nM. Several compounds had excellent subcutaneous AUC and bioavailability in rats. Although tripeptide compound 40 was 97% orally bioavailable, larger pentapeptides generally had low oral bioavailability. The X-ray crystal structure of compounds 24 and 45 bound to the protease demonstrated the close interaction of the macrocycle with the Ala156 methyl group and S4 pocket. The strategy of macrocyclization has been proved to be successful in improving potency (>20-fold greater than that of 1) and in structural depeptization.

  12. How molecular should your molecular model be? On the level of molecular detail required to simulate biological networks in systems and synthetic biology.

    Gonze, Didier; Abou-Jaoudé, Wassim; Ouattara, Djomangan Adama; Halloy, José


    The recent advance of genetic studies and the rapid accumulation of molecular data, together with the increasing performance of computers, led researchers to design more and more detailed mathematical models of biological systems. Many modeling approaches rely on ordinary differential equations (ODE) which are based on standard enzyme kinetics. Michaelis-Menten and Hill functions are indeed commonly used in dynamical models in systems and synthetic biology because they provide the necessary nonlinearity to make the dynamics nontrivial (i.e., limit-cycle oscillations or multistability). For most of the systems modeled, the actual molecular mechanism is unknown, and the enzyme equations should be regarded as phenomenological. In this chapter, we discuss the validity and accuracy of these approximations. In particular, we focus on the validity of the Michaelis-Menten function for open systems and on the use of Hill kinetics to describe transcription rates of regulated genes. Our discussion is illustrated by numerical simulations of prototype systems, including the Repressilator (a genetic oscillator) and the Toggle Switch model (a bistable system). We systematically compare the results obtained with the compact version (based on Michaelis-Menten and Hill functions) with its corresponding developed versions (based on "elementary" reaction steps and mass action laws). We also discuss the use of compact approaches to perform stochastic simulations (Gillespie algorithm). On the basis of these results, we argue that using compact models is suitable to model qualitatively biological systems.

  13. Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems

    Marchi, Massimo; Ballone, Pietro


    This study deals with a novel molecular simulation technique, named adiabatic bias molecular dynamics (MD), which provides a simple and reasonably inexpensive route to generate MD trajectories joining points in conformational space separated by activation barriers. Because of the judicious way the biasing potential is updated during the MD runs, the technique allows with some additional effort the computation of the free energy change experienced during the trajectory. The adiabatic bias method has been applied to a nontrivial problem: The unfolding of an atomistic model of lysozyme. Here, the radius of gyration (Rg) was used as a convenient reaction coordinate. For changes in Rg between 19.7 and 28 Å, we observe a net loss of the native tertiary structure of lysozyme. At the same time, secondary structure elements such as α-helices are retained although some of the original order is diminished. The calculated free energy profile for the unfolding transition shows a monotonous increase with Rg and depends crucially on the nonbonded cutoff used in the potential model.

  14. A Comparative Study of Successful Central Nervous System Drugs Using Molecular Modeling

    Kim, Hyosub; Sulaimon, Segun; Menezes, Sandra; Son, Anne; Menezes, Warren J. C.


    Molecular modeling is a powerful tool used for three-dimensional visualization and for exploring electrostatic forces involved in drug transport. This tool enhances student understanding of structure-property relationships, as well as actively engaging them in class. Molecular modeling of several central nervous system (CNS) drugs is used to…

  15. The challenges for molecular nutrition research 4: the "nutritional systems biology level"

    Ommen, B. van; Cavallieri, D.; Roche, H.M.; Klein, U.I.; Daniel, H.


    Nutritional systems biology may be defined as the ultimate goal of molecular nutrition research, where all relevant aspects of regulation of metabolism in health and disease states at all levels of its complexity are taken into account to describe the molecular physiology of nutritional processes. T

  16. Teaching Applied Genetics and Molecular Biology to Agriculture Engineers. Application of the European Credit Transfer System

    Weiss, J.; Egea-Cortines, M.


    We have been teaching applied molecular genetics to engineers and adapted the teaching methodology to the European Credit Transfer System. We teach core principles of genetics that are universal and form the conceptual basis of most molecular technologies. The course then teaches widely used techniques and finally shows how different techniques…

  17. A Comparative Study of Successful Central Nervous System Drugs Using Molecular Modeling

    Kim, Hyosub; Sulaimon, Segun; Menezes, Sandra; Son, Anne; Menezes, Warren J. C.


    Molecular modeling is a powerful tool used for three-dimensional visualization and for exploring electrostatic forces involved in drug transport. This tool enhances student understanding of structure-property relationships, as well as actively engaging them in class. Molecular modeling of several central nervous system (CNS) drugs is used to…

  18. Molecular Iodine-Mediated Cyclization of Tethered Heteroatom-Containing Alkenyl or Alkynyl Systems

    Malose Jack Mphahlele


    Full Text Available Molecular iodine has established itself as a readily available and easy-to-handle electrophilic and oxidizing reagent used in various organic transformations. In this review attention is focused on the use of molecular iodine in promoting cyclization (iodocyclization and cyclodehydroiodination of tethered heteroatom-containing alkenyl or alkynyl systems.

  19. Evolution of dust and molecular hydrogen in the Magellanic System

    Yozin, Cameron


    We investigate the evolution of the interstellar medium (ISM) in self-consistent, chemodynamical simulations of the Magellanic Clouds (MCs) during their recent (z<0.3) past. An explicit modelling of dust and molecular hydrogen lifecycles enables the comparison of our models against the observed properties of the ISM, including elemental depletion from the gas-phase. Combining this model with a tidal-dominated paradigm for the formation for the Magellanic Stream and Bridge, we reproduce the age-metallicity relations, long gas depletion timescales, and presently observed dust and molecular hydrogen masses of the MCs to within their respective uncertainties. We find that these models' enrichment depends sensitively on the processing of dust within the ISM and the dynamical influence of external tides/stellar bars. The ratio of characteristic dust destruction timescales in our SMC and LMC models, a governing parameter of our models' evolution, is consistent with estimates based on observed supernova (SN) rates...

  20. Modeling molecular hydrogen emission in M dwarf exoplanetary systems

    Evonosky, William; France, Kevin; Kruczek, Nick E.; Youngblood, Allison; Measurements of the Ultraviolet Spectral Characteristics of Low-mass Exoplanet host Stars (MUSCLES)


    Exoplanets orbiting low-mass stars are prime candidates for atmospheric characterization due to their astronomical abundance and short orbital periods. These planets orbit stars that are often more active than main sequence solar-type stars. They are exposed to differing levels of ultraviolet radiation which can cause traditional “biosignature” gases to be generated abiotically, potentially causing false-positive identifications of life. We modeled the recently discovered molecular hydrogen emission in the ultraviolet spectra (1350 - 1650 Å) as arising from the stellar surface, excited by radiation generated in the upper chromosphere. The model was compared with observed hydrogen emission from the “Measurements of the Ultraviolet Spectral Characteristics of Low-mass Exoplanet host Stars” (MUSCLES) survey by conducting a grid search and implementing a chi-squared minimization routine. We considered only progressions from the [1, 4] and [1, 7] first excited electronic levels. Our modeling procedure varied the atomic hydrogen column density (in the chromosphere) as well as the photospheric molecular hydrogen column density and temperature. The model required as an input a reconstructed intrinsic Lyman α profile which served as the pumping radiation for the molecular hydrogen. We found that an atomic hydrogen column density of log10N(H I) = 14.13 ± 0.16 cm-2 represents a breaking point above which there is not enough Lyman α flux available to excite a significant molecular hydrogen population into the [1, 7] state. We also present H2 temperatures which may suggest that star spots on low mass stars persist longer, and encompass more area than star spots on solar-type stars.

  1. Chemical evolution on planetary surfaces: from simple gases to organic macrocycles

    Fox, Stefan; Strasdeit, Henry

    It is generally accepted that α-amino acids existed in the primordial ocean on the Hadean / early Archean Earth. They had been abiotically synthesized from smaller molecules such as H2 , CH4 , H2 O, NH3 , HCN, aldehydes, ketones, and alcohols [1-3]. Once the amino acids had been formed, they probably reacted to more complex molecules. One possibility is the thermal transformation at hot volcanic coasts. In a first step, amino acid-containing seawater evaporated in the vicinity of lava streams. A salt crust remained in which amino acids were embedded. In a second step, these embedded amino acids were thermally transformed to new compounds. In order to simulate this hot-volcanic-coast scenario artificial salt crusts with embedded amino acids were prepared and heated to 300-800 ° C in a slow stream of nitrogen gas. We found that in the salt crusts glycine, DL-alanine and -aminoisobutyric acid were chemically bonded to calcium or magnesium ions. This metal coordination prevents the sublimation of the amino acids and permits the thermal formation of pyridines, piperazine-2,5-diones, polycyclic aromatic hydrocarbons, and especially several alkylated pyrroles. Thus an abiotic source of pyrroles on young Earth-like planets may exist. Amino acids and pyrroles are building blocks of important biomolecules. It might seem plausible that amino acids formed peptides on the early Earth. However, in aqueous solution the condensation reaction is unfavorable, and even if short peptides would have formed they would have tended to hydrolyze. This argument is equally true for nucleic acid components [4]. In contrast to that, it is known that pyrrole, in aqueous HCl solutions, reacts with formaldehyde to form oligopyrroles [5]. Prebiotic oligopyrroles and their metal complexes may have been utilized by primitive metabolizing systems and later modified into porphyrin-like macrocycles such as chlorophyll. [1] Miller, S. L. (1953) Science, 117, 528. [2] Johnson, A. P., Cleaves, H. J

  2. A thiourea-functionalized metal-organic macrocycle for the catalysis of Michael additions and prominent size-selective effect.

    Yang, Lu; Zhao, Liang; Zhou, Zhen; He, Cheng; Sun, Hui; Duan, Chunying


    A discrete tetranuclear thiourea-based metal-organic macrocycle (MOM) with a large size was constructed by a well-designed organic ligand and nickel(ii) ions via self-assembly. Incorporating thiourea groups as hydrogen-bond donors into a metal-organic complex system leads to a new approach for synthesizing functionalized heterogeneous catalysts, as this not only introduces coordination sites serving as chelators, but also overcomes the issues of self-association via intermolecular H-bonding, often occurring in homogeneous systems. The packing structure of this material formed a confined environment suitable for the access of substrate molecules dragged by the strong hydrogen-bond interactions from the thiourea groups, thus achieving a high catalytic performance in Michael additions of nitrostyrenes to nitroalkanes, with remarkable yields and size-selectivity in heterogeneous phase. Moreover, a comparison of the IR spectrum of Ni-SPT with the spectra of dimethyl malonate- and β-nitrostyrene-impregnated Ni-SPT indicated that both substrate molecules, β-nitrostyrene and dimethyl malonate, were able to access the cavity of the trimeric subunit.

  3. Construction of metal-organic frameworks through coordination and hydrogen bonding interactions: Syntheses, structures and photoluminescent properties of metal complexes with macrocyclic ligand

    Ouyang, Xing-Mei; Li, Zhen-Wu; Okamura, Taka-aki; Li, Yi-Zhi; Sun, Wei-Yin; Tang, Wen-Xia; Ueyama, Norikazu


    A macrocyclic ligand L with two diethylenetriamine units linked by two rigid biphenylene spacers was used as building block for construction of metal-organic frameworks. A silver(I) complex with macrocyclic and open-chain mix-type ligands [Ag 2( L)( L')](ClO 4) 2 ( 1) [ L'=1,6-bis(4-imidazol-1'-ylmethylphenyl)-2,5-diazahexane] was obtained by reaction of L and L' together with AgClO 4·H 2O. It is interesting that the open-chain tetradentate ligand L' only served as a bidentate ligand to bridge the Ag 2L units into an infinite one-dimensional (1D) cationic chain. Neutral 1D chain coordination polymer [Cu 2( L)( μ-SO 4) 2]·3H 2O·3MeOH ( 2) is formed by sulfate bridges between the neighboring Cu 2L units. When L reacted with nickel(II) sulfate instead of copper(II) sulfate, a monomacrocycle molecular complex [Ni 2( L)(H 2O) 4(SO 4) 2] ( 3) was obtained in which the sulfate anion acts as monodentate ligands rather than as bridges. When Cd(II) salts were used for the reactions with L, another two neutral 1D coordination polymers, [Cd 2( L)( μ-Cl) 2Cl 2]·2H 2O ( 4) and [Cd 2( L)( μ-Br) 2Br 2] ( 5), with the same structure were isolated. All the synthesized complexes exhibit three-dimensional framework structures linked by various hydrogen bonds. The photoluminescent properties of the synthesized complexes were studied in the solid state at room temperature, and the Ag(I) and Cd(II) complexes were found to show strong blue luminescence.

  4. Synthesis and Crystal Structure of a Novel 1D Mercury(II) Iodide Coordination Polymer Containing 40-Membered Macrocycle%Synthesis and Crystal Structure of a Novel 1D Mercury(II) Iodide Coordination Polymer Containing 40-Membered Macrocycle

    GAN Xiao-Ping; KONG Ling; WU Peng; LV Chen; TU Yu-Long; CHEN Yi-Xin; ZHOU Hong-Ping; WU Jie-Ying; TIAN Yu-Peng


    A mercury coordination polymer [Hg3(TizT)216]n (Mr = 1921.72, TizT = 2,4,6- tri(imidazole- 1-yl)- 1,3,5-triazine) containing a 40-membered macrocycle which was constructed by four TizT ligands and four mercury(II) iodide molecules had been synthesized by the reaction of HgI2 with TizT. The complex was characterized by elemental analysis, FT-IR, ^1H NMR spectra and X-ray crystallography. The crystal of the complex belongs to the monoclinic system and C2/c space group with a = 35.840(5), b = 8.169(5), c = 14.980(5) A, β = 104.466(5)°, Z= 4, V= 4247(3) A^3, De = 3.006 g·cm^-3, μ= 15.223 mm^-1, F(000) = 3384, Rint = 0.0504, wR = 0.0833 and constructs a chair-like conformation of cyclohexane one by one, which forms a 1-D polymer through the fashion of fused ring aromatic hydrocarbon. The hydrogen bonds and π-π interactions shape the 2-D network structure. The two compounds excited weak fluorescence.


    New method for calculating molecular orbitals with application to cyclic systems: Stud; of the quantum mechanical problem of an electron bound to a configuration of N overlapping potentials. Reprinted from ’The Physical Review ’.

  6. Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology (Final Report)

    EPA announced the release of the final report, Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology. This report describes new approaches that are faster, less resource intensive, and more robust that can help ...

  7. Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology (Final Report)

    EPA announced the release of the final report, Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology. This report describes new approaches that are faster, less resource intensive, and more robust that can help ...

  8. Materials learning from life: concepts for active, adaptive and autonomous molecular systems.

    Merindol, Rémi; Walther, Andreas


    Bioinspired out-of-equilibrium systems will set the scene for the next generation of molecular materials with active, adaptive, autonomous, emergent and intelligent behavior. Indeed life provides the best demonstrations of complex and functional out-of-equilibrium systems: cells keep track of time, communicate, move, adapt, evolve and replicate continuously. Stirred by the understanding of biological principles, artificial out-of-equilibrium systems are emerging in many fields of soft matter science. Here we put in perspective the molecular mechanisms driving biological functions with the ones driving synthetic molecular systems. Focusing on principles that enable new levels of functionalities (temporal control, autonomous structures, motion and work generation, information processing) rather than on specific material classes, we outline key cross-disciplinary concepts that emerge in this challenging field. Ultimately, the goal is to inspire and support new generations of autonomous and adaptive molecular devices fueled by self-regulating chemistry.

  9. Interactions of mercury with different molecular weight fractions of humic substances in aquatic systems.

    Chakraborty, P.; Yao, K.M.; Chennuri, K.; Vudamala, K.; Babu, P.V.R.

    Interactions of mercury (Hg) with different molecular weight fractions of humic substances (HS) play an important role in controlling distribution, diffusion, speciation, and bioavailability of Hg in natural systems. This study suggests that Hg...

  10. Optical and transport properties of complex molecular systems


    Esta Tesis presenta el estudio de las propiedades ópticas y de transporte de sistemas de baja dimensionalidad a través de modelos de enlace fuerte. Nuestro trabajo se centra en dos tipos de sistemas: agregados moleculares lineales y moléculas de ADN.En los Capítulos 2, 3 y 4 se estudian las propiedades de localización de un Hamiltoniano de Frenkel desordenado unidimensional. El desorden se introduce en las energías de sitio y es correlacionado de largo alcance. Para correlaciones fuertes, se ...

  11. Controllable Optical Bistability in a Crystal of Molecular Magnets System

    LIU Ji-Bing; LU Xin-You; HAO Xiang-Ying; SI Liu-Gang; YANG Xiao-Xue


    We investigate the formation of opticai bistability (OB) in a crystal of molecular magnets contained in a unidirectional ring cavity. The crystal is subjected to one de magnetic field and two (probe and coupling) ac resonant magnetic field. The results show that OB can be controlled efficiently by adjusting the intensity of the control field, the detuning of probe magnetic field and the cooperation parameter. Furthermore, within certain parameter range, the optical multistablity (OM) can also be observed in the crystal medium. This investigation can be used for designing new types of nonelectronic devices for realizing switching process.

  12. Molecular Genetic and Gene Therapy Studies of the Musculoskeletal System


    Molecular Genetics Division, Ohio State University. For reporting purpose, the ’Smad2’ sign indicates a disabled copy of ’Smad2’ gene while the ’+’ sign...skeletal mass in third- and fourth-grade children : Effects of age, gender, ethnicity and body composition. Bone 20:73-78. 18. Thomas, T. and Burguera, B...strand buffer mix (250 mM Tris HCI (pH 8.3 at RT), 375 mM KCI, 15 mM MgCI, I ul of 0.1 M DTT and 1 ul of RNAse Out, recombinant RNAse inhibitor

  13. Radiative corrections and quantum gates in molecular systems

    Huffenberger, Kevin M


    We propose a method for quantum information processing using molecules coupled to an external laser field. This utilizes molecular interactions, control of the external field and an effective energy shift of the doubly-excited state of two coupled molecules. Such a level shift has been seen in the two-photon resonance experiments recently reported in Ref. [1]. Here we show that this can be explained in terms of the QED Lamb shift. We quantify the performance of the proposed quantum logic gates in the presence of dissipative mechanisms. The unitary transformations required for performing one- and two-qubit operations can be implemented with present day technology.

  14. Charge Transport by Superexchange in Molecular Host-Guest Systems

    Symalla, Franz; Friederich, Pascal; Massé, Andrea; Meded, Velimir; Coehoorn, Reinder; Bobbert, Peter; Wenzel, Wolfgang


    Charge transport in disordered organic semiconductors is generally described as a result of incoherent hopping between localized states. In this work, we focus on multicomponent emissive host-guest layers as used in organic light-emitting diodes (OLEDs), and show using multiscale ab initio based modeling that charge transport can be significantly enhanced by the coherent process of molecular superexchange. Superexchange increases the rate of emitter-to-emitter hopping, in particular if the emitter molecules act as relatively deep trap states, and allows for percolation path formation in charge transport at low guest concentrations.

  15. Peptide Macrocycles Featuring a Backbone Secondary Amine: A Convenient Strategy for the Synthesis of Lipidated Cyclic and Bicyclic Peptides on Solid Support

    Oddo, Alberto; Münzker, Lena; Hansen, Paul Robert


    A convenient strategy for the on-resin synthesis of macrocyclic peptides (3- to 13-mers) via intramolecular halide substitution by a diamino acid is described. The method is compatible with standard Fmoc/tBu SPPS and affords a tail-to-side-chain macrocyclic peptide featuring an endocyclic secondary...

  16. Molecular Cloning of Human Gene(s) Directing the Synthesis of Nervous System Cholinesterases


    Report No. 4 If MOLECULAR CLONING OF O HUMAN GENE(S) DIRECTING qTHE SYNTHESIS OF NERVOUS SYSTEM CHOLINESTERASES cc Annual/Final Report 0 N November...62734A I734A875 IAl 451 MOLECULAR CLONING OF HUMAN GEME(S) DIRECTING THE SYNTHESIS OF NERVOUS SYSTEM CHOLINESTERASE 12. PERSONAL AUTHOR(S) Hermona Soreq...important roles in regulating the pace and mode of function of particular types of synapses. For example, molecular cloning of the nicotinic (44-46) and the

  17. Intraindividual, randomized comparison of the macrocyclic contrast agents gadobutrol and gadoterate meglumine in breast magnetic resonance imaging

    Fallenberg, Eva M.; Renz, Diane M.; Hamm, Bernd [Charite - Universitaetsmedizin Berlin, Campus Virchow-Klinikum, Department of Radiology, Berlin (Germany); Karle, Bettina [Clinic of Radiation Therapy, Helios Clinics, Berlin (Germany); Schwenke, Carsten [SCOSSIS Statistical Consulting, Berlin (Germany); Ingod-Heppner, Barbara [Charite Universitaetsmedizin, Campus Charite Mitte, Institute of Pathology, Berlin (Germany); Reles, Angela [Charite Universitaetsmedizin, Charite-Partner-Practice, Interdisciplinary Breast Center, Berlin (Germany); Engelken, Florian J. [Charite - Universitaetsmedizin Berlin, Charite Campus Mitte, Department of Radiology, Berlin (Germany); Huppertz, Alexander; Taupitz, Matthias [Charite - Universitaetsmedizin Berlin, Campus Benjamin Franklin, Department of Radiology, Berlin (Germany)


    To compare intraindividually two macrocyclic contrast agents - gadobutrol and gadoterate meglumine (Gd-DOTA) - for dynamic and quantitative assessment of relative enhancement (RE) in benign and malignant breast lesions. This was an ethically approved, prospective, single-centre, randomized, crossover study in 52 women with suspected breast lesions referred for magnetic resonance imaging (MRI). Each patient underwent one examination with gadobutrol and one with Gd-DOTA (0.1 mmol/kg BW) on a 1.5 T system 1 - 7 days apart. Dynamic, T1-weighted, 3D gradient echo sequences were acquired under identical conditions. Quantitative evaluation with at least three regions of interest (ROI) per lesion was performed. Primary endpoint was RE during the initial postcontrast phase after the first and second dynamic acquisition, and peak RE. All lesions were histologically proven; differences between the examinations were evaluated. Forty-five patients with a total of 11 benign and 34 malignant lesions were assessed. Mean RE was significantly higher for gadobutrol than Gd-DOTA (p < 0.0001). Gadobutrol showed significantly less washout (64.4 %) than Gd-DOTA (75.4 %) in malignant lesions (p = 0.048) Gadobutrol has higher RE values compared with Gd-DOTA, whereas Gd-DOTA shows more marked washout in malignant lesions. This might improve the detection of breast lesions and influence the specificity of breast MRI-imaging. (orig.)

  18. Density functional theory based study of molecular interactions, recognition, engineering, and quantum transport in π molecular systems.

    Cho, Yeonchoo; Cho, Woo Jong; Youn, Il Seung; Lee, Geunsik; Singh, N Jiten; Kim, Kwang S


    CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium

  19. Systems biology for molecular life sciences and its impact in biomedicine.

    Medina, Miguel Ángel


    Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

  20. Synthesis and characterization of two novel bimetallic macrocyclic complexes generated from 1,2,4-triazole-containing semi-rigid ligands and M(NO3)2 units (M = Ni and Zn).

    Wu, Xiang Wen; Yin, Shi; Wu, Wan Fu; Ma, Jian Ping


    Bimetallic macrocyclic complexes have attracted the attention of chemists and various organic ligands have been used as molecular building blocks, but supramolecular complexes based on semi-rigid organic ligands containing 1,2,4-triazole have remained rare until recently. It is easier to obtain novel topologies by making use of asymmetric semi-rigid ligands in the self-assembly process than by making use of rigid ligands. A new semi-rigid ligand, 3-[(pyridin-4-ylmethyl)sulfanyl]-5-(quinolin-2-yl)-4H-1,2,4-triazol-4-amine (L), has been synthesized and used to generate two novel bimetallic macrocycle complexes, namely bis{μ-3-[(pyridin-4-ylmethyl)sulfanyl]-5-(quinolin-2-yl)-4H-1,2,4-triazol-4-amine}bis[(methanol-κO)(nitrato-κ(2)O,O')nickel(II)] dinitrate, [Ni2(NO3)2(C17H14N6S)2(CH3OH)2](NO3)2, (I), and bis{μ-3-[(pyridin-4-ylmethyl)sulfanyl]-5-(quinolin-2-yl)-4H-1,2,4-triazol-4-amine}bis[(methanol-κO)(nitrato-κ(2)O,O')zinc(II)] dinitrate, [Zn2(NO3)2(C17H14N6S)2(CH3OH)2](NO3)2, (II), by solution reactions with the inorganic salts M(NO3)2 (M = Ni and Zn, respectively) in mixed solvents. In (I), two Ni(II) cations with the same coordination environment are linked by L ligands through Ni-N bonds to form a bimetallic ring. Compound (I) is extended into a two-dimensional network in the crystallographic ac plane via N-H...O, O-H...N and O-H...O hydrogen bonds, and neighbouring two-dimensional planes are parallel and form a three-dimensional structure via π-π stacking. Compound (II) contains two bimetallic rings with the same coordination environment of the Zn(II) cations. The Zn(II) cations are bridged by L ligands through Zn-N bonds to form the bimetallic rings. One type of bimetallic ring constructs a one-dimensional nanotube via O-H...O and N-H...O hydrogen bonds along the crystallographic a direction, and the other constructs zero-dimensional molecular cages via O-H...O and N-H...O hydrogen bonds. They are interlinked into a two-dimensional network in the ac

  1. Classical molecular simulations of complex industrially-important systems on the Intel Paragon

    Cochran, H.D.; LoCascio, P.F.; Cummings, P.T. [Univ. of Tennessee, Knoxville, TN (United States)


    Advances in parallel supercomputing now make possible molecular-based engineering and science calculations that will soon revolutionize many technologies, such as those involving polymers and those involving aqueous electrolytes. We have developed a suite of message-passing codes for classical molecular simulation of such complex fluids and amorphous materials and have completed a number of demonstration calculations of problems of scientific and technological importance with each. In this overview paper we will outline the techniques for classical molecular simulation of these industrially-important systems on the Inter Paragon and we will summarize some of the important scientific and technical results of the varied applications, including the following: (1) Parallel codes for quatemion dynamics using techniques for handling long-range Coulombic forces allow study of ion pairing in supercritical aqueous electrolyte solutions. Ion pairing lies at the heart of technological problems with corrosion and solids deposition in industrial processes utilizing high temperature water. (2) Non-equilibrium, multiple time step molecular dynamics lets us investigate the rheology of molecular fluids. Such calculations enable the molecular-based design of new synthetic lubricants of importance in the automotive engines of the future. (3) Chain molecule Monte Carlo simulations in the Gibbs ensemble now permit calculation of phase equilibrium of long-chain molecular systems. With complementary equilibrium molecular dynamics (with multiple time steps) we have been able to gain fundamental insight into the technologically-important problem of liquid-liquid phase separation in polymer blends.

  2. Highly efficient synthesis of monodisperse poly(ethylene glycols) and derivatives through macrocyclization of oligo(ethylene glycols).

    Zhang, Hua; Li, Xuefei; Shi, Qiuyan; Li, Yu; Xia, Guiquan; Chen, Long; Yang, Zhigang; Jiang, Zhong-Xing


    A macrocyclic sulfate (MCS)-based approach to monodisperse poly(ethylene glycols) (M-PEGs) and their monofunctionalized derivatives has been developed. Macrocyclization of oligo(ethylene glycols) (OEGs) provides MCS (up to a 62-membered macrocycle) as versatile precursors for a range of monofunctionalized M-PEGs. Through iterative nucleophilic ring-opening reactions of MCS without performing group protection and activation, a series of M-PEGs, including the unprecedented 64-mer (2850 Da), can be readily prepared. Synthetic simplicity coupled with versatility of this new strategy may pave the way for broader applications of M-PEGs. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Discovery and Optimization of Macrocyclic Quinoxaline-pyrrolo-dihydropiperidinones as Potent Pim-1/2 Kinase Inhibitors.

    Cee, Victor J; Chavez, Frank; Herberich, Bradley; Lanman, Brian A; Pettus, Liping H; Reed, Anthony B; Wu, Bin; Wurz, Ryan P; Andrews, Kristin L; Chen, Jie; Hickman, Dean; Laszlo, Jimmy; Lee, Matthew R; Guerrero, Nadia; Mattson, Bethany K; Nguyen, Yen; Mohr, Christopher; Rex, Karen; Sastri, Christine E; Wang, Paul; Wu, Qiong; Wu, Tian; Xu, Yang; Zhou, Yihong; Winston, Jeffrey T; Lipford, J Russell; Tasker, Andrew S; Wang, Hui-Ling


    The identification of Pim-1/2 kinase overexpression in B-cell malignancies suggests that Pim kinase inhibitors will have utility in the treatment of lymphoma, leukemia, and multiple myeloma. Starting from a moderately potent quinoxaline-dihydropyrrolopiperidinone lead, we recognized the potential for macrocyclization and developed a series of 13-membered macrocycles. The structure-activity relationships of the macrocyclic linker were systematically explored, leading to the identification of 9c as a potent, subnanomolar inhibitor of Pim-1 and -2. This molecule also potently inhibited Pim kinase activity in KMS-12-BM, a multiple myeloma cell line with relatively high endogenous levels of Pim-1/2, both in vitro (pBAD IC50 = 25 nM) and in vivo (pBAD EC50 = 30 nM, unbound), and a 100 mg/kg daily dose was found to completely arrest the growth of KMS-12-BM xenografts in mice.

  4. A Strategy to Suppress Phonon Transport in Molecular Junctions Using pi-Stacked Systems

    Li, Qian; Strange, Mikkel; Duchemin, Ivan


    Molecular junctions are promising candidates for thermoelectric devices due to the potential to tune the electronic and thermal transport properties. However, a high figure of merit is hard to achieve, without reducing the phononic contribution to thermal conductance. Here, we propose a strategy...... to suppress phonon transport in graphene-based molecular junctions preserving high electronic power factor, using nonbonded pi-stackal systems. Using first-principles calculations, we find that the thermal conductance of pi-stacked systems can be reduced by about 95%, compared with that of a covalently bonded...... molecular junction. Phonon transmission of pi-stacked systems is largely attenuated in the whole frequency range, and the remaining transmission occurs mainly below 5 THz, where out-of-plane channels dominate. The figure of merit (ZT) of the pi-stacked molecular junction is dramatically enhanced because...

  5. Molecular techniques in the diagnosis of deep and systemic mycosis.

    Springer, Jan; Einsele, Hermann; Loeffler, Juergen


    Making an early and sensitive diagnosis of invasive fungal infections in high-risk patients is mandatory, because it has major consequences on the effectiveness of antifungal therapy. Molecular assays have the potential to become the cornerstone of diagnosis, allowing for rapid, reliable detection of minute amounts of fungal DNA in various specimens at a low cost. PCR is gaining popularity as the platforms become more automated and commercially available; however, further studies are needed to explore the diagnostic value in patient subgroups (ie, children) and to define whether the underlying disease or the use of antifungal prophylaxis may influence assay results. Individualized management of high-risk patients would be desirable to integrate preemptive therapy strategies, and individual host and genetic factors. Pharmacological and epidemiological considerations should also be evaluated.

  6. System among the corticosteroids: specificity and molecular dynamics

    Brookes, Jennifer C.; Galigniana, Mario D.; Harker, Anthony H.; Stoneham, A. Marshall; Vinson, Gavin P.


    Understanding how structural features determine specific biological activities has often proved elusive. With over 161 000 steroid structures described, an algorithm able to predict activity from structural attributes would provide manifest benefits. Molecular simulations of a range of 35 corticosteroids show striking correlations between conformational mobility and biological specificity. Thus steroid ring A is important for glucocorticoid action, and is rigid in the most specific (and potent) examples, such as dexamethasone. By contrast, ring C conformation is important for the mineralocorticoids, and is rigid in aldosterone. Other steroids that are less specific, or have mixed functions, or none at all, are more flexible. One unexpected example is 11-deoxycorticosterone, which the methods predict (and our activity studies confirm) is not only a specific mineralocorticoid, but also has significant glucocorticoid activity. These methods may guide the design of new corticosteroid agonists and antagonists. They will also have application in other examples of ligand–receptor interactions. PMID:21613285

  7. Stability of molecular dynamics simulations of classical systems

    Toxværd, Søren


    The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... an improved stability with a factor of , but the overhead of computer time is a factor of at least two. The conclusion is that the second-order “Verlet”-algorithm, most commonly used in MD, is superior. It gives the exact dynamics within the limit of the asymptotic expansion and this limit can be estimated...

  8. Bulk superconductivity at 38 K in a molecular system.

    Ganin, Alexey Y; Takabayashi, Yasuhiro; Khimyak, Yaroslav Z; Margadonna, Serena; Tamai, Anna; Rosseinsky, Matthew J; Prassides, Kosmas


    C(60)-based solids are archetypal molecular superconductors with transition temperatures (Tc) as high as 33 K (refs 2-4). Tc of face-centred-cubic (f.c.c.) A(3)C(60) (A=alkali metal) increases monotonically with inter C(60) separation, which is controlled by the A(+) cation size. As Cs(+) is the largest such ion, Cs(3)C(60) is a key material in this family. Previous studies revealing trace superconductivity in Cs(x)C(60) materials have not identified the structure or composition of the superconducting phase owing to extremely small shielding fractions and low crystallinity. Here, we show that superconducting Cs(3)C(60) can be reproducibly isolated by solvent-controlled synthesis and has the highest Tc of any molecular material at 38 K. In contrast to other A(3)C(60) materials, two distinct cubic Cs(3)C(60) structures are accessible. Although f.c.c. Cs(3)C(60) can be synthesized, the superconducting phase has the A15 structure based uniquely among fullerides on body-centred-cubic packing. Application of hydrostatic pressure controllably tunes A15 Cs(3)C(60) from insulating at ambient pressure to superconducting without crystal structure change and reveals a broad maximum in Tc at approximately 7 kbar. We attribute the observed Tc maximum as a function of inter C(60)separation--unprecedented in fullerides but reminiscent of the atom-based cuprate superconductors--to the role of strong electronic correlations near the metal-insulator transition onset.

  9. Including Quantum Effects in the Dynamics of Complex (i.e., Large)Molecular Systems

    Miller, William H.


    The development in the 1950's and 60's of crossed molecular beam methods for studying chemical reactions at the single-collision molecular level stimulated the need and desire for theoretical methods to describe these and other dynamical processes in molecular systems. Chemical dynamics theory has made great strides in the ensuing decades, so that methods are now available for treating the quantum dynamics of small molecular systems essentially completely. For the large molecular systems that are of so much interest nowadays (e.g. chemical reactions in solution, in clusters, in nano-structures, in biological systems, etc.), however, the only generally available theoretical approach is classical molecular dynamics (MD) simulations. Much effort is currently being devoted to the development of approaches for describing the quantum dynamics of these complex systems. This paper reviews some of these approaches, especially the use of semiclassical approximations for adding quantum effects to classical MD simulations, also showing some new versions that should make these semiclassical approaches even more practical and accurate.

  10. Development of ocular drug delivery systems using molecularly imprinted soft contact lenses.

    Tashakori-Sabzevar, Faezeh; Mohajeri, Seyed Ahmad


    Recently, significant advances have been made in order to optimize drug delivery to ocular tissues. The main problems in ocular drug delivery are poor bioavailability and uncontrollable drug delivery of conventional ophthalmic preparations (e.g. eye drops). Hydrogels have been investigated since 1965 as new ocular drug delivery systems. Increase of hydrogel loading capacity, optimization of drug residence time on the ocular surface and biocompatibility with the eye tissue has been the main focus of previous studies. Molecular imprinting technology provided the opportunity to fulfill the above-mentioned objectives. Molecularly imprinted soft contact lenses (SCLs) have high potentials as novel drug delivery systems for the treatment of eye disorders. This technique is used for the preparation of polymers with specific binding sites for a template molecule. Previous studies indicated that molecular imprinting technology could be successfully applied for the preparation of SCLs as ocular drug delivery systems. Previous research, particularly in vivo studies, demonstrated that molecular imprinting is a versatile and effective method in optimizing the drug release behavior and enhancing the loading capacity of SCLs as new ocular drug delivery systems. This review highlights various potentials of molecularly imprinted contact lenses in enhancing the drug-loading capacity and controlling the drug release, compared to other ocular drug delivery systems. We have also studied the effects of contributing factors such as the type of comonomer, template/functional monomer molar ratio, crosslinker concentration in drug-loading capacity, and the release properties of molecularly imprinted hydrogels.

  11. Immobilized copper(II) macrocyclic complex on MWCNTs with antibacterial activity

    Tarlani, Aliakbar, E-mail: [Inorganic Nanostructures and Catalysts Research Lab., Chemistry & Chemical Engineering Research Center of Iran, Pajoohesh Blvd., km 17, Karaj Hwy, Tehran 14968-13151 (Iran, Islamic Republic of); Narimani, Khashayar [Inorganic Nanostructures and Catalysts Research Lab., Chemistry & Chemical Engineering Research Center of Iran, Pajoohesh Blvd., km 17, Karaj Hwy, Tehran 14968-13151 (Iran, Islamic Republic of); Mohammadipanah, Fatemeh; Hamedi, Javad [Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran 14155-6455 (Iran, Islamic Republic of); University of Tehran Biocompound Collection (UTBC), Microbial Technology and Products Research Center, University of Tehran, Tehran (Iran, Islamic Republic of); Tahermansouri, Hasan [Department of Chemistry, Ayatollah Amoli Branch, Islamic Azad University, Amol (Iran, Islamic Republic of); Amini, Mostafa M. [Department of Chemistry, Shahid Behshti University, 1983963113, Tehran (Iran, Islamic Republic of)


    Graphical abstract: In an antibacterial test, grafted copper(II) macrocyclic complex on the surface of MWCNT showed higher antibacterial activity against Bacillus subtilis compared to the individual MWCNT-COOH and the complex. - Highlights: • Copper(II) tetraaza macrocyclic complex covalently bonded to modified MWCNT. • Grafting of the complex carried out via an interaction between −C(=O)Cl group and NH of the ligand. • The samples were subjected in an antibacterial assessment to compare their activity. • Immobilized complex showed higher antibacterial activity against Bacillus subtilis ATCC 6633 compared to separately MWCNT-C(C=O)-OH and CuTAM. - Abstract: In a new approach, a copper(II) tetraaza macrocyclic complex (CuTAM) was covalently bonded on modified multi-walled carbon nanotubes (MWCNTs). To achieve this purpose, MWCNTs were converted to MWCNT-COCl and then reacted to NH groups of TAM ligand. The prepared material was characterized by Fourier Transform Infrared (FT-IR), X-ray diffraction (XRD), Raman spectroscopy, thermal gravimetric analysis (TGA), and FESEM (field emission scanning electron microscopy). FT-IR and TGA demonstrated the presence of the organic moieties, and XRD proved that the structure of MWCNTs remained intact during the three modification steps. An increase in the I{sub D}/I{sub G} ratio in Raman spectra confirmed the surface modifications. Finally, the samples were subjected to an antibacterial assessment to compare their biological activity. The antibacterial test showed that the grafted complex on the surface of the nanotube (MWCNT-CO-CuTAM) has higher antibacterial activity against Bacillus subtilis ATCC 6633 than the MWCNT-COOH and CuTAM with 1000 and 2000 μg/mL.

  12. Effect of plagiochin E, an antifungal macrocyclic bis(bibenzyl), on cell wall chitin synthesis in Candida albicans

    Xiu-zhen WU; Ai-xia CHENG; Ling-mei SUN; Hong-xiang LOU


    Aim: To investigate the effect of plagiochin E (PLE), an antifungal macrocyclic bis(bibenzyl) isolated from liverwort Marchantia polymorpha L, on cell wall chitin synthesis in Candida albicans. Methods: The effect of PLE on chitin synthesis in Candida albicans was investigated at the cellular and molecular lev-els. First, the ultrastructural changes were observed under transmission electron microscopy (TEM). Second, the effects of PLE on chitin synthetase (Chs) activi-ties in vitro were assayed using 6-O-dansyl-N-acetylglucosamine as a fluorescent substrate, and its effect on chitin synthesis in situ was assayed by spheroplast regeneration. Finally, real-time RT-PCR was performed to assay its effect on the expression of Chs genes (CHS). Results: Observation under TEM showed that the structure of the cell wall in Candida albicans was seriously damaged, which suggested that the antifungal activity of PLE was associated with its effect on the cell wail. Enzymatic assays and spheroplast regeneration showed that PLE inhibited chitin synthesis in vitro and in situ. The results of the PCR showed that PLE significantly downregulated the expression of CHS1, and upregulated the expression of CHS2 and CHS3. Because different Chs is regulated at different stages of transcription and post-translation, the downregulation of CHS1 would decrease the level of Chs 1 and inhibit its activity, and the inhibitory effects of PLE on Chs2 and Chs3 would be at the post-translational level or by the inhibi-tion on the enzyme-active center. Conclusion: These results indicate that the antifungal activity of PLE would be attributed to its inhibitory effect on cell wall chitin synthesis in Candida albicans.

  13. A grass molecular identification system for forensic botany: a critical evaluation of the strengths and limitations.

    Ward, Jodie; Gilmore, Simon R; Robertson, James; Peakall, Rod


    Plant material is frequently encountered in criminal investigations but often overlooked as potential evidence. We designed a DNA-based molecular identification system for 100 Australian grasses that consisted of a series of polymerase chain reaction assays that enabled the progressive identification of grasses to different taxonomic levels. The identification system was based on DNA sequence variation at four chloroplast and two mitochondrial loci. Seventeen informative indels and 68 single-nucleotide polymorphisms were utilized as molecular markers for subfamily to species-level identification. To identify an unknown sample to subfamily level required a minimum of four markers or nine markers for species identification. The accuracy of the system was confirmed by blind tests. We have demonstrated "proof of concept" of a molecular identification system for trace botanical samples. Our evaluation suggests that the adoption of a system that combines this approach with DNA sequencing could assist the morphological identification of grasses found as forensic evidence.

  14. Parameter estimation method for improper fractional models and its application to molecular biological systems.

    Tian, Li-Ping; Liu, Lizhi; Wu, Fang-Xiang


    Derived from biochemical principles, molecular biological systems can be described by a group of differential equations. Generally these differential equations contain fractional functions plus polynomials (which we call improper fractional model) as reaction rates. As a result, molecular biological systems are nonlinear in both parameters and states. It is well known that it is challenging to estimate parameters nonlinear in a model. However, in fractional functions both the denominator and numerator are linear in the parameters while polynomials are also linear in parameters. Based on this observation, we develop an iterative linear least squares method for estimating parameters in biological systems modeled by improper fractional functions. The basic idea is to transfer optimizing a nonlinear least squares objective function into iteratively solving a sequence of linear least squares problems. The developed method is applied to the estimation of parameters in a metabolism system. The simulation results show the superior performance of the proposed method for estimating parameters in such molecular biological systems.

  15. Aspectos moleculares do Sistema Sangüíneo ABO Molecular aspects of ABO Blood Group System

    Ana Carla Batissoco


    Full Text Available O sistema ABO é o mais importante grupo sangüíneo na medicina transfusional. O gene ABO codifica as glicosiltransferases responsáveis pela transferência dos resíduos específicos de açúcar, GalNaca1-3 e Gala 1-3, ao substrato H e os convertem ao antígeno A ou B respectivamente. A estrutura do DNA dos três principais alelos do sistema ABO, A¹, B e O foi primeiramente descrita em 1990. Os avanços da genética molecular permitiram o entendimento da base molecular dos genes ABO e o conhecimento do polimorfismo dos alelos comuns a esse locus. Essa revisão tem como objetivo o estudo dos alelos variantes desse sistema, assim como a compreensão das mutações, deleções ou rearranjo de genes responsáveis pela ocorrência de alguns dos subgrupos do sistema ABO. As técnicas mais comumente utilizadas para a genotipagem ABO também são avaliadas, bem como suas vantagens e limitações.The ABO blood group is the most important blood group system in transfusion medicine. Antigens of the ABO system consist of A or B carbohydrate structure carried on the substrate H antigen The ABO gene is responsible for encoding for glycosyltransferases A or B that defines which specific carbohydrate is added to the end of H substance oligosaccharide chains, GalNacalpha1-3 and Galalpha1-3, respectively. The DNA structure of the three major alleles of the human blood group ABO system, A¹ and B, was first described in 1990. Advances of molecular genetics have allowed understanding of the molecular basis of the ABO blood group system and the knowledge of the common alleles polymorphisms of this locus. This review article has the purpose of describing the variants of these alleles and the underlying mutations, deletions or rearrangement of the genes responsible for the occurrence of ABO subgroups and O transferases inactivation. Finally, various methods available for ABO genotyping are also evaluated, as well as its advantages and limitations.

  16. Synthesis of NLO polycarbonates via the ring-opening polymerization of macrocyclic prepolymers

    Kulig, Joseph B.; Moore, Collin G.; Brittain, William J.; Gilmour, Sandra; Perry, Joseph W.


    The synthesis and characterization of polycarbonates and polyformals is described. Copolymers of bisphenol A (BPA) and either a triphenyloxazole (1) or phenylquinoxaline (2) monomer were prepared. The polycarbonate copolymers were prepared by ring-opening polymerization of macrocyclic prepolymers using a solvent-free process. Preliminary electro- optic measurements have been performed on the polycarbonate copolymers of BPA and 1. Polyformals have also been prepared by a conventional polymerization process involving the reaction of dichloromethane with different feed ratios of BPA and either 1 or 2. The glass transition temperature of either the polyformals or polycarbonates is dramatically increased by increasing mole fractions of monomers 1 and 2.

  17. "Cyclamen Red" colors based on a macrocyclic anthocyanin in carnation flowers.

    Gonnet, J F; Fenet, B


    The "cyclamen" red (or pink) colors in carnation flowers-cultivars Red Rox and eight others-are based on the presence of a new macrocyclic anthocyanin, pelargonidin 3,5-di-O-beta-glucoside(6' ', 6' "-malyl diester) identified by spectroscopic methods. The instability of the bridging malyl group with sugars in acidic medium readily causes the formation of the opened ring form, 3-O-(6' '-O-malylglucoside)-5-O-glucoside. The issue of cyclamen colors based in carnations on this original acylated pelargonidin derivative simulating those based on simpler cyanidin glycosides in Rosa cultivars is discussed using CIELAB colorimetric coordinates.

  18. Catalytic Hydrolysis of Phosphate Diester with Metal Complexesof Macrocyclic Tetraamine in Comicellar Solution

    XIANG Qing-Xiang; YU Xiao-Qi; YOU Jing-Song; YAN Qian-Shun; XIE Ru-Gang


    Four novel pyridine or benzene ring-containing pendant macrocyclic dioxotetraanines 2,6-dioxo-1,4,7,10-tetraazacy-clododeane ligands have been synthesized.Their metal com-plexes have been investigated as catalysts for the hydrolysis of bis(p-nitrophenyl) phosphate (BNPP) in aqueous comicellar solution.The results indicate that the hydrophobic interaction between substrate and metal complex, the nature of transition metal ion, and the micellar microenvironment are important factors for the hydrolysis, of BNPP.Large rate enhancement (up to over two-three orders magnitude) employing 5 hasbeen observed.

  19. Neighbor-directed histidine N(τ) alkylation. A route to imidazolium-containing phosphopeptide macrocycles

    Qian, Wen-Jian [National Cancer Inst., Frederick, MD (United States); Park, Jung-Eun [National Cancer Inst., Bethesda, MD (United States); Grant, Robert [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Lai, Christopher C. [National Cancer Inst., Frederick, MD (United States); Kelley, James A. [National Cancer Inst., Frederick, MD (United States); Yaffe, Michael B. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Lee, Kyung S. [National Cancer Inst., Bethesda, MD (United States); Burke, Terrence R. [National Cancer Inst., Frederick, MD (United States)


    Our recently discovered, selective, on-resin route to N(τ)-alkylated imidazolium-containing histidine residues affords new strategies for peptide mimetic design. In this, we demonstrate the use of this chemistry to prepare a series of macrocyclic phosphopeptides, in which imidazolium groups serve as ring-forming junctions. These cationic moieties subsequently serve to charge-mask the phosphoamino acid group that directed their formation. Furthermore, neighbor-directed histidine N(τ)-alkylation opens the door to new families of phosphopeptidomimetics for use in a range of chemical biology contexts.


    SUN Qiang; ZHANG Jinlan; XU Jiping


    Chelating resin with macrocyclic mercaptal group supported on macroporous polystyrene beads was synthesized, which showed good selectivity to Hg2+: its complexing capacity amounted to 30-60 mg Hg2+/g resin, two orders of magnitude greater than for other metal ions such as Ca2+, Zn2+,Cd2+, Pb2+ etc. This resin could restore the activity of urease which had been deactivated by poisoning with Hg2+. Its restoring power was far better than that of the mercapto-resin and common anionic exchange resins. It showed some promising use as an oral polymeric detoxifying drug for mercury poisoning.

  1. Carbohydrate-based aza-macrocycles by Richman-Atkins cyclization of glucopyranose precursors.

    Rathjens, Andreas; Thiem, Joachim


    2, 3-Di-ω-halo- as well as 2, 3-di-ω-toluenesulfonamide-alkylated glucopyranoside derivatives were prepared. Their condensation with α,ω-bis-toluenesulfonamide components under varying Richman-Atkins conditions with alkali carbonate in DMF led to carbohydrate-linked aza-macrocycles displaying 14-, 17-, 18-, 21-, 24-, and 25-membered ring structures. Isomeric aza-macrocylic coronands of 20- as well as 30-membered ring size containing two saccharides could be obtained employing Richman-Atkins condensations of two functionalized sugar building units.

  2. Kinetics of oxidation of nickel(II) aza macrocycles by peroxydisulphate in aqueous media

    J Lalitham; V R Vijayaraghavan


    The kinetics of the oxidation of nickel (II) hexaaza and nickel (II) pentaaza macrocycles by the peroxydisulphate anion, S2O8 2-, were studied in aqueous media. Effect of H on reaction rate was also studied. The rate increases with increase of S2OO8 2- concentration. Rates are almost independent of acid between H 4 and 2, giving overall a relatively simple second-order rate law followed by oxidation within the ion pair solvent shell. Using rate = +1/2 d[Ni(L)3+]/dt = k[Ni(L)2+][S2O8 2-], oxidation rate constants were determined.

  3. Synthesis and P1' SAR exploration of potent macrocyclic tissue factor-factor VIIa inhibitors

    Ladziata, Vladimir (Uladzimir); Glunz, Peter W.; Zou†, Yan; Zhang, Xiaojun; Jiang, Wen; Jacutin-Porte, Swanee; Cheney, Daniel L.; Wei, Anzhi; Luettgen, Joseph M.; Harper, Timothy M.; Wong, Pancras C.; Seiffert, Dietmar; Wexler, Ruth R.; Priestley, E. Scott (BMS)


    Selective tissue factor-factor VIIa complex (TF-FVIIa) inhibitors are viewed as promising compounds for treating thrombotic disease. In this contribution, we describe multifaceted exploratory SAR studies of S1'-binding moieties within a macrocyclic chemotype aimed at replacing cyclopropyl sulfone P1' group. Over the course of the optimization efforts, the 1-(1H-tetrazol-5-yl)cyclopropane P1' substituent emerged as an improved alternative, offering increased metabolic stability and lower clearance, while maintaining excellent potency and selectivity.

  4. New macrocyclic compounds using organotin complexes as intermediates: synthesis and characterization

    Harminder Kaur


    Full Text Available Background & Aim:A new series of macrocyclic compounds 1-4 have been synthesized using tin as templates.Method:Tin templates are formed by refluxing the solution of dibutyltin (IV oxide with orthophenylenediamine (L1H,4-chlorocatechol (L2H, butane dithiol (L3H and 3-carboxypropyldisulphide (L4H. Results:The reaction is visualizedby cleavage X-Sn-X (X= oxygen/ nitrogen/ sulphur atom bond of tin template when treated withadipoyldichloride. Conclusion:The compounds 1-4 are characterized with the aid of elemental analyses, IR and NMR(1H, 13C studies which confirmed their proposed framework.

  5. Application of Calixarenes as Macrocyclic Ligands for Uranium(VI: A Review

    Katarzyna Kiegiel


    Full Text Available Calixarenes represent a well-known family of macrocyclic molecules with broad range of potential applications in chemical, analytical, and engineering materials fields. This paper covers the use of calixarenes as complexing agents for uranium(VI. The high effectiveness of calix[6]arenes in comparison to other calixarenes in uranium(VI separation process is also presented. Processes such as liquid-liquid extraction (LLE, liquid membrane (LM separation, and ion exchange are considered as potential fields for application of calixarenes as useful agents for binding UO22+ for effective separation from aqueous solutions containing other metal components.

  6. Synthesis and antituberculosis activity of novel unfolded and macrocyclic derivatives of ent-kaurane steviol.

    Khaybullin, Ravil N; Strobykina, Irina Yu; Dobrynin, Alexey B; Gubaydullin, Aidar T; Chestnova, Regina V; Babaev, Vasiliy M; Kataev, Vladimir E


    New derivatives of steviol 1, the aglycone of the glycosides of Stevia rebaudiana, including a novel class of semisynthetic diterpenoids, namely macrocyclic ent-kauranes were synthesized. These compounds possess antituberculosis activity inhibiting the in vitro growth of Mycobacterium Tuberculosis (H37R(V) strain) with MIC 5-20 μg/ml that is close to MIC 1 μg/ml demonstrated by antituberculosis drug isoniazid in control experiment. For the first time it was found that the change of ent-kaurane geometry (as in steviol 1) of tetracyclic diterpenoid skeleton to ent-beyerane one (as in isosteviol 2) influences on antituberculosis activity.

  7. Cyclooctane metathesis catalyzed by silica-supported tungsten pentamethyl [(ΞSiO)W(Me)5]: Distribution of macrocyclic alkanes

    Riache, Nassima


    Metathesis of cyclic alkanes catalyzed by the new surface complex [(ΞSiO)W(Me)5] affords a wide distribution of cyclic and macrocyclic alkanes. The major products with the formula CnH2n are the result of either a ring contraction or ring expansion of cyclooctane leading to lower unsubstituted cyclic alkanes (5≤n≤7) and to an unprecedented distribution of unsubstituted macrocyclic alkanes (12≤n≤40), respectively, identified by GC/MS and by NMR spectroscopies.

  8. Modeling of molecular photocells: Application to two-level photovoltaic system with electron-hole interaction.

    Nemati Aram, Tahereh; Anghel-Vasilescu, Petrutza; Asgari, Asghar; Ernzerhof, Matthias; Mayou, Didier


    We present a novel simple model to describe molecular photocells where the energy conversion process takes place by a single molecular donor-acceptor complex attached to electrodes. By applying quantum scattering theory, an open quantum system method, the coherent molecular photocell is described by a wave function. We analyze photon absorption, energy conversion, and quantum yield of a molecular photocell by considering the effects of electron-hole interaction and non-radiative recombination. We model the exciton creation, dissociation, and subsequent effects on quantum yield in the energy domain. We find that depending on the photocell structure, the electron-hole interaction can normally decrease or abnormally increase the cell efficiency. The proposed model helps to understand the mechanisms of molecular photocells, and it can be used to optimize their yield.

  9. Molecular structure design and soft template synthesis of aza-, oxaaza- and thiaazamacrocyclic metal chelates in the gelatin matrix

    Oleg V. Mikhailov


    Full Text Available The data about of soft template synthesis proceeding in gelatin matrices in [3d-element M(II ion – (N,S- or (N,O,S-ambidentate ligson – mono- or dicarbonyl ligson] systems, have been considered and discussed. The chemical nature of the final products of template synthesis formed under these specific conditions, has been compared with the chemical nature of the final products formed by template synthesis in solutions. It has been noted that in many cases, the nature and chemical composition of these products differ substantially. Specific features of the DFT calculated molecular structures of the macrocyclic compounds that can be formed due to the template synthesis in the systems indicated above, have been discussed, too. The review covers the period 1990–2015.

  10. The molecular identity of the mitochondrial Ca2+ sequestration system.

    Starkov, Anatoly A


    There is ample evidence to suggest that a dramatic decrease in mitochondrial Ca(2+) retention may contribute to the cell death associated with stroke, excitotoxicity, ischemia and reperfusion, and neurodegenerative diseases. Mitochondria from all studied tissues can accumulate and store Ca(2+) , but the maximum Ca(2+) storage capacity varies widely and exhibits striking tissue specificity. There is currently no explanation for this fact. Precipitation of Ca(2+) and phosphate in the mitochondrial matrix has been suggested to be the major form of storage of accumulated Ca(2+) in mitochondria. How this precipitate is formed is not known. The molecular identity of almost all proteins involved in Ca(2+) transport, storage and formation of the permeability transition pore is also unknown. This review summarizes studies aimed at identifying these proteins, and describes the properties of a known mitochondrial protein that may be involved in Ca(2+) transport and the structure of the permeability transition pore. © 2010 The Author Journal compilation © 2010 FEBS.

  11. Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems.

    Chiu, Matt; Herbordt, Martin C


    The acceleration of molecular dynamics (MD) simulations using high-performance reconfigurable computing (HPRC) has been much studied. Given the intense competition from multicore and GPUs, there is now a question whether MD on HPRC can be competitive. We concentrate here on the MD kernel computation: determining the short-range force between particle pairs. In one part of the study, we systematically explore the design space of the force pipeline with respect to arithmetic algorithm, arithmetic mode, precision, and various other optimizations. We examine simplifications and find that some have little effect on simulation quality. In the other part, we present the first FPGA study of the filtering of particle pairs with nearly zero mutual force, a standard optimization in MD codes. There are several innovations, including a novel partitioning of the particle space, and new methods for filtering and mapping work onto the pipelines. As a consequence, highly efficient filtering can be implemented with only a small fraction of the FPGA's resources. Overall, we find that, for an Altera Stratix-III EP3ES260, 8 force pipelines running at nearly 200 MHz can fit on the FPGA, and that they can perform at 95% efficiency. This results in an 80-fold per core speed-up for the short-range force, which is likely to make FPGAs highly competitive for MD.

  12. Exciton Localization in Extended π-Electron Systems: Comparison of Linear and Cyclic Structures.

    Thiessen, Alexander; Würsch, Dominik; Jester, Stefan-S; Aggarwal, A Vikas; Idelson, Alissa; Bange, Sebastian; Vogelsang, Jan; Höger, Sigurd; Lupton, John M


    We employ five π-conjugated model materials of different molecular shape-oligomers and cyclic structures-to investigate the extent of exciton self-trapping and torsional motion of the molecular framework following optical excitation. Our studies combine steady state and transient fluorescence spectroscopy in the ensemble with measurements of polarization anisotropy on single molecules, supported by Monte Carlo simulations. The dimer exhibits a significant spectral red shift within ∼100 ps after photoexcitation which is attributed to torsional relaxation. This relaxation mechanism is inhibited in the structurally rigid macrocyclic analogue. However, both systems show a high degree of exciton localization but with very different consequences: while, in the macrocycle, the exciton localizes randomly on different parts of the ring, scrambling polarization memory, in the dimer, localization leads to a deterministic exciton position with luminescence characteristics of a dipole. Monte Carlo simulations allow us to quantify the structural difference between the emitting and absorbing units of the π-conjugated system in terms of disorder parameters.

  13. Coherent control of non-resonant two-photon transition in molecular system

    Zhang Hui; Zhang Shi-An; Wang Zu-Geng; Sun Zhen-Rong


    In this paper,we study theoretically and experimentally the coherent control of non-resonant two-photon transition in a molecular system (Perylene dissolved in chloroform solution) by shaping the femtosecond pulses with simple phase patterns (cosinusoidal and π phase step-function shape).The control efficiency of the two-photon transition probability is correlated with both the laser field and the molecular absorption bandwidth.Our results demonstrate that,the two-photon transition probability in a molecular system can be reduced but not completely eliminated by manipulating the laser field,and the control efficiency is minimal when the molecular absorption bandwidth is larger than twice the laser spectral bandwidth.

  14. Systems theoretic analysis of the central dogma of molecular biology: some recent results.

    Gao, Rui; Yu, Juanyi; Zhang, Mingjun; Tarn, Tzyh-Jong; Li, Jr-Shin


    This paper extends our early study on a mathematical formulation of the central dogma of molecular biology, and focuses discussions on recent insights obtained by employing advanced systems theoretic analysis. The goal of this paper is to mathematically represent and interpret the genetic information flow at the molecular level, and explore the fundamental principle of molecular biology at the system level. Specifically, group theory was employed to interpret concepts and properties of gene mutation, and predict backbone torsion angle along the peptide chain. Finite state machine theory was extensively applied to interpret key concepts and analyze the processes related to DNA hybridization. Using the proposed model, we have transferred the character-based model in molecular biology to a sophisticated mathematical model for calculation and interpretation.

  15. The type II secretion system: biogenesis, molecular architecture and mechanism.

    Korotkov, Konstantin V; Sandkvist, Maria; Hol, Wim G J


    Many gram-negative bacteria use the sophisticated type II secretion system (T2SS) to translocate a wide range of proteins from the periplasm across the outer membrane. The inner-membrane platform of the T2SS is the nexus of the system and orchestrates the secretion process through its interactions with the periplasmic filamentous pseudopilus, the dodecameric outer-membrane complex and a cytoplasmic secretion ATPase. Here, recent structural and biochemical information is reviewed to describe our current knowledge of the biogenesis and architecture of the T2SS and its mechanism of action.

  16. Quantitative Assessment of Molecular Dynamics Sampling for Flexible Systems.

    Nemec, Mike; Hoffmann, Daniel


    Molecular dynamics (MD) simulation is a natural method for the study of flexible molecules but at the same time is limited by the large size of the conformational space of these molecules. We ask by how much the MD sampling quality for flexible molecules can be improved by two means: the use of diverse sets of trajectories starting from different initial conformations to detect deviations between samples and sampling with enhanced methods such as accelerated MD (aMD) or scaled MD (sMD) that distort the energy landscape in controlled ways. To this end, we test the effects of these approaches on MD simulations of two flexible biomolecules in aqueous solution, Met-Enkephalin (5 amino acids) and HIV-1 gp120 V3 (a cycle of 35 amino acids). We assess the convergence of the sampling quantitatively with known, extensive measures of cluster number Nc and cluster distribution entropy Sc and with two new quantities, conformational overlap Oconf and density overlap Odens, both conveniently ranging from 0 to 1. These new overlap measures quantify self-consistency of sampling in multitrajectory MD experiments, a necessary condition for converged sampling. A comprehensive assessment of sampling quality of MD experiments identifies the combination of diverse trajectory sets and aMD as the most efficient approach among those tested. However, analysis of Odens between conventional and aMD trajectories also reveals that we have not completely corrected aMD sampling for the distorted energy landscape. Moreover, for V3, the courses of Nc and Odens indicate that much higher resources than those generally invested today will probably be needed to achieve convergence. The comparative analysis also shows that conventional MD simulations with insufficient sampling can be easily misinterpreted as being converged.

  17. Development of design information for molecular-sieve type regenerative CO2-removal systems

    Wright, R. M.; Ruder, J. M.; Dunn, V. B.; Hwang, K. C.


    Experimental and analytic studies were conducted with molecular sieve sorbents to provide basic design information, and to develop a system design technique for regenerable CO2-removal systems for manned spacecraft. Single sorbate equilibrium data were obtained over a wide range of conditions for CO2, water, nitrogen, and oxygen on several molecular sieve and silica gel sorbents. The coadsorption of CO2 with water preloads, and with oxygen and nitrogen was experimentally evaluated. Mass-transfer, and some limited heat-transfer performance evaluations were accomplished under representative operating conditions, including the coadsorption of CO2 and water. CO2-removal system performance prediction capability was derived.

  18. Structural aspects of molecular recognition in the immune system. Part II: Pattern recognition receptors


    The vertebrate immune system uses pattern recognition receptors (PRRs) to detect a large variety of molecular signatures (pathogen-associated molecular patterns, PAMPs) from a broad range of different invading pathogens. The PAMPs range in size from relatively small molecules, to others of intermediate size such as bacterial lipopolysaccharide, lipopeptides, and oligosaccharides, to macromolecules such as viral DNA, RNA, and pathogen-derived proteins such as flagellin. Underlying this functio...

  19. Systems vaccinology : molecular signatures of immunity to Bordetella pertussis

    Raeven, R.H.M.


    The worldwide resurgence of whooping cough (pertussis), even in highly vaccinated populations, demands improved pertussis vaccines. In this thesis a systems vaccinology approach is applied to deepen knowledge of the immune responses evoked by different pertussis vaccines and compare this with a Bord

  20. Molecular recognition of paired receptors in the immune system

    Kimiko eKuroki


    Full Text Available Cell surface receptors are responsible for regulating cellular function on the front line, the cell membrane. Interestingly, accumulating evidence clearly reveals that the members of cell surface receptor families have very similar extracellular ligand-binding regions but opposite signaling systems, either inhibitory or stimulatory. These receptors are designated as paired receptors. Paired receptors often recognize not only physiological ligands but also non-self ligands, such as viral and bacterial products, to fight infections. In this review, we introduce several representative examples of paired receptors, focusing on two major structural superfamilies, the immunoglobulin-like and the C-type lectin-like receptors, and explain how these receptors distinguish self and non-self ligands to maintain homeostasis in the immune system. We further discuss the evolutionary aspects of these receptors as well as the potential drug targets for regulating diseases.

  1. Anisotropic pressure molecular dynamics for atomic fluid systems

    Romero-Bastida, M [Facultad de Ciencias, Universidad Autonoma del Estado de Morelos, Avenida Universidad 1001, Chamilpa, Cuernavaca, Morelos 62209 (Mexico); Lopez-Rendon, R [Departamento de QuImica, Universidad Autonoma Metropolitana-Iztapalapa, Av San Rafael Atlixco 186, 09340 Mexico DF (Mexico)


    The MTK equations (Martyna G J, Tobias D J and Klein M L 1994 J. Chem. Phys. 101 4177-89), which simulate the constant-pressure, constant-temperature NPT ensemble, have been modified to simulate an anisotropic pressure along a single coordinate axis, thus rendering the NP{sub zz}T ensemble. The necessary theory of non-Hamiltonian systems is briefly reviewed in order to analytically prove that the proposed equations indeed sample the desired ensemble. A previously derived geometric integrator for the MTK equations is modified to take into account the anisotropic pressure and volume fluctuations. We choose a Lennard-Jones fluid as an illustrative example. The density distribution function, as well as various thermodynamic and interfacial properties of the model system in a liquid-vapour coexistence state, was computed to test the robustness of the proposed equations of motion to simulate the NP{sub zz}T ensemble.

  2. Novel molecular targets in the treatment of systemic lupus erythematosus

    Crispín, JoséC; Tsokos, George C.


    T cells from patients with systemic lupus erythematosus (SLE) display a number of biochemical abnormalities which include altered expression of key signaling molecules, heightened calcium responses, and skewed expression of transcription factors. These defects are involved in the altered behavior of SLE T cells and are probably central in the disease pathogenesis. The aim of this communication is to review the defects that have been consistently documented in SLE T cells, highlighting molecules and pathways that represent therapeutic targets. PMID:18190888

  3. Biomedical wellness monitoring system based upon molecular markers

    Ingram, Whitney


    We wish to assist caretakers with a sensor monitoring systems for tracking the physiological changes of homealone patients. One goal is seeking biomarkers and modern imaging sensors like stochastic optical reconstruction microscopy (STORM), which has achieved visible imaging at the nano-scale range. Imaging techniques like STORM can be combined with a fluorescent functional marker in a system to capture the early transformation signs from wellness to illness. By exploiting both microscopic knowledge of genetic pre-disposition and the macroscopic influence of epigenetic factors we hope to target these changes remotely. We adopt dual spectral infrared imaging for blind source separation (BSS) to detect angiogenesis changes and use laser speckle imaging for hypertension blood flow monitoring. Our design hypothesis for the monitoring system is guided by the user-friendly, veteran-preferred "4-Non" principles (noninvasive, non-contact, non-tethered, non-stop-to-measure) and by the NIH's "4Ps" initiatives (predictive, personalized, preemptive, and participatory). We augment the potential storage system with the recent know-how of video Compressive Sampling (CSp) from surveillance cameras. In CSp only major changes are saved, which reduces the manpower cost of caretakers and medical analysts. This CSp algorithm is based on smart associative memory (AM) matrix storage: change features and detailed scenes are written by the outer-product and read by the inner product without the usual Harsh index for image searching. From this approach, we attempt to design an effective household monitoring approach to save healthcare costs and maintain the quality of life of seniors.

  4. Response of Critical Speed to Different Macrocycle Phases during Linear Periodization on Young Swimmers

    João Bartholomeu NETO


    Full Text Available Sport training programs to young swimmers have to aggregate different physical stimulus to collaborate with overall physical development, which can lead to reach best results in competitions. Linear periodization seems to be a powerful tool that allow the organization of these stimulus. However, this model has been not studied. Regarding physical capacities, aerobic fitness is inversely related with fatigue and exercise performance. Although aerobic capacity evaluation used to be expensive, critical speed (CS is easy and non - expensive tool capable to make this measurement. Thus, the aim of this study was evaluate the effects of linear periodization in CS on well - trained young swimmers. Sixteen athletes (age: 14.06  1.22 years, height: 163.52  10.99 cm, weight: 57.4  12.7 kg, body mass index: 21.24  37; 7 ♀, were underwent to a linear macrocycle training with 23 weeks divided in four mesocycles: general endurance (i.e., 4 weeks, specific endurance (i.e., 8 weeks, competitive (i.e., 7 weeks and taper (i.e., 4 weeks. Results showed significantly improve on CS after competitive and taper mesocycle phases, which was composed by higher training intensity in comparison with other macrocycle phases. Therefore, the results of the present study indicate a collaboration of mesocycle intensity on the cumulative effects of linear periodization in CS improve on young swimmers.

  5. Tiered analytics for purity assessment of macrocyclic peptides in drug discovery: Analytical consideration and method development.

    Qian Cutrone, Jingfang Jenny; Huang, Xiaohua Stella; Kozlowski, Edward S; Bao, Ye; Wang, Yingzi; Poronsky, Christopher S; Drexler, Dieter M; Tymiak, Adrienne A


    Synthetic macrocyclic peptides with natural and unnatural amino acids have gained considerable attention from a number of pharmaceutical/biopharmaceutical companies in recent years as a promising approach to drug discovery, particularly for targets involving protein-protein or protein-peptide interactions. Analytical scientists charged with characterizing these leads face multiple challenges including dealing with a class of complex molecules with the potential for multiple isomers and variable charge states and no established standards for acceptable analytical characterization of materials used in drug discovery. In addition, due to the lack of intermediate purification during solid phase peptide synthesis, the final products usually contain a complex profile of impurities. In this paper, practical analytical strategies and methodologies were developed to address these challenges, including a tiered approach to assessing the purity of macrocyclic peptides at different stages of drug discovery. Our results also showed that successful progression and characterization of a new drug discovery modality benefited from active analytical engagement, focusing on fit-for-purpose analyses and leveraging a broad palette of analytical technologies and resources.

  6. A supramolecular ruthenium macrocycle with high catalytic activity for water oxidation that mechanistically mimics photosystem II

    Schulze, Marcus; Kunz, Valentin; Frischmann, Peter D.; Würthner, Frank


    Mimicking the ingenuity of nature and exploiting the billions of years over which natural selection has developed numerous effective biochemical conversions is one of the most successful strategies in a chemist's toolbox. However, an inability to replicate the elegance and efficiency of the oxygen-evolving complex of photosystem II (OEC-PSII) in its oxidation of water into O2 is a significant bottleneck in the development of a closed-loop sustainable energy cycle. Here, we present an artificial metallosupramolecular macrocycle that gathers three Ru(bda) centres (bda = 2,2‧-bipyridine-6,6‧-dicarboxylic acid) that catalyses water oxidation. The macrocyclic architecture accelerates the rate of water oxidation via a water nucleophilic attack mechanism, similar to the mechanism exhibited by OEC-PSII, and reaches remarkable catalytic turnover frequencies >100 s-1. Photo-driven water oxidation yields outstanding activity, even in the nM concentration regime, with a turnover number of >1,255 and turnover frequency of >13.1 s-1.

  7. Synthesis, characterization, and photoactivated DNA cleavage by copper (II)/cobalt (II) mediated macrocyclic complexes.

    Naik, H R Prakash; Naik, H S Bhojya; Aravinda, T; Lamani, D S


    We report the synthesis of new photonuclease consisting of two Co(II)/Cu(II) complexes of macrocyclic fused quinoline. Metal complexes are [MLX(2)], type where M = Co(II) (5), Cu(II) (6), and X = Cl, and are well characterized by elemental analysis, Fourier transform infrared spectroscopy, (1)H-NMR and electronic spectra. We have shown that photocleavage of plasmid DNA is markedly enhanced when this ligand is irradiated in the presence of Cu(II), and more so than that of cobalt. The chemistry of ternary and binary Co(II) complexes showing efficient light induced (360 nm) DNA cleavage activity is summarized. The role of the metal in photoinduced DNA cleavage reactions is explored by designing complex molecules having macrocyclic structure. The mechanistic pathways are found to be concentration dependent on Co(II)/Cu(II) complexes and the photoexcitation energy photoredox chemistry. Highly effective DNA cleavage ability of 6 is attributed to the effective cooperation of the metal moiety.

  8. Coherent versus incoherent excitation energy transfer in molecular systems.

    Chang, Hung-Tzu; Cheng, Yuan-Chung


    We investigate the Markovian limit of a polaronic quantum master equation for coherent resonance energy transfer proposed recently by Jang et al. [J. Chem. Phys. 129, 101104 (2008)]. An expression for the rate of excitation energy transfer (EET) is derived and shown to exhibit both coherent and incoherent contributions. We then apply this theory to calculated EET rates for model dimer systems, and demonstrate that the small-polaron approach predicts a variety of dynamical behaviors. Notably, the results indicate that the EET dynamical behaviors can be understood by the interplay between noise-assisted EET and dynamical localization, while both are well captured by the polaron theory. Finally, we investigate bath correlation effects on the rate of EET and show that bath correlations (or anti-correlations) can either enhance or suppress EET rate depending on the strength of individual system-bath couplings. In summary, we introduce the small-polaron approach as an intuitive physical framework to consolidate our understanding of EET dynamics in the condensed phase.

  9. Molecular alteration of a muscarinic acetylcholine receptor system during synaptogenesis

    Large, T.H.; Cho, N.J.; De Mello, F.G.; Klein, W.L.


    Biochemical properties of the muscarinic acetylcholine receptor system of the avian retina were found to change during the period when synapses form in ovo. Comparison of ligand binding to membranes obtained before and after synaptogenesis showed a significant increase in the affinity, but not proportion, of the high affinity agonist-binding state. There was no change in receptor sensitivity to antagonists during this period. Pirenzepine binding, which can discriminate muscarinic receptor subtypes, showed the presence of a single population of low affinity sites (M2) before and after synaptogenesis. The change in agonist binding was not due to the late development of receptor function. However, detergent-solubilization of membranes eliminated differences in agonist binding between receptors from embryos and hatched chicks, suggesting a developmental change in interactions of the receptor with functionally related membrane components. A possible basis for altered interactions was obtained from isoelectric point data showing that the muscarinic receptor population underwent a transition from a predominantly low pI form (4.25) in 13 day embryos to a predominantly high pI form (4.50) in newly hatched chicks. The possibility that biochemical changes in the muscarinic receptor play a role in differentiation of the system by controlling receptor position on the surface of nerve cells is discussed.

  10. Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

    Sushko, Gennady B; Verkhovtsev, Alexey V; Volkov, Sergey N; Solov'yov, Andrey V


    The concept of molecular mechanics force field has nowadays been widely accepted for studying various processes in biomolecular systems. In this paper we suggest a modification for the standard CHARMM force field, that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, in this paper we provide several case studies where dynamical topology is necessary. In particular, it is shown, that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation or collision induced damage, transformation and fragmentation processes involving biomolecular systems.

  11. A Haptic-Enhanced System for Molecular Sensing

    Comai, Sara; Mazza, Davide

    The science of haptics has received an enormous attention in the last decade. One of the major application trends of haptics technology is data visualization and training. In this paper, we present a haptically-enhanced system for manipulation and tactile exploration of molecules.The geometrical models of molecules is extracted either from theoretical or empirical data using file formats widely adopted in chemical and biological fields. The addition of information computed with computational chemistry tools, allows users to feel the interaction forces between an explored molecule and a charge associated to the haptic device, and to visualize a huge amount of numerical data in a more comprehensible way. The developed tool can be used either for teaching or research purposes due to its high reliance on both theoretical and experimental data.

  12. Molecular mechanism of vitamin D in the cardiovascular system.

    Li, Yan Chun


    Vitamin D deficiency is a global health problem that has various adverse consequences. Vitamin D is mainly synthesized in the skin by sunlight (UV light) irradiation; therefore, vitamin D status is influenced by geographic locations, seasonal changes, and skin pigmentations. The kidney is involved in the biosynthesis of 1,25-dihydroxyvitamin D and the reuptake of filtered 25-hydroxyvitamin D from the proximal tubules, thus, vitamin D deficiency is highly prevalent in patients with kidney disease who have renal insufficiency. There is a growing body of epidemiological and clinical evidence in the literature that links vitamin D deficiency to cardiovascular disease. The discovery of the vitamin D hormone functioning as an endocrine inhibitor of the renin-angiotensin system provides an explanation for this association. This review will discuss the mechanism underlying the connection between vitamin D and cardiovascular disease and its physiological and therapeutic implications.

  13. Ipomoeassin F, a new cytotoxic macrocyclic glycoresin from the leaves of Ipomoea squamosa from the Suriname rainforest.

    Cao, Shugeng; Norris, Andrew; Wisse, Jan H; Miller, James S; Evans, Randy; Kingston, David G I


    A new cytotoxic macrocyclic glycoresin, ipomoeassin F (6), has been isolated from the leaves of Ipomoea squamosa. The structure was elucidated by the interpretation of spectral data. Compound 6 was strongly active in the A2780 (human ovarian cancer cell line) assay with an IC(50) value of 0.036 microM.

  14. Diverse organo-peptide macrocycles via a fast and catalyst-free oxime/intein-mediated dual ligation.

    Satyanarayana, Maragani; Vitali, Francesca; Frost, John R; Fasan, Rudi


    Macrocyclic Organo-Peptide Hybrids (MOrPHs) can be prepared from genetically encoded polypeptides via a chemoselective and catalyst-free reaction between a trifunctional oxyamino/amino-thiol synthetic precursor and an intein-fusion protein incorporating a bioorthogonal keto group.

  15. Isonitrile iron(II) complexes with chiral N2P2 macrocycles in the enantioselective transfer hydrogenation of ketones.

    Bigler, Raphael; Mezzetti, Antonio


    Bis(isonitrile) iron(II) complexes bearing a C2-symmetric N2P2 macrocyclic ligand, which are easily prepared from the corresponding bis(acetonitrile) analogue, catalyze the asymmetric transfer hydrogenation (ATH) of a broad scope of ketones in excellent yields (up to 98%) and with high enantioselectivity (up to 91% ee).

  16. Azalomycin F4a 2-ethylpentyl ester, a new macrocyclic lactone, from mangrove actinomycete Streptomyces sp.211726

    Gan Jun Yuan; Kui Hong; Hai Peng Lin; Jia Li


    Azalomycin F4a 2-ethylpentyl ester,a new 36-membered macrocyclic lactone antibiotic,was isolated from mangrove actinomycete Streptomyces sp.211726.Its structure was elucidated on the basis of spectroscopic data.The compound showed broad-spectrum antifungal activity and moderate cytotoxicity against human colon tumor cell HCT-116.

  17. Phases of polymer systems in solution studied via molecular dynamics

    Anderson, Joshua Allen [Iowa State Univ., Ames, IA (United States)


    Polymers are amazingly versatile molecules with a tremendous range of applications. Our lives would be very different without them. There would be no multitudes of plastic encased electronic gizmos, no latex paint on the walls and no rubber tires, just to name a few of the many commonplace polymer materials. In fact, life as we know it wouldn’t exist without polymers as two of the most essential types of molecules central to cellular life, Proteins and DNA, are both polymers! [1] With their wide range of application to a variety of uses, polymers are still a very active field in basic research. Of particular current interest is the idea of combining polymers with inorganic particles to form novel composite materials. [2] As computers are becoming faster, they are becoming all the more powerful tools for modeling and simulating real systems. With recent advances in computing on graphics processing units (GPUs) [3–7], questions can now be answered via simulation that could not even be asked before. This thesis focuses on the use of computer simulations to model novel polymerinorganic composite systems in order to predict what possible phases can form and under what conditions. The goal is to provide some direction for future experiments and to gain a deeper understanding of the fundamental physics involved. Along the way, there are some interesting and essential side-tracks in the areas of equilibrating complicated phases and accelerating the available computer power with GPU computing, both of which are necessary steps to enable the study of polymer nanocomposites.

  18. Structural insight into RNA recognition motifs: versatile molecular Lego building blocks for biological systems.

    Muto, Yutaka; Yokoyama, Shigeyuki


    'RNA recognition motifs (RRMs)' are common domain-folds composed of 80-90 amino-acid residues in eukaryotes, and have been identified in many cellular proteins. At first they were known as RNA binding domains. Through discoveries over the past 20 years, however, the RRMs have been shown to exhibit versatile molecular recognition activities and to behave as molecular Lego building blocks to construct biological systems. Novel RNA/protein recognition modes by RRMs are being identified, and more information about the molecular recognition by RRMs is becoming available. These RNA/protein recognition modes are strongly correlated with their biological significance. In this review, we would like to survey the recent progress on these versatile molecular recognition modules.

  19. Semiclassical "Divide-and-Conquer" Method for Spectroscopic Calculations of High Dimensional Molecular Systems

    Ceotto, Michele; Di Liberto, Giovanni; Conte, Riccardo


    A new semiclassical "divide-and-conquer" method is presented with the aim of demonstrating that quantum dynamics simulations of high dimensional molecular systems are doable. The method is first tested by calculating the quantum vibrational power spectra of water, methane, and benzene—three molecules of increasing dimensionality for which benchmark quantum results are available—and then applied to C60 , a system characterized by 174 vibrational degrees of freedom. Results show that the approach can accurately account for quantum anharmonicities, purely quantum features like overtones, and the removal of degeneracy when the molecular symmetry is broken.

  20. Relationship between Multi-Phase Formation and Molecular Structure for Liquid Crystal System

    LI Zhenxin; MA Heng; LI Shipu


    A mechanical model of liquid crystals ( LCs ) was used to explain the phase formation and thermal properties. The LC phases in the model are micro-machine systems consisting of an ensemble of molecular rotors, and some dynamic parameters in a semi-experiment molecular orbit method. A novel explanation on the multi-phase formation of LC system is obtained. It is found that the value of the critical rotational velocity is a key parameter for the characterization of each homologous series. The dipole moment of the molecules was also discussed.

  1. Mimicking Biological Delivery Through Feedback-Controlled Drug Release Systems Based on Molecular Imprinting.

    Kryscio, David R; Peppas, Nicholas A


    Intelligent drug delivery systems (DDS) are able to rapidly detect a biological event and respond appropriately by releasing a therapeutic agent; thus, they are advantageous over their conventional counterparts. Molecular imprinting is a promising area that generates a polymeric network which can selectively recognize a desired analyte. This field has been studied for a variety of applications over a long period of time, but only recently has it been investigated for biomedical and pharmaceutical applications. Recent work in the area of molecularly imprinted polymers in drug delivery highlights the potential of these recognitive networks as environmentally responsive DDS that can ultimately lead to feedback controlled recognitive release systems.

  2. Applications of quantum and classical connections in modeling atomic, molecular and electrodynamic systems

    Popa, Alexandru


    Applications of Quantum and Classical Connections in Modeling Atomic, Molecular and Electrodynamical Systems is a reference on the new field of relativistic optics, examining topics related to relativistic interactions between very intense laser beams and particles. Based on 30 years of research, this unique book connects the properties of quantum equations to corresponding classical equations used to calculate the energetic values and the symmetry properties of atomic, molecular and electrodynamical systems. In addition, it examines applications for these methods, and for the calculation of

  3. Efficient access to new chemical space through flow--construction of druglike macrocycles through copper-surface-catalyzed azide-alkyne cycloaddition reactions.

    Bogdan, Andrew R; James, Keith


    A series of 12- to 22-membered macrocycles, with druglike functionality and properties, have been generated by using a simple and efficient copper-catalyzed azide-acetylene cycloaddition reaction, conducted in flow in high-temperature copper tubing, under environmentally friendly conditions. The triazole-containing macrocycles have been generated in up to 90 % yield in a 5 min reaction, without resorting to the high-dilution conditions typical of macrocyclization reactions. This approach represents a very efficient method for constructing this important class of molecules, in terms of yield, concentration, and environmental considerations.

  4. Novel approaches for treating musculoskeletal diseases: molecular orthopedics and systems medicine.

    Mashayekhi, Kaveh; O'Brien, Margaret; Zugun-Eloae, Florin; Labusca, Luminita


    Molecular medicine uses knowledge about cell structure and function for disease, diagnostics, stage characterisation and treatment. The advent of genomic technologies is considerably leading to developments in the field of molecular medicine. The accumulation of detailed information about gene expression, epigenetic variability, protein transcription and functional modulation is contributing to a new era in medicine. Rapid and early diagnostic procedures, molecular characterisation of degenerative and proliferative diseases and personalized therapies are predicted to lead to advancements in health prevention and treatment of disease. Diagnostic tools and therapies based on local and /or general modulation of cellular processes for traumatic or degenerative musculoskeletal conditions are becoming available. A logical consequence of the information derived from extensive data gathering, systems biology and systemic medicine has lead to significant improvements in understanding biological structure and function in a simultaneous bottom top and integrative, holistic manner. The description of disease mechanism at an intimate, subcellular level has a dual benefit. A thorough understanding of the crosstalk involved in molecular pathways both in the normal and the diseased state are expanding scientific knowledge and simultaneously are enabling design cell-targeted and individualized therapies. This paper presents a brief overview of current molecular based treatments available to the orthopedic surgeon and introduces the concept of systemic medicine from the perspective of musculoskeletal pathology.

  5. Kinetics and mechanism of the stepwise complex formation of Cu(II) with tren-centered tris-macrocycles.

    Soibinet, Matthieu; Gusmeroli, Deborah; Siegfried, Liselotte; Kaden, Thomas A; Palivan, Cornelia; Schweiger, Arthur


    The stepwise complexation kinetics of Cu2+ with three tetratopic ligands L1, L2 and L3, tren-centred macrocycles with different bridges connecting the 14-membered macrocycles with the tren unit, have been measured by stopped-flow photodiode array techniques at 25 degrees C, I= 0.5 M (KNO3), and pH = 4.96. The reaction between the first Cu2+ and the ligand consists of several steps. In a rapid reaction Cu2+ first binds to the flexible and more reactive tren-unit. In this intermediate a translocation from the tren unit to the macrocyclic ring, which forms the thermodynamic more stable complex, takes place. This species can react further with a second Cu2+ to give a heterotopic dinuclear species with one Cu2+ bound by the tren-unit and the other coordinated by the macrocycle. A further translocation occurs to give the homoditopic species with two Cu2+ in the macrocycles. Finally a slow rearrangement of the dinuclear complex gives the final species. The rates of the translocation are dependent on the length and rigidity of the bridge, whereas the complexation rates with the tren unit are little affected by it. VIS spectra of the species obtained by fitting the kinetic results, EPR-spectra taken during the reaction, and ES mass spectra of the products confirm the proposed mechanism. The addition of a second, third and fourth equivalent of Cu2+ proceeds in an analogous way, but is complicated by the fact that we start and end with a mixture of species. These steps were evaluated in a qualitative way only.

  6. A ditopic O(4)S(2) macrocycle and its hard, soft, and hard/soft metal complexes exhibiting endo-, exo-, or endo/exocyclic coordination: synthesis, crystal structures, NMR titration, and physical properties.

    Ryu, Hyunsoo; Park, Ki-Min; Ikeda, Mari; Habata, Yoichi; Lee, Shim Sung


    A 20-membered O4S2 macrocycle (L(2)) was synthesized as a ditopic ligating system toward hard and soft metal ions simultaneously. Five complexes (3-7) of L(2) with different structures and coordination modes, including discrete to infinite forms, mono- to heteronuclear, and endo- to exo- and endo/exocoordination, were prepared and structurally characterized. First, the reaction of L(2) with Pb(ClO4)2·3H2O afforded a typical endocyclic mononuclear perchlorato complex [Pb(L(2))(ClO4)2] (3) in which one lead(II) is surrounded by the macrocycle adopting a "tight and bent" conformation. Meanwhile, the reaction with a softer metal salt AgNO3 resulted in the formation of the dinuclear bis(macrocycle) complex [Ag2(L(2))2(NO3)2] (4) in which two exocyclic silver(I) ions are doubly linked by two nitrate ions. The treatment of L(2) with CuI gave a mixture of the exocyclic monomer complex [Cu(L(2))I] (5) and the exocyclic dimer complex [(Cu2I2)(L(2))2] (6), which were separated manually because of their brick and rhomboid shapes of the crystals, respectively. Furthermore, the reaction of L(2) with a mixture of CuI and NaI afforded a photoluminescent heteronuclear complex [Na2(Cu6I8)(L(2))2(CH3CN)4]n (7) in the endo/exocyclic coordination mode. In this case, the endocyclic sodium(I) complex units are linked by the double-open cubanes-type cluster Cu6I8, yielding a two-dimensional network. The structural and binding properties of the complex of L(2) with silver(I) nitrate in solution were monitored by the NMR titration. Photophysical and thermal properties for complex 7 were also investigated and discussed.

  7. Role of multipole moments in electric-field-induced order of dense molecular systems.

    Acebal, Pablo; Carretero, Luis; Blaya, Salvador


    A new model is developed to describe the orientational order of dense molecular systems under an applied external electric field as a function of the n-particle distribution functions of a system under no external perturbation. From an approximation of this expression, the effects of several variables on this orientational order, such as the microscopic properties of the oriented molecules (the molecular geometry and multipole moments) and the solvent or matrix properties, are studied. The theoretical predictions show that, for a correct description of the orientational order, quadrupole and octupole moments must be included, as they play an important role in the orientational order achieved, depending on the molecular geometry. Furthermore, to verify the validity of the model, theoretical predictions are compared with experimental results, and show a good concordance.

  8. Boron Subphthalocyanine Based Molecular Triad Systems for the Capture of Solar Energy.

    Storm, Freja E; Olsen, Stine T; Hansen, Thorsten; De Vico, Luca; Jackson, Nicholas E; Ratner, Mark A; Mikkelsen, Kurt V


    In this study a number of chromophores based on boron subphthalocyanines are investigated for use in the future design of organic photovoltaic devices based on molecular triad systems. The computational study is performed at the TD-DFT CAM-B3LYP/6-311G(d) level of theory. The absorption spectra of these chromophores are simulated using TD-DFT and compared to experimental results. All investigated chromophores absorb light in the visible range and thus are suitable for absorption of sunlight in solar cell applications. On the basis of energy-level alignments, suitable combinations of moieties for a molecular triad system are proposed. The molecular triads will be used in future work as the functional part of organic photovoltaic devices, where the chromophore will be used both to absorb the incoming solar radiation and to increase the distance between the separated charges on donor and acceptor units to increase the lifetime of the charge-separated state.

  9. Flexibility and explicit solvent in molecular-dynamics-based docking of protein-glycosaminoglycan systems.

    Samsonov, Sergey A; Gehrcke, Jan-Philip; Pisabarro, M Teresa


    We present Dynamic Molecular Docking (DMD), a novel targeted molecular dynamics-based protocol developed to address ligand and receptor flexibility as well as the inclusion of explicit solvent in local molecular docking. A class of ligands for which docking performance especially benefits from overcoming these challenges is the glycosaminoglycans (GAGs). GAGs are periodic, highly flexible, and negatively charged polysaccharides playing an important role in the extracellular matrix via interaction with proteins such as growth factors and chemokines. The goal of our work has been to develop a proof of concept for an MD-based docking approach and to analyze its applicability for protein-GAG systems. DMD exploits the electrostatics-driven attraction of a ligand to its receptor, treats both as entirely flexible, and considers solvent explicitly. We show that DMD has high predictive significance for systems dominated by electrostatic attraction and demonstrate its capability to reliably identify the receptor residues contributing most to binding.

  10. Linear pi-conjugated systems derivatized with C60-fullerene as molecular heterojunctions for organic photovoltaics.

    Roncali, Jean


    This tutorial review covers recent contributions in the area of linear pi-conjugated systems bound to fullerenes in view of their application as active materials in photovoltaic devices. The first part discusses the concepts of double-cable polymer and molecular hetero-junction and presents several examples of chemically or electrochemically synthesized C60-derivatized conjugated polymers. The second and main part of the article concerns the various classes of C60-derivatized pi-conjugated oligomers designed in view of their utilization in single-component photovoltaic devices. Thus, C60-containing pi-conjugated systems such as oligoarylenevinylenes, oligoaryleneethynylenes and oligothiophenes are discussed on the basis of the relationships between molecular structure, photophysical properties and performances of the derived photovoltaic devices. A brief last section presents some recent examples of surface-attached molecular hetero-junctions based on self-assembled monolayers and discusses possible routes for future research.

  11. Autonomous Agents: The Origins and Co-Evolution of Reproducing Molecular Systems

    Kauffman, Stuart


    The central aim of this award concerned an investigation into, and adequate formulation of, the concept of an "autonomous agent." If we consider a bacterium swimming upstream in a glucose gradient, we are willing to say of the bacterium that it is going to get food. That is, we are willing, and do, describe the bacterium as acting on its own behalf in an environment. All free living cells are, in this sense, autonomous agents. But the bacterium is "just" a set of molecules. We define an autonomous agent as a physical system able to act on its own behalf in an environment, then ask, "What must a physical system be to be an autonomous agent?" The tentative definition for a molecular autonomous agent is that it must be self-reproducing and carry out at least one thermodynamic work cycle. The work carried out in this grant involved, among other features, the development of a detailed model of a molecular autonomous agent, and study of the kinetics of this system. In particular, a molecular autonomous agent must, by the above tentative definition, not only reproduce, but must carry out at least one work cycle. I took, as a simple example of a self-reproducing molecular system, the single-stranded DNA hexamer 3'CCGCGG5' which can line up and ligate its two complementary trimers, 5'CCG3' and 5'CGG3'. But the two ligated trimers constitute the same molecular sequence in the 3' to 5' direction as the initial hexamer, hence this system is autocatalytic. On the other hand the above system is not yet an autonomous agent. At the minimum, autonomous agents, as I have defined them, are a new class of chemical reaction network. At a maximum, they may constitute a proper definition of life itself.

  12. Advances of Molecular Imaging for Monitoring the Anatomical and Functional Architecture of the Olfactory System.

    Zhang, Xintong; Bi, Anyao; Gao, Quansheng; Zhang, Shuai; Huang, Kunzhu; Liu, Zhiguo; Gao, Tang; Zeng, Wenbin


    The olfactory system of organisms serves as a genetically and anatomically model for studying how sensory input can be translated into behavior output. Some neurologic diseases are considered to be related to olfactory disturbance, especially Alzheimer's disease, Parkinson's disease, multiple sclerosis, and so forth. However, it is still unclear how the olfactory system affects disease generation processes and olfaction delivery processes. Molecular imaging, a modern multidisciplinary technology, can provide valid tools for the early detection and characterization of diseases, evaluation of treatment, and study of biological processes in living subjects, since molecular imaging applies specific molecular probes as a novel approach to produce special data to study biological processes in cellular and subcellular levels. Recently, molecular imaging plays a key role in studying the activation of olfactory system, thus it could help to prevent or delay some diseases. Herein, we present a comprehensive review on the research progress of the imaging probes for visualizing olfactory system, which is classified on different imaging modalities, including PET, MRI, and optical imaging. Additionally, the probes' design, sensing mechanism, and biological application are discussed. Finally, we provide an outlook for future studies in this field.

  13. WeGET: predicting new genes for molecular systems by weighted co-expression

    Szklarczyk, R.; Megchelenbrink, W.; Cizek, P.; Ledent, M.; Velemans, G.; Szklarczyk, D.; Huynen, M.A.


    We have developed the Weighted Gene Expression Tool and database (WeGET, for the prediction of new genes of a molecular system by correlated gene expression. WeGET utilizes a compendium of 465 human and 560 murine gene expression datasets that have been collected from

  14. Anticipatory dynamics of biological systems: from molecular quantum states to evolution

    Igamberdiev, Abir U.


    Living systems possess anticipatory behaviour that is based on the flexibility of internal models generated by the system's embedded description. The idea was suggested by Aristotle and is explicitly introduced to theoretical biology by Rosen. The possibility of holding the embedded internal model is grounded in the principle of stable non-equilibrium (Bauer). From the quantum mechanical view, this principle aims to minimize energy dissipation in expense of long relaxation times. The ideas of stable non-equilibrium were developed by Liberman who viewed living systems as subdivided into the quantum regulator and the molecular computer supporting coherence of the regulator's internal quantum state. The computational power of the cell molecular computer is based on the possibility of molecular rearrangements according to molecular addresses. In evolution, the anticipatory strategies are realized both as a precession of phylogenesis by ontogenesis (Berg) and as the anticipatory search of genetic fixation of adaptive changes that incorporates them into the internal model of genetic system. We discuss how the fundamental ideas of anticipation can be introduced into the basic foundations of theoretical biology.

  15. Exploring coherent transport through π-stacked systems for molecular electronic devices

    Li, Qian; Solomon, Gemma


    transport and thermoelectric response in the π-stacked structures by investigating five representative stacked molecular junctions. We found that a π-stacked system of two substituted anthracenes exhibits good thermopower and a high power factor, suggesting that increased conjugation can enhance...

  16. Non-Sequential Double Recombination High Harmonic Generation in Molecular-like Systems

    Hansen, Kenneth Christian Klochmann; Madsen, Lars Bojer

    Non-sequential double recombination (NSDR) high harmonic generation (HHG) is a strongly correlated two-electron HHG process where two electrons combine their potential and kinetic energy into emitting a single photon. We have studied this process in a molecular-like system and found that the two...

  17. Origami: A Versatile Modeling System for Visualising Chemical Structure and Exploring Molecular Function

    Davis, James; Leslie, Ray; Billington, Susan; Slater, Peter R.


    The use of "Origami" is presented as an accessible and transferable modeling system through which to convey the intricacies of molecular shape and highlight structure-function relationships. The implementation of origami has been found to be a versatile alternative to conventional ball-and-stick models, possessing the key advantages of being both…

  18. Molecular characterization of a functional type VI secretion system from a clinical isolate of Aeromonas hydrophila

    Our laboratory recently molecularly characterized the type II secretion system (T2SS)-associated cytotoxic enterotoxin (Act) and the T3SS-secreted AexU effector from a diarrheal isolate SSU of Aeromonas hydrophila. The role of these toxin proteins in the pathogenesis of A. hydrop...

  19. Molecular Characterization of a Functional Type VI Secretion System from a Clinical Isolate of Aeromonas hydrophilia

    Our laboratory recently molecularly characterized the type II secretion system (T2SS)-associated cytotoxic enterotoxin (Act) and the T3SS-secreted AexU effector from a diarrheal isolate SSU of Aeromonas hydrophila. The role of these toxin proteins in the pathogenesis of A. hydrop...

  20. Molecular Dynamics Simulation of Valveless Pumping in a Closed Nanofluidic Tube System

    Hansen, Jesper S.; Ottesen, Johnny T.


    In this paper we perform a realistic nonequilibrium molecular dynamics simulation of valveless pumping in a closed nanofluidic tube system. It is shown that the simple pumping mechanism can generate a uni-directional mean flow on very small length and times scales, thereby overcoming the technical...

  1. Chemical descriptors, convexity and structure of density matrices in molecular systems

    Bochicchio, Roberto C


    The electron energy and density matrices in molecular systems are convex in respect of the number of particles. So that, the chemical descriptors based on their derivatives present the hamper of discontinuities for isolated systems and consequently higher order derivatives are undefined. The introduction of the interaction between the physical domain with an environment induces a coherent structure for the density matrix in the grand-canonical formulation suppressing the discontinuities leading to the proper definitions of the descriptors.

  2. Vibrational vs. electronic coherences in 2D spectrum of molecular systems

    Butkus, Vytautas; Valkunas, Leonas; Abramavicius, Darius


    The two-dimensional spectroscopy has recently revealed oscillatory behavior of excitation dynamics in molecular systems. However, in the majority of cases it is strongly debated if excitonic or vibrational wavepackets, or evidences of quantum transport have been observed. In this letter, the method for distinguishing between vibrational and excitonic wavepacket motion is presented, based on the phase and amplitude relationships of oscillations of distinct peaks, which has been revealed using fundamental analysis of two-dimensional spectrum of two representative systems.

  3. New Developments in Sleep Research: Molecular Genetics, Gene Expression, and Systems Neurobiology

    Kilduff, Thomas S.; Lein, Ed S; de la Iglesia, Horacio; Sakurai, Takeshi; Fu, Ying-Hui; Shaw, Paul


    Understanding the mechanisms that underlie the control of sleep and wakefulness is a major research area in neuroscience. This mini-symposium review highlights some recent developments at the gene, molecular, cellular, and systems level that have advanced this field. The studies discussed below utilize organisms ranging from flies to humans and focus on the interaction between the sleep homeostatic and circadian systems, the consequences of mutations in genes involved in the circadian clock o...

  4. Standoff characterization of high-molecular components of oil disperse systems

    Ganeeva, Y. M.; Yusupova, T. N.; Romanov, G. V.; Bashkirtseva, N. Y.; Rafailov, Michael K.


    Here we report work done toward standoff characterization of high-molecular components responsible for forming nano-structures in oil disperse system. Complex physical and chemical studies have been conducted specifically on bitumen extracted from rich and poor grade oil sand from Canada. Standoff characterization of oil disperse system highmolecular components is discussed here based on prospective of ultra-fast broadband tunable MWIR laser absorption spectroscopy.


    Ethiop.,3(1), 17-24 (1 939), ... Binucleating copper(II) and cobaltilll complexes of the ligand,. 4,16,20 ... to serve as simple model for multi-metal centered catalysts. ... catalysis in the four electron reduction of dioxygen to water (11,12).

  6. Elucidation of molecular kinetic schemes from macroscopic traces using system identification.

    Fribourg, Miguel; Logothetis, Diomedes E; González-Maeso, Javier; Sealfon, Stuart C; Galocha-Iragüen, Belén; Las-Heras Andrés, Fernando; Brezina, Vladimir


    Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic) processes from the overall (macroscopic) response remains a crucial challenge in the understanding of many aspects of physiology. Here we have devised a hybrid computational-analytical method to accomplish this task, the SYStems-based MOLecular kinetic scheme Extractor (SYSMOLE). SYSMOLE utilizes system-identification input-output analysis to obtain a transfer function between the stimulus and the overall cellular response in the Laplace-transformed domain. It then derives a Markov-chain state molecular kinetic scheme uniquely associated with the transfer function by means of a classification procedure and an analytical step that imposes general biological constraints. We first tested SYSMOLE with synthetic data and evaluated its performance in terms of its rate of convergence to the correct molecular kinetic scheme and its robustness to noise. We then examined its performance on real experimental traces by analyzing macroscopic calcium-current traces elicited by membrane depolarization. SYSMOLE derived the correct, previously known molecular kinetic scheme describing the activation and inactivation of the underlying calcium channels and correctly identified the accepted mechanism of action of nifedipine, a calcium-channel blocker clinically used in patients with cardiovascular disease. Finally, we applied SYSMOLE to study the pharmacology of a new class of glutamate antipsychotic drugs and their crosstalk mechanism through a heteromeric complex of G protein-coupled receptors. Our results indicate that our methodology can be successfully

  7. Elucidation of molecular kinetic schemes from macroscopic traces using system identification

    González-Maeso, Javier; Sealfon, Stuart C.; Galocha-Iragüen, Belén; Brezina, Vladimir


    Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic) processes from the overall (macroscopic) response remains a crucial challenge in the understanding of many aspects of physiology. Here we have devised a hybrid computational-analytical method to accomplish this task, the SYStems-based MOLecular kinetic scheme Extractor (SYSMOLE). SYSMOLE utilizes system-identification input-output analysis to obtain a transfer function between the stimulus and the overall cellular response in the Laplace-transformed domain. It then derives a Markov-chain state molecular kinetic scheme uniquely associated with the transfer function by means of a classification procedure and an analytical step that imposes general biological constraints. We first tested SYSMOLE with synthetic data and evaluated its performance in terms of its rate of convergence to the correct molecular kinetic scheme and its robustness to noise. We then examined its performance on real experimental traces by analyzing macroscopic calcium-current traces elicited by membrane depolarization. SYSMOLE derived the correct, previously known molecular kinetic scheme describing the activation and inactivation of the underlying calcium channels and correctly identified the accepted mechanism of action of nifedipine, a calcium-channel blocker clinically used in patients with cardiovascular disease. Finally, we applied SYSMOLE to study the pharmacology of a new class of glutamate antipsychotic drugs and their crosstalk mechanism through a heteromeric complex of G protein-coupled receptors. Our results indicate that our methodology can be successfully

  8. Metal-macrocycle framework (MMF): supramolecular nano-channel surfaces with shape sorting capability.

    Tashiro, Shohei; Kubota, Ryou; Shionoya, Mitsuhiko


    Hollow nanostructures for the functional assembly of chemical groups with inner surface geometry and regulable stoichiometry enable steric design of interior reaction centers. Herein we report a metal-macrocycle framework (MMF) that forms single-crystalline nanochannels with five distinct enantiomeric pairs of guest binding pockets. During crystal-soaking experiments, the MMF crystals can encapsulate aromatic molecules with high site selectivity. First, constitutional isomers of dibromobenzene are captured and sorted into different binding pockets. Second, each of the optical isomers of (1R/1S)-1-(3-chlorophenyl)ethanol is included diastereoselectively into one of an enantiomeric pair of binding pockets. An advantage of this strategy is that the interior walls can be "repainted" via replacement of the trapped molecules with alternatives. Such guest uptake behaviors would allow highly regioselective or stereoselective reactions within the nanochannel.

  9. Strontium-selective membrane electrodes based on some recently synthesized benzo-substituted macrocyclic diamides.

    Shamsipur, M; Rouhani, S; Sharghi, H; Ganjali, M R; Eshghi, H


    Eight different recently synthesized macrocyclic diamides were studied to characterize their abilities as strontium ion carriers in PVC membrane electrodes. The electrode based on 1,13-diaza-2,3;11,12-dibenzo-4,7,10-trioxacyclopentadecane-14,15-dione exhibits a Nernstian response for Sr(2+) ions over a wide concentration range (1.0 × 10(-)(1)-3.2 × 10(-)(5) M) with a limit of detection of 8.0 × 10(-)(6) M (0.7 ppm). The response time of the sensor is ∼10 s, and the membrane can be used for more than three months without observing any deviation. The electrode revealed comparatively good selectivities with respect to many alkali, alkaline earth, and transition metal ions. It was used as an indicator electrode in potentiometric titration of carbonate ions with a strontium ion solution.

  10. Cobalt(II)-selective membrane electrode based on a recently synthesized benzo-substituted macrocyclic diamide.

    Shamsipur, M; Poursaberi, T; Rouhani, S; Niknam, K; Sharghi, H; Ganjali, M R


    A PVC-membrane electrode based on a recently synthesized 18-membered macrocyclic diamide is presented. The electrode reveals a Nernstian potentiometric response for Co2+ over a wide concentration range (2.0 x 10(-6)-1.0 x 10(-2) M). The electrode has a response time of about 10 s and can be used for at least 2 months without any divergence. The proposed sensor revealed very good selectivities for Co2+ over a wide variety of other metal ions, and could be used over a wide pH range (3.0-8.0). The detection limit of the sensor is 6.0 x 10(-7) M. It was successfully applied to the direct determination and potentiometric titration of cobalt ion.

  11. Tetranuclear manganese(II) complexes of sulfonylcalix[4]arene macrocycles: synthesis, structure, spectroscopic and magnetic properties.

    Lamouchi, Meriem; Jeanneau, Erwann; Pillonnet, Anne; Brioude, Arnaud; Martini, Matteo; Stéphan, Olivier; Meganem, Faouzi; Novitchi, Ghenadie; Luneau, Dominique; Desroches, Cédric


    Two tetranuclear manganese(II) complexes {K(+)[Mn(4)(ThiaSO(2))(2)(OH)](-)} (1) and {K(+)[Mn(4)(ThiaSO(2))(2)(F)](-)} (2) have been synthesized under solvothermal conditions in methanol with p-tert-butylsulfonylcalix[4]arene (ThiaSO(2)). For both complexes, the structure has been established from single-crystal X-ray diffraction. The two complexes are best described as manganese squares sandwiched between two thiacalixarene macrocycles. In both complexes, in the center of the square formed by the four manganese(II) atoms, the unexpected presence of μ(4)-OH(-) or μ(4)-F(-) gives a negative charge to the cluster. The two tetranuclear complexes exhibit strong orange luminescence behavior resulting from the symbiosis between the ThiaSO(2) and the Mn(2+). Despite similar chemical formulation, (1) and (2) present difference in emission intensity and lifetime τ.

  12. Synthesis of Macrocyclic Ionophore for the Development of Highly Selective Chloride Sensor

    Sameena Mehtab


    Full Text Available The macrocyclic ligands 3,8,12,17-tetramethyl-2,18,9,11-bipyridyl-1,4,7,10,13,16-hexaazacyclooctadecanetetrahydro bromide has been synthesized and explored as suitable ionophores for chloride selective membrane sensors. It displays Nernstian behavior (59.2 mV decade-1 across the range of 4.1 × 10-8 to 1.0 × 10-2 M. The detection limit of the electrode is ~ 15 nM and the response time and life times are 14 s and eight weeks respectively over a wide pH range (3.5 - 9.5. Interference from other anions is very low and it can be used as indicator electrode in the potentiometric titration of chloride ions and to determine chloride in agricultural soil water samples.

  13. Graphene supported non-precious metal-macrocycle catalysts for oxygen reduction reaction in fuel cells

    Choi, Hyun-Jung; Ashok Kumar, Nanjundan; Baek, Jong-Beom


    Fuel cells are promising alternative energy devices owing to their high efficiency and eco-friendliness. While platinum is generally used as a catalyst for the oxygen reduction reaction (ORR) in a typical fuel cell, limited reserves and prohibitively high costs limit its future use. The development of non-precious and durable metal catalysts is being constantly conceived. Graphene has been widely used as a substrate for metal catalysts due to its unique properties, thus improving stability and ORR activities. In this feature, we present an overview on the electrochemical characteristics of graphene supported non-precious metal containing macrocycle catalysts that include metal porphyrin and phthalocyanine derivatives. Suggested research and future development directions are discussed.

  14. Dereplication of macrocyclic trichothecenes from extracts of filamentous fungi through UV and NMR profiles.

    Sy-Cordero, Arlene A; Graf, Tyler N; Wani, Mansukh C; Kroll, David J; Pearce, Cedric J; Oberlies, Nicholas H


    Macrocyclic trichothecenes (MTs), which have potent cytotoxicity, have been isolated from many different fungal species. These compounds were evaluated clinically by the US National Cancer Institute in the 1970s and 1980s. However, they have yet to be advanced into viable drugs because of severe side effects. Our team is investigating a diverse library of filamentous fungi for new anticancer leads. To avoid reisolating MTs through bioactivity-directed fractionation studies, a protocol for their facile dereplication was developed. The method uses readily available photodiode array detectors to identify one of two types of characteristic UV spectra for these compounds. In addition, diagnostic signals can be observed in the (1)H-NMR spectra, particularly for the epoxide and conjugated diene moieties, even at the level of a crude extract. Using these techniques in a complementary manner, MTs can be dereplicated rapidly.

  15. Synthesis and properties of new bolaform and macrocyclic galactose-based surfactants obtained by olefin metathesis.

    Satgé, Céline; Granet, Robert; Verneuil, Bernard; Champavier, Yves; Krausz, Pierre


    A series of galactose-based surfactants with various structures likely to display new interesting properties were synthesized. Four monocatenary surfactants were elaborated by microwave-assisted galactosylation of undecanol or 10-undecenol. These compounds were slightly soluble in water. Their tensioactive properties were determined at 45 degrees C. Olefin metathesis was used to synthesize the two single-chain bolaforms from undec-10-enyl galactopyranosides; two pseudomacrocyclic bolaforms were prepared by grafting two carbamates at O-4 and O-4' sugar positions of the single-chain bolaforms. These four surfactants are insoluble in water and undergo monolayer compression. Cyclization of these bolaforms by olefin metathesis led to macrocyclic surfactant analogues of archaeobacterial membrane components.

  16. HPLC Enantioseparation of Phenylcarbamic Acid Derivatives by Using Macrocyclic Chiral Stationary Phases

    Hroboňová Katarína


    Full Text Available The HPLC by using chiral stationary phases based on macrocyclic antibiotics, dimethylphenyl carbamate cyklofructan 7 and β-cyclodextrin in terms of polar-organic separation mode (mobile phase methanol/acetonitrile/acetic acid/triethylamine were used for enantioseparation of alkoxy derivatives of phenylcarbamic acid. The effect of the analyte structures on the efficiency of enantioseparation was investigated. The most suitable stationary phase was teicoplanin aglycone, where the separations of the enantiomers were obtained (the resolution value from 0.65 to 2.90, depending on the structure of the analyte. Significant effect on the resolution of the enantiomers has position of alkoxy substituent in the hydrophobic part of the molecule. The enantiorecognition was achieved for 3-alkoxysubstituted derivatives.

  17. Validation of a screening method for rapid control of macrocyclic lactone mycotoxins in maize flour samples.

    Zougagh, Mohammed; Téllez, Helena; Sánchez, Alberto; Chicharro, Manuel; Ríos, Angel


    A procedure for the analytical validation of a rapid supercritical fluid extraction amperometric screening method for controlling macrocyclic lactone mycotoxins in maize flour samples has been developed. The limit established by European legislation (0.2 mg kg(-1)), in reference to zearalenone (ZON) mycotoxin, was taken as the reference threshold to validate the proposed method. Natural ZON metabolites were also included in this study to characterize the final screening method. The objective was the reliable classification of samples as positive or negative samples. The cut-off level was fixed at a global concentration of mycotoxins of 0.17 mg kg(-1). An expanded unreliability zone between 0.16 and 0.23 mg kg(-1) characterized the screening method for classifying the samples. A set of 30 samples was used for the final demonstration of the reliability and usefulness of the method.

  18. Immune and nervous systems share molecular and functional similarities: memory storage mechanism.

    Habibi, L; Ebtekar, M; Jameie, S B


    One of the most complex and important features of both the nervous and immune systems is their data storage and retrieval capability. Both systems encounter a common and complex challenge on how to overcome the cumbersome task of data management. Because each neuron makes many synapses with other neurons, they are capable of receiving data from thousands of synaptic connections. The immune system B and T cells have to deal with a similar level of complexity because of their unlimited task of recognizing foreign antigens. As for the complexity of memory storage, it has been proposed that both systems may share a common set of molecular mechanisms. Here, we review the molecular bases of memory storage in neurons and immune cells based on recent studies and findings. The expression of certain molecules and mechanisms shared between the two systems, including cytokine networks, and cell surface receptors, are reviewed. Intracellular signaling similarities and certain mechanisms such as diversity, memory storage, and their related molecular properties are briefly discussed. Moreover, two similar genetic mechanisms used by both systems is discussed, putting forward the idea that DNA recombination may be an underlying mechanism involved in CNS memory storage.

  19. Diversity-oriented approach to macrocyclic cyclophane derivatives by Suzuki-Miyaura cross-coupling and olefin metathesis as key steps.

    Kotha, Sambasivarao; Chavan, Arjun S; Shaikh, Mobin


    Palladium-catalyzed Suzuki-Miyaura (SM) cross-coupling reaction with allylboronic acid pinacol ester and titanium assisted cross-metathesis (CM)/ring-closing metathesis (RCM) cascade has been used to synthesize macrocyclic cyclophane derivatives.

  20. Metal Vector Manipulated Molecular Self-Assembly from Werner System to Cotton System

    YU Shu-Yan; ZHANG Zhong-Xing; HUANG Hui; LI Sheng-Hui; HUANG Hai-Ping


    A definition of metal vector was given to coordinatively unsaturated metals or asymmetrically coordinated metal complexes in which the metal center is partly blocked by inert chelating ligand(s), thus possess specific reactivity and directionality, such as cis-coordinated square Pd(Ⅱ) or Pt(Ⅱ) complexes. Metal vectors have been extensively used in coordination catalysis and molecular assembly. In 1990, Fujita [ 1 ] first demonstrated the utility of cis-coordinated square Pd(Ⅱ)or Pt(Ⅱ) complexes as a right angular 2D metal vector in the formation of molecular square, a cyclic tetramer with nano-cavity and unique molecular recognition. So far, much attention has been paid to the use of the mononuclear coordination centers (Werner-type metal vectors) in molecular assembly.As late as 1999, Cotton et al. [2] reported the use of cis-coordinated metal-metal bonded dimetal units (Cotton-type metal vectors) to direct assembly of molecular squares.This presentation includes two parts: 1) Werner-type metal vector directed molecular assembly; [3]2) Cotton-type metal vector directed molecular assembly.[4]Firstly, the Werner-type metal vector, cis-coordinated Pd(Ⅱ) nitrate, was used to direct a 6-component self-assembly. This leads to the formation of a molecular bowl or crown with syn,syn,syn conformation. These structures are analogues of calix[3]arenes and can function as anion receptors. Interestingly, an nitrate is found to distort from a trigonal plane into a trigonal pyramid when binding to the bottom of the molecular bowl.Secondly, the Cotton-type metal vector, cis-diRh(Ⅱ, Ⅱ), was used to assemble di- or poly-carboxylate anions into neutral supermolecules. Most interestingly, a calixarene-based carceplex with four cis-diRh(Ⅱ, Ⅱ) fastners was obtained[5].All self-assembling entities were studied by both X-ray crystallographic analysis and solution NMR spectra, which are consistent with the presence of assembling structures even in solution.

  1. Theory of quantum and classical connections in modeling atomic, molecular and electrodynamical systems

    Popa, Alexandru


    Quantum and Classical Connections in Modeling Atomic, Molecular and Electrodynamic Systems is intended for scientists and graduate students interested in the foundations of quantum mechanics and applied scientists interested in accurate atomic and molecular models. This is a reference to those working in the new field of relativistic optics, in topics related to relativistic interactions between very intense laser beams and particles, and is based on 30 years of research. The novelty of this work consists of accurate connections between the properties of quantum equations and correspon

  2. Real-time observation of vibrational revival in the fastest molecular system

    Rudenko, A.; Ergler, Th.; Feuerstein, B.; Zrost, K.; Schröter, C. D.; Moshammer, R.; Ullrich, J.


    After preparing a coherent vibrational wave packet in the hydrogen molecular ion by ionizing neutral H2 molecules with a 6.5 fs, 760 nm laser pulse at 3 × 1014 W/cm2, we map its spatio-temporal evolution by the fragmentation induced with a second 6.5 fs laser pulse of doubled intensity. In this proof-of-principle experiment, we visualize the oscillations of this most fundamental molecular system, observe a dephasing of the vibrational wave packet and its subsequent revival. Whereas the experi...

  3. Synthesis of a TREN in which the aryl substituents are part of a 45 atom macrocycle.

    Cain, Matthew F; Forrest, William P; Peryshkov, Dmitry V; Schrock, Richard R; Müller, Peter


    A substituted TREN has been prepared in which the aryl groups in (ArylNHCH2CH2)3N are substituted at the 3- and 5-positions with a total of six OCH2(CH2)nCH═CH2 groups (n = 1, 2, 3). Molybdenum nitride complexes, [(ArylNCH2CH2)3N]Mo(N), have been isolated as adducts that contain B(C6F5)3 bound to the nitride. Two of these [(ArylNCH2CH2)3N]Mo(NB(C6F5)3) complexes (n = 1 and 3) were crystallographically characterized. After removal of the borane from [(ArylNCH2CH2)3N]Mo(NB(C6F5)3) with PMe3, ring-closing olefin metathesis (RCM) was employed to join the aryl rings with OCH2(CH2)nCH═CH(CH2)nCH2O links (n = 1-3) between them. RCM worked best with a W(O)(CHCMe3)(Me2Pyr)(OHMT)(PMe2Ph) catalyst (OHMT = hexamethylterphenoxide, Me2Pyr = 2,5-dimethylpyrrolide) and n = 3. The macrocyclic ligand was removed from the metal through hydrolysis and isolated in 70-75% yields relative to the borane adducts. Crystallographic characterization showed that the macrocyclic TREN ligand in which n = 3 contains three cis double bonds. Hydrogenation produced a TREN in which the three links are saturated, i.e., O(CH2)10O.

  4. Virtual libraries of tetrapyrrole macrocycles. Combinatorics, isomers, product distributions, and data mining.

    Taniguchi, Masahiko; Du, Hai; Lindsey, Jonathan S


    A software program (PorphyrinViLiGe) has been developed to enumerate the type and relative amounts of substituted tetrapyrrole macrocycles in a virtual library formed by one of four different classes of reactions. The classes include (1) 4-fold reaction of n disubstituted heterocycles (e.g., pyrroles or diiminoisoindolines) to form β-substituted porphyrins, β-substituted tetraazaporphyrins, or α- or β-substituted phthalocyanines; (2) combination of m aminoketones and n diones to form m × n pyrroles, which upon 4-fold reaction give β-substituted porphyrins; (3) derivatization of an 8-point tetrapyrrole scaffold with n reagents, and (4) 4-fold reaction of n aldehydes and pyrrole to form meso-substituted porphyrins. The program accommodates variable ratios of reactants, reversible or irreversible reaction (reaction classes 1 and 2), and degenerate modes of formation. Pólya's theorem (for enumeration of cyclic entities) has also been implemented and provides validation for reaction classes 3 and 4. The output includes the number and identity of distinct reaction-accessible substituent combinations, the number and identity of isomers thereof, and the theoretical mass spectrum. Provisions for data mining enable assessment of the number of products having a chosen pattern of substituents. Examples include derivatization of an octa-substituted phthalocyanine with eight reagents to afford a library of 2,099,728 members (yet only 6435 distinct substituent combinations) and reversible reaction of six distinct disubstituted pyrroles to afford 2649 members (yet only 126 distinct substituent combinations). In general, libraries of substituted tetrapyrrole macrocycles occupy a synthetically accessible region of chemical space that is rich in isomers (>99% or 95% for the two examples, respectively).

  5. Macrocyclic nickel(II) complexes: Synthesis, characterization, superoxide scavenging activity and DNA-binding

    Ramadan, Abd El-Motaleb M.


    A new series of nickel(II) complexes with the tetraaza macrocyclic ligand have been synthesized as possible functional models for nickel-superoxide dismutase enzyme. The reaction of 5-amino-3-methyl-1-phenylpyrazole-4-carbaldehyde (AMPC) with itself in the presence of nickel(II) ion yields, the new macrocyclic cationic complex, [NiL(NO3)2], containing a ligand composed of the self-condensed AMPC (4 mol) bound to a single nickel(II) ion. A series of metathetical reactions have led to the isolation of a number of newly complexes of the types [NiL]X2; X = ClO4 and BF4, [NiLX2], X = Cl and Br (Scheme 1). Structures and characterizations of these complexes were achieved by several physicochemical methods namely, elemental analysis, magnetic moment, conductivity, and spectral (IR and UV-Vis) measurements. The electrochemical properties and thermal behaviors of these chelates were investigated by using cyclic voltammetry and thermogravimetric analysis (TGA and DTG) techniques. A distorted octahedral stereochemistry has been proposed for the six-coordinate nitrato, and halogeno complexes. For the four-coordinate, perchlorate and fluoroborate, complex species a square-planar geometry is proposed. The measured superoxide dismutase mimetic activities of the complexes indicated that they are potent NiSOD mimics and their activities are compared with those obtained previously for nickel(II) complexes. The probable mechanistic implications of the catalytic dismutation of O2rad - by the synthesized nickel(II) complexes are discussed. The DNA-binding properties of representative complexes [NiLCl2] and [NiL](PF4)2 have been investigated by the electronic absorption and fluorescence measurements. The results obtained suggest that these complexes bind to DNA via an intercalation binding mode and the binding affinity for DNA follows the order: [NiLCl2] □ [NiL](PF4)2.

  6. Macrocyclic beta-sheet peptides that mimic protein quaternary structure through intermolecular beta-sheet interactions.

    Khakshoor, Omid; Demeler, Borries; Nowick, James S


    This paper reports the design, synthesis, and characterization of a family of cyclic peptides that mimic protein quaternary structure through beta-sheet interactions. These peptides are 54-membered-ring macrocycles comprising an extended heptapeptide beta-strand, two Hao beta-strand mimics [JACS 2000, 122, 7654] joined by one additional alpha-amino acid, and two delta-linked ornithine beta-turn mimics [JACS 2003, 125, 876]. Peptide 3a, as the representative of these cyclic peptides, contains a heptapeptide sequence (TSFTYTS) adapted from the dimerization interface of protein NuG2 [PDB ID: 1mio]. 1H NMR studies of aqueous solutions of peptide 3a show a partially folded monomer in slow exchange with a strongly folded oligomer. NOE studies clearly show that the peptide self-associates through edge-to-edge beta-sheet dimerization. Pulsed-field gradient (PFG) NMR diffusion coefficient measurements and analytical ultracentrifugation (AUC) studies establish that the oligomer is a tetramer. Collectively, these experiments suggest a model in which cyclic peptide 3a oligomerizes to form a dimer of beta-sheet dimers. In this tetrameric beta-sheet sandwich, the macrocyclic peptide 3a is folded to form a beta-sheet, the beta-sheet is dimerized through edge-to-edge interactions, and this dimer is further dimerized through hydrophobic face-to-face interactions involving the Phe and Tyr groups. Further studies of peptides 3b-3n, which are homologues of peptide 3a with 1-6 variations in the heptapeptide sequence, elucidate the importance of the heptapeptide sequence in the folding and oligomerization of this family of cyclic peptides. Studies of peptides 3b-3g show that aromatic residues across from Hao improve folding of the peptide, while studies of peptides 3h-3n indicate that hydrophobic residues at positions R3 and R5 of the heptapeptide sequence are important in oligomerization.

  7. Lighting porphyrins and phthalocyanines for molecular photovoltaics.

    Martínez-Díaz, M Victoria; de la Torre, Gema; Torres, Tomás


    The field of organic photovoltaics (OPV) represents one of the most promising technological areas. Porphyrins and phthalocyanines are perfectly suited for their integration in light energy conversion systems. These colored macrocycles exhibit very attractive physical properties, particularly very high extinction coefficients in the visible and near IR regions, where the maximum of the solar photon flux occurs, that is necessary for efficient photon harvesting, besides a rich redox chemistry, as well as photoinduced electron transfer and semiconducting capabilities.

  8. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems.

    Sophie S Abby

    Full Text Available Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose.Macromolecular System Finder (MacSyFinder provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems. Models are used to search for molecular systems in complete genomes or in unstructured data like metagenomes. The components of the systems are searched by sequence similarity using Hidden Markov model (HMM protein profiles. The assignment of hits to a given system is decided based on compliance with the content and organization of the system model. A graphical interface, MacSyView, facilitates the analysis of the results by showing overviews of component content and genomic context. To exemplify the use of MacSyFinder we built models to detect and class CRISPR-Cas systems following a previously established classification. We show that MacSyFinder allows to easily define an accurate "Cas-finder" using publicly available protein profiles.MacSyFinder is a standalone application implemented in Python. It requires Python 2.7, Hmmer and makeblastdb (version 2.2.28 or higher. It is freely available with its source code under a GPLv3 license at It is compatible with all platforms supporting Python and Hmmer/makeblastdb. The "Cas-finder" (models and HMM profiles is distributed as a compressed tarball archive as Supporting Information.

  9. Peptide macrocycles featuring a backbone secondary amine: a convenient strategy for the synthesis of lipidated cyclic and bicyclic peptides on solid support.

    Oddo, Alberto; Münzker, Lena; Hansen, Paul R


    A convenient strategy for the on-resin synthesis of macrocyclic peptides (3- to 13-mers) via intramolecular halide substitution by a diamino acid is described. The method is compatible with standard Fmoc/tBu SPPS and affords a tail-to-side-chain macrocyclic peptide featuring an endocyclic secondary amine. This functional group is still reactive toward acylation, allowing for the continuation of the synthesis. An application to the synthesis of lipidated cyclic and bicyclic antimicrobial peptides is presented.

  10. A chemical system that mimics decoding operations.

    Giansante, Carlo; Ceroni, Paola; Venturi, Margherita; Sakamoto, Junji; Schlüter, A Dieter


    The chemical information stored in equilibrium mixtures of molecular species is larger than the sum of information carried by the individual molecules. Protonation equilibria in dilute dichloromethane solution of a shape-persistent macrocycle bearing two 2,2'-bipyridine units and two Coumarin 2 moieties (see figure) can be exploited to mimic decoding operations.

  11. Parametric Sensitivity Analysis for Stochastic Molecular Systems using Information Theoretic Metrics

    Tsourtis, Anastasios; Katsoulakis, Markos A; Harmandaris, Vagelis


    In this paper we extend the parametric sensitivity analysis (SA) methodology proposed in Ref. [Y. Pantazis and M. A. Katsoulakis, J. Chem. Phys. 138, 054115 (2013)] to continuous time and continuous space Markov processes represented by stochastic differential equations and, particularly, stochastic molecular dynamics as described by the Langevin equation. The utilized SA method is based on the computation of the information-theoretic (and thermodynamic) quantity of relative entropy rate (RER) and the associated Fisher information matrix (FIM) between path distributions. A major advantage of the pathwise SA method is that both RER and pathwise FIM depend only on averages of the force field therefore they are tractable and computable as ergodic averages from a single run of the molecular dynamics simulation both in equilibrium and in non-equilibrium steady state regimes. We validate the performance of the extended SA method to two different molecular stochastic systems, a standard Lennard-Jones fluid and an al...

  12. Third international conference on intelligent systems for molecular biology (ISMB-95): Summary. Final report



    The specific aims of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB-95) were to: convene a critical mass of researchers applying advanced computational techniques to problems in molecular biology; promote interchange of problems and solutions between computer scientists and molecular biologists; create education opportunities in this cross-disciplinary field for students and senior researchers wishing to either apply or benefit from these techniques; produce an archival proceedings as a forum for rapid dissemination of new results in a peer-reviewed manner; produce a set of tutorial materials for education and training of researchers interested in this field; maintain the momentum generated by the highly successful previous conferences in the series, and establish a regular event that will help to solidify the field; and foster the involvement of women and minorities in the field.

  13. Intramolecular charge ordering in the multi molecular orbital system (TTM-TTP)I3

    Bonnet, Marie-Laure; Robert, Vincent; Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu


    Starting from the structure of the (TTM-TTP)I3 molecular-based material, we examine the characteristics of frontier molecular orbitals using ab initio (CASSCF/CASPT2) configurations interaction calculations. It is shown that the singly occupied and second-highest-occupied molecular orbitals are close to each other, i.e., this compound should be regarded as a two-orbital system. By dividing virtually the [TTM-TTP] molecule into three fragments, an effective model is constructed to rationalize the origin of this picture. In order to investigate the low-temperature, symmetry breaking experimentally observed in the crystal, the electronic distribution in a pair of [TTM-TTP] molecules is analyzed from CASPT2 calculations. Our inspection supports and explains the speculated intramolecular charge ordering which is likely to give rise to low-energy magnetic properties.

  14. Cyano-bridged structures based on [MnIIN3O2-macrocycle)]2+: a synthetic, structural, and magnetic study.

    Bonadio, Federica; Senna, Maria-Cristina; Ensling, Jürgen; Sieber, Andreas; Neels, Antonia; Stoeckli-Evans, Helen; Decurtins, Silvio


    Reactions between the complex [MnII(L)]2+, where L is a N3O2 macrocyclic ligand, and different cyanometalate precursors such as [M(CN)n]m- (M(III) = Cr, Fe; M(II) = Fe, Ni, Pd, Pt) lead to cyano-bridged molecular assemblies exhibiting a variety of structural topologies. The reaction between [MnII(L)]2+ and [FeII(CN)6]4- forms a trinuclear complex with formula [(MnII(L)(H2O))2(FeII(micro-CN)2(CN)4)] x 2MeOH x 10H2O (1) which crystallizes in the triclinic space group P1. The reaction between [MnII(L)]2+ and [M(II)(CN)4]2-, where M(II) = Ni (2), Pd (3), Pt (4), gives rise to three isostructural linear chain compounds with stoichiometry [(MnII(L))(M(II)(micro-CN)2(CN)2)]n and which crystallize in the monoclinic space group C2/c. The self-assembly between [MnII(L)]2+ with [M(III)(CN)6]3-, where M(III) = Cr (5), Fe (6, 7, 8), forms three types of compounds. Compounds 5 and 6 are isostructural (monoclinic, space group P2(1)/n), and the structures comprise anionic linear chains [(MnII(L))(M(III)(micro-CN)2(CN)4)]n(n-) with cationic trinuclear complexes [(MnII(L)(H2O))2(M(III)(micro-CN)2(CN)4)]+ as counterions. Using an excess of K3[FeIII(CN)6], an analogous compound to 6 but with K+ as counterion is obtained (7), which crystallizes in the triclinic space group P1. Compound 8 consists of 2-D layers with formula [(MnII(L))3(FeIII(micro-CN)4(CN)2)(FeIII(micro-CN)2(CN)4)]n x 2nMeOH; it crystallizes in the monoclinic space group P2(1)/n. The magnetic properties were investigated for all samples. In particular, compound 5, which shows antiferromagnetic exchange interactions between Mn(II) and Cr(III) ions through cyanide bridging ligands, has been studied in detail; the magnetic exchange parameter amounts to J = -7.5(7) cm(-1). Compound 8 shows a magnetically ordered phase below 6.4 K which is confirmed by Mössbauer spectroscopy; two hyperfine split spectra were observed below Tc from which IJI values of 2.1 and 1.6 cm(-1) could be deduced.

  15. [Molecular genetics of familial tumour syndromes of the central nervous system].

    Murnyák, Balázs; Szepesi, Rita; Hortobágyi, Tibor


    Although most of the central nervous system tumours are sporadic, rarely they are associated with familial tumour syndromes. These disorders usually present with an autosomal dominant inheritance and neoplasia develops at younger age than in sporadic cases. Most of these tumours are bilateral, multiplex or multifocal. The causative mutations occur in genes involved in cell cycle regulation, cell growth, differentiation and DNA repair. Studying these hereditary cancer predisposition syndromes associated with nervous system tumours can facilitate the deeper understanding of the molecular background of sporadic tumours and the development of novel therapeutic agents. This review is an update on hereditary tumour syndromes with nervous system involvement with emphasis on molecular genetic characteristics and their clinical implications.

  16. An analytic approach to 2D electronic PE spectra of molecular systems

    Szoecs, V., E-mail: [Institute of Chemistry, Comenius University, Mlynska dolina CH2, 842 15 Bratislava (Slovakia)


    Graphical abstract: The three-pulse photon echo (3P-PE) spectra of finite molecular systems using direct calculation from electronic Hamiltonians allows peak classification from 3P-PE spectra dynamics. Display Omitted Highlights: {yields} RWA approach to electronic photon echo. {yields} A straightforward calculation of 2D electronic spectrograms in finite molecular systems. {yields} Importance of population time dynamics in relation to inter-site coherent coupling. - Abstract: The three-pulse photon echo (3P-PE) spectra of finite molecular systems and simplified line broadening models is presented. The Fourier picture of a heterodyne detected three-pulse rephasing PE signal in the {delta}-pulse limit of the external field is derived in analytic form. The method includes contributions of one and two-excitonic states and allows direct calculation of Fourier PE spectrogram from corresponding Hamiltonian. As an illustration, the proposed treatment is applied to simple systems, e.g. 2-site two-level system (TLS) and n-site TLS model of photosynthetic unit. The importance of relation between Fourier picture of 3P-PE dynamics (corresponding to nonzero population time, T) and coherent inter-state coupling is emphasized.

  17. Self-assembly of intramolecular charge-transfer compounds into functional molecular systems.

    Li, Yongjun; Liu, Taifeng; Liu, Huibiao; Tian, Mao-Zhong; Li, Yuliang


    Highly polarized compounds exhibiting intramolecular charge transfer (ICT) are used widely as nonlinear optical (NLO) materials and red emitters and in organic light emitting diodes. Low-molecular-weight donor/acceptor (D/A)-substituted ICT compounds are ideal candidates for use as the building blocks of hierarchically structured, multifunctional self-assembled supramolecular systems. This Account describes our recent studies into the development of functional molecular systems with well-defined self-assembled structures based on charge-transfer (CT) interactions. From solution (sensors) to the solid state (assembled structures), we have fully utilized intrinsic and stimulus-induced CT interactions to construct these functional molecular systems. We have designed some organic molecules capable of ICT, with diversity and tailorability, that can be used to develop novel self-assembled materials. These ICT organic molecules are based on a variety of simple structures such as perylene bisimide, benzothiadiazole, tetracyanobutadiene, fluorenone, isoxazolone, BODIPY, and their derivatives. The degree of ICT is influenced by the nature of both the bridge and the substituents. We have developed new methods to synthesize ICT compounds through the introduction of heterocycles or heteroatoms to the π-conjugated systems or through extending the conjugation of diverse aromatic systems via another aromatic ring. Combining these ICT compounds featuring different D/A units and different degrees of conjugation with phase transfer methodologies and solvent-vapor techniques, we have self-assembled various organic nanostructures, including hollow nanospheres, wires, tubes, and ribbonlike architectures, with controllable morphologies and sizes. For example, we obtained a noncentrosymmetric microfiber structure that possessed a permanent dipole along its fibers' long axis and a transition dipole perpendicular to it; the independent NLO responses of this material can be separated and

  18. Time-dependent theoretical treatments of the dynamics of electrons and nuclei in molecular systems

    Deumens, E.; Diz, A.; Longo, R.; Öhrn, Y.


    An overview is presented of methods for time-dependent treatments of molecules as systems of electrons and nuclei. The theoretical details of these methods are reviewed and contrasted in the light of a recently developed time-dependent method called electron-nuclear dynamics. Electron-nuclear dynamics (END) is a formulation of the complete dynamics of electrons and nuclei of a molecular system that eliminates the necessity of constructing potential-energy surfaces. Because of its general formulation, it encompasses many aspects found in other formulations and can serve as a didactic device for clarifying many of the principles and approximations relevant in time-dependent treatments of molecular systems. The END equations are derived from the time-dependent variational principle applied to a chosen family of efficiently parametrized approximate state vectors. A detailed analysis of the END equations is given for the case of a single-determinantal state for the electrons and a classical treatment of the nuclei. The approach leads to a simple formulation of the fully nonlinear time-dependent Hartree-Fock theory including nuclear dynamics. The nonlinear END equations with the ab initio Coulomb Hamiltonian have been implemented at this level of theory in a computer program, ENDyne, and have been shown feasible for the study of small molecular systems. Implementation of the Austin Model 1 semiempirical Hamiltonian is discussed as a route to large molecular systems. The linearized END equations at this level of theory are shown to lead to the random-phase approximation for the coupled system of electrons and nuclei. The qualitative features of the general nonlinear solution are analyzed using the results of the linearized equations as a first approximation. Some specific applications of END are presented, and the comparison with experiment and other theoretical approaches is discussed.

  19. MR Imaging Findings in Molecular Subtypes of Breast Cancer According to BIRADS System.

    Navarro Vilar, Lidia; Alandete Germán, Salvador Pascual; Medina García, Rosana; Blanc García, Esther; Camarasa Lillo, Natalia; Vilar Samper, José


    To evaluate magnetic resonance imaging (MRI) findings, according to Breast Imaging-Reporting and Data System (BI-RADS), and to relate them with molecular subtypes of breast cancer. The MRI findings were reviewed retrospectively in 201 women diagnosed of invasive breast cancer confirmed by surgery and were compared with the molecular subtypes. Following the BI-RADS, MRI findings included disease type, size, enhancement, morphology and contrast kinetics. In mass-like lesion types were studied shape, margin and enhancement, and in nonmass-like lesion types, distribution modifiers and internal enhancement. Chi-squared analysis showed significant association (p < 0.01) between molecular subtypes and lesion type on MRI and histologic grade. Shape, margin and mass enhancement (p < 0.05) also showed significant association among molecular subtypes. Triple negative were more frequently unifocal and mass-like lesion, high histologic grade, round shape, smooth margin, and rim enhancement. Luminal-A were more frequently low grade, mass-like lesion, irregular shape and spiculated or irregular margin. Luminal-B were more frequently moderate-low grade, mass-like lesion, nonirregular shape and spiculated margin. HER-2-enriched were more frequently moderate grade, nonmass-like lesion and multicentric lesions were more present than in other subtypes. There are significantly different MRI features, according to BI-RADS, between the molecular subtypes breast cancer.

  20. Effect of molecular weight on the electrophoretic deposition of carbon black nanoparticles in moderately viscous systems.

    Modi, Satyam; Panwar, Artee; Mead, Joey L; Barry, Carol M F


    Electrophoretic deposition from viscous media has the potential to produce in-mold assembly of nanoparticles onto three-dimensional parts in high-rate, polymer melt-based processes like injection molding. The effects of the media's molecular weight on deposition behavior were investigated using a model system of carbon black and polystyrene in tetrahydrofuran. Increases in molecular weight reduced the electrophoretic deposition of the carbon black particles due to increases in suspension viscosity and preferential adsorption of the longer polystyrene chains on the carbon black particles. At low deposition times (≤5 s), only carbon black deposited onto the electrodes, but the deposition decreased with increasing molecular weight and the resultant increases in suspension viscosity. For longer deposition times, polystyrene codeposited with the carbon black, with the amount of polystyrene increasing with molecular weight and decreasing with greater charge on the polystyrene molecules. This deposition behavior suggests that use of lower molecular polymers and control of electrical properties will permit electrophoretic deposition of nanoparticles from polymer melts for high-rate, one-step fabrication of nano-optical devices, biochemical sensors, and nanoelectronics.

  1. The macrocyclic peptide antibiotic micrococcin P(1) is secreted by the food-borne bacterium Staphylococcus equorum WS 2733 and inhibits Listeria monocytogenes on soft cheese.

    Carnio, M C; Höltzel, A; Rudolf, M; Henle, T; Jung, G; Scherer, S


    Staphylococcus equorum WS 2733 was found to produce a substance exhibiting a bacteriostatic effect on a variety of gram-positive bacteria. The metabolite was purified to homogeneity by ammonium sulfate precipitation and semipreparative reversed-phase high-performance liquid chromatography. Electrospray mass spectrometry confirmed the high purity of the compound and revealed a molecular mass of 1,143 Da. By two-dimensional nuclear magnetic resonance spectroscopy the substance was identified as micrococcin P(1) which is a macrocyclic peptide antibiotic that has not yet been reported for the genus Staphylococcus. A total of 95 out of 95 Listeria strains and 130 out of 135 other gram-positive bacteria were inhibited by this substance, while none of 37 gram-negative bacteria were affected. The antilisterial potential of this food-grade strain as a protective starter culture was evaluated by its in situ application in cheese-ripening experiments under laboratory conditions. A remarkable growth reduction of Listeria monocytogenes could be achieved compared to control cheese ripened with a nonbacteriocinogenic type strain of Staphylococcus equorum. In order to prove that inhibition was due to micrococcin P(1), a micrococcin-deficient mutant was constructed which did not inhibit L. monocytogenes in cheese-ripening experiments.

  2. The Macrocyclic Peptide Antibiotic Micrococcin P1 Is Secreted by the Food-Borne Bacterium Staphylococcus equorum WS 2733 and Inhibits Listeria monocytogenes on Soft Cheese

    Carnio, Markus C.; Höltzel, Alexandra; Rudolf, Melanie; Henle, Thomas; Jung, Günther; Scherer, Siegfried


    Staphylococcus equorum WS 2733 was found to produce a substance exhibiting a bacteriostatic effect on a variety of gram-positive bacteria. The metabolite was purified to homogeneity by ammonium sulfate precipitation and semipreparative reversed-phase high-performance liquid chromatography. Electrospray mass spectrometry confirmed the high purity of the compound and revealed a molecular mass of 1,143 Da. By two-dimensional nuclear magnetic resonance spectroscopy the substance was identified as micrococcin P1 which is a macrocyclic peptide antibiotic that has not yet been reported for the genus Staphylococcus. A total of 95 out of 95 Listeria strains and 130 out of 135 other gram-positive bacteria were inhibited by this substance, while none of 37 gram-negative bacteria were affected. The antilisterial potential of this food-grade strain as a protective starter culture was evaluated by its in situ application in cheese-ripening experiments under laboratory conditions. A remarkable growth reduction of Listeria monocytogenes could be achieved compared to control cheese ripened with a nonbacteriocinogenic type strain of Staphylococcus equorum. In order to prove that inhibition was due to micrococcin P1, a micrococcin-deficient mutant was constructed which did not inhibit L. monocytogenes in cheese-ripening experiments. PMID:10831414

  3. The system-biological GLOBE 3D Genome Platform. : A new holistic genome viewer for molecular genetics

    M. Lesnussa (Michael); F.N. Kepper (Nick); H.J.F.M.M. Eussen (Bert); T.A. Knoch (Tobias)


    textabstractGenomes are tremendous co-evolutionary holistic systems for molecular storage, processing and fabrication of information. Their system-biological complexity remains, however, still largely mysterious, despite immense sequencing achievements and huge advances in the understanding of the

  4. A portable molecular beam epitaxy system for in situ x-ray investigations at synchrotron beamlines.

    Slobodskyy, T; Schroth, P; Grigoriev, D; Minkevich, A A; Hu, D Z; Schaadt, D M; Baumbach, T


    A portable synchrotron molecular beam epitaxy (MBE) system is designed and applied for in situ investigations. The growth chamber is equipped with all the standard MBE components such as effusion cells with shutters, main shutter, cooling shroud, manipulator, reflection high energy electron diffraction setup, and pressure gauges. The characteristic feature of the system is the beryllium windows which are used for in situ x-ray measurements. An UHV sample transfer case allows in vacuo transfer of samples prepared elsewhere. We describe the system design and demonstrate its performance by investigating the annealing process of buried InGaAs self-organized quantum dots.

  5. Replica exchange molecular simulation of Lennard-Jones particles in a two-dimensional confined system

    Doi, Hideo; Yasuoka, Kenji


    Confined systems exhibit interesting properties that are applied to the fields of lubrication, adhesion and nanotechnology. The replica exchange molecular simulation method was applied to calculate the phase equilibrium points of Lennard-Jones particles in a two-dimensional confined system. The liquid-solid phase equilibrium points and the solid structure with a dependency of the slit width were determined and the order parameter of the solid structure was analyzed. Such confined systems are shown to be favorable for manipulation of the phase equilibrium points.

  6. Molecular features determining different partitioning patterns of papain and bromelain in aqueous two-phase systems.

    Rocha, Maria Victoria; Nerli, Bibiana Beatriz


    The partitioning patterns of papain (PAP) and bromelain (BR), two well-known cysteine-proteases, in polyethyleneglycol/sodium citrate aqueous two-phase systems (ATPSs) were determined. Polyethyleneglycols of different molecular weight (600, 1000, 2000, 4600 and 8000) were assayed. Thermodynamic characterization of partitioning process, spectroscopy measurements and computational calculations of protein surface properties were also carried out in order to explain their differential partitioning behavior. PAP was observed to be displaced to the salt-enriched phase in all the assayed systems with partition coefficients (KpPAP) values between 0.2 and 0.9, while BR exhibited a high affinity for the polymer phase in systems formed by PEGs of low molecular weight (600 and 1000) with partition coefficients (KpBR) values close to 3. KpBR values resulted higher than KpPAP in all the cases. This difference could be assigned neither to the charge nor to the size of the partitioned biomolecules since PAP and BR possess similar molecular weight (23,000) and isoelectric point (9.60). The presence of highly exposed tryptophans and positively charged residues (Lys, Arg and His) in BR molecule would be responsible for a charge transfer interaction between PEG and the protein and, therefore, the uneven distribution of BR in these systems.

  7. A Pilot-Scale System for Carbon Molecular Sieve Hollow Fiber Membrane Manufacturing

    Karvan, O.


    Carbon molecular sieve (CMS) membranes offer advantages over traditional polymeric membrane materials, but scale-up of manufacturing systems has not received much attention. In the recent decade, there has been a dramatic increase in fundamental research on these materials with a variety of applications being studied. The results from a pilot-scale CMS production system are presented. This system was designed based on extensive laboratory research, and hollow fiber membranes produced in this system show similar performance compared to membranes produced using a smaller bench-scale system. After optimizing the system design, a 93% recovery of the precursor fibers for use in membrane module preparation were obtained. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. A Molecular Thermodynamic Model for Interfacial Tension in Surfactant-Oil-Water System


    An interfacial equation of state based on perturbation theory for surfactant-oil-water system has been developed. By combining the interfacial equation of state with Boudh-Hir and Mansoori's model, a molecular ther- modynamic model has been proposed. The interfacial tension of surfactant-oil-water systems can be calculated from the surface tensions of pure oil and water by this model. The inteffacial tension data for sodium dodecyl sulphate- heptane-water system, polyoxyethylene n-octylphenol-heptane-water system and hexadecyl trimethyl ammonium bromide-heptane-water system have been correlated. By using the adjustable parameters obtained, the interfacial tensions of these systems at other temperatures have been predicted. Both the correlated and the predicted values are satisfactory.

  9. [Chiral separation of drugs based on macrocyclic antibiotics using HPLC, supercritical fluid chromatography (SFC) and capillary electrochromatography (CEC)].

    Dungelová, J; Lehotay, J; Rojkovicová, T; Cizmárik, J


    Separation of enantiomers by means of high-performance liquid chromatography (HPLC), supercritical fluid chromatography (SFC), and capillary electrochromatography (CEC) is of great importance in pharmaceutical analyses. In recent years, separation of various types of racemates employs most frequently chiral stationary phases based on macrocyclic antibiotics. This class of chiral selectors includes vancomycin, teikoplanin, ristocetin A, teikoplanin without saccharide components, avoparcin, etc. The review paper describes the properties of selected antibiotics, the effect of chromatographic conditions on enantioselectivity (effect of the composition of the mobile phase, effect of pH of the mobile phase, effect of temperature), and the study of possible mechanisms of interaction, which play an important role in the separation of enantiomers. Examples of the use of macrocyclic antibiotics in the separation of various compounds by means of the HPLC, SFC, and CEC methods follow.

  10. Synthesis of Chiral Macrocyclic or Linear Pyridine Carboxamides from Pyridine-2,6-dicarbonyl Dichloride as Antimicrobial Agents

    Abd El-Galil E Amr


    Full Text Available A series of chiral linear and macrocyclic bridged pyridines has been prepared starting from pyridine-2,6-dicarbonyl dichloride (2. The coupling of 1 with D-alanyl methyl ester gave 2,6-bis-D-alanyl pyridine methyl ester (3. Hydrazinolysis of 3 with hydrazine hydrate afforded bis-hydrazide 4. The latter was reacted with thiophene-2-carbaldehyde, phthalic anhydride or cyclohexanone to afford bis-carboxamide pyridine derivatives 5-7, respectively. Compound 4 was coupled with p-methoxy- or p-nitroaceto-phenone to yield compounds 8 and 9. In addition, 4 was reacted with 1,2,4,5-benzenetetra-carboxylic acid dianhydride or 1,4,5,8-naphthalenetetracarboxylic acid dianhydride to afford the macrocyclic octacarboxaamide pyridines 10 and 11. The detailed synthesis, spectroscopic data and antimicrobial screening for the synthesized compounds are reported.

  11. Quantitative computational models of molecular self-assembly in systems biology

    Thomas, Marcus; Schwartz, Russell


    Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

  12. Hybrid artificial photosynthetic systems comprising semiconductors as light harvesters and biomimetic complexes as molecular cocatalysts.

    Wen, Fuyu; Li, Can


    Solar fuel production through artificial photosynthesis may be a key to generating abundant and clean energy, thus addressing the high energy needs of the world's expanding population. As the crucial components of photosynthesis, the artificial photosynthetic system should be composed of a light harvester (e.g., semiconductor or molecular dye), a reduction cocatalyst (e.g., hydrogenase mimic, noble metal), and an oxidation cocatalyst (e.g., photosystem II mimic for oxygen evolution from water oxidation). Solar fuel production catalyzed by an artificial photosynthetic system starts from the absorption of sunlight by the light harvester, where charge separation takes place, followed by a charge transfer to the reduction and oxidation cocatalysts, where redox reaction processes occur. One of the most challenging problems is to develop an artificial photosynthetic solar fuel production system that is both highly efficient and stable. The assembly of cocatalysts on the semiconductor (light harvester) not only can facilitate the charge separation, but also can lower the activation energy or overpotential for the reactions. An efficient light harvester loaded with suitable reduction and oxidation cocatalysts is the key for high efficiency of artificial photosynthetic systems. In this Account, we describe our strategy of hybrid photocatalysts using semiconductors as light harvesters with biomimetic complexes as molecular cocatalysts to construct efficient and stable artificial photosynthetic systems. We chose semiconductor nanoparticles as light harvesters because of their broad spectral absorption and relatively robust properties compared with a natural photosynthesis system. Using biomimetic complexes as cocatalysts can significantly facilitate charge separation via fast charge transfer from the semiconductor to the molecular cocatalysts and also catalyze the chemical reactions of solar fuel production. The hybrid photocatalysts supply us with a platform to study the

  13. Chemoinformatics in the New Era: From Molecular Dynamics to Systems Dynamics.

    Wang, Guanyu


    Chemoinformatics, due to its power in gathering information at the molecular level, has a wide array of important applications to biology, including fundamental biochemical studies and drug discovery and optimization. As modern "omics" based profiling and network based modeling and simulation techniques grow in sophistication, chemoinformatics now faces a great opportunity to include systems-level control mechanisms as one of its pillar components to extend and refine its various applications. This viewpoint article, through the example of computer aided targeting of the PI3K/Akt/mTOR pathway, outlines major steps of integrating systems dynamics simulations into molecular dynamics simulations to facilitate a higher level of chemoinformatics that would revolutionize drug lead optimization, personalized therapy, and possibly other applications.

  14. A systems biology approach identifies molecular networks defining skeletal muscle abnormalities in chronic obstructive pulmonary disease.

    Nil Turan


    Full Text Available Chronic Obstructive Pulmonary Disease (COPD is an inflammatory process of the lung inducing persistent airflow limitation. Extensive systemic effects, such as skeletal muscle dysfunction, often characterize these patients and severely limit life expectancy. Despite considerable research efforts, the molecular basis of muscle degeneration in COPD is still a matter of intense debate. In this study, we have applied a network biology approach to model the relationship between muscle molecular and physiological response to training and systemic inflammatory mediators. Our model shows that failure to co-ordinately activate expression of several tissue remodelling and bioenergetics pathways is a specific landmark of COPD diseased muscles. Our findings also suggest that this phenomenon may be linked to an abnormal expression of a number of histone modifiers, which we discovered correlate with oxygen utilization. These observations raised the interesting possibility that cell hypoxia may be a key factor driving skeletal muscle degeneration in COPD patients.

  15. Organic molecular beam deposition system and initial studies of organic layer growth

    Andreasson, M [Applied Semiconductor Physics, Microtechnology and Nanoscience, Chalmers University of Technology, S-41296 Goeteborg (Sweden); Ilver, L [Department of Experimental Physics, Chalmers University of Technology, S-41296 Goeteborg (Sweden); Kanski, J [Department of Experimental Physics, Chalmers University of Technology, S-41296 Goeteborg (Sweden); Andersson, T G [Applied Semiconductor Physics, Microtechnology and Nanoscience, Chalmers University of Technology, S-41296 Goeteborg (Sweden)


    This work describes an organic molecular beam deposition system with substrate entry/exit chamber, buffer chamber and with the possibility to transfer substrate from a III-V molecular beam deposition system. Flux calibrations of organic molecules and the initial growth of organic layers are described. For this purpose, the molecules 3,4,9,10 perylene tetra carboxylic dianhydride and copper phtalocyanine were used. Layers were grown on oxidized and hydrogen passivated Si(100), Indium tin oxide and glass respectively. The growth was investigated with atomic force microscopy, reflection high energy electron diffraction and ultraviolet photoemission spectroscopy. An investigation with x-ray photoelectron and Raman spectroscopy on the effect of atmospheric exposure is also included, showing little effect of surface pollution when the samples were handled carefully. The initial formation (monolayers) of copper phtalocyanine thin films was studied by ultraviolet photoemission spectroscopy.

  16. Molecular Chaperones, Cochaperones, and Ubiquitination/Deubiquitination System: Involvement in the Production of High Quality Spermatozoa

    Rosaria Meccariello


    Full Text Available Spermatogenesis is a complex process in which mitosis, meiosis, and cell differentiation events coexist. The need to guarantee the production of qualitatively functional spermatozoa has evolved into several control systems that check spermatogenesis progression/sperm maturation and tag aberrant gametes for degradation. In this review, we will focus on the importance of the evolutionarily conserved molecular pathways involving molecular chaperones belonging to the superfamily of heat shock proteins (HSPs, their cochaperones, and ubiquitination/deubiquitination system all over the spermatogenetic process. In this respect, we will discuss the conserved role played by the DNAJ protein Msj-1 (mouse sperm cell-specific DNAJ first homologue and the deubiquitinating enzyme Ubpy (ubiquitin-specific processing protease-y during the spermiogenesis in both mammals and nonmammalian vertebrates.

  17. Complement System Part I – Molecular Mechanisms of Activation and Regulation

    Merle, Nicolas S.; Church, Sarah Elizabeth; Fremeaux-Bacchi, Veronique; Roumenina, Lubka T.


    Complement is a complex innate immune surveillance system, playing a key role in defense against pathogens and in host homeostasis. The complement system is initiated by conformational changes in recognition molecular complexes upon sensing danger signals. The subsequent cascade of enzymatic reactions is tightly regulated to assure that complement is activated only at specific locations requiring defense against pathogens, thus avoiding host tissue damage. Here, we discuss the recent advances describing the molecular and structural basis of activation and regulation of the complement pathways and their implication on physiology and pathology. This article will review the mechanisms of activation of alternative, classical, and lectin pathways, the formation of C3 and C5 convertases, the action of anaphylatoxins, and the membrane-attack-complex. We will also discuss the importance of structure–function relationships using the example of atypical hemolytic uremic syndrome. Lastly, we will discuss the development and benefits of therapies using complement inhibitors. PMID:26082779

  18. Through-space electronic communication of zinc phthalocyanine with substituted [60]Fullerene bearing O2Nxaza-crown macrocyclic ligands

    Ghanbari, Bahram; Shahhoseini, Leila; Mahlooji, Niloofar; Gholamnezhad, Parisa; Taheri Rizi, Zahra


    Two new macrocyclic ligands containing 17- and 19-membered O2N3-donor aza-crowns anchored to [60]Fullerene were synthesized and characterized by employing HPLC, electrospray ionization mass (ESI-MS), 1H and 13C NMR, UV-vis, IR spectroscopies, as well as powder X-ray diffraction (PXRD) and thermogravimetric analysis (TGA) in solid state. TGA measurements revealed that upon linking each of these macrocycle rings to [60]Fullerene, the decomposition point measured for [60]Fullerene moiety was increased, indicating on the promoted stability of [60]Fullerene backbone during binding to these macrocyclic ligands. Moreover, the ground state non-covalent interactions of [60]Fullerene derivatives of O2Nx (x = 2, and 3) aza-crown macrocyclic ligands namely, L1-L4 with zinc phthalocyanine (ZnPc) were also investigated by UV-vis absorption, steady state and time resolved fluorescence spectrophotometry in N-methyl-2-pyrrolidone (NMP). The calculation of Stern-Volmer constants (KSV) indicated on existence of an efficient quenching mechanism comprising of the excited singlet state of ZnPc in the presence of L1-L4. The observation of an appropriate correlation between decrease in fluorescence intensity and lifetime parameters led us to propose the occurrence of a static mechanism for the fluorescence quenching of ZnPc in the presence of L1-L3. The binding constants (KBH) of L1-L4/ZnPc were also determined applying the fluorescence quenching experiments. Meanwhile, the incompatibility of both KSV and KBH values found for L4 was also described in terms of structural features using DFT calculations using the B3LYP functional and 6-31G* basis set.

  19. Tools for Chemical Biology: New Macrocyclic Compounds from Diversity-Oriented Synthesis and Toward Materials from Silver(I) Acetylides

    Madsen, Charlotte Marie

    Part I The formation of a library of diverse macrocyclic compounds with different functionalities and ring sizes in a few steps from two easily accessible α,ω-diol building blocks is presented. The building blocks are combined by esteriffcations in four different ways leading to the formation of ...... of uoro-iodoadamantanes. However, overall the results provide a good starting point for the synthesis of new triptycene and adamantane-containing molecules that can interact with carbon nanotubes....

  20. Modulation of lipopolysaccharide-induced proinflammatory cytokine production by satratoxins and other macrocyclic trichothecenes in the murine macrophage.

    Chung, Yong-Joo; Jarvis, Bruce; Pestka, James


    The satratoxins and other macrocyclic trichothecene mycotoxins are produced by Stachybotrys, a mold that is often found in water-damaged dwellings and office buildings. To test the potential immunomodulatory effects of these mycotoxins, RAW 264.7 murine macrophage cells were treated with various concentrations of satratoxin G (SG), isosatratoxin F (iSF), satratoxin H (SH), roridin A (RA), and verrucarin A (VA) for 48 h in the presence or absence of suboptimal concentra-tion of lipopolysaccharide (LPS, 50 ng/ml), and tumor necrosis factor-alpha (TNF-alpha ) and interleukin-6 (IL-6) production were assayed by enzyme-linked immunosorbent assay (ELISA). In LPS-stimulated cultures, TNF-alpha supernatant concentrations were significantly increased in the presence of 2.5, 2.5, and 1 ng/ml of SG, SH, and RA, respectively, whereas IL-6 concentrations were not affected by the same concentrations these macrocyclic trichothecenes. When cells that were treated with LPS and SG (2.5 ng/ml) were evaluated by real-time polymerase chain reaction (PCR),TNF-alpha mRNA was found to increase at 24, 36, and 48 h compared to control cells. At higher concentrations, cytokine production and cell viability were markedly impaired in LPS-stimulated cells. Without LPS stimulation, neither TNF-alpha, nor IL-6 was induced. These results indicate that low concentrations of macrocyclic trichothecenes superinduce expression of TNF-alpha, whereas higher concentrations of these toxins are cytotoxic and concurrently reduce cytokine production. The capacity of satratoxins and other macrocyclic trichothecenes to alter cytokine production may play an etiologic role in outbreaks of Stachybotrys-associated human illnesses.