Sample records for synthesis molecular structure

  1. Synthesis, molecular structure, spectroscopic investigations and ...

    Indian Academy of Sciences (India)

    cates an easy outlook of the makeup of the molec- ular orbitals in a certain energy range. The energy split between the HOMOs and LUMOs are the crit- ical parameters in special molecular electrical trans- port properties which help in the measure of elec- tron conductivity.42 The HOMO represents the ability to donate an ...

  2. Synthesis, molecular structure, spectroscopic investigations and ...

    Indian Academy of Sciences (India)

    The spectroscopic properties of the title compound have beeninvestigated by using IR, UV–Vis and ¹H NMR techniques. The molecular geometry and spectroscopic data of the title compound have been calculated by using the density functional method (B3LYP) invoking 6-311G(d,p) basis set. UV-Vis spectra of the two ...

  3. Synthesis, molecular structure, spectroscopic investigations and ...

    Indian Academy of Sciences (India)

    MS received 29 December 2015; revised 9 April 2016; accepted 25 May 2016 ... B, open form blue. Scheme 1. Structures and Photochromic reaction of the title compound. 2. Experimental. 2.1 Materials and measurements. The mid-IR spectra were obtained in the ... segment is put between two parallel Au(111) surfaces,.

  4. Synthesis, molecular structures and ESI-mass studies of copper (I ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 127; Issue 10. Synthesis, molecular structures and ESI-mass studies of copper(I) complexes with ligands incorporating N, S and P donor atoms. Tarlok S Lobana Arvinder Kaur Rohit Sharma Madhu Bala Amanpreet K Jassal Courtney E Duff Jerry P Jasinski. Volume ...

  5. Synthesis and molecular structure of chiral metallo-based sterically overcrowded alkenes

    NARCIS (Netherlands)

    Wiel, Matthijs K.J. ter; Meetsma, Auke; Feringa, Bernard


    A four step synthesis of pyridyl-2-yl-thioxanthen-9-ylidene-isoquinolines is described. The corresponding palladium complexes are the first examples of a novel class of chiral, metallo-based, sterically overcrowded alkenes. The crystal and molecular structure of the palladium dichloride complex

  6. Synthesis and molecular structure of manganese complexes with ...

    Indian Academy of Sciences (India)


    Manganese-dioxygen complexes are assumed to play significant roles in physiologically important enzymatic reactions including superoxide dismutation, decomposition of hydrogen peroxide and dioxygen evolution from water catalysed by manganese containing proteins 1. Accordingly, the characterization of structurally ...

  7. Efficient synthesis and molecular structure of 2-hydroxyisophthaldehyde

    NARCIS (Netherlands)

    Zondervan, C; van den Beuken, E.K; Kooijman, H.; Spek, A.L.; Feringa, B.L.


    A new highly effective procedure has been developed for the preparation of 2-hydroxyisophthaldehyde from 2,6-dimethylphenol. The X-ray crystal structure shows infinite chains of molecules joined by hydrogen bonds. (C) 1997 Published by Elsevier Science Ltd.

  8. Synthesis, reactivity, and electronic structure of molecular uranium nitrides


    Cleaves, Peter A.


    The study of metal-ligand multiple bonding offers insight into the electronic structure and bond of metal systems. Until recently, for uranium, such systems were limited to uranyl, and terminal chalcogenide, imide and carbene complexes. In 2012, this was extended to nitrides with the first preparation of a uranium–nitride (U≡N) species isolable under standard conditions, namely [U(TrenTIPS)(N)][Na(12C4)2] (52), which is prepared by the two-electron reduction of sodium azide with a trivalent u...

  9. New Diethyl Ammonium Salt of Thiobarbituric Acid Derivative: Synthesis, Molecular Structure Investigations and Docking Studies

    Directory of Open Access Journals (Sweden)

    Assem Barakat


    Full Text Available The synthesis of the new diethyl ammonium salt of diethylammonium(E-5-(1,5-bis(4-fluorophenyl-3-oxopent-4-en-1-yl-1,3-diethyl-4,6-dioxo-2-thioxohexaydropyrimidin-5-ide 3 via a regioselective Michael addition of N,N-diethylthiobarbituric acid 1 to dienone 2 is described. In 3, the carboanion of the thiobarbituric moiety is stabilized by the strong intramolecular electron delocalization with the adjacent carbonyl groups and so the reaction proceeds without any cyclization. The molecular structure investigations of 3 were determined by single-crystal X-ray diffraction as well as DFT computations. The theoretically calculated (DFT/B3LYP geometry agrees well with the crystallographic data. The effect of fluorine replacement by chlorine atoms on the molecular structure aspects were investigated using DFT methods. Calculated electronic spectra showed a bathochromic shift of the π-π* transition when fluorine is replaced by chlorine. Charge decomposition analyses were performed to study possible interaction between the different fragments in the studied systems. Molecular docking simulations examining the inhibitory nature of the compound show an anti-diabetic activity with Pa (probability of activity value of 0.229.

  10. Molecular structure design and soft template synthesis of aza-, oxaaza- and thiaazamacrocyclic metal chelates in the gelatin matrix

    Directory of Open Access Journals (Sweden)

    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.

  11. Synthesis, three-dimensional structure, conformation and correct chemical shift assignment determination of pharmaceutical molecules by NMR and molecular modeling

    International Nuclear Information System (INIS)

    Azeredo, Sirlene O.F. de; Sales, Edijane M.; Figueroa-Villar, José D.


    This work includes the synthesis of phenanthrenequinone guanylhydrazone and phenanthro[9,10-e][1,2,4]triazin-3-amine to be tested as intercalate with DNA for treatment of cancer. The other synthesized product, 2-[(4-chlorophenylamino)methylene]malononitrile, was designed for future determination of its activity against leishmaniasis. A common problem about some articles on the literature is that some previously published compounds display error of their molecular structures. In this article it is shown the application of several procedures of nuclear magnetic resonance (NMR) to determine the complete molecular structure and the non questionable chemical shift assignment of the synthesized compounds, and also their analysis by molecular modeling to confirm the NMR results. To determine the capacity of pharmacological compounds to interact with biological targets is determined by docking. This work is to motivate the application of NMR and molecular modeling on organic synthesis, being a process that is very important for the study of the prepared compounds as interactions with biological targets by NMR. (author)

  12. Synthesis, three-dimensional structure, conformation and correct chemical shift assignment determination of pharmaceutical molecules by NMR and molecular modeling

    Energy Technology Data Exchange (ETDEWEB)

    Azeredo, Sirlene O.F. de; Sales, Edijane M.; Figueroa-Villar, José D., E-mail: [Instituto Militar de Engenharia (IME), Rio de Janeiro, RJ (Brazil). Grupo de Ressonância Magnética Nuclear e Química Medicinal


    This work includes the synthesis of phenanthrenequinone guanylhydrazone and phenanthro[9,10-e][1,2,4]triazin-3-amine to be tested as intercalate with DNA for treatment of cancer. The other synthesized product, 2-[(4-chlorophenylamino)methylene]malononitrile, was designed for future determination of its activity against leishmaniasis. A common problem about some articles on the literature is that some previously published compounds display error of their molecular structures. In this article it is shown the application of several procedures of nuclear magnetic resonance (NMR) to determine the complete molecular structure and the non questionable chemical shift assignment of the synthesized compounds, and also their analysis by molecular modeling to confirm the NMR results. To determine the capacity of pharmacological compounds to interact with biological targets is determined by docking. This work is to motivate the application of NMR and molecular modeling on organic synthesis, being a process that is very important for the study of the prepared compounds as interactions with biological targets by NMR. (author)

  13. Synthesis and Structural Characterization of New Light Molecular Weight Inorganic Oxidizers and Related Derivatives. Volume: 2 (United States)


    results from ab initio calculations and contrary to the VSEPR concept of repelling points on a sphere, the minimum energy structures of these main group...trigonal prism, or a pentagonal bipyramid. 5 According to the VSEPR model of "repelling points on a sphere", 5 the preferred structures should be the...34 VSEPR arguments 5 or classical, directionally localized molecular orbitals, can be rationalized in terms of a bonding scheme, first noticed49 for XeF5

  14. Synthesis and molecular structure of (monoaqua) oxovanadium (IV) thiosemicarbazide-diacetate monohydrate

    International Nuclear Information System (INIS)

    Gerbeleu, N.V.; Bologa, A.O.; Burshtein, I.F.; Filippova, I.G.; Kiosse, G.A.


    This paper describes the structure for a new complex of oxovanadium (IV) with H 2 L. This compound was obtained by mixing warm aqueous solutions containing 1.0 g VOSO 4 .2H 2 O and H 2 L at room temperature. The coordinates and the individual temperature factors of the basis atoms in the structure VOLH 2 O .H 2 O are presented. It is shown that the vanadium atom in both complexes has a distorted octahedral environment. The geometrical isomerism is accompanied by differences in the conformations of the molecular ligand. Two geometrical isomers of a previously unknown type are concurrently present in the VOLH 2 O structure. The formation of these isomers is made possible by the different arrangement of inequivalent branches of the organic ligand. This type of isomerism should be expected in the complexes of other metals with H 2 L and in the coordination compounds of metals with other B-type tripod ligands

  15. Synthesis, molecular modeling and structural characterization of vanillin derivatives as antimicrobial agents (United States)

    Sun, Juan; Yin, Yong; Sheng, Gui-Hua; Yang, Zhi-Bo; Zhu, Hai-Liang


    Two vanillin derivatives have been designed and synthesized and their biological activities were also evaluated for antimicrobial activity. Their chemical structures are characterized by single crystal X-ray diffraction studies, 1H NMR, MS, and elemental analysis. Structural stabilization of them followed by intramolecular as well as intermolecular H-bonds makes these molecules as perfect examples in molecular recognition with self-complementary donor and acceptor units within a single molecule. Docking simulations have been performed to position compounds into the FtsZ active site to determine their probable binding model. Compound 3a shows the most potent biological activity, which may be a promising antimicrobial leading compound for the further research.

  16. Synthesis, crystal and molecular structure of two biologically active aromatic sulfonamides and their hydrochloride salts (United States)

    Remko, Milan; Kožíšek, Jozef; Semanová, Jana; Gregáň, Fridrich


    4-Sulfamoyl-N-(3-morpholinopropyl) benzamide (P10), N-(3-morpholinopropyl)benzene-1,4-disulfonamide (P20) and their hydrochloride salts (P11 and P22) were prepared. The X-ray molecular structure of these compounds was determined. The gas-phase structure of these drugs was computed using Becke3LYP/6-31G(d) and Becke3LYP/6-311 + G(d,p) model chemistries. The conformational behavior of these systems in water was examined using the solvation CPCM model. In the solid state, gas phase and in solution the conformations of the basic compounds P10 and P20 possess a characteristic L-shaped structure stabilized via an intramolecular hydrogen bonding system of the N sbnd H⋯N type. This hydrogen bond is not present in P11 and P22. A network of intermolecular hydrogen bonds mediated by the Cl atoms and crystal-packing forces in P11 and P22 stabilize a more extended structure in the solid state.

  17. Synthesis, Molecular Structure and Spectroscopic Investigations of Novel Fluorinated Spiro Heterocycles

    Directory of Open Access Journals (Sweden)

    Mohammad Shahidul Islam


    Full Text Available This paper describes an efficient and regioselective method for the synthesis of novel fluorinated spiro-heterocycles in excellent yield by cascade [5+1] double Michael addition reactions. The compounds 7,11-bis(4-fluorophenyl-2,4-dimethyl- 2,4-diazaspiro[5.5] undecane-1,3,5,9-tetraone (3a and 2,4-dimethyl-7,11-bis (4-(trifluoromethylphenyl-2,4-diazaspiro[5.5]undecane-1,3,5,9-tetraone (3b were characterized by single-crystal X-ray diffraction, FT-IR and NMR techniques. The optimized geometrical parameters, infrared vibrational frequencies and NMR chemical shifts of the studied compounds have also been calculated using the density functional theory (DFT method, using Becke-3-Lee-Yang-Parr functional and the 6-311G(d,p basis set. There is good agreement between the experimentally determined structural parameters, vibrational frequencies and NMR chemical shifts of the studied compounds and those predicted theoretically. The calculated natural atomic charges using NBO method showed higher polarity of 3a compared to 3b.The calculated electronic spectra are also discussed based on the TD-DFT calculations.

  18. Synthesis, crystal structure, DNA binding and molecular docking studies of zinc(II) carboxylates (United States)

    Muhammad, Niaz; Ikram, Muhammad; Wadood, Abdul; Rehman, Sadia; Shujah, Shaukat; Erum; Ghufran, Mehreen; Rahim, Shahnaz; Shah, Muzamil; Schulzke, Carola


    New zinc(II) carboxylate complexes [Zn(3-F-C6H4CH2COO)2]n (1), [Zn3(3-F-C6H4CH2COO)6(Phen)2] (2) and [Zn3(3-F-C6H4CH2COO)6(bipy)2] (3) were synthesized and characterized by atomic absorption, single crystal structural analysis and IR studies. Complex 1 crystallizes as a coordination polymer constituting a web of μ - η1,η1 carboxylate bridged tetrahedral zinc centers. Complexes 2 and 3 comprise trinuclear zinc centers with two terminal fivefold coordinated slightly distorted square-pyramidal and central sixfold coordinated octahedral zinc centers. The complexes were also assessed for their DNA binding ability by UV/- Vis spectroscopy and their behavior rationalized theoretically by molecular docking studies. A DNA binding study has shown groove binding interactions with the complexes.

  19. Molecular iron(III) phosphonates: synthesis, structure, magnetism, and Mössbauer studies. (United States)

    Goura, Joydeb; Bag, Prasenjit; Mereacre, Valeriu; Powell, Annie K; Chandrasekhar, Vadapalli


    The reaction of Fe(ClO4)2·6H2O with t-BuPO3H2 or Cl3CPO3H2 in the presence of an ancillary pyrazole phenolate as a coligand, H2phpzH [H2phpzH = 3(5)-(2-hydroxyphenyl)pyrazole], afforded tetra- and pentanuclear Fe(III) phosphonate complexes [Fe4(t-BuPO3)4(HphpzH)4]·5CH3CN·5CH2Cl2 (1) and [HNEt3]2[Fe5(μ3-O)(μ-OH)2 (Cl3CPO3)3(HphpzH)5(μ-phpzH]·3CH3CN·2H2O (2). Single-crystal X-ray structural analysis reveals that 1 possesses a cubic double-4-ring (D4R) core similar to what is found in zeolites. The molecular structure of 2 reveals it to be pentanuclear. It crystallizes in the chiral P1 space group. Magnetic studies on 1 and 2 have also been carried out, which reveal that the bridging phosphonate ligands mediate weak antiferromagnetic interactions between the Fe(III) ions. Magnetization dynamics of 1 and 2 have been corroborated by a Mössbauer spectroscopy analysis.

  20. Chiral lactic hydrazone derivatives as potential bioactive antibacterial agents: Synthesis, spectroscopic, structural and molecular docking studies (United States)

    Noshiranzadeh, Nader; Heidari, Azam; Haghi, Fakhri; Bikas, Rahman; Lis, Tadeusz


    A series of novel chiral lactic-hydrazone derivatives were synthesized by condensation of (S)-lactic acid hydrazide with salicylaldehyde derivatives and characterized by elemental analysis and spectroscopic studies (FT-IR, 1H NMR and 13C NMR spectroscopy). The structure of one compound was determined by single crystal X-ray analysis. Antibacterial activity of the synthesized compounds was studied against Staphylococcus aureus, Streptococcus pneumonia, Escherichia coli and Pseudomonas aeruginosa as bacterial cultures by broth microdilution method. All of the synthesized compounds showed good antibacterial activity with MIC range of 64-512 μg/mL. Compounds (S,E)-2-hydroxy-N-(2-hydroxy-5-nitrobenzylidene)propanehydrazide (5) and (S,E)-2-hydroxy-N-((3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl)propanehydrazide (7) were the most effective antibacterial derivatives against S. aureus and E. coli respectively with a MIC value of 64 μg/mL. Bacterial biofilm formation assay showed that these compounds significantly inhibited biofilm formation of P. aeruginosa. Also, in silico molecular docking studies were performed to show lipoteichoic acid synthase (LtaS) inhibitory effect of lactic hydrazone derivatives. The association between electronic and structural effects of some substituents on the benzylidene moiety and the biological activity of these chiral compounds were studied. Structural studies show that compound with higher hydrogen bonding interactions show higher antibacterial activity. The results show chiral hydrazone derivatives based on lactic acid hydrazide could be used as potential lead compounds for developing novel antibacterial agents.

  1. Quaternary Alkylammonium Conjugates of Steroids: Synthesis, Molecular Structure, and Biological Studies

    Directory of Open Access Journals (Sweden)

    Bogumił Brycki


    Full Text Available The methods of synthesis as well as physical, spectroscopic (1H-NMR, 13C-NMR, and FT-IR, ESI-MS, and biological properties of quaternary and dimeric quaternary alkylammonium conjugates of steroids are presented. The results were contrasted with theoretical calculations (PM5 methods and potential pharmacological properties (PASS. Alkylammonium sterols exhibit a broad spectrum of antimicrobial activity comparable to squalamine.

  2. On the synthesis of vanadium containing molecular sieves by experimental design from a VOSO4.5H2O.Al(iPrO)3.Pr2NH.H2O gel: occurrence of VAPO-41 as a secondary structure in the synthesis of VAPO-11

    NARCIS (Netherlands)

    Weckhuysen, B.M.; Frunza, L.; Voort, P. van der; Vansant, E.F.; Schoonheydt, R.A.


    An experimental design was applied to the hydrothermal synthesis of VAPO-11 molecular sieve (AEL structure)from a VOSO4.5H2O.Al(iPrO)3.Pr2NH.H2O gel. The influence of five synthesis parameters (synthesis temperature, synthesis time, vanadium content, water content and template content) on the

  3. Synthesis, Molecular Structure, and Electrochemistry of 1-Ferrocenyl-1,2-dicarba-closo-dodecaboranes

    Czech Academy of Sciences Publication Activity Database

    Korotvička, A.; Šnajdr, I.; Štěpnička, P.; Císařová, I.; Janoušek, Zbyněk; Kotora, M.

    -, č. 15 (2013), s. 2789-2798 ISSN 1434-1948 Grant - others:GA ČR(CZ) GAP207/11/0338; GAČR(CZ) GAP207/11/0705 Program:GA Institutional support: RVO:61388963 Keywords : carboranes * metallocenes * structure elucidation * electrochemistry * addition Subject RIV: CA - Inorganic Chemistry Impact factor: 2.965, year: 2013

  4. Synthesis, characterization, and molecular structure of tetraethylammonium pentakis(isothiocyanato)bis(2,2'-bipyridine)uranate(IV)

    International Nuclear Information System (INIS)

    Wiley, R.O.; Von Dreele, R.B.; Brown, T.M.


    The synthesis of tetraethylammonium pentakis(isothiocyanato)bis(2,2'-bipyridine)uranate(IV) has been accomplished, and it was characterized by classical physical methods. The crystal and molecular structure was determined from single-crystal x-ray data collected by the theta-2theta technique on an automated diffractometer. The compound consists of pentakis(isothiocyanato)bis (2,2'-bipyridine)uranate(IV) anions and disordered tetraethylammonium cations. Uranium is bound to nine nitrogen atoms in a highly distorted monocapped square antiprism in which one bipyridine occupies a position bridging the cap and the near square while the other bipyridine spans the opposite edge of the far square. Distortion from the ideal geometry is caused by the small ligand bite of the bipyridine ligand. An alternative description of the coordination geometry is derived from the seven-coordinate pentagonal bipyramid in which each bipyridine ligand is assumed to occupy an axial position with the five thiocyanato ligands forming the pentagonal girdle. The U-N bond distances vary from 2.35 to 2.47 A for the thiocyanato ligands and from 2.61 to 2.65 A for the bipyridine ligands. The structure was solved by standard heavy-atom techniques and refined by large-block matrix least squares to a final R value of 0.083 for 3878 independent observed reflections. The compound crystallized in the monoclinic space group P2 1 /c, Z = 4, with lattice parameters a = 14.427 (10) A, b = 18.612 (17) A, c = 15.710 (10) A, and β = 105.17 (7) 0 , rho/sub obsd/ = 1.57 g cm -3

  5. Synthesis, molecular structure, spectral analysis and cytotoxic activity of two new aroylhydrazones (United States)

    Singh, Ravindra Kumar; Singh, Ashok Kumar; Siddiqui, Sahabjada; Arshad, Mohammad; Jafri, Asif


    Two new aroylhydrazones viz 4-nitro-N‧-(1-(pyridin-2-yl)ethylidene)benzohydrazide, NPHY (4) and 4-nitro-N‧-(1-(thiophen-2-yl)ethylidene)benzohydrazide, NPHT (5) have been prepared and characterized by 1H NMR, 13C NMR, FT-IR, UV-Visible spectroscopy and mass spectrometry. All quantum calculations were performed at DFT level of theory using B3LYP functional and 6-31G (d,p) as basis set. TD-DFT calculated electronic transitions are found to be in good agreement with experimental findings. The assignments for normal vibrational modes have been done by computing Potential Energy Distribution (PED) using Gar2ped. HOMO-LUMO analysis was performed and reactivity descriptors were also computed. Global electrophilicity index (ω) of 6.12-6.26 eV shows these aroylhydrazones to be strong electrophiles. Intramolecular interactions were analyzed by 'Atoms in molecule' (AIM) approach. Also, the computed first static hyperpolarizabilities (β0) of these hydrazones indicate their future application as an attractive non-linear optical (NLO) material. Cytotoxicity evaluated by MTT assay, suggested that the synthesized aroylhydrazones significantly reduce the cell viability of breast cancer cell lines (MCF7) and human prostate adenocarcinoma (DU145) in a dose dependent manner. Cytotoxic potencies (IC50) of these hydrazones against MCF7 and DU145 cell lines were found in range of 54.67-85.67 μM. The result of ROS activity provides supportive data for molecular mechanism of these hydrazones, which is related to apoptotic cellular death. Nuclear condensation assay performed by DAPI staining shows fragmented and condensed nuclei in MCF7 cells, suggesting cell death by apoptosis.

  6. Synthesis, Structure and Solid State Properties of Cyclohexanemethylamine Substituted Phenalenyl Based Molecular Conductor

    Directory of Open Access Journals (Sweden)

    Robert C. Haddon


    Full Text Available We report the preparation, crystallization and solid state characterization of a cyclohexanemethylamine substituted spirobiphenalenyl radical; in the solid state the compound is iso-structural with its dehydro-analog (benzylamine-substitued compound, and the molecules packed in a one-dimensional fashion that we refer to as a π-step stack. Neighboring molecules in the stack interact via the overlap of one pair of active (spin bearing carbon atoms per phenalenyl unit. The magnetic susceptibility measurement indicates that in the solid state the radical remains paramagnetic and the fraction of Curie spins is 0.75 per molecule. We use the analytical form of the Bonner-Fisher model for the S = 1/2 antiferromagnetic Heisenberg chain of isotropically interacting spins with intrachain spin coupling constant J = 6.3 cm−1, to fit the experimentally observed paramagnetism [χp (T] in the temperature range 4–330 K. The measured room temperature conductivity (σRT = 2.4 × 10–3 S/cm is comparable with that of the iso-structural benzyl radical, even though the calculated band dispersions are smaller than that of the unsaturated analog.

  7. Synthesis, molecular structure investigations and antimicrobial activity of 2-thioxothiazolidin-4-one derivatives (United States)

    Barakat, Assem; Al-Najjar, Hany J.; Al-Majid, Abdullah Mohammed; Soliman, Saied M.; Mabkhot, Yahia Nasser; Al-Agamy, Mohamed H. M.; Ghabbour, Hazem A.; Fun, Hoong-Kun


    A variety of 2-thioxothiazolidin-4-one derivatives were prepared and their in vitro antimicrobial activities were studied. Most of these compounds showed significant antibacterial activity specifically against Gram-positive bacteria, among which compounds 4a,e,g, 5b,e,g,h and 6f exhibit high levels of antimicrobial activity against Bacillus subtilis ATCC 10400 with Minimum Inhibitory Concentration (MIC) value of 16 μg/mL. All compounds have antifungal activity against Candida albicans. Unfortunately, however, none of the compounds were active against Gram-negative bacteria. The chemical structure of 3 was confirmed by X-ray single crystal diffraction technique. DFT calculations of 3 have been performed on the free C10H7Cl2NO2S2, 3a and the H-bonded complex, C10H7Cl2NO2S2·H2O, 3b to explore the effect of the H-bonding interactions on the geometric and electronic properties of the studied systems. A small increase in bond length was observed in the C12-O6 due to the H-bonding interactions between 3a and water molecule. MEP study has been used to recognize the most reactive sites towards electrophilic and nucleophilic attacks as well as the possible sites for the H-bonding interactions. The TD-DFT calculations have been used to predict theoretically the electronic spectra of the studied compound. The most intense transition band is predicted at 283.9 nm due to the HOMO-2/HOMO-1 to LUMO transitions. NBO analyses were carried out to investigate the stabilization energy of the various intramolecular charge transfer interactions within the studied molecules.

  8. SUPPLEMENTARY INFORMATION Synthesis and Molecular ...

    Indian Academy of Sciences (India)


    S28: Binding mode for compounds, MTX docked and minimized in the DHFR binding pocket, with residues involved in its recognition Molecular docking structure and ligand protein binding sites of. MTX- a)-Best possible pose of compound MTX (boll and stick structure) showing hydrogen bond. (red color line) and bond ...

  9. Structure-activity relationships of β-hydroxyphosphonate nucleoside analogues as cytosolic 5'-nucleotidase II potential inhibitors: synthesis, in vitro evaluation and molecular modeling studies. (United States)

    Meurillon, Maïa; Marton, Zsuzsanna; Hospital, Audrey; Jordheim, Lars Petter; Béjaud, Jérôme; Lionne, Corinne; Dumontet, Charles; Périgaud, Christian; Chaloin, Laurent; Peyrottes, Suzanne


    The cytosolic 5'-nucleotidase II (cN-II) has been proposed as an attractive molecular target for the development of novel drugs circumventing resistance to cytotoxic nucleoside analogues currently used for treating leukemia and other malignant hemopathies. In the present work, synthesis of β-hydroxyphosphonate nucleoside analogues incorporating modifications either on the sugar residue or the nucleobase, and their in vitro evaluation towards the purified enzyme were carried out in order to determine their potency towards the inhibition of cN-II. In addition to the biochemical investigations, molecular modeling studies revealed important structural features for binding affinities towards the target enzyme. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  10. Valency and molecular structure

    CERN Document Server

    Cartmell, E


    Valency and Molecular Structure, Fourth Edition provides a comprehensive historical background and experimental foundations of theories and methods relating to valency and molecular structures. In this edition, the chapter on Bohr theory has been removed while some sections, such as structures of crystalline solids, have been expanded. Details of structures have also been revised and extended using the best available values for bond lengths and bond angles. Recent developments are mostly noted in the chapter on complex compounds, while a new chapter has been added to serve as an introduction t

  11. Structure-based design, synthesis and molecular modeling studies of thiazolyl urea derivatives as novel anti-parkinsonian agents. (United States)

    Azam, Faizul; Prasad, Medapati Vijaya Vara; Thangavel, Neelaveni; Shrivastava, Anil Kumar; Mohan, Govind


    Synthesis of 1-(substituted aryl)-3-(thiazol-2-yl)urea derivatives was undertaken as our efforts to discover novel antiparkinsonian agents with improved pharmacological profile in haloperidol-induced catalepsy and oxidative stress in mice. Furfuryl, 2- and/or 3-methoxy substituted phenyl derivatives emerged as potent agents. With exception of 2-chloro,5-trifluoromethyl substituted analog, halogen substituted derivatives exhibited moderate antiparkinsonian activity. The results of biochemical investigations from brain homogenate of mice outline the importance of neuroprotective/antioxidant therapy for Parkinson's disease (PD), supporting the notion that the oxidative stress may play a significant role in the pathophysiological mechanisms underlying PD. Molecular docking studies of these compounds with adenosine A(2A) receptor exhibited very good binding interactions and warrants further studies to confirm their binding with human A(2A) receptor for the design and development of potent antagonists. Parameters for Lipinski's rule of 5 were calculated computationally because pharmacokinetic and metabolic behaviors in the body often are linked to the physical properties of a compound. None of the synthesized compounds violated Lipinski's rule, making them suitable drug candidate for the treatment of PD.

  12. Stereodivergent synthesis with a programmable molecular machine (United States)

    Kassem, Salma; Lee, Alan T. L.; Leigh, David A.; Marcos, Vanesa; Palmer, Leoni I.; Pisano, Simone


    It has been convincingly argued that molecular machines that manipulate individual atoms, or highly reactive clusters of atoms, with Ångström precision are unlikely to be realized. However, biological molecular machines routinely position rather less reactive substrates in order to direct chemical reaction sequences, from sequence-specific synthesis by the ribosome to polyketide synthases, where tethered molecules are passed from active site to active site in multi-enzyme complexes. Artificial molecular machines have been developed for tasks that include sequence-specific oligomer synthesis and the switching of product chirality, a photo-responsive host molecule has been described that is able to mechanically twist a bound molecular guest, and molecular fragments have been selectively transported in either direction between sites on a molecular platform through a ratchet mechanism. Here we detail an artificial molecular machine that moves a substrate between different activating sites to achieve different product outcomes from chemical synthesis. This molecular robot can be programmed to stereoselectively produce, in a sequential one-pot operation, an excess of any one of four possible diastereoisomers from the addition of a thiol and an alkene to an α,β-unsaturated aldehyde in a tandem reaction process. The stereodivergent synthesis includes diastereoisomers that cannot be selectively synthesized through conventional iminium-enamine organocatalysis. We anticipate that future generations of programmable molecular machines may have significant roles in chemical synthesis and molecular manufacturing.

  13. Synthesis and Structural Characterization of a CHA-type AlPO4Molecular Sieve with Penta-Coordinated Framework Aluminum Atoms. (United States)

    Park, Gi Tae; Jo, Donghui; Ahn, Nak Ho; Cho, Jung; Hong, Suk Bong


    The structure-directing effects of a series of polymethylimidazolium cations with different numbers of methyl groups as organic structure-directing agents (OSDAs) in the synthesis of aluminophosphate (AlPO 4 )-based molecular sieves in both fluoride and hydroxide media are investigated. On the one hand, among the OSDAs studied here, the smallest 1,3-dimethylimidazolium and the largest 1,2,3,4,5-pentamethylimidazolium cations were found to direct the synthesis of a new variant of the triclinic chabazite (CHA)-type AlPO 4 material, designated AlPO 4 -34(t) V , and the one-dimensional small-pore silicoaluminophosphate (SAPO) molecular sieve STA-6 in hydroxide media, respectively. On the other hand, the intermediate-sized 1,2,3,4-tetramethylimidazolium cation gave SSZ-51, a two-dimensional large-pore SAPO material, in fluoride media. Synchrotron powder X-ray diffraction and Rietveld analyses reveal that as-made AlPO 4 -34(t) V contains penta-coordinated framework Al species connected by hydroxyl groups, as well as tetrahedral framework Al, which contrasts with the distortions arising from the two F - or OH - bridges between octahedral Al atoms in all already known AlPO 4 -34 materials. The presence of Al-OH-Al linkages in this triclinic AlPO 4 -34 molecular sieve has been further corroborated by thermal analysis, variable-temperature IR,27Al magic-angle spinning NMR, and dispersion-corrected density functional theory calculations.

  14. Synthesis, pharmacological characterization, and structure-activity relationship studies of small molecular agonists for the orphan GPR88 receptor. (United States)

    Jin, Chunyang; Decker, Ann M; Huang, Xi-Ping; Gilmour, Brian P; Blough, Bruce E; Roth, Bryan L; Hu, Yang; Gill, Joseph B; Zhang, X Peter


    GPR88 is an orphan G-protein-coupled receptor (GPCR) enriched in the striatum. Genetic deletion and gene expression studies have suggested that GPR88 plays an important role in the regulation of striatal functions and is implicated in psychiatric disorders. The signal transduction pathway and receptor functions of GPR88, however, are still largely unknown due to the lack of endogenous and synthetic ligands. In this paper, we report the synthesis of a GPR88 agonist 2-PCCA and its pure diastereomers, which were functionally characterized in both transiently and stably expressing GPR88 HEK293 cells. 2-PCCA inhibited isoproterenol-stimulated cAMP accumulation in a concentration-dependent manner in cells expressing GPR88 but not in the control cells, suggesting that the observed cAMP inhibition is mediated through GPR88 and that GPR88 is coupled to Gαi. 2-PCCA did not induce calcium mobilization in GPR88 cells, indicating no Gαq-mediated response. A structure-activity relationship (SAR) study of 2-PCCA was also conducted to explore the key structural features for GPR88 agonist activity.

  15. Photoionization and molecular structure

    International Nuclear Information System (INIS)

    Palma, A.


    A presentation is here given of the theoretical work on photoionization and molecular structure carried out by the author and coworkers. The implications of the photoionization process on the molecular geometry are emphasized. In particular, the ionization effect on deep orbitals is considered and it is shown that, contrary to traditional thinking, these orbitals have relevant effects on the molecular geometry. The problem of calculating photoionization relative intensities for the full spectrum is also considered, and the results of the present model are compared with experimental and other theoretical results. (author)

  16. Synthesis, Molecular Structure and Reactivity of 5-Methylidene-1,2,3,5-tetrahydroimidazo[2,1-b]quinazolines

    Directory of Open Access Journals (Sweden)

    Maria Gdaniec


    Full Text Available Synthesis of novel 5-methylidene-1,2,3,5-tetrahydro[2,1-b]-quinazolinederivatives 2-4 with potential biological activities mediated by α-adrenergic and/orimidazoline receptors was performed by reacting 2-chloro-4,5-dihydroimidazole (1 withthe corresponding 2-aminoacetophenones. Compound 2, which incorporates an enaminemoiety, underwent a 1,3-dipolar cycloaddition reaction with the appropriate nitrones 5-9to give 1,2,3,5-tetrahydro-imidazo[2,1-b]quinazolin-5,5'-spiro-2',3'-diphenylisoxazol-idines 10-14. Reactions of the title compounds 2 and 4 with dimethyl acetylene-dicarboxylate (DMAD afforded dimethyl 2-(2,3-dihydroimidazo[2,1-b]quinazolin-5(1H-ylidenemethylbut-2-enedioates 15, 16. Imidazo[2,1-b]quinazoline 2 was furthertreated with acetyl chloride, benzoyl chloride and mesyl chloride to give the 1-substitutedderivatives 17, 18 and 19, respectively. The structures of all new compounds obtainedwere confirmed by elemental analysis and spectral data (IR, 1H- and 13C-NMR as well asX-ray crystallographic analysis of 3 and 18.

  17. Synthesis and structure of interaction products of quinoline-2(1H)-thione with molecular iodine. (United States)

    Chernov'yants, Margarita S; Starikova, Zoya A; Kolesnikova, Tatiana S; Karginova, Anastasia O; Lyanguzov, Nikolay V


    The behavior of quinoline-2(1H)-thione, which is a potential antithyroid drug toward molecular iodine, was investigated. The ability of quinoline-2(1H)-thione to form the outer-sphere charge-transfer complex C9H7NS·I2 with iodine molecular in dilute chloroform solution has been studied by UV-vis spectroscopy (lgβ=3.85). The crystal structure of the new salt 2-(quinoline-2-yldisulfanyl)quinolinium triiodide - product of irreversible oxidation of quinoline-2(1H)-thione was determined by X-ray diffraction. The 2-(quinoline-2-yldisulfanyl)quinolinium cations form dimers through π-π-stacking interaction between quinoline rings. Strong intramolecular interactions are observed between iodine - sulfur atoms and iodine - hydrogen atoms with shortened contacts (less of sum of van der Waals contacts). It is noteworthy that two perfectly centrosymmetrical anions I3(-) form a very short contact I(3)⋯I(3') 3.7550(5) so we can state the formation of the dianion I(6)(2-). Therefore the formation and topology of polyiodide species depend on the characteristics, such as shape, size and charge, etc., of the counter cation, 2-(quinoline-2-yldisulfanyl)quinolinium, which is considered as templating agent. Copyright © 2015. Published by Elsevier B.V.

  18. Identification of novel benzimidazole derivatives as anti-Trypanosoma cruzi agents: solid-phase synthesis, structure-activity relationships and molecular docking studies. (United States)

    Ríos, Natalia; Varela, Javier; Birriel, Estefania; González, Mercedes; Cerecetto, Hugo; Merlino, Alicia; Porcal, Williams


    In this paper, we report the solid-phase synthesis of 33 novel 1,2,5-tri-substituted benzimidazole derivatives and their in vitro activity on cruzipain and Trypanosoma cruzi epimastigotes. Seven compounds were potent inhibitors of T. cruzi growth with IC50 values in the range 6-16 µM. Applying structure-activity relationships and principal component analysis strategies we were able to determine ring substituent effects and physicochemical properties that are important for the antichagasic activity of these novel derivatives, as well as get an insight into their possible mechanisms of action. Molecular docking studies revealed the binding orientation of the ligands in the active site of cruzipain providing new guidelines for the further design of better inhibitors. Compound 2a constitute a promising hit compound for novel anti-T. cruzi agents showing that the benzimidazole scaffold may represent an interesting therapeutic alternative for the treatment of Chagas disease.

  19. Understanding molecular structure from molecular mechanics. (United States)

    Allinger, Norman L


    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  20. Synthesis, Molecular Structure Optimization, and Cytotoxicity Assay of a Novel 2-Acetyl-3-amino-5-[(2-oxopropylsulfanyl]-4-cyanothiophene

    Directory of Open Access Journals (Sweden)

    Yahia N. Mabkhot


    Full Text Available A novel thiophene-containing compound, 2-acetyl-3-amino-5-[(2-oxopropylsulfanyl]-4-cyanothiophene (4 was synthesized by reaction of malononitrile with CS2 in the presence of K2CO3 under reflux in DMF and the subsequent reaction with chloroacetone followed by cyclization. This compound has been characterized by means of FT-IR, 1H-NMR, 13C-NMR, and mass spectrometry as well as elemental analysis. In addition, the molecular structures of compound 4 was determined by X-ray crystallography. The geometry of the molecule is stabilized by an intramolecular interaction between N1–H1···O1 to form S6 graf set ring motif. In the crystal, molecules are linked via N1–H2···O1 and C7–H7A···N2 interactions to form a three-dimensional network. Molecular structure and other spectroscopic properties of compound 4 were calculated using DFT B3LYP/6-31G (d,p method. Results revealed a good agreement between the optimized geometric parameters and the observed X-ray structure. Furthermore, and by employing the natural bond orbital (NBO method, the intramolecular charge transfer (ICT interactions along with natural atomic charges at different sites, were calculated; results indicated strong n→π* ICT from LP(1N5→BD*(2C15-C16 (63.23 kcal/mol. In addition, the stabilization energy E(2 of the LP(2O3→ BD*(1N5-H6 ICT (6.63 kcal/mol indicated the presence of intramolecular N-H···OH bonding. Similarly, calculations of the electronic spectra of compound 4 using, TD-DFT revealed a good agreement with the experimental data. Finally, compound 4 was evaluated for its in vitro cytotoxic effect against PC-3 and HeLa cell lines, as an anticancer agent, and found to be nontoxic.

  1. Silica Synthesis by Sponges: Unanticipated Molecular Mechanism (United States)

    Morse, D. E.; Weaver, J. C.


    substitutions of specific amino acid sidechains, in conjunction with computer-assisted molecular modeling and biomimetic synthesis, allowed us to probe the determinants of catalytic activity and confirm the identification of the amino acid sidechains required for hydrolysis of the silicon alkoxides. If, as suggested by the data of others, silicic acid is conjugated with organic moieties after its transport into the cell, the catalytic mechanism described here may be important in biosilicification by sponges. As is often the case, we have been better able to answer mechanistic questions about "how" silica can be formed biologically, than "why" the diversity of structures is elaborated. Studies of spicule formation during cellular regeneration in Tethya aurantia reveal that synthesis of the larger silica needles (megascleres) and smaller starburst-shaped microscleres may be independently regulated, presumably at the genetic level. The spatial segregation of these morphologically-distinct spicule types within the sponge further suggests an adaptive significance of the different skeletal elements.

  2. Synthesis, molecular structure, spectroscopic properties and stability of (Z)-N-methyl-C-2,4,6-trimethylphenylnitrone (United States)

    Lasri, Jamal; Ismail, Ali I.; Haukka, Matti; Soliman, Saied M.


    New N-methyl-C-2,4,6-trimethylphenylnitrone 1 has been synthesized starting from N-methylhydroxylamine and mesitaldehyde. The product was fully characterized using different spectroscopic techniques; FTIR, NMR, UV-Vis, high resolution mass spectrometry and X-ray diffraction. The relative stability and percent of population of its two possible isomers (E and Z) were calculated using the B3LYP/6-311++G(d,p) method in gas phase and in solution. In agreement with the X-ray results, it was found that Z-isomer is the most stable one in both gas phase and solution. The molecular geometry, vibrational frequencies, gauge-including atomic orbital (GIAO), and chemical shift values were also calculated using the same level of theory. The TD-DFT results of the studied nitrone predicted a π-π∗ transition band at 285.1 nm (fosc = 0.3543) in the gas phase. The rest of the spectral bands undergo either hyperchromic or hypsochromic shifts in the presence of solvent. Polarizability and HOMO-LUMO gap values were used to predict the nonlinear optical properties (NLO) of the studied compound. NBO analysis has been used to determine the most accurate Lewis structure of the studied molecule.

  3. Synthesis and Molecular Structures of (E-non-2-enoic Acid and (E-dec-2-enoic Acid

    Directory of Open Access Journals (Sweden)

    Marcel Sonneck


    Full Text Available The molecular structures of (E-non-2-enoic acid (C9 and (E-dec-2-enoic acid (C10 are reported. The title compounds were crystallized by slow evaporation of ethanolic solutions at −30 °C. C9 crystallizes in the monoclinic space group P21/c and C10 in the triclinic space group P-1, each with 4 molecules in the unit cell. The unit cell parameters for C9 are: a = 10.6473(4 Å, b = 5.2855(2 Å, c = 17.0313(7 Å; β = 106.0985(10° and V = 920.87(6 Å3. The unit cell parameters for C10 are: a = 4.1405(2 Å, b = 15.2839(6 Å, c = 17.7089(7 Å; α = 68.3291(11°, β = 83.3850(13°, γ = 85.0779(12° and V = 1033.39(8 Å3.

  4. Synthesis, X-Ray Crystal Structures, Biological Evaluation, and Molecular Docking Studies of a Series of Barbiturate Derivatives

    Directory of Open Access Journals (Sweden)

    Assem Barakat


    Full Text Available A series of barbiturates derivatives synthesized and screened for different set of bioassays are described. The molecular structures of compounds 5a, 5d, and 5f were solved by single-crystal X-ray diffraction techniques. The results of bioassay show that compounds 4a, 4b, 4c, 4d, 4e, 4f, and 4g are potent antioxidants in comparison to the tested standards, butylated hydroxytoluene (BHT, and N-acetylcysteine. Compounds 4a–4e (IC50=101.8±0.8–124.4±4.4 μM and 4g (IC50=104.1±1.9 μM were more potent antioxidants than the standard (BHT, IC50=128.8±2.1 μM. The enzyme inhibition potential of these compounds was also evaluated, in vitro, against thymidine phosphorylase, α-glucosidase, and β-glucuronidase enzymes. Compounds 4c, 4h, 4o, 4p, 4q, 5f, and 5m were found to be potent α-glucosidase inhibitors and showed more activity than the standard drug acarbose, whereas compounds 4v, and 5h were found to be potent thymidine phosphorylase inhibitors, more active than the standard drug, 7-deazaxanthine. All barbiturates derivatives (4a–4x, 4z, and 5a–5m were found to be noncytotoxic against human prostate (PC-3, Henrietta Lacks cervical (HeLa and Michigan Cancer Foundation-7 breast (MCF-7 cancer cell lines, and 3T3 normal fibroblast cell line, except 4y which was cytotoxic against all the cell lines.

  5. Rational assembly of soluble copper(II) phosphonates: synthesis, structure and magnetism of molecular tetranuclear copper(II) phosphonates. (United States)

    Chandrasekhar, Vadapalli; Senapati, Tapas; Dey, Atanu; Sañudo, E Carolina


    The reactions of the dinuclear copper complexes [Cu(2)(L)(OAc)] [H(3)L = N,N'-(2-hydroxypropane-1,3-diyl)bis(salicylaldimine) or [Cu(2)(L')(OAc)] (H(3)L' = N,N'-(2-hydroxypropane-1,3-diyl)bis(4,5-dimethylsalicylaldimine)] with various phosphonic acids, RPO(3)H(2) (R = t-Bu, Ph, c-C(5)H(9), c-C(6)H(11) or 2,4,6-i-Pr(3)-C(6)H(2)), leads to the replacement of the acetate bridge affording tetranuclear copper(II) phosphonates, [Cu(4)(L)(2)(t-BuPO(3))](CH(3)OH)(2)(C(6)H(6)) (1), [Cu(4)(L)(2)(PhPO(3))(H(2)O)(2)(NMe(2)CHO)](H(2)O)(2) (2), [Cu(4)(L')(2)(C(5)H(9)PO(3))](CH(3)OH)(2) (3), [Cu(4)(L')(2)(C(6)H(11)PO(3)](MeOH)(4)(H(2)O)(2) (4) and [Cu(4)(L')(2)(C(30)H(46)P(2)O(5))](PhCH(3)) (5). The molecular structures of 1-4 reveal that a [RPO(3)](2-) ligand is involved in holding the four copper atoms together by a 4.211 coordination mode. In 5, an in situ formed [(RPO(2))(2)O](4-) ligand bridges two pairs of the dinuclear subunits. Magnetic studies on these complexes reveal that the phosphonate ligand is an effective conduit for magnetic interaction among the four copper centers present; a predominantly antiferromagnetic interaction is observed at low temperatures.

  6. Synthesis, molecular structure, biological properties and molecular docking studies on Mn(II), Co(II) and Zn(II) complexes containing bipyridine-azide ligands. (United States)

    Thamilarasan, Vijayan; Jayamani, Arumugam; Sengottuvelan, Nallathambi


    Metal complexes of the type Mn(bpy)2(N3)2 (1), Co(bpy)2(N3)2·3H2O (2) and Zn2(bpy)2(N3)4 (3) (Where bpy = 2,2-bipyridine) have been synthesized and characterized by elemental analysis and spectral (FT-IR, UV-vis) studies. The structure of complexes (1-3) have been determined by single crystal X-ray diffraction studies and the configuration of ligand-coordinated metal(II) ion was well described as distorted octahedral coordination geometry for Mn(II), Co(II) and distorted square pyramidal geometry for Zn(II) complexes. DNA binding interaction of these complexes (1-3) were investigated by UV-vis absorption, fluorescence circular dichroism spectral and molecular docking studies. The intrinsic binding constants Kb of complexes 1, 2 and 3 with CT-DNA obtained from UV-vis absorption studies were 8.37 × 10(4), 2.23 × 10(5) and 5.52 × 10(4) M(-1) respectively. The results indicated that the three complexes are able to bind to DNA with different binding affinity, in the order 2 > 1 > 3. Complexes (1-3) exhibit a good binding propensity to bovine serum albumin (BSA) proteins having relatively high binding constant values. Gel electrophoresis assay demonstrated the ability of the complexes 1-3 promote the cleavage ability of the pBR322 plasmid DNA in the presence of the reducing agent 3-mercaptopropionic acid (MPA) but with different cleavage mechanisms: the complex 3 cleaves DNA via hydrolytic pathway (T4 DNA ligase assay), while the DNA cleavage by complexes 1 and 2 follows oxidative pathway. The chemical nuclease activity follows the order: 2 > 1 > 3. The effects of various activators were also investigated and the nuclease activity efficacy followed the order MPA > GSH > H2O2 > Asc. The cytotoxicity studies of complexes 1-3 were tested in vitro on breast cancer cell line (MCF-7) and they found to be active. Copyright © 2014. Published by Elsevier Masson SAS.

  7. Synthesis, characterization, antimicrobial activity and molecular ...

    African Journals Online (AJOL)

    Synthesis, characterization, antimicrobial activity and molecular docking studies of combined pyrazol-barbituric acid pharmacophores. Assem Barakat, Bandar M. Al-Qahtani, Abdullah M. Al-Majid, M. Ali Mohammed Rafi Shaik, Mohamed H.M. Al-Agamy, Abdul Wadood ...

  8. Synthesis, structure-activity relationship and molecular docking of cyclohexenone based analogous as potent non-nucleoside reverse-transcriptase inhibitors (United States)

    Nazar, Muhammad Faizan; Abdullah, Muhammad Imran; Badshah, Amir; Mahmood, Asif; Rana, Usman Ali; Khan, Salah Ud-Din


    The chalcones core in compounds is advantageously chosen effective synthons, which offer exciting perspectives in biological and pharmacological research. The present study reports the successful development of eight new cyclohexenone based anti-reverse transcriptase analogous using rational drug design synthesis principles. These new cyclohexenone derivatives (CDs) were synthesized by following a convenient route of Robinson annulation, and the molecular structure of these CDs were later confirmed by various analytical techniques such as 1H NMR, 13C NMR, FT-IR, UV-Vis spectroscopy and mass spectrometry. All the synthesized compounds were screened theoretically and experimentally against reverse transcriptase (RT) and found potentially active reverse transcriptase (RT) inhibitors. Of the compounds studied, the compound 2FC4 showed high interaction with RT at non-nucleoside binding site, contributing high free binding energy (ΔG -8.01 Kcal) and IC50 (0.207 μg/ml), respectively. Further results revealed that the compounds bearing more halogen groups, with additional hydrophobic character, offered superior anti-reverse transcriptase activity as compared to rest of compounds. It is anticipate that the present study would be very useful for the selection of potential reverse transcriptase inhibitors featuring inclusive pharmacological profiles.

  9. Synthesis of functionalized molecular motors

    NARCIS (Netherlands)

    ter Wiel, MKJ; Feringa, BL


    Synthetic routes to two molecular motors are reported. The sterically hindered central olefinic bond connecting the two halves of these C,symmetric molecules was prepared by a McMurry reaction. In this way, a motor with two five-membered rings and a motor with two six-membered rings were prepared,

  10. Stereoselective green synthesis and molecular structures of highly functionalized spirooxindole-pyrrolidine hybrids - A combined experimental and theoretical investigation (United States)

    Kumar, Raju Suresh; Almansour, Abdulrahman I.; Arumugam, Natarajan; Soliman, Saied M.; Kumar, Raju Ranjith; Altaf, Mohammad; Ghabbour, Hazem A.; Krishnamoorthy, Bellie Sundaram


    Highly functionalized spirooxindole-pyrrolidine hybrids have been synthesized stereoselectively through a [3 + 2] cycloaddition strategy in an ionic liquid, 1-butyl-3-methylimidazolium bromide ([bmim]Br). The structure of these spiro heterocyclic hybrids was elucidated using one and two dimensional NMR spectroscopy, single crystal X-ray crystallographic studies and Density Functional Theory (DFT) calculations. The calculated geometric parameters are in good agreement with the experimental data obtained from the X-ray structures. The Natural Bond Orbital (NBO) calculations on these molecules confirm the electron rich carbonyl oxygen and electron deficient NH groups. The 1H and 13C NMR chemical shifts calculated using GIAO method are in good agreement with the experimental data. The DFT computed polarizability values also suggest the possible NLO activity of these molecules.

  11. 2-Substituted 7-trifluoromethyl-thiadiazolopyrimidones as alkaline phosphatase inhibitors. Synthesis, structure activity relationship and molecular docking study. (United States)

    Jafari, Behzad; Ospanov, Meirambek; Ejaz, Syeda Abida; Yelibayeva, Nazym; Khan, Shafi Ullah; Amjad, Sayyeda Tayyeba; Safarov, Sayfidin; Abilov, Zharylkasyn A; Turmukhanova, Mirgul Zh; Kalugin, Sergey N; Ehlers, Peter; Lecka, Joanna; Sévigny, Jean; Iqbal, Jamshed; Langer, Peter


    Alkaline Phosphatases (APs) play a key role in maintaining a ratio of phosphate to inorganic pyrophosphate (P i /PP i ) and thus regulate extracellular matrix calcification during bone formation and growth. Among different isozymes of AP, aberrant increase in the level of tissue non-specific alkaline phosphatase (TNAP) is strongly associated with vascular calcification and end-stage renal diseases. In this context, we synthesized a novel series of fluorinated pyrimidone derivatives, i.e., 2-bromo-7-trifluoromethyl-5-oxo-5H-1,3,4-thiadiazolepyrimidones. The bromine functionality was further used for derivatisation by nucleophilic aromatic substitution using amines as nucleophiles as well as by Palladium catalysed Suzuki-Miyaura reactions. The synthesized derivatives were found potent but non-selective inhibitors of both isozymes of AP. Arylated thiadiazolopyrimidones exhibited stronger inhibitory activities than 2-amino-thiadiazolopyrimidones. The binding modes and possible interactions of the most active inhibitor within the active site of the enzyme were observed by molecular docking studies. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  12. Six-coordinate oxo-vanadium(V) dimer complex with methoxy bridging: synthesis, crystal structure, biological activity and molecular docking

    Czech Academy of Sciences Publication Activity Database

    Heidari, F.; Fatemi, S.J.A.; Yousef Ebrahimipour, S.; Ebrahimnejad, H.; Castro, J.; Dušek, Michal; Eigner, Václav


    Roč. 76, Feb (2017), s. 1-4 ISSN 1387-7003 R&D Projects: GA MŠk(CZ) LO1603; GA ČR(CZ) GA14-03276S EU Projects: European Commission(XE) CZ.2.16/3.1.00/24510 Institutional support: RVO:68378271 Keywords : oxo-vanadium(V) * Schiff base complex * antimicrobial activity * X-ray crystal structure Subject RIV: CA - Inorganic Chemistry OBOR OECD: Inorganic and nuclear chemistry Impact factor: 1.640, year: 2016

  13. Triphenylphosphane Pt(II) complexes containing biologically active natural polyphenols: Synthesis, crystal structure, molecular modeling and cytotoxic studies. (United States)

    Dell'Anna, Maria Michela; Censi, Valentina; Carrozzini, Benedetta; Caliandro, Rocco; Denora, Nunzio; Franco, Massimo; Veclani, Daniele; Melchior, Andrea; Tolazzi, Marilena; Mastrorilli, Piero


    Platinum complexes bearing phosphane ligands in cis configuration with deprotonated flavonoids (3-hydroxyflavone, quercetin) and deprotonated ethyl gallate were synthesized starting from cis-[PtCl 2 (PPh 3 ) 2 ]. In all cases, O,O' chelate structures were obtained. While quercetin and ethyl gallate complexes are quite stable in solution, the 3-hydroxyflavonate complex undergoes a slow aerobic photodegradation in solution with formation of salicylic and benzoic acids. The X-ray diffraction structures of quercetin and ethyl gallate complexes are reported. Cell cycle studies (in the dark) of the complexes in two human cell lines revealed that the cytotoxic activity of the complex bearing 3-hydroxyflavonate is higher than those exhibited by 3-hydroxyflavone or by cis-[PtCl 2 (PPh 3 ) 2 ] alone. Density functional theory studies on the hydrolysis pathway for the 3-hydroxyflavone and ethyl gallate complexes explained the different cytotoxic activity observed for the two compounds on the basis of the different intermediates formed during hydrolysis (relatively inert hydroxy Pt complexes for ethyl gallate and monoaqua complexes for 3-hydroxyflavone). Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Synthesis, crystal structures, molecular docking and urease inhibition studies of Ni(II) and Cu(II) Schiff base complexes (United States)

    Sangeeta, S.; Ahmad, K.; Noorussabah, N.; Bharti, S.; Mishra, M. K.; Sharma, S. R.; Choudhary, M.


    [Ni(L)2] 1 and [Cu(L)2] 2 [HL = 2-((E)-(2-methoxyphenylimino)methyl)-4,6-dichlorophenol] Schiff base complexes have been successfully synthesized and were characterized by FT-IR, UV-Vis, fluorescence spectroscopy and thermogravimetric analysis. The crystal structures of the two complexes were determined through X-ray crystallography. Its inhibitory activity against Helicobacter pylori urease was evaluated in vitro and showed strong inhibitory activity against H. pylori urease compared with acetohydroxamic acid (IC50 = 42.12 μmolL-1), which is a positive reference. A docking analysis using the AutoDock 4.0 program could explain the inhibitory activity of the complex against urease.

  15. Structural synthesis of parallel robots

    CERN Document Server

    Gogu, Grigore

    This book represents the fifth part of a larger work dedicated to the structural synthesis of parallel robots. The originality of this work resides in the fact that it combines new formulae for mobility, connectivity, redundancy and overconstraints with evolutionary morphology in a unified structural synthesis approach that yields interesting and innovative solutions for parallel robotic manipulators.  This is the first book on robotics that presents solutions for coupled, decoupled, uncoupled, fully-isotropic and maximally regular robotic manipulators with Schönflies motions systematically generated by using the structural synthesis approach proposed in Part 1.  Overconstrained non-redundant/overactuated/redundantly actuated solutions with simple/complex limbs are proposed. Many solutions are presented here for the first time in the literature. The author had to make a difficult and challenging choice between protecting these solutions through patents and releasing them directly into the public domain. T...

  16. Synthesis, XRD single crystal structure analysis, vibrational spectral analysis, molecular dynamics and molecular docking studies of 2-(3-methoxy-4-hydroxyphenyl) benzothiazole (United States)

    Sarau Devi, A.; Aswathy, V. V.; Sheena Mary, Y.; Yohannan Panicker, C.; Armaković, Stevan; Armaković, Sanja J.; Ravindran, Reena; Van Alsenoy, C.


    The vibrational spectra and corresponding vibrational assignments of 2-(3-methoxy-4-hydroxyphenyl)benzothiazole is reported. Single crystal XRD data of the title compound is reported and the orientation of methoxy group is cis to nitrogen atom of the thiazole ring. The phenyl ring breathing modes of the title compound are assigned at 1042 and 731 cm-1 theoretically. The charge transfer within the molecule is studied using frontier molecular orbital analysis. The chemical reactivity descriptors are calculated theoretically. The NMR spectral data predicted theoretically are in good agreement with the experimental data. The strong negative region spread over the phenyl rings, nitrogen atom and oxygen atom of the hydroxyl group in the MEP plot is due to the immense conjugative and hyper conjugative resonance charge delocalization of π-electrons. Molecule sites prone to electrophilic attacks have been determined by analysis of ALIE surfaces, while Fukui functions provided further insight into the local reactivity properties of title molecule. Autoxidation properties have been investigated by calculation of bond dissociation energies (BDEs) of hydrogen abstraction, while BDEs of the rest of the single acyclic bonds were valuable for the further investigation of degradation properties. Calculation of radial distribution functions was performed in order to determine which atoms of the title molecule have pronounced interactions with water molecules. The title compound forms a stable complex with aryl hydrocarbon receptor and can be a lead compound for developing new anti-tumor drug. Antimicrobial properties of the title compound was screened against one bacterial culture Escherchia coli and four fungal cultures viz., Aspergillus niger, Pencillum chrysogenum, Saccharomyces cerevisiae and Rhyzopus stolonifer.

  17. Detonation-synthesis nanodiamonds: synthesis, structure, properties and applications

    International Nuclear Information System (INIS)

    Dolmatov, Valerii Yu


    The review outlines the theoretical foundations and industrial implementations of modern detonation synthesis of nanodiamonds and chemical purification of the nanodiamonds thus obtained. The structure, key properties and promising fields of application of detonation-synthesis nanodiamonds are considered.


    African Journals Online (AJOL)

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    dimensional supramolecular framework. ... The growing interest in the field of the crystal engineering of inorganic-organic hybrid materials .... Synthesis, structure and photoluminescence of (HgCl3)n(C6NO2H6)n(C6NO2H5)n nH2O. Bull. Chem.

  19. Synthesis, Molecular Structure and Cytotoxicity of Molecular Materials Based on Water Soluble Half-Sandwich Rh(III) and Ir(III) Tetranuclear Metalla-Cycles (United States)

    Gupta, Gajendra; Murray, Benjamin S.; Dyson, Paul J.; Therrien, Bruno


    The neutral dinuclear complexes [(η5-C5Me5)2Rh2(μ-dhnq)Cl2] (1) and [(η5-C5Me5)2Ir2(μ-dhnq)Cl2] (2) (dhnqH2 = 5,8-dihydroxy-1,4-naphthoquinone) were obtained from the reaction of [(η5-C5Me5)M(μ-Cl)Cl]2 (M = Rh, Ir) with dhnqH2 in the presence of CH3COONa. Treatment of 1 or 2 in methanol with linear ditopic ligands L (L = pyrazine, 4,4′-bipyridine or 1,2-bis(4-pyridyl)ethylene), in the presence of AgCF3SO3, affords the corresponding tetranuclear metalla-rectangles [(η5-C5Me5)4M4(μ-dhnq)2(μ-L)2]4+ (L = pyrazine, M = Rh, 3; M = Ir, 4; L = 4,4′-bipyridine, M = Rh, 5; M = Ir, 6; L = 1,2-bis(4-pyridyl)ethylene, M = Rh, 7; M = Ir, 8). All complexes were isolated as their triflate salts and were fully characterized by infrared, 1H and 13C NMR spectroscopy, and some representative complexes by single-crystal X-ray structure analysis. The X-ray structures of 3, 5 and 6 confirm the formation of the tetranuclear metalla-cycles, and suggest that complexes 5 and 6 possess a cavity of sufficient size to encapsulate small guest molecules. In addition, the antiproliferative activity of the metalla-cycles 3–8 was evaluated against the human ovarian A2780 (cisplatin sensitive) and A2780cisR (cisplatin resistant) cancer cell lines and on non-tumorigenic human embryonic kidney HEK293 cells. All cationic tetranuclear metalla-rectangles were found to be highly cytotoxic, with IC50 values in the low micromolar range. PMID:28788394

  20. Synthesis, Molecular Structure and Cytotoxicity of Molecular Materials Based on Water Soluble Half-Sandwich Rh(III and Ir(III Tetranuclear Metalla-Cycles

    Directory of Open Access Journals (Sweden)

    Gajendra Gupta


    Full Text Available The neutral dinuclear complexes [(η5-C5Me52Rh2(μ-dhnqCl2] (1 and [(η5-C5Me52Ir2(μ-dhnqCl2] (2 (dhnqH2 = 5,8-dihydroxy-1,4-naphthoquinone were obtained from the reaction of [(η5-C5Me5M(μ-ClCl]2 (M = Rh, Ir with dhnqH2 in the presence of CH3COONa. Treatment of 1 or 2 in methanol with linear ditopic ligands L (L = pyrazine, 4,4′-bipyridine or 1,2-bis(4-pyridylethylene, in the presence of AgCF3SO3, affords the corresponding tetranuclear metalla-rectangles [(η5-C5Me54M4(μ-dhnq2(μ-L2]4+ (L = pyrazine, M = Rh, 3; M = Ir, 4; L = 4,4′-bipyridine, M = Rh, 5; M = Ir, 6; L = 1,2-bis(4-pyridylethylene, M = Rh, 7; M = Ir, 8. All complexes were isolated as their triflate salts and were fully characterized by infrared, 1H and 13C NMR spectroscopy, and some representative complexes by single-crystal X-ray structure analysis. The X-ray structures of 3, 5 and 6 confirm the formation of the tetranuclear metalla-cycles, and suggest that complexes 5 and 6 possess a cavity of sufficient size to encapsulate small guest molecules. In addition, the antiproliferative activity of the metalla-cycles 3–8 was evaluated against the human ovarian A2780 (cisplatin sensitive and A2780cisR (cisplatin resistant cancer cell lines and on non-tumorigenic human embryonic kidney HEK293 cells. All cationic tetranuclear metalla-rectangles were found to be highly cytotoxic, with IC50 values in the low micromolar range.

  1. Synthesis and Characterisation of Aluminophosphate Molecular Sieves

    Energy Technology Data Exchange (ETDEWEB)

    Halvorsen, E.N.


    Catalysts are very important in petrochemical processes. One of the properties that make crystalline, microporous materials attractive for catalytic purposes is their well-defined structure and ability to act as shape selective catalysts. This doctoral thesis presents the synthesis and characterization of a number of crystalline, microporous aluminophosphates and silicoaluminophosphates. 99 refs., 50 figs., 12 tabs.

  2. Synthesis, characterization and molecular modelling of a novel dipyridamole supramolecule - X-ray structure, quantum mechanics and molecular dynamics study to comprehend the hydrogen bond structure-activity relationship (United States)

    Vepuri, Suresh B.; Devarajegowda, H. C.; Soliman, Mahmoud E.


    Hydrochloride salt formation for Active Pharmaceutical Ingredients (APIs) is the primary choice to impart aqueous solubility and to promote dissolution. Dipyridamole (DIP) is a cardiovascular drug which is practically insoluble in water. We discovered a new form of DIP called as dipyridamole hydrochloride trihydrate (DIPHT), which was prepared by an unusual method of reacting the DIP with hydrated hydrochloric acid (HCl) that was liberated in situ by the reaction of ferric chloride with water. The liberated HCl was consumed as reagent in situ by the scavenger (API) and was converted to a hydrochloride trihydrate. The product was characterized by FTIR, mass spectroscopy, PXRD and DSC. Supramolecular structure of this novel DIPHT was revealed by single crystal XRD. A sustained intramolecular hydrogen bond alliance was found in DIP and the DIPHT. Stability of this hydrogen bond was further evaluated by means of molecular modelling studies. We performed electron calculations using quantum mechanics (QM) on both the base and salt structures to compare their geometry and molecular orbital energy levels. Molecular Dynamics (MD) simulations were also conducted in explicit solvent models to provide more insights into the hydrogen bond strength and conformational preferences of the base and salt structure. Together with QM and MD, we were able to explain the influence of hydrogen bonds on proton uptake activity of DIP and stability of DIP and DIPHT. DIPHT which can dissolve faster than DIP in water may enhance the dissolution and bioavailability of the drug. As the current drug development research is shifting to repurpose the existing drugs in order to subside the untoward risks in new drug development, we believe that DIPHT with its intrinsic aqueous solubility could bring more application for DIP and generate interest within the pharmaceutical industry.

  3. synthesis and structures

    Indian Academy of Sciences (India)

    Priya Saxena


    Aug 29, 2017 ... complexes as well as for biological applications.16–24. Of particular mention here are the nickel and palladium complexes of ..... tion and indexing were performed with CrysAlisPro software suite.42 WinGX module was used to perform all the cal- culations.43 The structures were solved by direct methods.

  4. Catalytic NH3 Synthesis using N2 /H2 at Molecular Transition Metal Complexes: Concepts for Lead Structure Determination using Computational Chemistry. (United States)

    Hölscher, Markus; Leitner, Walter


    While industrial NH 3 synthesis based on the Haber-Bosch-process was invented more than a century ago, there is still no molecular catalyst available which reduces N 2 in the reaction system N 2 /H 2 to NH 3 . As the many efforts of experimentally working research groups to develop a molecular catalyst for NH 3 synthesis from N 2 /H 2 have led to a variety of stoichiometric reductions it seems justified to undertake the attempt of systematizing the various approaches of how the N 2 molecule might be reduced to NH 3 with H 2 at a transition metal complex. In this contribution therefore a variety of intuition-based concepts are presented with the intention to show how the problem can be approached. While no claim for completeness is made, these concepts intend to generate a working plan for future research. Beyond this, it is suggested that these concepts should be evaluated with regard to experimental feasibility by checking barrier heights of single reaction steps and also by computation of whole catalytic cycles employing density functional theory (DFT) calculations. This serves as a tool which extends the empirically driven search process and expands it by computed insights which can be used to rationalize the various challenges which must be met. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Structural biology of Molecular machines

    Indian Academy of Sciences (India)


    a structural biology perspective. TANWEER HUSSAIN. Molecular Reproduction, Development and Genetics (MRDG). Indian Institute of Science (IISc). Bangalore. Symposium on “Molecular Machines: a multidiscipline enterprise” 1st July 2017. 28th mid-year meeting of Indian Academy of Sciences at IISc, Bangalore ...

  6. Synthesis, crystal structure, Hirshfeld surface analysis, spectroscopic characterization, reactivity study by DFT and MD approaches and molecular docking study of a novel chalcone derivative (United States)

    Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan; Van Alsenoy, C.


    In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-(trifluoromethyl)phenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in monoclinic crystal system in P21/c space group, unit cell parameters a = 16.7629 (12) Å, b = 13.9681 (10) Å, c = 5.8740 (4) Å, β = 96.3860 (12)° and Z = 4. Hirshfeld surface analysis revealed that the molecular structure is dominated by H⋯H, C⋯H/H⋯C, Br⋯F/F⋯Br and F⋯F contacts. The FT-IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. Average local ionization energies (ALIE) and Fukui functions have been used as quantum-molecular descriptors to locate the molecule sites that could be of importance from the aspect of reactivity. Degradation properties have been assessed by calculations of bond dissociation energies (BDE) for hydrogen abstraction and the rest of the single acyclic bonds, while molecular dynamics (MD) simulations were used in order to calculate radial distribution functions and determine the atoms with significant interactions with water. In order to understand how the title molecule inhibits and hence increases the catalytic efficiency of MOA-B enzyme, molecular docking study was performed.

  7. Titanium(IV) in the organic-structure-directing-agent-free synthesis of hydrophobic and large-pore molecular sieves as redox catalysts. (United States)

    Wang, Jingui; Yokoi, Toshiyuki; Kondo, Junko N; Tatsumi, Takashi; Zhao, Yanli


    Titanium(IV) incorporated into the framework of molecular sieves can be used as a highly active and sustainable catalyst for the oxidation of industrially important organic molecules. Unfortunately, the current process for the incorporation of titanium(IV) requires a large amount of expensive organic molecules used as organic-structure-directing agents (OSDAs), and this significantly increases the production costs and causes environmental problems owing to the removal of OSDAs by pyrolysis. Herein, an OSDA-free process was developed to incorporate titanium(IV) into BEA-type molecular sieves for the first time. More importantly, the hydrophobic environment and the robust, 3 D, and large pore structure of the titanium(IV)-incorporated molecular sieves fabricated from the OSDA-free process created a catalyst that was extremely active and selective for the epoxidation of bulky cyclooctene in comparison to Ti-incorporated BEA-type molecular sieves synthesized with OSDAs and commercial titanosilicate TS-1. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Prediction of molecular crystal structures

    CERN Document Server

    Beyer, T


    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of parac...


    African Journals Online (AJOL)

    Preferred Customer

    Cg1, Cg2 and Cg3 are the centroids of Mo1-O2-C8-N2-N1, C9-C14 and. C1-C6 benzene rings. Figure 1. Molecular structure of the complex at 30% probability displacement. IR spectra. The hydrazone ligands showed stretching bands attributed to C=O, C=N, C–OH and NH at. 1656, 1637, 1155 and 1237, and 3211 cm–1, ...

  10. Prediction of molecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, Theresa


    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  11. Synthesis, characterization, crystal structure, in-vitro anti-inflammatory and molecular docking studies of 5-mercapto-1-substituted tetrazole incorporated quinoline derivative (United States)

    Sureshkumar, K.; Maheshwaran, V.; Dharma Rao, T.; Themmila, Khamrang; Ponnuswamy, M. N.; Kadhirvel, Saraboji; Dhandayutham, Saravanan


    A novel 5-mercapto-1-substituted tetrazole incorporated quinoline analog was synthesized. The compound 2-Cyclopropyl-4-(4-fluorophenyl)-3-{1-[2-(4-methoxybenzyloxy)ethyl]1H-tetrazol-5-ylsulfanylmethyl}quinoline was characterized by IR, Mass, 1H and 13C NMR spectroscopic techniques. Molecular structure was confirmed by using single crystal X-ray diffraction technique. Thermal behavior was studied by using TGA and DSC techniques. Further, in vitro anti-inflammatory and in silico docking analysis has been carried out to study the activity of the compound.

  12. Synthesis, crystal structure analysis, spectral investigations, DFT computations and molecular dynamics and docking study of 4-benzyl-5-oxomorpholine-3-carbamide, a potential bioactive agent (United States)

    Murthy, P. Krishna; Sheena Mary, Y.; Shyma Mary, Y.; Panicker, C. Yohannan; Suneetha, V.; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Suchetan, P. A.


    4-benzyl-5-oxomorpholine-3-carbamide has been synthesized; single crystals were grown by slow evaporation solution growth technique at room temperature and characterized by single crystal X-ray diffraction, FT-IR, FT-Raman and 1H-NMR. The compound crystallizes in the monoclinic space group P21/n. The molecular geometry of the compound was optimized by using Density Functional Theory (DFT/B3LYP) method with 6-311++G(d,p) basis set in the ground state and geometric parameters are in agreement with the X-ray analysis results of the structure. The experimental vibrational spectra were compared with the calculated spectra and each vibrational wave number was assigned on the basis of potential energy distribution (PED). The electronic and charge transfer properties have been explained on the basis of highest occupied molecular orbital's (HOMOs) and lowest unoccupied molecular orbital's (LUMOs). Besides molecular electrostatic potential (MEP), frontier molecular orbital's (FMOs), some global reactivity descriptors, thermodynamic properties, non-linear optical (NLO) behavior and Mullikan charge analysis of the title compound were computed with the same method in gas phase, theoretically. Potential reactive sites of the title compound have been identified by average local ionization energy and Fukui functions, both mapped to the electron density surface. Bond dissociation energies for all single acyclic bonds have been calculated in order to investigate autoxidation and degradation properties of the title compound. Atoms with pronounced interactions with water molecules have been detected by calculations of radial distribution functions after molecular dynamics simulations. The experimental results are compared with the theoretical calculations using DFT methods for the fortification of the paper. Further the docking studies revealed that the title compound as a docked ligand forms a stable complex with pyrrole inhibitor with a binding affinity value of -7.5 kcal/mol. This

  13. Design, synthesis and anti-HIV evaluation of novel diarylnicotinamide derivatives (DANAs) targeting the entrance channel of the NNRTI binding pocket through structure-guided molecular hybridization. (United States)

    Liu, Zhaoqiang; Chen, Wenmin; Zhan, Peng; De Clercq, Erik; Pannecouque, Christophe; Liu, Xinyong


    Through a structure-based molecular hybridization approach, a novel series of diarylnicotinamide derivatives (DANAs) targeting the entrance channel of HIV-1 NNRTIs binding pocket (NNIBP) were rationally designed, synthesized and evaluated for their anti-HIV activities in MT-4 cells together with the inhibition against the reverse transcriptase (RT) in an enzymatic assay. Encouragingly, most of the new DANAs were found to be active against wild-type HIV-1 with an EC50 in the range of 0.027-4.54 μM. Among them, compound 6b11 (EC50 = 0.027 μM, SI > 12518) and 6b5 (EC50 = 0.029 μM, SI = 2471) were identified as the most potent inhibitors, which were more potent than the reference drugs nevirapine (EC50 = 0.31 μM) and delavirdine (EC50 = 0.66 μM). Some DANAs were also active at micromolar concentrations against the K103N + Y181C resistant mutant. Compound 6b11 exhibited the highest enzymatic inhibition activity (IC50 = 20 nM), which is equal to that of efavirenz (EC50 = 20 nM) and 31 times higher than that of nevirapine (EC50 = 0.62 μM). Preliminary structure-activity relationships (SARs) and molecular modeling of these new DANAs have been discussed. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  14. Novel 2-amino-1,3,4-thiadiazoles and their acyl derivatives: Synthesis, structural characterization, molecular docking studies and comparison of experimental and computational results (United States)

    Er, Mustafa; Isildak, Gamze; Tahtaci, Hakan; Karakurt, Tuncay


    This study aims to synthesize and characterize compounds containing 2-amino-1,3,4-thiadiazole and compare experimental results to theoretical results. For this purpose, firstly mono, di and tetra 2-amino-1,3,4-thiadiazole compounds (2a-c, 14, 20 and 25) were synthesized in relatively high yields (74-87%). The target compounds (3-11, 15-17, 21-23 and 26-28) were then synthesized in moderate to high yields (65-85%) from the reactions of 2-amino-1,3,4-thiadiazole compounds with various acyl chloride derivatives. The structures of all synthesized compounds were elucidated by IR, 1H NMR, 13C NMR, elemental analyses and mass spectroscopy techniques. The structures of 2b (C9H8N4O2S) and 2c (C11H13N3O2S) were also elucidated by X-ray diffraction analysis. Lastly, IR spectrum, 1H NMR and 13C NMR chemical shift values, frontier molecular orbital (FMO) values of these molecules containing heteroatoms were examined using the Becke-3- Lee-Yang-Parr (B3LYP) method with the 6-31G(d) basis set. Two different molecular structures containing 2-amino-1,3,4-thiadiazole (2b, 2c) were used in our study to examine these properties. Also, compounds 2b and 2c form a stable complex with beta-Lactamase as can be understood from the binding affinity values and the results show that the compound might inhibit the beta-Lactamase enzyme. It was found that theoretical and experimental results obtained in the experiment were compatible with each other and with the values found in the literature.

  15. Ruthenium-Catalyzed Synthesis of Dialkoxymethane Ethers Utilizing Carbon Dioxide and Molecular Hydrogen. (United States)

    Thenert, Katharina; Beydoun, Kassem; Wiesenthal, Jan; Leitner, Walter; Klankermayer, Jürgen


    The synthesis of dimethoxymethane (DMM) by a multistep reaction of methanol with carbon dioxide and molecular hydrogen is reported. Using the molecular catalyst [Ru(triphos)(tmm)] in combination with the Lewis acid Al(OTf)3 resulted in a versatile catalytic system for the synthesis of various dialkoxymethane ethers. This new catalytic reaction provides the first synthetic example for the selective conversion of carbon dioxide and hydrogen into a formaldehyde oxidation level, thus opening access to new molecular structures using this important C1 source. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Synthesis and characterization of core–shell magnetic molecularly ...

    Indian Academy of Sciences (India)

    Abstract. In this study, simple, effective and general processes were used for the synthesis of a new nano- molecularly imprinted polymers (MIPs) layer on magnetic Fe3O4 nanoparticles (NPs) with uniform core–shell struc- ture by combining surface imprinting and nanotechniques. The first step for the synthesis of magnetic ...

  17. Synthesis, molecular structure, vibrational spectroscopy, optical investigation and DFT study of a novel hybrid material: 3,3‧-diammoniumdiphenylsulfone hexachloridostannate monohydrate (United States)

    Kessentini, A.; Dammak, T.; Belhouchet, M.


    In his work we investigate a new halogenotin (IV) organic inorganic material. The structure, determined by single-crystal X-ray diffraction at 293 K of 3,3‧-diammoniumdiphenylsulfone hexachloridostannate monohydrate abbreviated 3,3‧(DDS)SnCl6, can be viewed as inorganic layers built from (SnCl6)2- octahedra and H2O molecules, between which, the organic entities [C12H14N2O2S]2+ are inserted. Experimental room-temperature X-ray studies were supported by theoretical methods using density functional theory (DFT). The detailed examination of the vibrational spectra of our material was correlated by DFT calculation using the unit cell parameters obtained from the experiment data. The optical properties in the UV-visible region have been explored by the UV-visible absorption. This material shows a single absorption band centred at 325 nm (318 eV). The energy difference between Occupied, HOMO and Lowest Unoccupied, LUMO orbital which is called energy gap can be used to predict the strength and stability of metal complexes, as well as in determining molecular electrical transport properties. For the calculation of excitation energies in the optical studies we used Time-Dependent Density Functional Theory (TD-DFT). In addition, Mulliken population method and molecular electrostatic potential (MEP) of the title material have been theoretically studied by GAUSSIAN 03 package.

  18. Synthesis, crystal structure, vibrational profiling, DFT studies and molecular docking of N-(4-chloro-2-{[2-(1H-indol-2-ylcarbonyl) hydrazinyl](oxo)acetyl}phenyl)acetamide.DMSO: A new antiproliferative agent (United States)

    Al-Wabli, Reem I.; Salman, Asmaa; Shyni, V.; Ghabbour, Hazem A.; Joe, I. Hubert; Almutairi, Maha S.; Maklad, Yousreya A.; Attia, Mohamed I.


    Cancer is one of the most serious health problems worldwide and it is considered the second major cause of mankind deaths. We report the synthesis and spectroscopic characterization of N-(4-chloro-2-{[2-(1H-indol-2-ylcarbonyl)hydrazinyl](oxo)acetyl}phenyl)acetamide (CICHOPA, 5) as a new antiproliferative glyoxylamide derivative. Molecular structure of CICHOPA (5) was unequivocally confirmed via X-ray analysis and it was crystallized in the monoclinic, P21/c, a = 14.3956 (4) Å, b = 8.9307 (3) Å, c = 34.9507 (10) Å, β = 94.439 (1)°, V = 4479.9 (2) Å3, Z = 8. The in vitro anticancer potential of the title molecule 5 was examined toward four types of human cancer cell lines. Vibrational profile of the CICHOPA molecule was investigated with the aid of density functional theory approach. Natural bond orbital, and natural population analyses as well as HOMO and LUMO molecular orbitals studies were carried out in order to explore the possible intermolecular delocalization or hyperconjugation in the title compound. The binding mode of compound 5 to its target protein was predicted through a molecular docking investigation. The in vitro antiproliferative activity of the title compound 5 was examined against four human cancer cell lines and showed growth inhibitory activity at concentrations of 25 and 50 μM.

  19. Synthesis, spectroscopic characterization and electronic structure of ...

    Indian Academy of Sciences (India)


    Copper(I) carbene complex; carbene complex synthesis; Cu(I)–carbene electronic structure. 1. Introduction. Metal carbene complexes are arguably the most ver- satile organometallic reagents that have been devel- oped for organic synthesis.1 Different reactions of these complexes have been reported since their dis-.

  20. Rotational spectra and molecular structure

    CERN Document Server

    Wollrab, James E


    Physical Chemistry, A Series of Monographs: Rotational Spectra and Molecular Structure covers the energy levels and rotational transitions. This book is divided into nine chapters that evaluate the rigid asymmetric top molecules and the nuclear spin statistics for asymmetric tops. Some of the topics covered in the book are the asymmetric rotor functions; rotational transition intensities; classes of molecules; nuclear spin statistics for linear molecules and symmetric tops; and classical appearance of centrifugal and coriolis forces. Other chapters deal with the energy levels and effects of ce

  1. Molecular clips based on propanediurea : synthesis and physical properties

    NARCIS (Netherlands)

    Jansen, Robertus Johannes


    This thesis describes the synthesis and physical properties of a series of molecular clips derived from the concave molecule propanediurea. These molecular clips are cavity-containing receptors that can bind a variety of aromatic guests. This binding is a result of hydrogen bonding and pi-pi

  2. CSMB | Center For Structural Molecular Biology (United States)

    Federal Laboratory Consortium — The Center for Structural Molecular Biologyat ORNL is dedicated to developing instrumentation and methods for determining the 3-dimensional structures of proteins,...

  3. Uncertainties of Molecular Structural Parameters

    International Nuclear Information System (INIS)

    Császár, Attila G.


    performed. Simply, there are significant disagreements between the same bond lengths measured by different techniques. These disagreements are, however, systematic and can be computed via techniques of quantum chemistry which deal not only with the motions of the electrons (electronic structure theory) but also with the often large amplitude motions of the nuclei. As to the relevant quantum chemical computations, since about 1970 electronic structure theory has become able to make quantitative predictions and thus challenge (or even overrule) many experiments. Nevertheless, quantitative agreement of quantum chemical results with experiment can only be expected when the motions of the atoms are also considered. In the fourth age of quantum chemistry we are living in an era where one can bridge quantitatively the gap between ‘effective’, experimental and ‘equilibrium’, computed structures at even elevated temperatures of interest thus minimizing any real uncertainties of structural parameters. The connections mentioned are extremely important as they help to understand the true uncertainty of measured structural parameters. Traditionally it is microwave (MW) and millimeterwave (MMW) spectroscopy, as well as gas-phase electron diffraction (GED), which yielded the most accurate structural parameters of molecules. The accuracy of the MW and GED experiments approached about 0.001Å and 0.1º under ideal circumstances, worse, sometimes considerably worse, in less than ideal and much more often encountered situations. Quantum chemistry can define both highly accurate equilibrium (so-called Born-Oppenheimer, r e BO , and semiexperimental, r e SE ) structures and, via detailed investigation of molecular motions, accurate temperature-dependent rovibrationally averaged structures. Determining structures is still a rich field for research, understanding the measured or computed uncertainties of structures and structural parameters is still a challenge but there are firm and well

  4. An Optimized Synthesis, Molecular Structure and Characterization of Benzylic Derivatives of 1,2,4-Triazin-3,5(2H,4H-dione

    Directory of Open Access Journals (Sweden)

    Long-Chih Hwang


    Full Text Available 4-Benzyl-1,2,4-triazin-3,5(2H,4H-dione (3-benzyl-6-azauracil, 2, and 2,4-dibenzyl-1,2,4-triazin-3,5(2H,4H-dione (1,3-dibenzyl-6-azauracil, 3 were synthesized by the reaction of 1,2,4-triazin-3,5(2H,4H-dione (6-azauracil, 1 with benzyl bromide and potassium carbonate in dry acetone via the 18-crown-6-ether catalysis. In these reaction methods, we developed more convenient and efficient methodologies to afford compounds 2 and 3 in good yields. These compounds were characterized by 1H- and 13C-NMR, MS spectrum, IR spectroscopy and elemental analysis. The structure of 2 was verified by 2D-NMR measurements, including gHSQC and gHMBC measurements. A single-crystal X-ray diffraction experiment indicated that compound 3, with the molecular formula C17H15N3O2, crystallized from a CH3OH/CH2Cl2 diffusion solvent system in a monoclinic space group P21/c with a = 13.7844(13, b = 8.5691(8, c = 13.0527(12 Å, β = 105.961(2°, V = 1482.3(2 Å3, Z = 4, resulting in a density Dcalc of 1.314 g/cm3. The crystal structure of compound 3 is tightly stabilized by contact with five other molecules from the six short contacts formed by intermolecular C−O···H−Car, C−H···Car, and weakly π···π stacking interactions. The dihedral angle 31.90° is formed by the mean planes of the benzene rings of the N-2 and N-4 benzyl groups.

  5. Molecular catalysts structure and functional design

    CERN Document Server

    Gade, Lutz H


    Highlighting the key aspects and latest advances in the rapidly developing field of molecular catalysis, this book covers new strategies to investigate reaction mechanisms, the enhancement of the catalysts' selectivity and efficiency, as well as the rational design of well-defined molecular catalysts. The interdisciplinary author team with an excellent reputation within the community discusses experimental and theoretical studies, along with examples of improved catalysts, and their application in organic synthesis, biocatalysis, and supported organometallic catalysis. As a result, readers wil

  6. Synthesis and characterization of core–shell magnetic molecularly ...

    Indian Academy of Sciences (India)

    In this study, simple, effective and general processes were used for the synthesis of a new nanomolecularly imprinted polymers (MIPs) layer on magnetic Fe3O4 nanoparticles (NPs) with uniform core–shell structure by combining surface imprinting and nanotechniques. The first step for the synthesis of magnetic NPs was ...


    African Journals Online (AJOL)

    Preferred Customer

    2Department of Chemistry, University of Aveiro, CICECO, 3810-193 Aveiro, Portugal. (Received October 14 ... The principal feature of ionothermal synthesis is that the ionic liquids (ILs) act as both the “designed” green solvents ... purification except [EMI]Br. [EMI]Br was synthesized from the reaction of ethylbromide with.

  8. Solvothermal synthesis of high molecular weight dithienogermole ...

    Indian Academy of Sciences (India)

    cation of the resulting organic products by the Soxhlet extraction gave the target polymers with high molecular weight and low polydispersity index (PDI). The higher molecular weight of pDTG-PH may be ascribed to high solubility of the polymers than those of pDTG-BTA. The long branched alkyl chain in acceptor part may.

  9. Organoactinide chemistry: synthesis, structure, and solution dynamics

    International Nuclear Information System (INIS)

    Brennan, J.G.


    This thesis considers three aspects of organoactinide chemistry. In chapter one, a bidentate phosphine ligand was used to kinetically stabilize complexes of the type Cp 2 MX 2 . Ligand redistribution processes are present throughout the synthetic work, as has often been observed in uranium cyclopentadienyl chemistry. The effects of covalent M-L bonding on the solution and solid state properties of U(III) coordination complexes are considered. In particular, the nature of the more subtle interaction between the metal and the neutral ligand are examined. Using relative basicity data obtained in solution, and solid state structural data (and supplemented by gas phase photoelectron measurements), it is demonstrated that the more electron rich U(III) centers engage in significant U → L π-donation. Trivalent uranium is shown to be capable of acting either as a one- or two-electron reducing agent toward a wide variety of unsaturated organic and inorganic molecules, generating molecular classes unobtainable via traditional synthetic approaches, as well as offering an alternative synthetic approach to molecules accessible via metathesis reactions. Ligand redistribution processes are again observed, but given the information concerning ligand lability, this reactivity pattern is applied to the synthesis of pure materials inaccessible from redox chemistry. 214 refs., 33 figs., 10 tabs

  10. Solvothermal synthesis of high molecular weight dithienogermole ...

    Indian Academy of Sciences (India)

    dithiadiazole alternate polymers were synthesized by the solvothermal method. Optical properties and molecular weight were investigated by UV–Vis absorption spectroscopy and Gel Permeation Chromatography. Compared with the results achieved ...

  11. Carbonic anhydrase inhibition of Schiff base derivative of imino-methyl-naphthalen-2-ol: Synthesis, structure elucidation, molecular docking, dynamic simulation and density functional theory calculations (United States)

    Abbas, Saghir; Nasir, Hafiza Huma; Zaib, Sumera; Ali, Saqib; Mahmood, Tariq; Ayub, Khurshid; Tahir, Muhammad Nawaz; Iqbal, Jamshed


    In the present study, we have designed and synthesized a Schiff base derivative 3 and characterized by FT-IR, 1H and 13C NMR spectroscopy. Single crystal X-ray diffraction and NMR studies were also performed. The synthetic compound was screened for its inhibitory potential against carbonic anhydrase II. The experimental results were validated by molecular docking and dynamic simulations of compound 3 in the active pocket of enzyme. Important binding interactions with the key residues in the active site of the carbonic anhydrase enzyme were revealed. Moreover, supramolecular assembly of the title compound was analyzed by density functional theory (DFT) calculations. These studies rendered a more clear understanding for the demonstration of novel molecular mechanism involved in CA II inhibition by the synthesized compound.

  12. Tetrapodal Molecular Switches and Motors : Synthesis and Photochemistry

    NARCIS (Netherlands)

    Chen, Kuang-Yen; Wezenberg, Sander J.; Carroll, Gregory T.; London, Gabor; Kistemaker, Jos C. M.; Pijper, Thomas C.; Feringa, Ben L.


    The design, synthesis, and dynamic behavior of a series of novel tetrapodal molecular switches and motors containing common functional groups for attachment to various inorganic and organic surfaces are presented. Using a Diels-Alder reaction, an anthracene unit with four functionalized alkyl

  13. Synthesis, molecular and crystalline architectures, and properties of ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 125; Issue 4. Synthesis, molecular and crystalline architectures, and properties of a mononuclear complex [CoII (benzidine)2(NCS)2(OH2)2]. Subhasish Kundu Subhasis Roy Kishalay Bhar Rajarshi Ghosh Chia-Her Lin Joan Ribas Barindra Kumar Ghosh. Volume 125 ...

  14. Synthesis and molecular docking of new hydrazones derived from ...

    African Journals Online (AJOL)

    Synthesis and molecular docking of new hydrazones derived from ethyl isonipecotate and their biological activities. A Munir, Aziz-ur Rehman, M.A. Abbasi, S.Z. Siddiqui, A Nasir, S.G. Khan, S Rasool, S.A.A. Shah ...

  15. Synthesis, evaluation and molecular modelling studies of some ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 122; Issue 2. Synthesis, evaluation and molecular modelling studies of some novel 3-(3 ... The compounds have been characterized on the basis of elemental analysis and spectral data. All the compounds were evaluated for their HIV-1 RT inhibitory activity. Among ...

  16. Structure-based development of novel triazoles and related thiazolotriazoles as anticancer agents and Cdc25A/B phosphatase inhibitors. Synthesis, in vitro biological evaluation, molecular docking and in silico ADME-T studies. (United States)

    Rostom, Sherif A F; Badr, Mona H; Abd El Razik, Heba A; Ashour, Hayam M A


    Synthesis of twenty nine new 1,2,4-triazoles and some derived thiazolothiadiazoles (structurally-relevant to some reported triazoles with anticancer and/or Cdc25A/B inhibitory activities) is described in this study. The obtained NCI's in vitro antitumor data revealed that five analogs (12, 15, 18, 19 and 22) displayed considerable tumor percentage growth inhibitory activity (GI%), among which the analog 18 possessed a special antitumor potential and spectrum. Additionally, the same five analogs showed a marginal GI effect on the normal breast epithelial cell line MCF-10A indicating higher selectivity towards cancer cells. The same active analogs 12, 15, 18, 19 and 22 were further assessed for their in vitro Cdc25A/B phosphatase inhibitory activity (a possible antitumor target), where 18 and 22 displayed a distinctive inhibitory affinity towards the Cdc25B isozyme (6.7 and 8.4 μM, respectively). Docking of 12, 15, 18, 19 and 22 with the active site of human Cdc25B phosphatase enzyme demonstrated superior binding profile by the top-scoring analog 18 relative to a reported Cdc25 phosphatase ligand. In silico calculations of molecular properties revealed that all of the active compounds comply with Lipinski's RO5 and Veber's criteria for good bioavailability suggesting good drug-likeness upon oral administration with a predicted high safety profile. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  17. Synthesis and Studies of Sulfur-Containing Heterocyclic Molecules for Molecular Electronics

    DEFF Research Database (Denmark)

    Mazzanti, Virginia

    This work describes the synthesis and studies of sulfur containing π conjugated heterocycles, which are considered interesting motifs in the field of molecular electronics. The first project, which is covered in Chapter 1, concerns the functionalization of tetracycle dibenzo[bc,fg][1,4]dithiapent......This work describes the synthesis and studies of sulfur containing π conjugated heterocycles, which are considered interesting motifs in the field of molecular electronics. The first project, which is covered in Chapter 1, concerns the functionalization of tetracycle dibenzo[bc,fg][1...... the synthesis of dimeric structures of redox active system tetrathiafulvalene (TTF). Molecules with different conjugation pathways bridging two TTFs were synthesized and studied using CV and DPV in order to probe the electronic interaction between these two redox units. The last aspect of this thesis, which...

  18. Synthesis, characterization, antimicrobial activity and molecular ...

    African Journals Online (AJOL)

    construction of supramolecular blocks. In this context, Pyrazole derivatives are of particular interest because ... construction of new heterocycles. Their anti- microbial properties and molecular docking were ...... residues Thr58, Lys57 and Arg56 respectively of protein (Figure 2a), Alternatively, docking simulation with gyrase ...

  19. Structured synthesis of MEMS using evolutionary approaches

    DEFF Research Database (Denmark)

    Fan, Zhun; Wang, Jiachuan; Achiche, Sofiane


    In this paper, we discuss the hierarchy that is involved in a typical MEMS design and how evolutionary approaches can be used to automate the hierarchical synthesis process for MEMS. The paper first introduces the flow of a structured MEMS design process and emphasizes that system-level lumped...... the integrated design automation idea using these evolutionary approaches....

  20. Synthesis, spectroscopy and supramolecular structures of two ...

    Indian Academy of Sciences (India)



    May 16, 2007 ... Indian Academy of Sciences. 243. #. Dedicated to Prof. Dr. Werner Weisweiler on the occasion of his 69th birthday. *For correspondence. Synthesis, spectroscopy and supramolecular structures of two magnesium 4-nitrobenzoate complexes. #. BIKSHANDARKOIL R SRINIVASAN,. 1,. * JYOTI V SAWANT,.

  1. Hydrothermal synthesis, crystal structure and luminescence property ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 127; Issue 12. Hydrothermal synthesis, crystal structure and luminescence property of a three dimensional Sm(III) coordination polymer with 2,5-pyridinedicarboxylic acid. Kranthi Kumar Gangu Anima S Dadhich Saratchandra Babu Mukkamala. Volume 127 Issue 12 ...

  2. Synthesis, crystal structure, thermal analysis and dielectric

    Indian Academy of Sciences (India)

    Annual Meetings · Mid Year Meetings · Discussion Meetings · Public Lectures · Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Bulletin of Materials Science; Volume 39; Issue 5. Synthesis, crystal structure, thermal analysis and dielectric properties of two mixed trichlorocadmiates (II).

  3. Synthesis, properties and supramolecular structure of ...

    Indian Academy of Sciences (India)

    Synthesis, properties and supramolecular structure of piperazinediium thiosulfate monohydrate. +. BIKSHANDARKOIL R SRINIVASANa*, ASHISH R NAIKa. , SUNDER N DHURIa. ,. CHRISTIAN NÄTHERb and WOLFGANG BENSCHb. aDepartment of Chemistry, Goa University, Goa 403 206, India. bInstitut für ...

  4. Synthesis, molecular and electronic structure of a stacked half-sandwich dititanium complex incorporating a cyclic p-faced bridging ligand

    Czech Academy of Sciences Publication Activity Database

    Gyepes, R.; Pinkas, Jiří; Císařová, I.; Kubišta, Jiří; Horáček, Michal; Mach, Karel


    Roč. 6, č. 96 (2016), s. 94149-94159 ISSN 2046-2069 R&D Projects: GA ČR(CZ) GAP207/12/2368 Institutional support: RVO:61388955 Keywords : atoms * carbon * electronic structure Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.108, year: 2016

  5. Synthesis and characterization of low-dimensional molecular magnetic materials (United States)

    Liu, Chen

    This dissertation presents experimental results from the synthesis and structural, magnetic characterization of representative low-dimensional molecule-based magnetic materials. Most of the materials reported in this dissertation, both coordination polymers and cuprate, are obtained as the result of synthesizing and characterizing spin ladder systems; except the material studied in Chapter 2, ferricenyl(III)trisferrocenyl(II)borate, which is not related to the spin ladder project. The interest in spin ladder systems is due to the discovery of high-temperature superconductivity in doped cuprates possessing ladder-like structures, and it is hoped that investigation of the magnetic behavior of ladder-like structures will help us understand the mechanism of high-temperature superconductivity. Chapter 1 reviews fundamental knowledge of molecular magnetism, general synthetic strategies for low-dimensional coordination polymers, and a brief introduction to the current status of research on spin ladder systems. Chapter 2 presents a modified synthetic procedure of a previously known monomeric complex, ferricenyl(III)trisferrocenyl(II)borate, 1. Its magnetic properties were characterized and previous results have been disproved. Chapter 3 investigates the magnetism of [CuCl2(CH3CN)] 2, 2, a cuprate whose structure consists of isolated noninterpenetrating ladders formed by the stacking of Cu(II) dimers. This material presents an unexpected ferromagnetic interaction both within the dimeric units and between the dimers, and this behavior has been rationalized based on the effect of its terminal nonbridging ligands. In Chapter 4, the synthesis and magnetism of two ladder-like coordination polymers, [Co(NO3)2(4,4'-bipyridine) 1.5(MeCN)]n, 3, and Ni2(2,6-pyridinedicarboxylic acid)2(H2O)4(pyrazine), 4, are reported. Compound 3 possesses a covalent one-dimensional ladder structure in which Co(II) ions are bridged through bipyridine molecules. Compared to the materials discussed in

  6. Fluorescence Titrations of Bio-relevant Complexes with DNA: Synthesis, Structural Investigation, DNA Binding/Cleavage, Antimicrobial and Molecular Docking Studies. (United States)

    Arun, Thesingu Rajan; Subramanian, Ramasamy; Packianathan, Seemon; Raman, Natarajan


    In the present work, we attempted to develop new metal complexes (Cu(II), Co(II), Ni(II) and Zn(II)) of the imine ligand which was synthesized from 9,10-phenanthrenequinone and para-anisidine. With an intention to make the complexes most stable, very special chelating amino acid has been coordinated to the metal centre. The resultant metal complexes have been characterized by variety of techniques including FT-IR, UV-Vis., (1)H NMR, (13)C NMR, powder XRD, EPR and mass spectral studies. The interaction of the complexes with DNA has been effectively examined and explored by fluorescence titration, UV-Vis absorption, viscometer titration, cyclic voltammetry (CV) and differential pulse voltammetry. Moreover, molecular docking analysis has been performed to understand the nature of binding of the complexes with DNA. These studies prove that CT DNA interaction of the complexes follows intercalation mode. The metal complexes exhibit effective cleavage of pUC19 DNA by an oxidative cleavage mechanism. The antimicrobial screening indicates that these complexes are good antimicrobial agents against various organisms.

  7. [UO2(NH3)5]Br2·NH3: synthesis, crystal structure, and speciation in liquid ammonia solution by first-principles molecular dynamics simulations. (United States)

    Woidy, Patrick; Bühl, Michael; Kraus, Florian


    Pentaammine dioxido uranium(VI) dibromide ammonia (1/1), [UO2(NH3)5]Br2·NH3, was synthesized in the form of yellow crystals by the reaction of uranyl bromide, UO2Br2, with dry liquid ammonia. The compound crystallizes orthorhombic in space group Cmcm and is isotypic to [UO2(NH3)5]Cl2·NH3 with a = 13.2499(2), b = 10.5536(1), c = 8.9126(1) Å, V = 1246.29(3) Å(3) and Z = 4 at 123 K. The UO2(2+) cation is coordinated by five ammine ligands and the coordination polyhedron can be best described as pentagonal bipyramid. Car-Parrinello molecular dynamics simulations are reported for [UO2(NH3)5](2+) in the gas phase and in liquid NH3 solution (using the BLYP density functional). According to free-energy simulations, solvation by ammonia has only a small effect on the uranyl-NH3 bond strength.

  8. Synthesis and structures of metal chalcogenide precursors (United States)

    Hepp, Aloysius F.; Duraj, Stan A.; Eckles, William E.; Andras, Maria T.


    The reactivity of early transition metal sandwich complexes with sulfur-rich molecules such as dithiocarboxylic acids was studied. Researchers recently initiated work on precursors to CuInSe2 and related chalcopyrite semiconductors. Th every high radiation tolerance and the high absorption coefficient of CuInSe2 makes this material extremely attractive for lightweight space solar cells. Their general approach in early transition metal chemistry, the reaction of low-valent metal complexes or metal powders with sulfur and selenium rich compounds, was extended to the synthesis of chalcopyrite precursors. Here, the researchers describe synthesis, structures, and and routes to single molecule precursors to metal chalcogenides.

  9. Synthesis, spectral characteristics, and the crystal and molecular structures of 2,3-dimethyl-1-phenyl-4-(N-phthalimido)pyrazolone-5

    International Nuclear Information System (INIS)

    Sokol, V. I.; Strashnova, S. B.; Kovalchukova, O. V.; Sergienko, V. S.; Davydov, V. V.; Zaitsev, B. E.; Evtushenko, Yu. M.


    2,3-Dimethyl-1-phenyl-4-(N-phthalimido)pyrazolone-5 (I) is synthesized and isolated in the form of single crystals. The crystal structure of compound I is determined using X-ray diffraction. The phthalimide and pyrazolone rings in the molecule are not coplanar: the angle between their median planes is 56.4 o . The bond lengths in the rings level off, which indicates the delocalization of the electron density. The spectral characteristics (IR and electronic spectra) of molecule I are determined.

  10. Synthesis and Molecular Structures of Two [1,4-bis(3-pyridyl)-2,3-diazo-1,3-butadiene]-dichloro-Zn(II) Coordination Polymers


    Lee, Gene-Hsiang; Wang, Hsin-Ta


    Two novel coordination polymers with 3D metal-organic frameworks (MOFs) have been synthesized by reacting 1,4-bis(3-pyridyl)-2,3-diazo-1,3-butadiene (L) with zinc dichloride. Both compounds have the same repeating unit consisting of a distorted tetrahedral Zn(II) center coordinated by two chlorides and two pyridyl nitrogen atoms of two bridging bismonodentate L ligands, however, different structural conformations have been found, one forming a helical chain and the other producing a square-wa...

  11. Synthesis, Characterization, Tautomeric Structure and Solvatochromic Behavior of Novel 4-(5-Arylazo-2-Hydroxystyryl-1-Methylpyridinium Iodide as Potential Molecular Photoprobe

    Directory of Open Access Journals (Sweden)

    Farag Altalbawy


    Full Text Available A novel series of the title compound 4-(5-arylazo-2-hydroxystyryl-1-methylpyridinium iodide 6 has been synthesized via condensation reactions of the arylazosalicylaldehyde derivatives 4a–i with 1-methyl-picolinium iodide 5. The structures of the new arylazo compounds were characterized by 1H NMR, IR, mass spectroscopy, as well as spectral and elemental analyses. The electronic absorption spectra of arylazomerocyanine compounds 6 were measured in different buffer solutions and solvents. The pK′s and pK*′s in both the ground and excited states, respectively, were determined for the series and their correlations with the Hammett equation were examined. The results indicated that the title arylazomerocyanine dyes 6 exist in the azo form 6A in both ground and excited states. The substituent and solvent effects (solvatochromism of the title compound arylazomerocyanine dyes were determined using the Kamlet-Taft equation and subsequently discussed.

  12. A MnII6MnIII6 single-strand molecular wheel with a reuleaux triangular topology: synthesis, structure, magnetism, and DFT studies. (United States)

    Zartilas, Sotiris; Papatriantafyllopoulou, Constantina; Stamatatos, Theocharis C; Nastopoulos, Vassilios; Cremades, Eduard; Ruiz, Eliseo; Christou, George; Lampropoulos, Christos; Tasiopoulos, Anastasios J


    The use of the anion of 3-methyl-1,3,5-pentanetriol (mpt(3-)) in manganese carboxylate chemistry has afforded the new Mn(II/III)12 cluster [Mn(II)6Mn(III)6(mpt)6(CH3CO2)12(py)6]·3CH3CN (1·3CH3CN). Complex 1 was isolated in moderate yield by the reaction of Mn(CH3CO2)2·4H2O and H3mpt in a 2.6:1 molar ratio in a solvent mixture of acetonitrile and pyridine. The structure of 1 consists of alternating [Mn(II)2(CH3CO2)3(py)](+) and [Mn(III)2(μ-OR)2(CH3CO2)(py)](3+) dimeric units (three of each dimer), linked at each end by two alkoxo and one acetate bridges; the mpt(3-) ligands adopt the η(2):η(2):η(2):μ4 coordination mode. The overall metal topology of this new Mn12 wheel resembles a guitar plectrum, or a Reuleaux triangle. Complex 1 displays an unprecedented structural topology, being the first example of a Mn(II)6Mn(III)6 wheel constructed from alternating homovalent dimers and the only known Mn12 loop with the trigonal symmetry of a Reuleaux triangle (all other reported loops were ellipsoids). Variable-temperature, solid-state direct- and alternating-current magnetization studies were carried out on complex 1, revealing the presence of antiferromagnetic exchange interactions between the metal ions in the molecule, which lead to a spin ground-state value S = 0; the exchange coupling parameters J were calculated using density functional theory employing a hybrid B3LYP functional.


    African Journals Online (AJOL)

    B. S. Chandravanshi

    The V atoms in the complexes are in octahedral coordination. Thermal stabilities of the complexes have also been studied. KEY WORDS: Oxovanadium complex, Aroylhydrazone ligand, Crystal structure, X-ray diffraction, Thermal property. INTRODUCTION. Coordination chemistry of vanadium has attracted considerable ...

  14. Synthesis, structure elucidation, biological screening, molecular modeling and DNA binding of some Cu(II) chelates incorporating imines derived from amino acids (United States)

    Abdel-Rahman, Laila H.; Abu-Dief, Ahmed M.; Ismael, Mohammed; Mohamed, Mounir A. A.; Hashem, Nahla Ali


    Three tridentate Schiff bases amino acids were prepared by direct condensation of 3-methoxysalicylaldehyde (MS) or 4-diethylaminosalicylaldehyde (DS) with α-amino acid ligands [L-phenylalanine (P), L-histidine (H) and DL-tryptophan (T)]. The prepared Schiff bases amino acids were investigated by melting points, elemental analysis, 1HNMR and 13CNMR, IR, UV-Vis spectra, conductivity and magnetic measurements analyses. Subsequently, copper was introduced and Cu(II) complexes formed. These complexes were analyzed by thermal and elemental analyses and further investigated by FT-IR and UV/Vis spectroscopies. The experimental results indicating that all Cu(II) complexes contain hydrated water molecules (except DSPCu complex) and don't contain coordinated water molecules. The kinetic and thermal parameters were extracted from the thermal data using Coast and Redfern method. The molar conductance values of the Schiff base amino acid ligands and their Cu(II) complexes were relatively low, showing that these compounds have non-electrolytic nature. Magnetic susceptibility measurements showed the diamagnetic nature of the Schiff base amino acid ligands and paramagnetic nature of their complexes. Additionally, a spectrophotometric method was determined to extract their stability constants. It was found that the complexes possess 1:2 (M:L) stoichiometry. The results suggested that 3-methoxysalicylaldehyde and 4-diethylaminosalicylaldehyde amino acid Schiff bases behave as monobasic tridentate ONO ligands and coordinate Cu(II) ions in octahedral geometry according to the general formula [Cu(HL)2]·nH2O. To further understanding the structural and electronic properties of these complexes, Density Functional Theory (DFT) calculations were employed and provided a satisfactory description. The optimized structures of MST Schiff base ligand and its complex were calculated using DFT. The antimicrobial activity of the Schiff base ligands and their complexes were screened against some

  15. Metal based pharmacologically active agents: Synthesis, structural characterization, molecular modeling, CT-DNA binding studies and in vitro antimicrobial screening of iron(II) bromosalicylidene amino acid chelates (United States)

    Abdel-Rahman, Laila H.; El-Khatib, Rafat M.; Nassr, Lobna A. E.; Abu-Dief, Ahmed M.; Ismael, Mohamed; Seleem, Amin Abdou


    In recent years, great interest has been focused on Fe(II) Schiff base amino acid complexes as cytotoxic and antitumor drugs. Thus a series of new iron(II) complexes based on Schiff bases amino acids ligands have been designed and synthesized from condensation of 5-bromosalicylaldehyde (bs) and α-amino acids (L-alanine (ala), L-phenylalanine (phala), L-aspartic acid (aspa), L-histidine (his) and L-arginine (arg)). The structure of the investigated iron(II) complexes was elucidated using elemental analyses, infrared, ultraviolet-visible, thermogravimetric analysis, as well as conductivity and magnetic susceptibility measurements. Moreover, the stoichiometry and the stability constants of the prepared complexes have been determined spectrophotometrically. The results suggest that 5-bromosalicylaldehyde amino acid Schiff bases (bs:aa) behave as dibasic tridentate ONO ligands and coordinate to Fe(II) in octahedral geometry according to the general formula [Fe(bs:aa)2]ṡnH2O. The conductivity values between 37 and 64 ohm-1 mol-1 cm2 in ethanol imply the presence of nonelectrolyte species. The structure of the complexes was validated using quantum mechanics calculations based on accurate DFT methods. Geometry optimization of the Fe-Schiff base amino acid complexes showed that all complexes had octahedral coordination. In addition, the interaction of these complexes with (CT-DNA) was investigated at pH = 7.2, by using UV-vis absorption, viscosity and agarose gel electrophoresis measurements. Results indicated that the investigated complexes strongly bind to calf thymus DNA via intercalative mode and showed a different DNA binding according to the sequence: bsari > bshi > bsali > bsasi > bsphali. Moreover, the prepared compounds are screened for their in vitro antibacterial and antifungal activity against three types of bacteria, Escherichia coli, Pseudomonas aeruginosa and Bacillus cereus and three types of anti fungal cultures, Penicillium purpurogenium, Aspergillus

  16. Synthesis, characterization and computational studies of 3-{(E)-[(2-hydroxyphenyl)imino]methyl}benzene-1,2-diol and molecular structure of its zwitterionic form (United States)

    Ezeorah, Julius Chigozie; Ossai, Valentine; Obasi, Lawrence Nnamdi; Elzagheid, Mohamed I.; Rhyman, Lydia; Lutter, Michael; Jurkschat, Klaus; Dege, Necmi; Ramasami, Ponnadurai


    The Schiff base 3-{(E)-[(2-hydroxyphenyl)imino]methyl}benzene-1,2-diol was synthesized by the condensation of 2,3-dihydroxybenzaldehyde and 2-aminophenol in water at room temperature. The crystal was grown using two solvents (dry methanol and 60% methanol). The compound was characterized using elemental microanalysis, IR, NMR, UV spectroscopies and single-crystal X-ray diffraction crystallography. The X-ray structure reveals that the Schiff base crystallizes as a methanol solvate in dry methanol with triclinic crystal system, space group P-1 and Z = 2 in the unit cell and as a non-methanol solvate in 60% methanol with triclinic crystal system, space group P-1 and Z = 4 in the unit cell. The compound showed absorption bands at 272, 389, 473 and 602 nm in DMSO. These bands were assigned as π → π ∗, n → π∗ and n-σ∗ transitions. The 473 and 602 nm bands in DMSO reveal that the compound exists in tautomeric forms. The presence of N-H, C-O and Cdbnd N stretching vibrations in the IR spectrum indicates that the compound is zwitterionic in the solid state. This study was supplemented using density functional theory method.

  17. Synthesis, molecular structure and DFT studies of tricarbonylrhenium(I) complexes containing nitrogen based bis, tris, tetrakis-(di-2-pyridylaminomethyl)benzene ligands (United States)

    Sangilipandi, S.; Sutradhar, Dipankar; Kaminsky, Werner; Chandra, Asit K.; Mohan Rao, K.


    The reactions of rhenium starting precursor with the corresponding N,N‧-bidentate 2,2‧-dipyridylamine ligands (L1-L5) in toluene medium under nitrogen atmosphere leads to the formation of mononuclear tricarbonylrhenium(I) complexes. These complexes are denoted by general formula fac-[Re(L) (CO)3Br] (1-5); where, L = 1,2-bis(di-2-pyridylaminomethyl)benzene (L1), 1,3-bis(di-2-pyridylaminomethyl)benzene (L2), 1,4-bis(di-2-pyridylaminomethyl)benzene (L3), 1,3,5-tris(di-2-pyridylaminomethyl)benzene (L4) and 1,2,4,5-tetrakis(di-2-pyridylaminomethyl)benzene (L5). All these complexes have been synthesized and characterized by FT-IR, 1H NMR, UV-Vis and mass spectroscopic techniques. Emission spectrum for these complexes has also been investigated and found that complex (5) shows maximum emission as compared to other complexes. Moreover, two of the complexes (2 &4) were structurally determined by single crystal X-ray diffraction analysis. The time-dependent DFT calculations were carried out for the complexes (2, 4 &5) which show good agreement with the experimental absorption data.

  18. Synthesis and Molecular Structures of Two [1,4-bis(3-pyridyl-2,3-diazo-1,3-butadiene]-dichloro-Zn(II Coordination Polymers

    Directory of Open Access Journals (Sweden)

    Hsin-Ta Wang


    Full Text Available Two novel coordination polymers with 3D metal-organic frameworks (MOFs have been synthesized by reacting 1,4-bis(3-pyridyl-2,3-diazo-1,3-butadiene (L with zinc dichloride. Both compounds have the same repeating unit consisting of a distorted tetrahedral Zn(II center coordinated by two chlorides and two pyridyl nitrogen atoms of two bridging bismonodentate L ligands, however, different structural conformations have been found, one forming a helical chain and the other producing a square-wave chain. The intermolecular C−H···Cl hydrogen bonds in 1 and 2 play important roles in the formation of three-dimensional coordination polymers. Compound 1 crystallized in an orthorhombic space group Pna21 with a = 7.9652(3, b = 21.4716(7, c = 8.2491(3Å, V = 1410.81(9 Å 3 and Z = 4. Compound 2 crystallized in a monoclinic space group P21/n with a = 9.1752(3, b = 14.5976(4, c = 10.3666(3 Å , β = 98.231(2°, V = 1374.16(7 Å 3 and Z = 4.

  19. MFI-molecular sieve membranes:synthesis, characterization and modelling


    Jareman, Fredrik


    This work concerns evaluation by permeation measurements and modeling of thin (<2µm) MFI molecular sieve membranes and, to a smaller extent, synthesis of such materials. The membranes have been synthesized on graded a-alumina microfiltration filters using The seed film method. Scanning electron microscopy and x-ray diffraction were used for characterization in addition to permeation measurements. Mathematical models describing membrane flux for real membranes and defect distributions were ...

  20. Molecular Structure of Nucleic Acids

    Indian Academy of Sciences (India)

    chain, that is, after 34 A. The distance of a phosphorus atom from the fibre axis is 10. A. As the phosphates are on the outside, cations have easy access to them. The structure is an open one, and its water content is rather high. At lower water contents we would expect the bases to tilt so that the structure could become more.

  1. Molecular Structure of Nucleic Acids

    Indian Academy of Sciences (India)

    A structure for nucleic acid has already been proposed by Pauling and Corey [1]. They kindly made'their manuscript available to us in advance of publication. Their model consists of three inter-twined chains, with the phosphates near the fibre axis, and the bases on the outside. In our opinion, this structure is unsatisfactory ...

  2. Synthesis, structural and electrical characterizations of thermally ...

    African Journals Online (AJOL)

    Synthesis, structural and electrical characterizations of thermally evaporated Cu 2 SnS 3 thin films. ... The surface profilometer shows that the deposited films are rough. The XRD spectra identified the ... The electrical resistivity of the deposited Cu2SnS3 film is 2.55 x 10-3 Ωcm. The conductivity is in the order of 103 Ω-1cm-1.

  3. Synthesis, Crystal Structure, Density Function Theory, Molecular ...

    African Journals Online (AJOL)

    have been broadly utilized in medicinal chemistry and drug design because of extensive variety of biological activities such as antimicrobial, anti- convulsant, anticancer, anti-inflammatory, analgesic, hypolipidimic and immunomodulatory activities [1]. The use of phthalimide as primary amine protecting group is extensively ...

  4. Marine Nucleosides: Structure, Bioactivity, Synthesis and Biosynthesis

    Directory of Open Access Journals (Sweden)

    Ri-Ming Huang


    Full Text Available Nucleosides are glycosylamines that structurally form part of nucleotide molecules, the building block of DNA and RNA. Both nucleosides and nucleotides are vital components of all living cells and involved in several key biological processes. Some of these nucleosides have been obtained from a variety of marine resources. Because of the biological importance of these compounds, this review covers 68 marine originated nucleosides and their synthetic analogs published up to June 2014. The review will focus on the structures, bioactivities, synthesis and biosynthetic processes of these compounds.

  5. Exploring RNA structure by integrative molecular modelling

    DEFF Research Database (Denmark)

    Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice


    on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded...

  6. Collisional and photon induced molecular synthesis within ice mantles

    International Nuclear Information System (INIS)

    Mason, N.J.; Dawes, A.; Tegeder, P.; Holtom, P.


    Multilayers of molecules condensed on bulk surfaces at temperatures below 270 K are of great importance in several areas of modern physical and chemical research, for example in the terrestrial stratosphere where they play a key role in the heterogeneous catalytic destruction of ozone on the surfaces of ice crystals in polar stratospheric clouds. The interactions of photons, electrons and ions with a molecular adsorbate produces highly reactive species (radicals, cations, anions) which can subsequently react with neighbouring molecules to form new products and hence initiate further chemical and physical processes. To date, few studies of molecules synthesis by collisions within multilayers has been done and are largely restricted to ion-molecule reactions. Neutral atom/molecule-molecule collisions stimulated by photon, electron and ion impact were studied. A prototype instrument in which multilayers of ice with co-adsorbed molecular species may be formed on a cold substrate at temperatures compatible with the terrestrial atmosphere, the interstellar medium or planetary bodies was constructed. Using UV irradiation, electrons and ions films were bombarded. Molecular synthesis within the mantle was proved by a combination of FTIR, UV-vis and mass spectrometry as a function of incident flux, energy and polarization. First results of synchrotron irradiation of water film are given. (nevyjel)

  7. The Molecular Industrial Revolution: Automated Synthesis of Small Molecules. (United States)

    Trobe, Melanie; Burke, Martin D


    Today we are poised for a transition from the highly customized crafting of specific molecular targets by hand to the increasingly general and automated assembly of different types of molecules with the push of a button. Creating machines that are capable of making many different types of small molecules on demand, akin to that which has been achieved on the macroscale with 3D printers, is challenging. Yet important progress is being made toward this objective with two complementary approaches: 1) Automation of customized synthesis routes to different targets by machines that enable the use of many reactions and starting materials, and 2) automation of generalized platforms that make many different targets using common coupling chemistry and building blocks. Continued progress in these directions has the potential to shift the bottleneck in molecular innovation from synthesis to imagination, and thereby help drive a new industrial revolution on the molecular scale. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. "Intelligent" design of molecular materials: Understanding the concepts of design in supramolecular synthesis of network solids (United States)

    Moulton, Brian D.

    This work endeavors to delineate modern paradigms for crystal engineering, i.e. the design and supramolecular synthesis of functional molecular materials. Paradigms predicated on an understanding of the geometry of polygons and polyhedra are developed. The primary focus is on structural determination by single crystal X-ray crystallography, structural interpretation using a suite of graphical visualization and molecular modeling software, and on the importance of proper graphical representation in the presentation and explanation of crystal structures. A detailed analysis of a selected series of crystal structures is presented. The reduction of these molecular networks to schematic representations that illustrate their fundamental connectivity facilitates the understanding of otherwise complex supramolecular solids. Circuit symbols and Schlafli notation are used to describe the network topologies, which enables networks of different composition and metrics to be easily compared. This reveals that molecular orientations in the crystals and networks are commensurate with networks that can be derived from spherical close packed lattices. The development of a logical design strategy for a new class of materials based on our understanding of the chemical composition and topology of these networks is described. The synthesis and crystal structure of a series of new materials generated by exploitation of this design strategy is presented, in addition to a detailed analysis of the topology of these materials and their relationship to a 'parent' structure. In summary, this dissertation demonstrates that molecular polygons can self-assemble at their vertexes to produce molecular architectures and crystal structures that are consistent with long established geometric dogma. The design strategy represents a potentially broad ranging approach to the design of nanoporous structures from a wide range of chemical components that are based on molecular shape rather than chemical

  9. Dihydroazulene Photochromism:Synthesis, Molecular Electronics and Hammett Correlations

    DEFF Research Database (Denmark)

    Broman, Søren Lindbæk

    This thesis describes the development of a versatile synthetic protocol for preparation of a large selection of dihydroazulenes (DHAs) with both electron withdrawing and donating groups. By UV-Vis and NMR spectroscopies and even in a single-molecule junction, their ability to undergo a light...... will be discussed in detail. The second chapter describes the design and synthesis of DHA/VHFs intended for use in molecular electronics and their solution and single-molecule junction switching properties. By the expansion of the recently reported procedure for functionalization of this system by Suzuki cross...

  10. New 1,2,4-triazine bearing compounds: molecular modeling, synthesis and biotesting

    Directory of Open Access Journals (Sweden)

    Negrutska V. V.


    Full Text Available Aim. To enlarge a spectrum of biologically active compounds in the series of the 1,2,4-triazino[5,6-b] [1,4]benzothiazine (1,2,4-TBT derivatives and reveal among them efficient inhibitors of RNA synthesis Methods. The methods of structure optimization of the 3-oxo-1,2,4-TBT by fragment-oriented substitution, the molecular doking of new structures in a virtual target, the rational chemical synthesis of the theoretically predicted compounds and their testing in the system of transcription in vitro. Results. The series of 1,2,4-TBT derivatives with substituents in the benzene and triazine cycles of a base molecule were synthesized. The testing of synthesized compounds in the in vitro transcription system directed by T7 RNA polymerase revealed the structure- and concentration-dependent inhibition of the RNA synthesis by some of these compounds. The experimental and virtual screening data for all investigated compounds have a good correlation. It was found that most effective derivative is the 3-oxo-8-butyl-1,2,4-TBT which completely inhibited transcription at the concentration of 6 mg/ml. Conclusions. The biotesting results allow us to assume that the inhibition of RNA synthesis is caused by binding of the 3-oxo- 8-butyl-1,2,4-TBT to both free RNA polymerase molecules and those including in a transcriptional complex with DNA

  11. Structure, bioactivity, and synthesis of methylated flavonoids. (United States)

    Wen, Lingrong; Jiang, Yueming; Yang, Jiali; Zhao, Yupeng; Tian, Miaomiao; Yang, Bao


    Methylated flavonoids are an important type of natural flavonoid derivative with potentially multiple health benefits; among other things, they have improved bioavailability compared with flavonoid precursors. Flavonoids have been documented to have broad bioactivities, such as anticancer, immunomodulation, and antioxidant activities, that can be elevated, to a certain extent, by methylation. Understanding the structure, bioactivity, and bioavailability of methylated flavonoids, therefore, is an interesting topic with broad potential applications. Though methylated flavonoids are widely present in plants, their levels are usually low. Because developing efficient techniques to produce these chemicals would likely be beneficial, we provide an overview of their chemical and biological synthesis. © 2017 New York Academy of Sciences.

  12. Synthesis of Structures Related to Antifreeze Glycoproteins


    Fyrner, Timmy


    In this thesis, synthesis of structures related to antifreeze glycoproteins (AFGPs) are presented. Synthetic routes to a protected carbohydrate derivative, 2,3,4,6-tetra-O-benzyl-β-galactopyranosyl-(1→3)-2-deoxy-2-azido-4,6-di-O-benzyl-β-D-thio-1-galactopyranoside, and a tBu-Ala-Thr-Ala-Fmoc tripeptide, are described. These compounds are meant to be used in the assembly of AFGPs and analogues thereof. A Gal-GlcN disaccharide was synthesized via glycosylation between the donor, bromo-2-O-benzo...

  13. How We Teach Molecular Structure to Freshmen. (United States)

    Hurst, Michael O.


    Currently molecular structure is taught in general chemistry using three theories, this being based more on historical development rather than logical pedagogy. Electronegativity is taught with a confusing mixture of definitions that do not correspond to modern practice. Valence bond theory and VSEPR are used together in a way that often confuses…

  14. Molecular structure, vibrational spectroscopic studies and natural ...

    Indian Academy of Sciences (India)

    Home; Journals; Pramana – Journal of Physics; Volume 74; Issue 5. Molecular structure ... The entropy of the title compound was also performed at HF using the hybrid functional BLYP and B3LYP with 6-31 G(d,p) as basis set levels of theory. Natural bond orbital (NBO) analysis of the title molecule is also carried out.

  15. Wall grid structure for interior scene synthesis

    KAUST Repository

    Xu, Wenzhuo


    We present a system for automatically synthesizing a diverse set of semantically valid, and well-arranged 3D interior scenes for a given empty room shape. Unlike existing work on layout synthesis, that typically knows potentially needed 3D models and optimizes their location through cost functions, our technique performs the retrieval and placement of 3D models by discovering the relationships between the room space and the models\\' categories. This is enabled by a new analytical structure, called Wall Grid Structure, which jointly considers the categories and locations of 3D models. Our technique greatly reduces the amount of user intervention and provides users with suggestions and inspirations. We demonstrate the applicability of our approach on three types of scenarios: conference rooms, living rooms and bedrooms.

  16. Synthesis, molecular and crystalline architectures, and properties of ...

    Indian Academy of Sciences (India)

    The construction1 of coordination compounds of cobalt(II) of different nuclearities is the centre of attrac- tion due to interesting structural and physico-chemical properties.1–5 ... Design SQUID MPMS-XL magnetometer working in the 2–300 K range. ..... Complex 1 adopts a molecular architecture cor- responding to the gross ...

  17. Marine Biotoxins: Laboratory Culture and Molecular Structure (United States)


    4 (B) 108.3 12.1 6.4 - (L) GT - Cambierdiscus toxicus PL - Prorocentrum lima KB - Kahala Beach L - lethal + - toxic symptoms - 15 - Table IV. DaM for...on reverse if necessary and identify by block number) FIELD GROUP SUB-GROUP Mice, Lab Animals, Maitotoxin, RA I, BD, Marine Toxin , 076 13 Ciquatoxin...most potent naturally occurring toxins known. Their physiological actions are diverse, as are their molecular structures, not all of which have been

  18. Boronate esters: Synthesis, characterization and molecular base receptor analysis (United States)

    Gómez-Jaimes, Gelen; Barba, Victor


    The synthesis of three boronate esters obtained by reacting 4-fluorophenylboronic (1), 4-iodophenylboronic (2) and 3,4-chlorophenylboronic (3) acids with 2,4,5-trihidroxybenzaldehyde is reported. The structural characterization was determined by spectroscopic and spectrometric techniques. The boron atom was evaluated to acts as Lewis acid center in the reaction with pyridine (Py), triethylamine (TEA) and fluoride anion (F-). The titration method was followed by UV-Vis and 11B NMR spectroscopy; results indicate the good interaction with the fluoride ion but poor coordination towards pyridine in solution.

  19. Synthesis, Molecular Structure and Characterization of Allylic Derivatives of 6-Amino-3-methyl-1,2,4-triazolo[3,4-f][1,2,4]-triazin-8(7H-one

    Directory of Open Access Journals (Sweden)

    Gene-Hsiang Lee


    Full Text Available 1-Allyl- (2 and 7-allyl-6-amino-3-methyl-1,2,4-triazolo[3,4-f][1,2,4]triazin-8(7H-one (3 were obtained via the 18-crown-6-ether catalyzed room temperature reactionof 6-amino-3-methyl-1,2,4-triazolo[3,4-f][1,2,4]triazin-8(7H-one (1 with potassiumcarbonate and allyl bromide in dry acetone. The structures of these two derivatives wereverified by 2D-NMR measurements, including gHSQC and gHMBC measurements. Theminor compound 2 may possess aromatic character. A single crystal X-ray diffractionexperiment indicated that the major compound 3 crystallizes from dimethyl sulfoxide in themonoclinic space group P21/n and its molecular structure includes an attached dimethylsulfoxide molecule, resulting in the molecular formula C10H16N6O2S. Molecular structuresof 3 are linked by extensive intermolecular N-H···N hydrogen bonding [graph set C 1 (7]. 1Each molecule is attached to the dimethyl sulfoxide oxygen via N-H···O intermolecularhydrogen bonding. The structure is further stabilized by π-π stacking interactions.

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

    Directory of Open Access Journals (Sweden)

    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

  1. Synthesis, structures and theoretical investigation of (United States)

    Weigend; Wirth; Ahlrichs; Fenske


    The silylated derivative of thiophosphoric acid (S)P(SSiMe3)3 is used as a convenient starting compound for the synthesis of multinuclear Cu and Au cluster complexes. (S)P(SSiMe3)3 reacts with CuCI/PPh3 and [AuCClPPh3] to give the following compounds: [Cu4(P2S6)(PPh3)4] (1), [Cu6(P2S6)Cl2-(PPh3)6] (2) and [Au4(P2S6)(PPh3)4](3). According to X-ray structure determination, these compounds contain P2S6(4-) ions, in which S atoms act as ligands for Cu+ and Au+ ions. Although 1 and 3 have the same stoichiometry, bonding of the metal ions to the P2S6 skeleton displays small but remarkable differences. Au is twofold coordinated, whereas Cu shows a threefold coordination. Ab initio calculations have been carried out to rationalise these structural differences. The theoretical treatment of the corresponding Ag compound indicates the latter to be less stable.

  2. Synthesis, antiproliferative activity and molecular docking of Colchicine derivatives. (United States)

    Huczyński, Adam; Majcher, Urszula; Maj, Ewa; Wietrzyk, Joanna; Janczak, Jan; Moshari, Mahshad; Tuszynski, Jack A; Bartl, Franz


    In order to create more potent anticancer agents, a series of five structurally different derivatives of Colchicine have been synthesised. These compounds were characterised spectroscopically and structurally and their antiproliferative activity against four human tumour cell lines (HL-60, HL-60/vinc, LoVo, LoVo/DX) was evaluated. Additionally the activity of the studied compounds was calculated using computational methods involving molecular docking of the Colchicine derivatives to β-tubulin. The experimental and computational results are in very good agreement indicating that the antimitotic activity of Colchicine derivatives can be readily predicted using computational modeling methods. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

  3. Drug Development of the Antimalarial Agent Artemisinin: Total Synthesis, Analog Synthesis, and Structure-Activity Relationship Studies (United States)


    jHoluenesulfonyl hydrazide in tetrahydrofuran (THF), solvolysis of the ketal group and subsequent hydrazone formation was observed. Under base...ARTEMISININ: TOTAL SYNTHESIS , ANALOG SYNTHESIS , AND STRUCTURE-ACTIVITY RELATIONSHIP STUDIES mc Mitchell A. Avery, Ph.D. SRI International...Antimalarial Agent Artemisinin: Total Synthesis , Analog Synthesis and Structure-Activity Relationship Studies 12 PERSONAL AUTHOR(S) Mitchell A

  4. Synthesis, characterization and biodistribution of bisphosphonates Sm-153 complexes: correlation with molecular modeling interaction studies

    Energy Technology Data Exchange (ETDEWEB)

    Neves, M. E-mail:; Gano, L.; Pereira, N.; Costa, M.C.; Costa, M.R.; Chandia, M.; Rosado, M.; Fausto, R


    Bisphosphonates (BPs) are characterized by a P-C-P backbone structure and two phosphonic acid groups bonded to the same carbon, and are established as osteoclast-mediated bone resorption inhibitors. The nature of the groups attached to the central carbon atom are responsible in determining the potency of bisphosphonates as anti-resorption drugs. However, it is not yet clear the exact relationship between their molecular structure and pharmacologic activities. In this study, molecular geometries of pamidronate, alendronate and neridronate, differing only in the length of the aliphatic chains, were predicted by molecular mechanics and their interactions with hydroxyapatite, the main bone mineral component, were examined. We report the synthesis and radiochemical characterization of {sup 153}Sm complexes with pamidronate, alendronate and neridronate. Hydroxyapatite binding and biodistribution studies of these complexes have shown a good correlation with the theoretical molecular modeling interaction studies. So, it is possible to conclude that computational chemistry techniques are a good approach to evaluate specific interactions and may play a relevant role in determining the relative ability of BPs to mineral bone, and open new perspectives to the design of new BPs with increased pharmacological activity. These techniques could be extended to BPs as ligands to carrier radioactive metals, aiming for new bone therapeutic radiopharmaceuticals.

  5. Propagator theory of atomic and molecular structure

    International Nuclear Information System (INIS)

    Oehrn, Y.


    It is not at all obvious which methods of use in quantum chemistry can be characterized as being without wavefunctions. There are, however, a number of methods that purpose to calculate atomic and molecular electronic structure and properties without the explicit use of many-electron wavefunctions. Fully realizing the arbitrariness of any classification of such methods as well as the absence of sharp boundaries between any choice of groups, the author separates the three kinds of approaches: (i) Local Density Energy Functional Methods, (ii) Density Matrix Methods, (iii) Propagator or Green's Function Methods. (Auth.)

  6. Synthesis, structure and low temperature study of electric transport ...

    Indian Academy of Sciences (India)

    Synthesis, structure and low temperature study of electric transport and magnetic properties of GdSr2MnCrO7. Devinder ... Keywords. Chemical synthesis; X-ray diffraction; electrical properties; magnetic properties. Abstract. The layered perovskite oxide, GdSr2MnCrO7, has been prepared by the standard ceramic method.

  7. Halogenated Symmetrical Tetraazapentacenes: Synthesis, Structures, and Properties. (United States)

    Engelhart, Jens U; Paulus, Fabian; Schaffroth, Manuel; Vasilenko, Vladislav; Tverskoy, Olena; Rominger, Frank; Bunz, Uwe H F


    We herein describe the synthesis and property evaluation of several brominated and chlorinated tetraazapentacenes. The targets were obtained by thermal condensation of 2,5-dihydroxyquinone with 4,5-dichloro-, 2,6-dichloro-, and 4,5-dibromo-1,2-phenylenediamine, followed by oxidation with hot acidic dichromate. Double alkynylation, reductive deoxygenation, and subsequent oxidation using MnO2 furnishes the target compounds. Absorption spectra, electrochemistry, and single crystal structures of the targets are reported. The 1,4,8,11-tetrachlorotetraazapentacene (1,4,8,11-tetrachloroquinoxalino[2,3-b]phenazine) carrying its chlorine atoms in the peri-positions packs in a herringbone type arrangement, while the isomer (2,3,9,10-tetrachloroquinoxalino[2,3-b]phenazine, with the chlorine atoms in the east and west positions) packs in one-dimensional stacks. In all cases, the reduction potentials and the calculated LUMO-positions are decreased by the introduction of the halogen atoms.

  8. Synthesis of cationic diphosphine ruthenium complexes with nido-dicarbaundecaborate anions. Molecular structure of [RuCl(dppe)2]+[7,8-nido-C2B9H12]-

    International Nuclear Information System (INIS)

    Cheredilin, D.N.; Dolgushin, F.M.; Balagurova, E.V.; Godovikov, I.A.; Chizhevskij, I.T.


    Five new diphosphine ruthenium(II) complexes with nido-dicarbaundecaborate anions were synthesized. The composition and structure of the complexes were confirmed by data of 1 H, 31 P{ 1 H} NMR and elementary analysis. The crystal and molecular structure of solvated complex [RuCl(dppe) 2 + [7,8-nido-C 2 B 9 H 12 ] - ·CH 2 Cl 2 was ascertained by the method of X-ray diffraction analysis. It is shown that coordination sphere of ruthenium atom in the complex cation is a distorted trigonal bipyramid. The distances from ruthenium atom to phosphorus atoms are 2.398(1) and 2.391(1) A, while the angle P-Ru-P equals 175.85(5) Deg [ru

  9. Molecular Models of Genetic and Organismic Structures

    CERN Document Server

    Baianu, I C


    In recent studies we showed that the earlier relational theories of organismic sets (Rashevsky,1967), Metabolic-Replication (M,R)-systems (Rosen,1958)and molecular sets (Bartholomay,1968) share a joint foundation that can be studied within a unified categorical framework of functional organismic structures (Baianu,1980. This is possible because all relational theories have a biomolecular basis, that is, complex structures such as genomes, cells,organs and biological organisms are mathematically represented in terms of biomolecular properties and entities,(that are often implicit in their representation axioms. The definition of organismic sets, for example, requires that certain essential quantities be determined from experiment: these are specified by special sets of values of general observables that are derived from physicochemical measurements(Baianu,1970; Baianu,1980; Baianu et al, 2004a.)Such observables are context-dependent and lead directly to natural transformations in categories and Topoi, that are...

  10. [Molecular structure and fractal analysis of oligosaccharide]. (United States)

    Liu, Wen-long; Wang, Lu-man; He, Dong-qi; Zhang, Tian-lan; Gou, Bao-di; Li, Qing


    To propose a calculation method of oligosaccharides' fractal dimension, and to provide a new approach to studying the drug molecular design and activity. By using the principle of energy optimization and computer simulation technology, the steady structures of oligosaccharides were found, and an effective way of oligosaccharides fractal dimension's calculation was further established by applying the theory of box dimension to the chemical compounds. By using the proposed method, 22 oligosaccharides' fractal dimensions were calculated, with the mean 1.518 8 ± 0.107 2; in addition, the fractal dimensions of the two activity multivalent oligosaccharides which were confirmed by experiments, An-2 and Gu-4, were about 1.478 8 and 1.516 0 respectively, while C-type lectin-like receptor Dectin-1's fractal dimension was about 1.541 2. The experimental and computational results were expected to help to find a class of glycoside drugs whose target receptor was Dectin-1. Fractal dimension, differing from other known macro parameters, is a useful tool to characterize the compound molecules' microscopic structure and function, which may play an important role in the molecular design and biological activity study. In the process of oligosaccharides drug screening, the fractal dimension of receptor and designed oligosaccharides or glycoclusters can be calculated respectively. The oligosaccharides with fractal dimension close to that of target receptor should then take priority compared with others, to get the drug molecules with latent activity.

  11. Synthesis, Characterization (Molecular-Morphological) and Theoretical Morphology Predictions of Poly(cyclohexadiene) Containing Linear Triblock Terpolymers

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Rajeev [ORNL; Dadmun, Mark D [ORNL; Sumpter, Bobby G [ORNL; Mays, Jimmy [ORNL; Avgeropoulos, Apostolos [University of Athens, Athens, Greece; Zafeiropoulos, N.E. [University of Athens, Athens, Greece; Misichoronis, K. [University of Athens, Athens, Greece; Rangou, S. [University of Athens, Athens, Greece; Ashcraft, E. [University of Tennessee, Knoxville (UTK)


    The synthesis via anionic polymerization of six linear triblock terpolymers with various sequences of blocks such as PS (polystyrene), PB (polybutadiene), PI (polyisoprene) and PCHD (poly(1,3-cyclohexadiene)) is reported. The synthesis of the terpolymers was accomplished by the use of anionic polymerization with high vacuum techniques and sequential monomer addition. Molecular characterization of the samples was performed via size exclusion chromatography and membrane osmometry to measure polydispersity indices and the number-average molecular weights, respectively. Proton nuclear magnetic resonance spectroscopy was adopted to verify the type of microstructure for the polydienes as well as to calculate the molar composition. Structural characterization was performed via transmission electron microscopy and small angle X-ray scattering and several morphologies were observed including one which has not been reported previously. Real-space self-consistent field theory (SCFT) without a priori knowledge about the symmetry of the periodic structures was used to elucidate the thermodynamics of the synthesized triblock copolymers.

  12. Synthesis and crystal structure of a wheel-shaped supramolecular ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 126; Issue 5. Synthesis and crystal structure of a wheel-shaped supramolecular coordination complex. Deepak Gupta Palanisamy Rajakannu Bhaskaran Shankar Firasat Hussain Malaichamy Sathiyendiran. Special issue on Chemical Crystallography Volume 126 ...

  13. Synthesis, structure and Hirshfeld surface analysis, vibrational and ...

    Indian Academy of Sciences (India)

    dimensional architecture. Hirshfeld surface analysis for visually analysing intermolecular interactions in crystal structures employing molecular sur- face contours and 2D fingerprint plots has been used to scrutinize molecular shapes. The vibration ...

  14. Synthesis and Molecular Modeling of Thermally Stable DNA G-Quadruplexes with Anthraquinone Insertions

    DEFF Research Database (Denmark)

    Gouda, Alaa S.; Amine, Mahasen S.; Pedersen, Erik Bjerregaard


    Two new phosphoramidite building blocks for DNA synthesis were synthesized from 1,5- and 2,6-dihydroxyanthraquinones through alkylation with 3-bromo-1-propanol followed by DMT-protection. The novel synthesized 1,5- and 2,6-disubstituted anthraquinone monomers H15 and H26 are incorporated into a G......-quadruplex by single and double replacements of TGT and TT loops. Monomers H15 and H26 were found to destabilize G-quadruplex structures for all single replacements of TGT or TT loops. The largest destabilization was observed when H26 linker replaced a TT loop. In contrast, the presence of anthraquinone monomers...... anthraquinone-modified quadruplexes revealed no change of the antiparallel structure when compared with the wild type under potassium buffer conditions. The significantly increased thermostabilities were interpreted by molecular modeling of anthraquinone-modified G-quadruplexes....

  15. Utilization of molecular species of diglycerides in the synthesis of lecithin

    NARCIS (Netherlands)

    Mudd, J.B.; Golde, L.M.G. van; Deenen, L.L.M. van


    1. 1. The synthesis of lecithin by rat liver microsomes was measured in the presence of [14C]CDP-choline and three molecular species of diglycerides derived from rat liver lecithin containing four, two and one double bond. The rate of synthesis of lecithin was the same regardless of the fatty acid

  16. Manipulation of molecular structures with magnetic fields

    NARCIS (Netherlands)

    Boamfa, M.I.


    The present thesis deals with the use of magnetic fields as a handle to manipulate matter at a molecular level and as a tool to probe molecular properties or inter molecular interactions. The work consists of in situ optical studies of (polymer) liquid crystals and molecular aggregates in high

  17. Algorithmic dimensionality reduction for molecular structure analysis. (United States)

    Brown, W Michael; Martin, Shawn; Pollock, Sara N; Coutsias, Evangelos A; Watson, Jean-Paul


    Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated algorithms for nonlinear dimensionality reduction for representation of trans, trans-1,2,4-trifluorocyclo-octane conformation--a molecule whose structure can be described on a 2-manifold in a Cartesian coordinate phase space. We describe an efficient approach for a deterministic enumeration of ring conformations. We demonstrate a drastic improvement in dimensionality reduction with the use of nonlinear methods. We discuss the use of dimensionality reduction algorithms for estimating intrinsic dimensionality and the relationship to the Whitney embedding theorem. Additionally, we investigate the influence of the choice of high-dimensional encoding on the reduction. We show for the case studied that, in terms of reconstruction error root mean square deviation, Cartesian coordinate representations and encodings based on interatom distances provide better performance than encodings based on a dihedral angle representation.

  18. Algorithmic dimensionality reduction for molecular structure analysis (United States)

    Brown, W. Michael; Martin, Shawn; Pollock, Sara N.; Coutsias, Evangelos A.; Watson, Jean-Paul


    Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated algorithms for nonlinear dimensionality reduction for representation of trans, trans-1,2,4-trifluorocyclo-octane conformation—a molecule whose structure can be described on a 2-manifold in a Cartesian coordinate phase space. We describe an efficient approach for a deterministic enumeration of ring conformations. We demonstrate a drastic improvement in dimensionality reduction with the use of nonlinear methods. We discuss the use of dimensionality reduction algorithms for estimating intrinsic dimensionality and the relationship to the Whitney embedding theorem. Additionally, we investigate the influence of the choice of high-dimensional encoding on the reduction. We show for the case studied that, in terms of reconstruction error root mean square deviation, Cartesian coordinate representations and encodings based on interatom distances provide better performance than encodings based on a dihedral angle representation. PMID:18715062

  19. Algorithmic dimensionality reduction for molecular structure analysis (United States)

    Brown, W. Michael; Martin, Shawn; Pollock, Sara N.; Coutsias, Evangelos A.; Watson, Jean-Paul


    Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated algorithms for nonlinear dimensionality reduction for representation of trans, trans-1,2,4-trifluorocyclo-octane conformation-a molecule whose structure can be described on a 2-manifold in a Cartesian coordinate phase space. We describe an efficient approach for a deterministic enumeration of ring conformations. We demonstrate a drastic improvement in dimensionality reduction with the use of nonlinear methods. We discuss the use of dimensionality reduction algorithms for estimating intrinsic dimensionality and the relationship to the Whitney embedding theorem. Additionally, we investigate the influence of the choice of high-dimensional encoding on the reduction. We show for the case studied that, in terms of reconstruction error root mean square deviation, Cartesian coordinate representations and encodings based on interatom distances provide better performance than encodings based on a dihedral angle representation.

  20. Synthesis of High-Molecular-Weight Multifunctional Glycerol Polyhydroxyurethanes PHUs

    Directory of Open Access Journals (Sweden)

    Bassam Nohra


    Full Text Available Glycerol carbonate acrylate is a 5-membered cyclic carbonate synthesized from glycerol that is used as a chemical coupling agent and has proven highly suitable for use in the synthesis of multifunctional polyhydroxyurethanes (PHUs. The multifunctionality of the structure of PHUs is determined by the density of the carbon-amine groups generated by the Aza-Michael reaction and that of the urethane groups and adjacent primary and secondary hydroxyl groups generated by aminolysis. Glycerol carbonate acrylate is polymerized with polyfunctional mono-, di-, tri, and tetra-amines, by type-AB polyaddition, either in bulk or in solution, through stepwise or one-pot reaction strategies in the absence of added catalysts. These approaches result in the generation of linear, interchain, and crosslinked structures, through the polyaddition of linear and branched amines to the ethylene and cyclic carbonate sites of glycerol carbonate acrylate. The resulting collection of organic molecules gives rise to polyethylene amino ester PHUs with a high molar mass, exceeding 20,000 g·mol−1, with uniform dispersity.

  1. Boron nitride ceramics from molecular precursors: synthesis, properties and applications. (United States)

    Bernard, Samuel; Salameh, Chrystelle; Miele, Philippe


    Hexagonal boron nitride (h-BN) attracts considerable interest because its structure is similar to that of carbon graphite while it displays different properties which are of interest for environmental and green technologies. The polar nature of the B-N bond in sp(2)-bonded BN makes it a wide band gap insulator with different chemistry on its surface and particular physical and chemical properties such as a high thermal conductivity, a high temperature stability, a high resistance to corrosion and oxidation and a strong UV emission. It is chemically inert and nontoxic and has good environmental compatibility. h-BN also has enhanced physisorption properties due to the dipolar fields near its surface. Such properties are closely dependent on the processing method. Bottom-up approaches consist of transforming molecular precursors into non-oxide ceramics with retention of the structural units inherent to the precursor molecule. The purpose of the present review is to give an up-to-date overview on the most recent achievements in the preparation of h-BN from borazine-based molecular single-source precursors including borazine and 2,4,6-trichloroborazine through both vapor phase syntheses and methods in the liquid/solid state involving polymeric intermediates, called the Polymer-Derived Ceramics (PDCs) route. In particular, the effect of the chemistry, composition and architecture of the borazine-based precursors and derived polymers on the shaping ability as well as the properties of h-BN is particularly highlighted.

  2. Design, synthesis and characterization of novel binary V(V)-Schiff base materials linked with insulin-mimetic vanadium-induced differentiation of 3T3-L1 fibroblasts to adipocytes. Structure-function correlations at the molecular level. (United States)

    Halevas, E; Tsave, O; Yavropoulou, M P; Hatzidimitriou, A; Yovos, J G; Psycharis, V; Gabriel, C; Salifoglou, A


    Among the various roles of vanadium in the regulation of intracellular signaling, energy metabolism and insulin mimesis, its exogenous activity stands as a contemporary challenge currently under investigation and a goal to pursue as a metallodrug against Diabetes mellitus II. In this regard, the lipogenic activity of vanadium linked to the development of well-defined anti-diabetic vanadodrugs has been investigated through: a) specifically designing and synthesizing Schiff base organic ligands L, bearing a variable number of terminal alcohols, b) a series of well-defined soluble binary V(V)-L compounds synthesized and physicochemically characterized, c) a study of their cytotoxic effect and establishment of adipogenic activity in 3T3-L1 fibroblasts toward mature adipocytes, and d) biomarker examination of a closely-linked molecular target involving or influenced by the specific V(V) forms, cumulatively delineating factors involved in potential pathways linked to V(V)-induced insulin-like activity. Collectively, the results a) project the importance of specific structural features in Schiff ligands bound to V(V), thereby influencing the emergence of its (a)toxicity and for the first time its insulin-like activity in pre-adipocyte differentiation, b) contribute to the discovery of molecular targets influenced by the specific vanadoforms seeking to induce glucose uptake, and c) indicate an interplay of V(V) structural speciation and cell-differentiation biological activity, thereby gaining insight into vanadium's potential as a future metallodrug in Diabetes mellitus. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Molecular motion and structure in plastics

    International Nuclear Information System (INIS)

    Doolan, K.R.; Baxter, M.


    Full text: When molten thermoplastics solidify, the polymeric chains form a completely amorphous structure or a mixture of crystalline and amorphous regions. Measurement of Nuclear Magnetic Resonance (NMR) relaxation times provides information about the configuration and molecular motion of polymeric chains in solid plastics. We are currently measuring the NMR relaxation times T 1 , T 2 , T 2 and T 1p as a function of temperature using a Bruker High Power pulsed NMR Spectrometer for several different classes of thermoplastics containing varying concentrations of inorganic filler materials. We present data here for T 1 , and T 2 obtained for polyethylenes, polypropylenes, polystyrenes and acrylics in the temperature range 100 K to 450 K. At temperatures below 320 K, all of the polyethylenes and polypropylenes and some of the polystyrenes and acrylics produced NMR signals after a single radio frequency (RF) pulse with rapidly and slowly decaying components corresponding to the rigid and flexible regions within the plastic. From these results we have estimated using Mathematica the amount of crystallinity within the polyethylenes and polypropylenes. For the impact modified polystyrenes and acrylics studied we have estimated the amounts of elastomeric phases present. We find that the initial rapid decay signal produced by polyethylenes and polypropylenes is Gaussian while the long tail is Lorentzian. All of the signal components from the polystyrenes and the acrylics were fitted using Lorentzian functions indicating their structures are highly amorphous. Addition of CaCO 3 filler to polypropylene resins appears to reduce the crystallinity of the material. We also present data for the activation energy of the molecular motion inducing longitudinal relaxation, from T 1 measurements

  4. Molecular dynamics investigations of BioH protein substrate specificity for biotin synthesis. (United States)

    Xue, Qiao; Cui, Ying-Lu; Zheng, Qing-Chuan; Zhang, Hong-Xing


    BioH, an enzyme of biotin synthesis, plays an important role in fatty acid synthesis which assembles the pimelate moiety. Pimeloyl-acyl carrier protein (ACP) methyl ester, which is long known to be a biotin precursor, is the physiological substrate of BioH. Azelayl methyl ester, which has a longer chain than pimeloyl methyl ester, conjugated to ACP is also indeed accepted by BioH with very low rate of hydrolysis. To date, the substrate specificity for BioH and the molecular origin for the experimentally observed rate changes of hydrolysis by the chain elongation have remained elusive. To this end, we have investigated chain elongation effects on the structures by using the fully atomistic molecular dynamics simulations combined with binding free energy calculations. The results indicate that the substrate specificity is determined by BioH together with ACP. The added two methylenes would increase the structural flexibility by protein motions at the interface of ACP and BioH, instead of making steric clashes with the side chains of the BioH hydrophobic cavity. On the other hand, the slower hydrolysis of azelayl substrate is suggested to be associated with the loose of contacts between BioH and ACP, and with the lost electrostatic interactions of two ionic/hydrogen bonding networks at the interface of the two proteins. The present study provides important insights into the structure-function relationships of the complex of BioH with pimeloyl-ACP methyl ester, which could contribute to further understanding about the mechanism of the biotin synthetic pathway, including the catalytic role of BioH.

  5. A Loose Coupling Mechanism of Synthesis of ATP by Proton Flux in the Molecular Machine of Living Cells (United States)

    Oosawa, Fumio; Hayashi, Shigeru


    A loose coupling mechanism is proposed for the molecular machine of living cells which performs the synthesis of ATP from ADP and inorganic phosphate by a proton flux across the membrane. The basic assumption is that a torque or rotational movement is produced in protein molecules by the proton flux and the ATP synthesis is promoted by the torque or rotational movement in the molecules. The first process is carried out by a mechanism similar to the bacterial flagellar motor where the coupling between the flow of protons and the rotation of the motor is loose. A structural model for the second process is also presented. The threshold of the potential difference of proton for the ATP synthesis can be low and the number of protons to synthesize one ATP molecule is not an integer but a variable number.

  6. Molecular structure input on the web

    Directory of Open Access Journals (Sweden)

    Ertl Peter


    Full Text Available Abstract A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential. The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

  7. Ionothermal synthesis and structural characterization of [Cu ...

    Indian Academy of Sciences (India)

    bSchool of Chemistry and Chemical Engineering, Harbin Normal University, No. 1 Shida Road Limin development Zone, Harbin 150025, P. R. China e-mail: MS received 29 December 2014; revised 2 April 2015; accepted 3 April 2015. Abstract. The ionothermal synthesis and spectroscopic, thermal ...

  8. Superheavy nuclei – cold synthesis and structure

    Indian Academy of Sciences (India)

    Abstract. The quantum mechanical fragmentation theory (QMFT), given for the cold synthesis of new and superheavy elements, is reviewed and the use of radioactive nuclear beams (RNB) and targets (RNT) is discussed. The QMFT is a complete theory of cold nuclear phenomena, namely, the cold fission, cold fusion and ...

  9. Superheavy nuclei–cold synthesis and structure

    Indian Academy of Sciences (India)

    The quantum mechanical fragmentation theory (QMFT), given for the cold synthesis of new and superheavy elements, is reviewed and the use of radioactive nuclear beams (RNB) and targets (RNT) is discussed. The QMFT is a complete theory of cold nuclear phenomena, namely, the cold fission, cold fusion and cluster ...

  10. Tautomerism in quinoxalines derived from the 1,4-naphthoquinone nucleus: acid mediated synthesis, X-ray molecular structure of 5-chlorobenzo[f]quinoxalin-6-ol and density functional theory calculations

    International Nuclear Information System (INIS)

    Gomez, Javier A.G.; Lage, Mateus R.; Carneiro, Jose Walkimar de M.; Resende, Jackson A.L.C.; Vargas, Maria D.


    The reaction of tert-butyl 2-(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-ylamino) ethylcarbamate with CF 3 COOH/CH 2 Cl 2 yields 5-chloro-3,4-dihydrobenzo[f]quinoxalin-6(2H)-one which undergoes acid-promoted dehydrogenation in the presence of water to give novel 5-chlorobenzo[f]quinoxalin-6-ol. The molecular structure of 5-chlorobenzo[f]quinoxalin-6-ol in the solid state, determined by an X-ray diffraction (XRD) study, and the solution data confirm that it exists as the enol-imine tautomer, both in the solid state and in solution, differently from 5-chloro-3,4-dihydrobenzo[f]quinoxalin-6(2H)-one, which exhibits the keto-amine arrangement. Density functional theory (DFT) calculations confirmed the preference of 5-chlorobenzo[f]quinoxalin-6-ol and of the derivatives containing H and CH 3 groups in place of the Cl atom for the enol-imine tautomer. It is suggested that the enol-imine structure is preferred for 5-chlorobenzo[f]quinoxalin-6-ol as a consequence of the higher aromatic character of this structure in comparison with the keto-amine form. DFT calculations carried out on the two tautomers of the benzo[a]phenazin-5(7H)-ones analogous to the benzo[f]quinoxalin-6(4H)-ones showed that the relative stabilities are dominated by solvation effects in the first case and the degree of aromaticity, in the latter. (author)

  11. Tautomerism in quinoxalines derived from the 1,4-naphthoquinone nucleus: acid mediated synthesis, X-ray molecular structure of 5-chlorobenzo[f]quinoxalin-6-ol and density functional theory calculations

    Energy Technology Data Exchange (ETDEWEB)

    Gomez, Javier A.G.; Lage, Mateus R.; Carneiro, Jose Walkimar de M.; Resende, Jackson A.L.C.; Vargas, Maria D., E-mail:, E-mail: [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Instituto de Quimica


    The reaction of tert-butyl 2-(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-ylamino) ethylcarbamate with CF{sub 3}COOH/CH{sub 2}Cl{sub 2} yields 5-chloro-3,4-dihydrobenzo[f]quinoxalin-6(2H)-one which undergoes acid-promoted dehydrogenation in the presence of water to give novel 5-chlorobenzo[f]quinoxalin-6-ol. The molecular structure of 5-chlorobenzo[f]quinoxalin-6-ol in the solid state, determined by an X-ray diffraction (XRD) study, and the solution data confirm that it exists as the enol-imine tautomer, both in the solid state and in solution, differently from 5-chloro-3,4-dihydrobenzo[f]quinoxalin-6(2H)-one, which exhibits the keto-amine arrangement. Density functional theory (DFT) calculations confirmed the preference of 5-chlorobenzo[f]quinoxalin-6-ol and of the derivatives containing H and CH{sub 3} groups in place of the Cl atom for the enol-imine tautomer. It is suggested that the enol-imine structure is preferred for 5-chlorobenzo[f]quinoxalin-6-ol as a consequence of the higher aromatic character of this structure in comparison with the keto-amine form. DFT calculations carried out on the two tautomers of the benzo[a]phenazin-5(7H)-ones analogous to the benzo[f]quinoxalin-6(4H)-ones showed that the relative stabilities are dominated by solvation effects in the first case and the degree of aromaticity, in the latter. (author)

  12. Synthesis, structural, spectroscopic, anti-cancer and molecular docking studies on novel 2-[(Anthracene-9-ylmethylene)amino]-2-methylpropane-1,3-diol using XRD, FTIR, NMR, UV-Vis spectra and DFT (United States)

    Pavitha, P.; Prashanth, J.; Ramu, G.; Ramesh, G.; Mamatha, K.; Venkatram Reddy, Byru


    The novel titled compound 2-[(Anthracene-9-ylmethylene)amino]-2-methylpropane-1,3-diol (AMD) has been synthesized by slow evaporation technique from mixed solvent system of methanol with anthracene-9-carbaldehyde and 2-amino-2-methylpropane-1,3-diol. The synthesized molecule AMD was characterized experimentally by single crystal XRD, FTIR, NMR and UV-Vis spectra and density functional theory (DFT) computations. The structure of the crystal has been determined as orthorhombic system with space group P 21 21 21 and the cell parameters are obtained using XRD data. The optimized ground state geometry of the molecule is determined by evaluating torsional potentials as a function of angle of free rotation around Csbnd C bonds of functional groups by DFT method employing B3LYP functional with 6-311++G(d,p) basis set. All the fundamental vibrations of the molecule are assigned unambiguously using potential energy distribution (PED) obtained in the DFT computations. The rms error between the observed and scaled frequencies is 6.20 cm-1. The values of dipole moment, polarizability and hyperpolarizability are evaluated to study the NLO behavior of the molecule. The HOMO-LUMO energies and thermodynamic parameters are also determined. The molecular electrostatic surface potential (MESP) is mapped to obtain the charge density distribution. The 1H and 13C NMR chemical shifts of the molecule are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. UV-visible spectrum of the compound is also recorded in the region 200-800 nm to know the type of electronic transitions involved. The anti-cancer activity of AMD is determined against human breast cancer cell line MCF-7 and human prostate cancer cell line PC-3 and correlated the results with study of molecular docking against pharmacological protein IDO-1 receptor.

  13. Molecular Nickel Phosphide Carbonyl Nanoclusters: Synthesis, Structure, and Electrochemistry of [Ni11P(CO)18]3- and [H6-nNi31P4(CO)39]n- (n = 4 and 5). (United States)

    Capacci, Chiara; Ciabatti, Iacopo; Femoni, Cristina; Iapalucci, Maria Carmela; Funaioli, Tiziana; Zacchini, Stefano; Zanotti, Valerio


    experiments. The molecular structures of the new clusters have been determined by single-crystal X-ray analysis. These represent the first examples of structurally characterized molecular nickel carbonyl nanoclusters containing interstitial phosphide atoms.

  14. Synthesis, structure and Hirshfeld surface analysis, vibrational and ...

    Indian Academy of Sciences (India)

    Hirshfeld surface analysis for visually analysing intermolecular interactions in crystal structures employing molecular surfacecontours and 2D fingerprint plots has been used to scrutinize molecular shapes. The vibration properties of this structure were studied by IR spectroscopy and Raman scattering. Vibration spectra ...

  15. Synthesis, Structure and Hirshfeld surface analysis, vibrational and ...

    Indian Academy of Sciences (India)


    lead to the formation of a three-dimensional architecture. Hirshfeld surface analysis for visually analyzing intermolecular interactions in crystal structures employing molecular surface contours and 2D fingerprint plots have been used to scrutinize molecular shapes. The vibration properties of this structure were studied by IR ...

  16. New palladium(II) and platinum(II) 5,5-diethylbarbiturate complexes with 2-phenylpyridine, 2,2'-bipyridine and 2,2'-dipyridylamine: synthesis, structures, DNA binding, molecular docking, cellular uptake, antioxidant activity and cytotoxicity. (United States)

    Icsel, Ceyda; Yilmaz, Veysel T; Kaya, Yunus; Samli, Hale; Harrison, William T A; Buyukgungor, Orhan


    Novel palladium(ii) and platinum(ii) complexes of 5,5-diethylbarbiturate (barb) with 2-phenylpyridine (Hppy), 2,2'-bipyridine (bpy) and 2,2'-dipyridylamine (dpya) have been prepared and characterized by elemental analysis, IR, UV-Vis, NMR and ESI-MS. Single-crystal diffraction measurements show that complex consists of binuclear [Pd2(μ-barb-κN,O)2(ppy-κN,C)2] moieties, while complexes are mononuclear, [M(barb-κN)2(L-κN,N')] (L = bpy or dpya). has a composition of [Pt(dpya-κN,N')2][Ag(barb-κN)2]2·4H2O and was assumed to have a structure of [Pt(barb-κN)(Hppy-κN)(ppy-κN,C)]·3H2O. The complexes were found to exhibit significant DNA binding affinity by a non-covalent binding mode, in accordance with molecular docking studies. In addition, complexes and displayed strong binding with supercoiled pUC19 plasmid DNA. Cellular uptake studies were performed to assess the subcellular localization of the selected complexes. A moderate radical scavenging activity of and was confirmed by DPPH and ABTS tests. Complexes , , and showed selectivity against HT-29 (colon) cell line.

  17. Synthesis and crystal structure of a ternary copper(II) complex of 2,2‧-bipyridine and picrate: Molecular docking, reactivity towards DNA and in vitro anticancer activity (United States)

    Zheng, Kang; Jiang, Man; Li, Yan-Tuan; Wu, Zhi-Yong; Yan, Cui-Wei


    A new mononuclear ternary copper(II) complex with mixed ligands of 2,2‧-bipyridine (bpy) and picrate (pic), namely [Cu(bpy)(pic)2], has been synthesized and characterized by elemental analysis, molar conductivity measurement, IR and electronic spectral studies, and single-crystal X-ray diffraction. The crystal structure analysis reveals the presence of two crystallographic independent molecules in an asymmetric unit. The copper(II) atoms are in elongated octahedral coordination geometries. A three-dimensional supermolecular network is formed through non-classical C-H⋯O hydrogen bonds. The DNA-binding properties of the copper(II) complex are investigated both theoretically and experimentally, revealing that the copper(II) complex can interact with HS-DNA in the mode of intercalation, and the molecular docking of the copper(II) complex with the self-complementary DNA duplex of sequence d(ACCGACGTCGGT)2 facilitates the binding events. The in vitro anticancer activities suggest that the copper(II) complex is active against the selected tumor cell lines.

  18. Synthesis and Molecular Structures of the Lowest Melting Odd- and Even-Numbered α,β-Unsaturated Carboxylic Acids—(E-Hept-2-Enoic Acid and (E-Oct-2-Enoic Acid

    Directory of Open Access Journals (Sweden)

    Marcel Sonneck


    Full Text Available The molecular structures of the two lowest melting odd- and even-numbered α,β-unsaturated carboxylic acids—(E-hept-2-enoic acid (C7 and (E-oct-2-enoic acid (C8—are herein reported. The title compounds were crystallized by slow evaporation of ethanolic solutions at −30 °C. C7 crystallizes in the triclinic space group P 1 ¯ with two molecules in the unit cell and C8 in the monoclinic space group C2/c with eight molecules in the unit cell. The unit cell parameters for C7 are: a = 5.3049(2 Å, b = 6.6322(3 Å, c = 11.1428(5 Å, α = 103.972(3°, β = 97.542(3°, γ = 90.104(3°, and V = 376.92(3 Å3 (T = 150(2 K. The unit cell parameters for C8 are: a = 19.032(10 Å, b = 9.368(5 Å, c = 11.520(6 Å, β = 123.033(11°, and V = 1721.80(16 Å3 (T = 200(2 K.

  19. Synthesis and Molecular Structure of 6-Amino-3-benzylmercapto-1,2,4-triazolo[3,4-f][1,2,4]triazin-8(7H-one

    Directory of Open Access Journals (Sweden)

    Gene-Hsiang Lee


    Full Text Available The title compound 6-amino-3-benzylmercapto-1,2,4-triazolo[3,4-f][1,2,4]-triazin-8(7H-one (4, molecular formula C11H10N6OS, was obtained by the reaction of3-amino-2-benzyl-6-hydrazino-1,2,4-triazin-5(2H-one (3 with carbon disulfide in awater/pyridine mixture. Compound 4 can also be synthesized by reacting6-amino-3(2Hmercapto-1,2,4-triazolo[3,4-f][1,2,4]triazin-8(7H-one (7 with benzylbromide in methanolic ammonia water. The compound crystallizes in the monoclinicspace group P21/c with a = 7.2926(15, b = 14.456(2, c = 11.436(2 å, β = 105.30(2°, V= 1162.9(4 å3 and Z = 4, resulting in a density Dcalc of 1.567 g/cm3. Molecules of 4 arelinked by extensive intermolecular N-H···N and N-H···O hydrogen bonding [graph set R22 (9]. The structure is further stabilized by π-π stacking interactions. 2

  20. Molecularly stabilised ultrasmall gold nanoparticles: synthesis, characterization and bioactivity (United States)

    Leifert, Annika; Pan-Bartnek, Yu; Simon, Ulrich; Jahnen-Dechent, Willi


    Gold nanoparticles (AuNPs) are widely used as contrast agents in electron microscopy as well as for diagnostic tests. Due to their unique optical and electrical properties and their small size, there is also a growing field of potential applications in medical fields of imaging and therapy, for example as drug carriers or as active compounds in thermotherapy. Besides their intrinsic optical properties, facile surface decoration with (bio)functional ligands renders AuNPs ideally suited for many industrial and medical applications. However, novel AuNPs may have toxicological profiles differing from bulk and therefore a thorough analysis of the quantitative structure-activity relationship (QSAR) is required. Several mechanisms are proposed that cause adverse effects of nanoparticles in biological systems. Catalytic generation of reactive species due to the large and chemically active surface area of nanomaterials is well established. Because nanoparticles approach the size of biological molecules and subcellular structures, they may overcome natural barriers by active or passive uptake. Ultrasmall AuNPs with sizes of 2 nm or less may even behave as molecular ligands. These types of potential interactions would imply a size and ligand-dependent behaviour of any nanomaterial towards biological systems. Thus, to fully understand their QSAR, AuNPs bioactivity should be analysed in biological systems of increasing complexity ranging from cell culture to whole animal studies.

  1. Functionalized imidazolium and benzimidazolium salts as paraoxonase 1 inhibitors: Synthesis, characterization and molecular docking studies. (United States)

    Karataş, Mert Olgun; Uslu, Harun; Alıcı, Bülent; Gökçe, Başak; Gencer, Nahit; Arslan, Oktay; Arslan, N Burcu; Özdemir, Namık


    Paraoxonase (PON) is a key enzyme in metabolism of living organisms and decreased activity of PON1 was acknowledged as a risk for atherosclerosis and organophosphate toxicity. The present study describes the synthesis, characterization, PON1 inhibitory properties and molecular docking studies of functionalized imidazolium and benzimidazolium salts (1a-5g). The structures of all compounds were elucidated by IR, NMR, elemental analysis and structures of compounds 2b and 2c were characterized by single-crystal X-ray diffraction. Compound 1c, a coumarin substituted imidazolium salt showed the best inhibitory effect on the activity of PON1 with good IC50 value (6.37 μM). Kinetic investigation was evaluated for this compound and results showed that this compound is competitive inhibitor of PON1 with Ki value of 2.39 μM. Molecular docking studies were also performed for most active compound 1c and one of least active compound 2c in order to determine the probable binding model into active site of PON1 and validation of the experimental results. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Materials-by-design: computation, synthesis, and characterization from atoms to structures (United States)

    Yeo, Jingjie; Jung, Gang Seob; Martín-Martínez, Francisco J.; Ling, Shengjie; Gu, Grace X.; Qin, Zhao; Buehler, Markus J.


    In the 50 years that succeeded Richard Feynman’s exposition of the idea that there is ‘plenty of room at the bottom’ for manipulating individual atoms for the synthesis and manufacturing processing of materials, the materials-by-design paradigm is being developed gradually through synergistic integration of experimental material synthesis and characterization with predictive computational modeling and optimization. This paper reviews how this paradigm creates the possibility to develop materials according to specific, rational designs from the molecular to the macroscopic scale. We discuss promising techniques in experimental small-scale material synthesis and large-scale fabrication methods to manipulate atomistic or macroscale structures, which can be designed by computational modeling. These include recombinant protein technology to produce peptides and proteins with tailored sequences encoded by recombinant DNA, self-assembly processes induced by conformational transition of proteins, additive manufacturing for designing complex structures, and qualitative and quantitative characterization of materials at different length scales. We describe important material characterization techniques using numerous methods of spectroscopy and microscopy. We detail numerous multi-scale computational modeling techniques that complements these experimental techniques: DFT at the atomistic scale; fully atomistic and coarse-grain molecular dynamics at the molecular to mesoscale; continuum modeling at the macroscale. Additionally, we present case studies that utilize experimental and computational approaches in an integrated manner to broaden our understanding of the properties of two-dimensional materials and materials based on silk and silk-elastin-like proteins.

  3. Synthesis of molecular imprinted beta cyclodextrins oligomers in water

    DEFF Research Database (Denmark)

    Yu, Donghong; Nielsen, Anne Louise; Bach, Lone


    hydrophobic molecules in aqueous solution, however, with limited selectivity. Templated synthesis of Cyclodextrin polymers was introduced by Komiyama. By use of simple templates, such as cholesterol, polymers with improved selectivity for the template molecules were achieved. In most of these stu...... complex formation between them prior to polymerization was proven by 2d-ROESY NMR. Water soluble CD dimmers were proven by MALDI-TOF MS to be the dominating products after synthesis....

  4. Organized Mesoporous Alumina: Synthesis, Structure and Potential in Catalysis

    Czech Academy of Sciences Publication Activity Database

    Čejka, Jiří


    Roč. 254, - (2003), s. 327-338 ISSN 0926-860X R&D Projects: GA AV ČR IAA4040001; GA ČR GA104/02/0571; GA MŠk ME 404 Institutional research plan: CEZ:AV0Z4040901 Keywords : organized mesoporous alumina * mesoporous molecular sieves * synthesis Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.825, year: 2003

  5. Synthesis, structures, nuclease activity, cytotoxicity, DFT and molecular docking studies of two nitrato bridged homodinuclear (Cu-Cu, Zn-Zn) complexes containing 2,2'-bipyridine and a chalcone derivative. (United States)

    Gaur, Ruchi; Choubey, Diksha Kumari; Usman, Mohammad; Ward, Benzamin D; Roy, Jagat Kumar; Mishra, Lallan


    Nitrato briged dinuclear complexes of type [Cu 2 (L) 2 (bpy) 2 (NO 3 )](NO 3 )·4H 2 O, 1 and [Zn 2 (L) 2 (bpy) 2 (NO 3 )](NO 3 )·4H 2 O, 2 (L=deprotonated form of free ligand LH, [1-(2-hydroxyphenyl)-3-(9-anthracenyl) propenone; bpy=2,2'bipyridine] are synthesized and characterized using a battery of physicochemical techniques and X-ray crystallography. A distorted square pyramidal geometry is assigned to them with N 2 O 3 coordination core around the metal ion. The co-ligand L binds the metal ions through its O,O' atoms in anti-syn mode. The metal centers in complexes 1 and 2 are separated via bridging nitrato group at a distance of 6.073Å and 5.635Å respectively. Their structures and absorption spectra are supported by the computational studies using density functional theory (DFT) and TD-DFT. Both complexes exhibit nuclease activity and cleave supercoiled (form I) DNA. The complex 1 preferentially binds major groove of DNA and follows an oxidative pathway whereas complex 2 binds with minor groove of DNA via hydrolytic pathway. Both complexes inhibit topoisomerase I relaxation activity with IC 50 values of 7 and 35μM. Molecular docking studies support the groove binding and topoisomerase I binding of the complexes. The complex 1 showed a significant cytotoxicity against HeLa cell lines (a cervical cancer cell lines) in vitro with IC 50 value calculated as 2.9±0.021μM as compared to 28.2±0. 044μΜ for complex 2. Complex 2 induces the cell apoptosis at a later-stage as compared to complex 1. The cell apoptosis and topoisomerase inhibition by complexes enable them to be potential candidates as future anticancer drugs. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Synthesis of Heteroaromatic Compounds by Oxidative Aromatization Using an Activated Carbon/Molecular Oxygen System

    Directory of Open Access Journals (Sweden)

    Masahiko Hayashi


    Full Text Available A variety of heteroaromatic compounds, such as substituted pyridines, pyrazoles, indoles, 2-substituted imidazoles, 2-substituted imidazoles, 2-arylbenzazoles and pyrimidin-2(1H-ones are synthesized by oxidative aromatization using the activated carbon and molecular oxygen system. Mechanistic study focused on the role of activated carbon in the synthesis of 2-arylbenzazoles is also discussed. In the final section, we will disclose the efficient synthesis of substituted 9,10-anthracenes via oxidative aromatization.

  7. Density functional studies of molecular structures of N-methyl ...

    Indian Academy of Sciences (India)


    studies. Sparse experimental data on the gas-phase geometry of DMF reported in the literature compares well with the DFT results on DMF. DFT emerges as a powerful method to calculate molecular structures. Keywords. Density functional theory; alkyl amides; molecular structure of alkyl amides; transition state search; ...

  8. Molecular genetic and molecular evolutionary studies on the bacteriochlorophyll synthesis genes of Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Burke-Agueero, Donald H. [Univ. of California, Berkeley, CA (United States)


    Rhodobacter capsulatus, purple bacterium capable of either aerobic or photosynthetic growth, has proven to be very useful in genetic studies of photosynthesis. Forty-four genes clustered together within a 46 kilobase region are required to establish photosynthetic ability in R. capsulatus. Approximately twenty of these genes are involved in bacteriochlorophyll synthesis of which eight ``bch`` genes are the subject of this thesis. Six of these genes were found to code for the two ring reductases. The first converts protochlorophyllide (PChlide) into a chlorin, the immediate precursor to chlorophyll a, and then into a bacteriochlorin. Each reductase is shown to be made up of three subunits. PChlide reductase is coded by the genes bchN, bchB, and bchL. Proteins with amino acid sequences markedly similar to those of bchN and bchL have been shown in other organisms to be required for chlorophyll synthesis; hence, their designation as chlN and chlB. A third chloroplast-encoded gene of heretofore unknown function shares amino acid identities with bchB and is probably the third subunit of the plant PChlide reductase. The bchA locus, which encodes the chlorin reductase, is found to be made up of three separate, translationally coupled genes, referred to as bchX, bchY, and bchZ. Amino acid similarities between bchX, bchL, and the nitrogenase reductase protein nifH suggest that all three classes of proteins share certain three-dimensional structural features, including elements that are central to the enzymatic mechanism of nifH. PChlide reductase and chlorin reductase are clearly derived from a common ancestor. Several lines of analysis suggests the ancestor of both enzyme systems reduced PChlide twice to produce bacteriochlorophyll supporting the concept bacteriochlorophyll as the ancestral reaction center pigment.

  9. Molecular genetic and molecular evolutionary studies on the bacteriochlorophyll synthesis genes of Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Burke-Agueero, D.H.


    Rhodobacter capsulatus, purple bacterium capable of either aerobic or photosynthetic growth, has proven to be very useful in genetic studies of photosynthesis. Forty-four genes clustered together within a 46 kilobase region are required to establish photosynthetic ability in R. capsulatus. Approximately twenty of these genes are involved in bacteriochlorophyll synthesis of which eight bch'' genes are the subject of this thesis. Six of these genes were found to code for the two ring reductases. The first converts protochlorophyllide (PChlide) into a chlorin, the immediate precursor to chlorophyll a, and then into a bacteriochlorin. Each reductase is shown to be made up of three subunits. PChlide reductase is coded by the genes bchN, bchB, and bchL. Proteins with amino acid sequences markedly similar to those of bchN and bchL have been shown in other organisms to be required for chlorophyll synthesis; hence, their designation as chlN and chlB. A third chloroplast-encoded gene of heretofore unknown function shares amino acid identities with bchB and is probably the third subunit of the plant PChlide reductase. The bchA locus, which encodes the chlorin reductase, is found to be made up of three separate, translationally coupled genes, referred to as bchX, bchY, and bchZ. Amino acid similarities between bchX, bchL, and the nitrogenase reductase protein nifH suggest that all three classes of proteins share certain three-dimensional structural features, including elements that are central to the enzymatic mechanism of nifH. PChlide reductase and chlorin reductase are clearly derived from a common ancestor. Several lines of analysis suggests the ancestor of both enzyme systems reduced PChlide twice to produce bacteriochlorophyll supporting the concept bacteriochlorophyll as the ancestral reaction center pigment.

  10. Synthesis, rotational dynamics, and photophysical characterization of a crystalline linearly conjugated phenyleneethynylene molecular dirotor. (United States)

    Hughs, Melissa; Jimenez, Miguel; Khan, Saeed; Garcia-Garibay, Miguel A


    We report the synthesis, crystal structure, solid-state dynamics, and photophysical properties of 6,13-bis((4-(3-(3-methoxyphenyl)-3,3-diphenylprop-1-yn-1-yl)phenyl)ethynyl)-5,7,12,14-tetrahydro-5,14:7,12-bis([1,2]benzeno)pentacene (1), a molecular dirotor with a 1,4-bis((4-ethynylphenyl)ethynyl)benzene (BEPEB) chromophore. The incorporation of a pentiptycene into the molecular dirotor provides a central stator and a fixed phenylene ring relative to which the two flanking ethynylphenylene rotators can explore various torsion angles; this allows the BEPEB fluorophore dynamics to persist in the solid state. X-ray diffraction studies have shown that molecular dirotor 1 is packed so that all the BEPEB fluorophores adopt a parallel alignment, this is ideal for the development of functional materials. Variable temperature, quadrupolar echo (2)H NMR studies have shown that phenylene rotator flipping has an activation energy of 9.0 kcal/mol and a room temperature flipping frequency of ∼2.6 MHz. Lastly, with measurements in solution, glasses, and crystals, we obtained evidence that the fluorescence excitation and emission spectra of the phenyleneethynylene chromophores is dependent on the extent of conjugation between the phenylene rings, as determined by their relative dihedral angles. This work provides a promising starting point for the development of molecular dirotors with polar groups whose amphidynamic nature will allow for the rapid shifting of solid-state absorption, fluorescence, and birefringence, in response to external electric fields.

  11. Hydrothermal synthesis, structure and characterization of new ...

    Indian Academy of Sciences (India)


    Keywords. Hydrothermal; crystal structure; solid electrolyte; iron (III) pyrophosphate. 1. Introduction ... tion, structure and electrical conductivity and the higher values of ..... type cavity structure. Acknowledgements. The authors would like to express their thanks to DST,. New Delhi, for financial assistance under the projects.

  12. Synthesis of molecular complexes for small molecule activation

    International Nuclear Information System (INIS)

    Andrez, Julie


    The redox chemistry of f-elements is drawing the attention of inorganic chemists due to their unusual reaction pathways. Notably low-valent f-element complexes have been shown to be able to activate small molecules such as CO 2 and N 2 in mild conditions. Compared to d-block metals, f-elements present a coordination chemistry dominated by electrostatic interactions and steric constraints. Molecular complexes of f-elements could thus provide new catalytic routes to transform small molecules into valuable chemicals. However the redox chemistry of low valent f-elements is dominated by single-electron transfers while the reductions of CO 2 and N 2 require multi-electronic processes. Accordingly the first approach of this PhD work was the use of redox active ligands as electron reservoir to support f-element centres increasing the electron number available for reduction events. The coordination of uranium with tridentate Schiff base ligand was investigated and led to isolation of a dinuclear electron-rich species able to undertake up to eight-electron reduction combining the redox activity of the ligands and the uranium centres. In order to obtain electron-rich compounds potentially able to polarize the C=O bond of CO 2 , the synthesis of hetero-bimetallic species supported by salophen Schiff base ligand was also studied. In a second approach we have used bulky ligands with strong donor-character to tune the reducing abilities of low valent f-elements. In this case a bimolecular electron-transfer process is often observed. The reactivity of the U(III) siloxid complex [U(OSi(OtBu) 3 ) 4 K] was further investigated. Notably, reaction with Ph 3 PS led to the formation of a terminal U(IV) sulfide complex with multiple U-S bond which was analysed by DFT studies to better understand the bonding nature. Preliminary studies on the role of the counter-cation (M) in the system [U(OSi(OtBu) 3 ) 4 M] on the outcome of the reactivity with CS 2 and CO 2 have also been performed. The

  13. Molecular structure and centrifugal distortion in methylthioethyne

    NARCIS (Netherlands)

    Engelsen, D. den


    The investigation of the microwave spectra of five isotopic species of methylthioethyne, HCCSCH3 enabled a fairly reliable calculation to be made of bond lengths and angles. The centrifugal distortion parameters are related to molecular vibrations.

  14. Synthesis, structure, and magnetic characterization of a C3-symmetric Mn(III)3Cr(III) assembly: molecular recognition between a trinuclear Mn(III) triplesalen complex and a fac-triscyano Cr(III) complex. (United States)

    Freiherr von Richthofen, Carl-Georg; Stammler, Anja; Bögge, Hartmut; DeGroot, Marty W; Long, Jeffrey R; Glaser, Thorsten


    The reaction of the tris(tetradentate) triplesalen ligand H(6)talen(t-Bu(2)), which provides three salen-like coordination environments bridged in a meta-phenylene arrangement by a phloroglucinol backbone, with Mn(II) salts under aerobic conditions, affords, in situ, the trinuclear Mn(III) triplesalen complex [(talen(t-Bu(2))){Mn(III)(solv)(n)}(3)](3+). This species then reacts with [(Me(3)tacn)Cr(CN)(3)] to form the tetranuclear complex [{(talen(t-Bu(2)))Mn(III)(3)}{(Me(3)tacn)Cr(CN)(3)}](3+) ([Mn(III)(3)Cr(III)](3+)). The regular ligand folding observed in the trinuclear triplesalen complex preorganizes the three metal ions for the reaction with three facially coordinated nitrogen atoms of [(Me(3)tacn)Cr(CN)(3)]. [{(talen(t-Bu(2)))(Mn(III)(MeOH))(3)}{(Me(3)tacn)Cr(CN)(3)}](ClO(4))(3) (1) was characterized by infrared spectroscopy, elemental analysis, mass spectrometry, electron absorption spectroscopy, and magnetic measurements. The molecular structure was established for the acetate-substituted derivative [{(talen(t-Bu(2)))(Mn(III)(MeOH))(2)(Mn(III)(OAc))}{(Me(3)tacn)Cr(CN)(3)}](ClO(4))(2) (2) by single-crystal X-ray diffraction. Variable-temperature-variable-field and mu(eff) versus T magnetic data have been analyzed in detail by full-matrix diagonalization of the appropriate spin-Hamiltonian, consisting of isotropic exchange, zero-field splitting, and Zeeman interaction components. Satisfactory reproduction of the experimental data has been obtained for the parameters J(Mn-Cr) = -0.12 +/- 0.04 cm(-1), J(Mn-Mn) = -0.70 +/- 0.03 cm(-1), and D(Mn) = -3.0 +/- 0.4 cm(-1). These generate a triply degenerate pseudo S(t) = 7/2 spin manifold, which cannot be appropriately described by a giant spin model and which exhibits a weak easy-axis magnetic anisotropy. This is corroborated by the onset of a frequency-dependent chi'' signal at low temperatures, demonstrating a slow relaxation of the magnetization indicative of 1 being a single-molecule magnet. Comparing the

  15. Algorithmic dimensionality reduction for molecular structure analysis


    Brown, W. Michael; Martin, Shawn; Pollock, Sara N.; Coutsias, Evangelos A.; Watson, Jean-Paul


    Dimensionality reduction approaches have been used to exploit the redundancy in a Cartesian coordinate representation of molecular motion by producing low-dimensional representations of molecular motion. This has been used to help visualize complex energy landscapes, to extend the time scales of simulation, and to improve the efficiency of optimization. Until recently, linear approaches for dimensionality reduction have been employed. Here, we investigate the efficacy of several automated alg...

  16. Similarity Measure for Molecular Structure: A Brief Review (United States)

    Bero, S. A.; Muda, A. K.; Choo, Y. H.; Muda, N. A.; Pratama, S. F.


    Similarity or distance measures have been used widely to calculate the similarity or dissimilarity between two samples of dataset. Cheminformatics is known as the domain that dealing with chemical information and both similarity and distance coefficient have been an important role for matching, searching and classification of chemical information. There are various types of similarity/distance coefficient used in molecular structure similarity searching. Generally, the calculation using similarity/distance coefficient is focusing more on 2-dimensional (2D) rather than 3-dimensional (3D) structure. In this paper, the popular similarity/distance coefficients for molecular structure will be reviewed together with the review on 3D molecular structure.

  17. Applications of the Cambridge Structural Database to molecular inorganic chemistry. (United States)

    Orpen, A Guy


    Applications of the data in the Cambridge Structural Database (CSD) to knowledge acquisition and fundamental research in molecular inorganic chemistry are reviewed. Various classes of application are identified, including the derivation of typical molecular dimensions and their variability and transferability, the derivation and testing of theories of molecular structure and bonding, the identification of reaction paths and related conformational analyses based on the structure correlation hypothesis, and the identification of common and presumably energetically favourable intermolecular interactions. In many of these areas, the availability of plentiful structural data from the CSD is set against the emergence of high-quality computational data on the geometry and energy of inorganic complexes.

  18. Design, synthesis, α-glucosidase inhibitory activity, molecular docking and QSAR studies of benzimidazole derivatives (United States)

    Dinparast, Leila; Valizadeh, Hassan; Bahadori, Mir Babak; Soltani, Somaieh; Asghari, Behvar; Rashidi, Mohammad-Reza


    In this study the green, one-pot, solvent-free and selective synthesis of benzimidazole derivatives is reported. The reactions were catalyzed by ZnO/MgO containing ZnO nanoparticles as a highly effective, non-toxic and environmentally friendly catalyst. The structure of synthesized benzimidazoles was characterized using spectroscopic technics (FT-IR, 1HNMR, 13CNMR). Synthesized compounds were evaluated for their α-glucosidase inhibitory potential. Compounds 3c, 3e, 3l and 4n were potent inhibitors with IC50 values ranging from 60.7 to 168.4 μM. In silico studies were performed to explore the binding modes and interactions between enzyme and synthesized benzimidazoles. Developed linear QSAR model based on density and molecular weight could predict bioactivity of newly synthesized compounds well. Molecular docking studies revealed the availability of some hydrophobic interactions. In addition, the bioactivity of most potent compounds had good correlation with estimated free energy of binding (ΔGbinding) which was calculated according to docked best conformations.

  19. Chlorosulfolipids: Structure, synthesis, and biological relevance


    Bedke, D. Karl; Vanderwal, Christopher D.


    Chlorosulfolipids have been isolated from freshwater algae and from toxic mussels. They appear to have a structural role in algal membranes and have been implicated in Diarrhetic Shellfish Poisoning. Further fascinating aspects of these compounds include their stereochemically complex polychlorinated structures and the resulting strong conformational biases, and their poorly understood (yet surely compelling) biosynthesis. Discussions of each of these topics and of efforts in structural and s...

  20. Synthesis, anti-microbial activity and molecular docking studies on ...

    Indian Academy of Sciences (India)

    inflammatory,6 anti-coagulant7 and as inhibitors of lipoxygenase8 and cyclooxygenase.9. Click chemistry10–12 has emerged as a reliable approach for the stereo selective synthesis of 1,2,3- triazole with desired properties. Cycloaddition of azide to alkyne in the presence of copper sulphate and sodium ascorbate to give 1 ...

  1. Mesoporous molecular sieve MCM-41 catalyzed one-pot synthesis ...

    African Journals Online (AJOL)

    An efficient synthesis of 3,4-dihydro-2(1H)-pyrimidinones and -thiones using MCM-41 as the catalyst from an aldehyde, β-keto ester, and urea or thiourea under solvent-free conditions is described. KEY WORDS: Biginelli reaction, Dihydropyrimidinones, MCM-41, One-pot, Reusable. Bull. Chem. Soc. Ethiop. 2011, 25(2) ...

  2. Molecular design, synthesis and evaluation of chemical biology tools

    NARCIS (Netherlands)

    Hoogenboom, Jorin


    Chapter 1 provides a perspective of synthetic organic chemistry as a discipline involved in the design, synthesis and evaluation of complex molecules. The reader is introduced with a brief history of synthetic organic chemistry, all the while dealing with different aspects of

  3. Synthesis, structure, redox and spectra of green iridium complexes ...

    Indian Academy of Sciences (India)


    3. *For correspondence. Synthesis, structure, redox and spectra of green iridium complexes of tridentate azo-aromatic ligands. MANASHI PANDA,a CHAYAN DAS,a CHEN-HSIUNG HUNGb and. SREEBRATA ... Mn(II)7 and Fe(II)8 but also produces stable anionic ..... the EPR of the oxidized complexes were not suc- cessful ...

  4. Synthesis and structure refinement of layered double hydroxides of ...

    Indian Academy of Sciences (India)


    )-oxygen bond in this compound as opposed to the Co–Ga hydroxide. These observations are supported by IR spectra. Keywords. Layered double hydroxide; Rietveld refinement; urea hydrolysis. 1. Introduction. The synthesis, structure and properties of layered double hydroxides (LDHs) have been widely studied in recent.

  5. Abstract: Synthesis, structure and density functional theory (DFT ...

    Indian Academy of Sciences (India)

    Ruthenium Complexes of Chelating Amido-functionalized N-heterocyclic Carbene Ligands: Synthesis, Structure and DFT Studies. Sachin Kumar,† Anantha Narayanan,† Mitta Nageswar Rao,† Mobin M. Shaikh§ and Prasenjit Ghosh*,†. †Department of Chemistry and. §National Single Crystal X-ray Diffraction Facility,.

  6. Synthesis, structure and applications of [cis-dioxomolybdenum (VI ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 123; Issue 2. Synthesis, structure and applications of [cis-dioxomolybdenum(VI)-(ONO)] type complexes. Rajan Deepan Chakravarthy Dillip Kumar Chand. Volume 123 Issue 2 March 2011 pp 187-199 ... ...

  7. Synthesis, crystal structure and catecholase activity of a Ni (II ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 126; Issue 6. Synthesis, crystal structure and catecholase activity of a Ni(II) complex derived from a tetradentate Schiff base ligand. Pradipta Kumar Basu Merry Mitra Amrita Ghosh Latibuddin Thander Chia -Her Lin Rajarshi Ghosh. Rapid Communications Volume 126 ...

  8. Synthesis, characterization, X-ray crystal structure, electrochemical ...

    Indian Academy of Sciences (India)

    DOI 10.1007/s12039-015-0978-8. Synthesis, characterization, X-ray crystal structure, electrochemical evaluation and anti-cancer studies of a mixed ligand Cu(II) complex of (E)-N -((2-hydroxynaphthalen-1-yl)methylene)acetohydrazide. IRAN SHEIKHSHOAIEa, S YOUSEF EBRAHIMIPOURa,∗, MAHDIEH SHEIKHSHOAIEa,.

  9. Synthesis, structure and applications of [cis-dioxomolybdenum (VI ...

    Indian Academy of Sciences (India)

    Oxo-molybdenum chemistry is of great interest since such units are found in the active sites of a majority of molybdo-enzymes. In order to mimic the biological systems, a number of oxo-molybdenum complexes have been synthesised and studied. This review describes synthesis, structure and applications of ...

  10. Synthesis, structure and luminescence properties of phosphates A1 ...

    Indian Academy of Sciences (India)

    Home; Journals; Bulletin of Materials Science; Volume 40; Issue 1. Synthesis, structure and luminescence properties of phosphates A 1 − 3 x Eu x Zr 2 (PO 4 ) 3 (A—alkali metal). ANTON KANUNOV BENOIT GLORIEUX ALBINA ORLOVA ELENA BOROVIKOVA GALINA ZAVEDEEVA. Volume 40 Issue 1 February 2017 pp 7- ...

  11. Synthesis and crystal structure of a wheel-shaped supramolecular ...

    Indian Academy of Sciences (India)

    Synthesis and crystal structure of a wheel-shaped supramolecular coordination complex. DEEPAK GUPTA, PALANISAMY RAJAKANNU, BHASKARAN SHANKAR,. FIRASAT HUSSAIN and MALAICHAMY SATHIYENDIRAN. ∗. Department of Chemistry, University of Delhi, Delhi 110 007, India e-mail:; ...

  12. Theoretical study of electron transport throughout some molecular structures (United States)

    Abbas, Mohammed A. A.; Hanoon, Falah H.; Al-Badry, Lafy F.


    The present work is a theoretical study of the electronic properties of some molecular structures. The system that takes into account in the study is left lead-donor-molecule-acceptor-right lead. The molecule, such as (phenyl, biphenyl, triphenyl, naphthalene, anthracene, and phenanthrene), is threaded by magnetic flux. This work contains two parts. First is computing density of states of the molecular structures as a closed system by density functional theory (DFT). Second is calculating the transmission probability and electric current of such molecular structures as an open system by steady-state theoretical model. Furthermore, the most important effects, taking into consideration are quantum interference, magnetic flux, and interface structure. Our results show that the connection of the molecule to the two leads, the number of rings, the magnetic flux, and the geometrical structure of the molecule play an important role in determining the energy gap of molecular structures.

  13. Synthesis, crystal structure, thermal analysis and dielectric ...

    Indian Academy of Sciences (India)

    In both the materials, the crystal structure has been determined by X-ray single crystal analysis at room temperature (293 K). The compound structures consist of K + (or NH 4 + ) cations and double chains of CdCl 6 octahedra sharing one edge extending along b -axis. The mixture of KA + /NH 4 + cations are located ...

  14. Hydrothermal synthesis, structure and characterization of new ...

    Indian Academy of Sciences (India)


    The structure has tunnel-type cavities and are congenial for ion transportation through them. The compound exhibits moderate thermal stability. Keywords. Hydrothermal; crystal structure; solid electrolyte; iron (III) pyrophosphate. 1. Introduction. NASICON and related compounds belong to the well known family of solid ...

  15. Synthesis, crystal structures, spectroscopic characterization and in ...

    Indian Academy of Sciences (India)

    Both the complexes were structurally characterized by single crystal XRD. The crystal structure of complex 1 displays a distorted square pyramidal geometry in which Schiff base is coordinated to the Cu(II) ion via ONO-donor in the axial mode, whereas, the chelating diamine displays axial and equatorial mode of binding via ...

  16. Bioinspired synthesis of new silica structures. (United States)

    Patwardhan, Siddharth V; Mukherjee, Niloy; Steintz-Kannan, Miriam; Clarson, Stephen J


    Silicon and oxygen are the two most abundant elements in the Earth's crust but despite the vast scientific literature on crystalline and amorphous silica, new chemistries, structures and applications continue to be discovered for compounds formed from these elements--thus we present here for the first time the formation of new amorphous silica structures that were uniquely synthesized by a bioinspired synthetic system.

  17. Lewis Structures Are Models for Predicting Molecular Structure, Not Electronic Structure (United States)

    Purser, Gordon H.


    This article argues against a close relationship between Lewis dot structures and electron structure obtained from quantum mechanical calculations. Lewis structures are a powerful tool for structure prediction, though they are classical models of bonding and do not predict electronic structure. The "best" Lewis structures are those that, when combined with the VSEPR model, allow the accurate prediction of molecular properties, such as polarity, bond length, bond angle, and bond strength. These structures are achieved by minimizing formal charges within the molecule, even if it requires an expanded octet on atoms beyond the second period. Lewis structures that show an expanded octet do not imply full d-orbital involvement in the bonding. They suggest that the presence of low-lying d-orbitals is important in producing observed molecular structures. Based on this work, the presence of electron density, not a large separation in charge, is responsible for the short bond lengths and large angles in species containing nonmetal atoms from beyond the second period. This result contradicts results obtained from natural population analysis, a method that attempts to derive Lewis structures from molecular orbital calculations.

  18. Biomineralization-inspired synthesis of functional organic/inorganic hybrid materials: organic molecular control of self-organization of hybrids. (United States)

    Arakaki, Atsushi; Shimizu, Katsuhiko; Oda, Mayumi; Sakamoto, Takeshi; Nishimura, Tatsuya; Kato, Takashi


    Organisms produce various organic/inorganic hybrid materials, which are called biominerals. They form through the self-organization of organic molecules and inorganic elements under ambient conditions. Biominerals often have highly organized and hierarchical structures from nanometer to macroscopic length scales, resulting in their remarkable physical and chemical properties that cannot be obtained by simple accumulation of their organic and inorganic constituents. These observations motivate us to create novel functional materials exhibiting properties superior to conventional materials--both synthetic and natural. Herein, we introduce recent progress in understanding biomineralization processes at the molecular level and the development of organic/inorganic hybrid materials by these processes. We specifically outline fundamental molecular studies on silica, iron oxide, and calcium carbonate biomineralization and describe material synthesis based on these mechanisms. These approaches allow us to design a variety of advanced hybrid materials with desired morphologies, sizes, compositions, and structures through environmentally friendly synthetic routes using functions of organic molecules.

  19. Constrained saccharides: a review of structure, biology, and synthesis. (United States)

    Rodriguez, Jacob; O'Neill, Sloane; Walczak, Maciej A


    Review primarily covers from 1995-2018Carbohydrate function, recognized in a multitude of biological processes, provides a precedent for developing carbohydrate surrogates that mimic the structure and function of bioactive compounds. In order to constrain highly flexible oligosaccharides, synthetic tethering techniques like those exemplified by stapled peptides are utilized to varying degrees of success. Naturally occurring constrained carbohydrates, however, exist with noteworthy cytotoxic and chemosensitizing properties. This review highlights the structure, biology, and synthesis of this intriguing class of molecules.

  20. Synthesis, crystal structure, theoretical study and luminescence ...

    Indian Academy of Sciences (India)

    phenanthroline) has been synthesized and characterized by elemental analysis, infrared spectroscopy, ultraviolet-visible spectroscopy, X-ray single crystal analysis and fluorescent analysis. Its crystal structure is monoclinic with space group 2/ and ...

  1. Synthesis and computer-aided structural investigation of potentially photochromic spirooxazines

    International Nuclear Information System (INIS)

    Chi, L.


    Quantum mechanical methods, PPP-MO and ZINDO, were used to predict the electronic spectra of the ring-opened forms and ring-closed forms respectively of a series of spirooxazines. Molecular mechanics was used to optimise the molecular geometry and to calculate the molecular final energy (steric energy) using the MM2 force field method. An all-valence-electron quantum mechanical method was employed to calculate the heats of formation using AM1 parameters, and the data were used to provide a measure of the stability of the molecules. This computer-aided structural investigation has provided an enhanced understanding of the spirooxazine system and methods with the potential to predict photochromic behaviour have emerged. The synthesis of a series of heterocyclic analogues of the well-known spironaphthoxazines based on quinolines, coumarin and pyrazolones were attempted. The properties of the compounds obtained were correlated with the results of the calculations. (author)

  2. Molecular dynamics modeling of structural battery components

    NARCIS (Netherlands)

    Verners, O.; Van Duin, A.C.T.; Wagemaker, M.; Simone, A.


    A crosslinked polymer based solid electrolyte prototype material –poly(propylene glycol) diacrylate– is studied using the reactive molecular dynamics force field ReaxFF. The focus of the study is the evaluation of the effects of equilibration and added plasticizer (ethylene carbonate) or anion

  3. Molecular structure of the lecithin ripple phase

    NARCIS (Netherlands)

    de Vries, AH; Yefimov, S; Mark, AE; Marrink, SJ


    Molecular dynamics simulations of lecithin lipid bilayers in water as they are cooled from the liquid crystalline phase show the spontaneous formation of rippled bilayers. The ripple consists of two domains of different length and orientation, connected by a kink. The organization of the lipids in

  4. Synthesis and structure of cerium nitrosocarbonylcyanmethanid complex

    International Nuclear Information System (INIS)

    Gerasimenko, H.; Scopenko, V.V.; Kapshuk, A.A.


    Full text: The complex compound [CeL 4 Dy 2 ]Na*2Ac (where L- nitrosocarbonylcyanmethanid, Dy -- dipyridile, Ac - acetone) were synthesised by interaction of cerium chloride and sodium nitrosocarbonylcyanmethanid from acetone solution. After two hours of mixing the dipyridil solution in acetone was added for complex stabilization. After filtration solution was put to desiccator for crystallisation. The complex was studied using IR- and UV-spectroscopy. The structure of the complex was determined using X-ray structure analysis. It was found that the structure of the complex belongs to orthorhombic Pna2(1) syngony with the unit cell parameters 17.010, 16.280 and 16.340Angstroms, respectively. It was found that cerium in the compound was eight co-ordinated. Four nitroso ligands were co-ordinated by bidentate bridge method and two dipyridiles by bidentate-cycle method

  5. Synthesis and Studies of Sulfur-Containing Heterocyclic Molecules for Molecular Electronics

    DEFF Research Database (Denmark)

    Mazzanti, Virginia

    This work describes the synthesis and studies of sulfur containing π conjugated heterocycles, which are considered interesting motifs in the field of molecular electronics. The first project, which is covered in Chapter 1, concerns the functionalization of tetracycle dibenzo[bc,fg][1,4]dithiapent...

  6. Synthesis of Polyimides in Molecular-Scale Confinement for Low-Density Hybrid Nanocomposites. (United States)

    Isaacson, Scott G; Fostvedt, Jade I; Koerner, Hilmar; Baur, Jeffery W; Lionti, Krystelle; Volksen, Willi; Dubois, Geraud; Dauskardt, Reinhold H


    In this work, we exploit a confinement-induced molecular synthesis and a resulting bridging mechanism to create confined polyimide thermoset nanocomposites that couple molecular confinement-enhanced toughening with an unprecedented combination of high-temperature properties at low density. We describe a synthesis strategy that involves the infiltration of individual polymer chains through a nanoscale porous network while simultaneous imidization reactions increase the molecular backbone stiffness. In the extreme limit where the confinement length scale is much smaller than the polymer's molecular size, confinement-induced molecular mechanisms give rise to exceptional mechanical properties. We find that polyimide oligomers can undergo cross-linking reactions even in such molecular-scale confinement, increasing the molecular weight of the organic phase and toughening the nanocomposite through a confinement-induced energy dissipation mechanism. This work demonstrates that the confinement-induced molecular bridging mechanism can be extended to thermoset polymers with multifunctional properties, such as excellent thermo-oxidative stability and high service temperatures (>350 °C).

  7. Microwave radiation hydrothermal synthesis and characterization of micro- and mesoporous composite molecular sieve Y/SBA-15

    Directory of Open Access Journals (Sweden)

    Wenyuan Wu


    Full Text Available A microwave radiation hydrothermal method to control synthesis of micro- and mesoporous Y/SBA-15 composite molecular sieves was reported. The synthesized SBA-15 and Y/SBA-15 were characterized by scanning electron microscopy (SEM and N2 adsorption–desorption. The three kinds of different concentrations of hydrochloric acid (0.75 M, 2 M and 3.25 M were used to investigate the effect on Y/SBA-15. The analysis results of the composite products indicated that the optimization synthesis condition employed zeolite type Y and TEOS as silicon sources under 0.75 M hydrochloric acid by the microwave radiation hydrothermal synthesis method. The N2 adsorption–desorption test results of micro–mesoporous composite molecular sieve type Y/SBA-15 in mesoporous extent indicated that SBET is 355.529 m2/g, D‾BET is 4.050 nm, and mesoporous aperture focuses on the distribution region of 5.3 nm. It was found that the received composite product has an appropriate proportion of smaller size, larger size pore structure and the thicker pore wall. In addition, its internal channels have a high degree of order and smooth flow in long-range channels.

  8. Synthesis, characterization and crystal structure of a ...

    African Journals Online (AJOL)

    The Mo atom in the complex is in octahedral coordination. Thermal stability of the complex has also been studied. KEY WORDS: Molybdenum complex, Hydrazone ligand, Crystal structure, X-ray diffraction, Thermal property. Bull. Chem. Soc. Ethiop. 2014, 28(3), 409-414. DOI: ...

  9. Synthesis, crystal structure, thermal analysis and dielectric ...

    Indian Academy of Sciences (India)

    [13] Perry C H and Lowdes R P 1969 J. Chem. Phys. 51 3648. [14] Sheldrick G M 1997 SHELXS9, Program for the Refinement of Crystal Structures (Germany: University of Gottingen). [15] Loukil M, Kabadou A, Salles Ph and Ben Salah A 2004 Chem. Phys. 300 247. [16] Rolies M M and De Ranter C J 1978 Acta Crystallogr.

  10. Synthesis, crystal structure, theoretical study and luminescence ...

    Indian Academy of Sciences (India)

    performed on complex 1 to rationalize its experimental absorption spectra. Complex 1 exhibits luminescence in EtOH ... potential applications in biological systems like, devel- opment of structural and functional models for ... to react with [WOnS4−n] (n = 0-2).11,12 These reactions result in the formation of a large number of ...

  11. Structure of bright-rimmed molecular clouds

    International Nuclear Information System (INIS)

    Wootten, A.; Sargent, A.; Knapp, G.; Huggins, P.J.


    Five bright-rimmed molecular clouds, NGC 1977, IC 1396, IC 1848 A, B35, and NGC 7822, have been mapped with 30'' resolution in the J = 2--1 lines of 12 co. For the first three, 13 CO maps have also been made. The spatial distributions of temperature, density, and molecular abundance in these clouds have been determined, particularly in the vicinity of the rims. In general, the gas densities increase close to the rims, but temperature enhancements occur over comparatively extended regions. Near the rims the gas kinematics is varied: velocity gradients are observed in several regions, and in IC 1396 line broadening is distinguishable. A detailed study of the excitation of 13 CO demonstrates that near the well-resolved rim in NGC 1977 where C I and carbon recombination lines have been observed, there is a definite decline in the CO abundance. These molecular clouds span a variety of stages of star formation, but in none does the interaction with the adjacent H II region appear to have substantially affected the course of the star-forming history of the cloud

  12. Synthesis and Supramolecular Chemistry of Novel Liquid Crystalline Crown Ether-Substituted Phthalocyanines : Toward Molecular Wires and Molecular Ionoelectronics

    NARCIS (Netherlands)

    Nostrum, Cornelus F. van; Picken, Stephen J.; Schouten, Arend-Jan; Nolte, Roeland J.M.


    The synthesis of the metal-free and the dihydroxysilicon derivatives of tetrakis[4’,5’-bis(decoxy)benzo-18-crown-6]phthalocyanine is described. The metal-free phthalocyanine is liquid crystalline and exhibits a crystalline phase to mesophase transition at 148 °C. The structures of the crystalline

  13. Crystal structure and pair potentials: A molecular-dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Parrinello, M.; Rahman, A.


    With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

  14. Synthesis, crystal structure, thermal analysis and dielectric ...

    Indian Academy of Sciences (India)

    2.2 X-ray structure determination. Two transparent parallelepipedic crystals with dimensions,. 0.20 × 0.12 × 0.04 and 0.26 × 0.14 × 0.12, were chosen from the preparation. The intensity data were collected on. An APEX II diffractometer with graphite–crystal monochro- mated MoKα radiation (0.71073 Å). Lorentz and polariz-.

  15. Synthesis, reactivity and structural studies of carboranyl thioethers and disulfides

    Czech Academy of Sciences Publication Activity Database

    Laromaine, A.; Teixidor, F.; Kivekäs, R.; Sillanpää, R.; Benakki, R.; Grüner, Bohumír; Vinas, C.

    -, č. 10 (2005), s. 1785-1795 ISSN 1477-9226 Grant - others:Generalitat de Catalunya(ES) 2001/SGR/0033 Keywords : molecular structure * crystal structure * closo-carboranes Subject RIV: CA - Inorganic Chemistry Impact factor: 3.003, year: 2005

  16. Synthesis, crystal structure, optical and electrochemical properties of ...

    Indian Academy of Sciences (India)

    Its molecular geometry in the ground state has also been calculated using density functional theory (DFT) at the B3LYP/6-31G∗∗ level and compared with its crystal structure. Results show that the optimized geometry can well reproduce the crystal structure. Furthermore, both absorption and emission spectra of 1 and 2 ...

  17. Hybrid structures for molecular level sensing (United States)

    Lemieux, Melburne Charles

    With substantial molecular mobility and segment dynamics relative to metals and ceramics, all polymeric materials, to some extent, are stimuli-responsive by exhibiting pronounced chemical and physical changes in the backbone, side chains, segments, or end groups induced by changes in the local environment. Thus, the push to incorporate polymeric materials as sensing/responsive nanoscale layers into next-generation miniaturized sensor applications is a natural progression. The significance and impact of this research is wide-ranging because it offers design considerations and presents results in perhaps two of the most critical broad areas of nanotechnology: ultrathin multifunctional polymer coatings and miniaturized sensors. In this work, direct evidence is given showing that polymer coatings comprised of deliberately selected molecular segments with very different chemistry can have switchable properties, and that the surface composition can be precisely controlled, and thus properties can be tuned: all in films on the order of 20 nm and less. Furthermore, active sensing layers in the form of plasma-polymerized polymers are successfully incorporated into actual silicon based microsensors resulting in a novel hybrid organic/inorganic materials platform for microfabricated MEMS sensors with record performance far beyond contemporary sensors in terms of detection sensitivity to various environments. The results produced in this research show thermal sensors with more than two orders of magnitude better sensitivity than what is attainable currently. In addition, a humidity response on the order of parts per trillion, which is four orders of magnitude more sensitive than current designs is achieved. Molecular interactions and forces for organic molecules are characterized at the picoscale to optimize polymeric nanoscale layer design that in turn optimize and lead to microscale hybrid sensors with unprecedented sensitivities.

  18. Synthesis and structure of vanillin azomethines

    Directory of Open Access Journals (Sweden)

    Jasmina M. Jovanović


    Full Text Available Vanillin is most prominent as the principal flavor and aroma compound in vanilla. Vanillin has been used as a chemical intermediate in the production of pharmaceuticals and other fine chemicals.The two intermediates, assigned as intermediates I and II, were prepared by using vanillin and 1-butylbromide or 2-chloroacetic acid, respectively. The condensation of intermediates with 2,3- -diaminopyridine gave azomethines. Their structure was established by using elemental microanalysis, as well as UV/Vis, FTIR and 1H-NMR spectra. Synthesized compounds were tested for their antifungal activity against Candida albicans, Candida lipolytica and Sacharomyces cerevisiae.

  19. MCM-41 ordered mesoporous molecular sieves synthesis and characterization

    Directory of Open Access Journals (Sweden)

    Rogério A.A. Melo


    Full Text Available The aim of this work was to study the hydrothermal synthesis of Si and SiAlMCM-41 performed under both autogenic pressure and refluxing conditions. XRD data showed that the MCM-41 phase may be formed by both processes and that the synthesized material in the presence of Al and/or under reflux presents the hexagonally arrangement of less ordered mesopores. However, as verified by XRD and physisorption data, the order was improved with higher synthesis times. 29Si and 1H - 29Si C/P MAS NMR spectra showed that a great part of the Si atoms exists as silanol groups which originate resonance peaks at -110, -100 and -91 ppm. The presence of Al atoms may generate Si(3Si, Al and Si(2Si, 2Al environments which might be contributing to resonance peaks at -100 and -91 ppm. The 27Al MAS NMR spectrum of the as synthesized AlSiMCM-41 showed a resonance peak of tetrahedral framework aluminum close to 53 ppm and two others, one close to 14 ppm attributed to Al(H2O6+3 species and the other a weak signal close to 32 ppm attributed to pentacoordinated Al. 27Al MAS NMR spectra of the calcined sample showed a peak at 0 ppm corresponding to an hexacoordinated extra-framework aluminum formed during calcination.

  20. Synthesis, molecular and crystalline architectures, and properties of ...

    Indian Academy of Sciences (India)

    OH2)2] (1) (bnzd = benzidine) has been isolated through a single-pot reaction of the molecular building components in MeOH–. H2O solvent mixture at room temperature and characterized by physico-chemical and spectroscopic methods.

  1. Synthesis, anti-microbial activity and molecular docking studies on ...

    Indian Academy of Sciences (India)

    100, where I = Zone of inhibition. 2.6 Docking studies. The protein in complex with simocyclinone (PDB ID: 2Y3P) was used as the template for molecular docking studies. GLIDE 9.5 and IFD script from Schrödinger,. LLC (New York) was employed as our primary docking engine.20 A hierarchical search protocol was utilized ...

  2. Systematic analysis of crystal and molecular structures

    Czech Academy of Sciences Publication Activity Database

    Hašek, Jindřich; Dohnálek, Jan


    Roč. 19, č. 2 (2012), s. 86-87 ISSN 1211-5894. [Struktura 2012. Kolokvium Krystalografické společnosti. 11.06.2012-14.06.2012, Klatovy] R&D Projects: GA ČR GA310/09/1407 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : structure databases * structure-function relations * organic and inorganic materials Subject RIV: EE - Microbiology, Virology

  3. Synthesis, structure, and properties of azatriangulenium salts

    DEFF Research Database (Denmark)

    Laursen, B.W.; Krebs, Frederik C


    A general synthetic route to novel nitrogen-bridged heterocyclic carbenium ions of the acridinium and triangulenium type has been developed and investigated. The synthetic method is based on nucleophilic aromatic substitution (SNAr) on the tris(2,6-dimethoxyphenyl)carbenium ion (1) with primary...... amines and, by virtue of its stepwise and irreversible nature, provides a powerful tool for the preparation of a wide variety of new heterocyclic carbenium salts. Several derivatives of the three new oxygen- and/or nitrogen-bridged triangulenium salts, azadioxa- (6), diazaoxa- (7......), and triazatriangulenium (4), have been synthesized and their physicochemical properties have been investigated. Crystal structures for compounds 2 b-PF6: 2d-PF6, 4b-BF4, 4c-BF4, 6e-BF4, and 8 are reported. The different packing modes found for the triazatriagulenium salts are discussed in relation to the electrostatic...

  4. Synthesis, crystal structures, hydrogen bonding graph-sets and ...

    African Journals Online (AJOL)

    Synthesis, crystal structures, hydrogen bonding graph-sets and theoretical studies of nickel (+II) co-ordinations with pyridine-2,6-dicarboxamide oxime. ... which crystallized in the monoclinic space group C2/c with a = 14.915(2), b = 0.895(2), c = 8.205(1) Å, β = 114.69(1), and Z = 4. The complex consists of discrete cations ...

  5. Structure of FD-895 revealed through total synthesis. (United States)

    Villa, Reymundo; Mandel, Alexander L; Jones, Brian D; La Clair, James J; Burkart, Michael D


    The total synthesis of FD-895 was completed through a strategy that featured the use of a tandem esterification ring-closing metathesis (RCM) process to construct the 12-membered macrolide and a modified Stille coupling to append the side chain. These studies combined with detailed analysis of all four possible C16-C17 stereoisomers were used to confirm the structure of FD-895 and identify an analog with an enhanced subnanomolar bioactivity.

  6. Aperture synthesis observations of NH3 in OMC-1 - Filamentary structures around Orion-KL

    International Nuclear Information System (INIS)

    Murata, Yasuhiro; Kawabe, Ryohei; Ishiguro, Masato; Morita, Kohichiro; Kasuga, Takashi


    Aperture synthesis observations of the Orion molecular cloud 1 (OMC-1) have been made in NH 3 (1, 1) and (2, 2) emission at 23.7 GHz, using the Nobeyama Millimeter Array (NMA), and obtained 16 arcsec resolution maps for OMC-1 and 8 arcsec resolution maps for the Orion-KL region. Filamentary structures extending over 0.5 pc from the Orion-KL region to the north and northwest directions were found. These structures are associated with the H2 finger structures and Herbig-Haro objects which are located at the blue-shifted side of the bipolar molecular outflow. The results suggest that these filaments are ambient molecular cloudlets with shocked surfaces caused by the strong stellar wind from the Orion-KL region. The 8 arcsec resolution NH 3 (2, 2) maps show the extended features around the hot core of Orion-KL. These extended features correspond to the rotating disk and shocked shell associated with the bipolar molecular outflow. 37 refs

  7. Diastereoselective synthesis and molecular docking studies of novel fused tetrahydropyridine derivatives as new inhibitors of HIV protease (United States)

    Mohammadi, Ali A.; Taheri, Salman; Amouzegar, Ali; Ahdenov, Reza; Halvagar, Mohammad Reza; Sadr, Ahmad Shahir


    An efficient one-pot, catalyst-free, and four-components procedure for the synthesis of novel 10b-hydroxy-4-nitro-5-phenyl-2,3,5,5a-tetrahydro-1H-imidazo[1,2-a]indeno[2,1-e]pyridin-6(10bH)-one derivatives from corresponding diamine, nitro ketene dithioacetal, aldehydes and 1,3-indandione in ethanol has been achieved upon a Knoevenagel condensation-Michael addition-tautomerism-cyclisation sequence. All the newly synthesized compounds were screened for molecular docking studies. Molecular docking studies were carried out using the crystal structure of HIV protease enzyme. Some of the compounds obtain minimum binding energy and good affinity toward the active pocket of HIV protease enzyme in compare with Saquinavir as a standard HIV protease inhibitor.

  8. Synthesis, Crystal Structures, Molecular Docking and MAO-B Inhibitory Activity of Transition Metal Complexes Derived from 2-(4-(Pyridin-2-yl)piperazin-1-yl)acetic Acid. (United States)

    Ren, Yan-Jie; Zhu, Jin-Long; Zhang, Li-Xin; Xu, Yin-Xiang; Qian, Shao-Song


    Three new complexes derived from 2-(4-(pyridin-2-yl)piperazin-1-yl)acetic acid (HL), [M(L)2(H2O)2] where M = CuII (1), ZnII (2) and CdII (3), have been synthesized and characterized by IR spectroscopy, elemental analysis and X-ray crystallography. The inhibitory activity of these three complexes against MAO-B was tested in vitro, and the molecular docking experiments were also carried out to rationalize their binding models. Both the experimental and docking simulation results indicated that complex 1 has the best inhibitory activity with IC50 value being 6.5 ± 0.31 μM.

  9. Poly[n]catenanes: Synthesis of molecular interlocked chains (United States)

    Wu, Qiong; Rauscher, Phillip M.; Lang, Xiaolong; Wojtecki, Rudy J.; de Pablo, Juan J.; Hore, Michael J. A.; Rowan, Stuart J.


    As the macromolecular version of mechanically interlocked molecules, mechanically interlocked polymers are promising candidates for the creation of sophisticated molecular machines and smart soft materials. Poly[n]catenanes, where the molecular chains consist solely of interlocked macrocycles, contain one of the highest concentrations of topological bonds. We report, herein, a synthetic approach toward this distinctive polymer architecture in high yield (~75%) via efficient ring closing of rationally designed metallosupramolecular polymers. Light-scattering, mass spectrometric, and nuclear magnetic resonance characterization of fractionated samples support assignment of the high-molar mass product (number-average molar mass ~21.4 kilograms per mole) to a mixture of linear poly[7-26]catenanes, branched poly[13-130]catenanes, and cyclic poly[4-7]catenanes. Increased hydrodynamic radius (in solution) and glass transition temperature (in bulk materials) were observed upon metallation with Zn2+.

  10. Characterising the Structure of Molecular Clouds (United States)

    Wong, Graeme Francis

    The Interstellar Medium contains the building blocks of matter in our Galaxy and plays a vital role in the evolution of low mass star formation. The poorly studied molecular clouds of Lupus and Chamaeleon contain ongoing low mass star formation, and are in close proximity to our Solar System. While on the other hand the Carina molecular cloud, poorly observed in radio wavelength, is an active region of star formation and host some of the brightest stars known within our Galaxy. Using tracers like carbon monoxide, atomic neutral carbon, and ammonia, we are able to measure the temperature and density of the gas cloud. This information allows us to understand the initial conditions of the formation of low mass stars. Observations conducted with the 22-m Mopra radio telescope (located at the edge of the Warrumbungle Mountains near Coonabarabran), in the Carbon monoxide (CO) isotopologues 12 CO, 13 CO, C17O, and C18O (1-0) transitions, have mapped the Chamaeleon II cloud, an intermediate mass cloud within the Chamaeleon. Through the sub-arcminute maps, comparisons have been made to previous low resolution (2.5') maps which have been to resolve some of the dense clumps previously identified. Optical depth, column density, and excitation temperature derived from the CO maps, are consistent with previous results. A detailed comparison between identified C18O clumps have shown the different conditions occurring within the clumps, some of which contain or are located near a population of young stellar objects. The Northern region of the Carina Nebular Complex, was observed with NANTEN2, a 4-m radio telescope (located in the Chilean Atacama desert), in the 12CO (4-3) and [C I] 3P1-3P0 emission lines. Previous observations towards this region has either been at poor resolution or had limited coverage. The presented observations, strike a balance between the two; observing in sub-arcmin resolution (0.6') and with an area of 0.9° X 0.5° mapped. Excitation temperature of the 12

  11. Synthesis and Characterization of Nanocrystalline Aluminophosphate AlPO4-5 Molecular Sieve

    Directory of Open Access Journals (Sweden)

    Asir Alnaama


    Full Text Available Nanocrystalline aluminophosphate AlPO4-5 molecular sieves were synthesized by hydrothermal method (HTS. Synthesis parameters like time and temperature of crystallization were investigated. Type of template (R and ratio of R/P2O5 were studied also. Characterization of the synthesized AlPO4-5 were done by powder X-ray diffraction (XRD, scanning electron microscopy (SEM/EDX, Fourier transform infrared (FTIR, differential scanning calorimetry-thermogravimetry analysis (DSC-TGA, and N2 adsorption-desorption BET analysis. XRD patterns results showed excellent crystallinity for two types of templates, di-n-propylamine (DPA and tetrapropyl ammonium hydroxide (TPAOH for alumminophosphate five (AFI structure. Nano-level for particle size of 66 nm was revealed by AFM test. Good thermal stability was obtained in DSC-TGA results. Best time and temperature of crystallization of 24h and 190 O C were got. Optimum R/P2O5 for two kind of template was established.

  12. Synthesis, estrogen receptor binding affinity and molecular docking of pyrimidine-piperazine-chromene and -quinoline conjugates. (United States)

    Parveen, Iram; Ahmed, Naseem; Idrees, Danish; Khan, Parvez; Hassan, Md Imtaiyaz


    Substituted 2-amino-7-((6-(4-(2-hydroxyethyl) piperazin-1-yl)-2-methylpyrimidin-4-yl)oxy)-4-phenyl-4H-chromene-3-carbonitriles and 2-amino-7-((6-(4-(2-hydroxyethyl)piperazin-1-yl)-2-methylpyrimidin-4-yl)oxy)-4-phenyl-1,4-dihydroquinoline-3-carbonitriles were synthesized via an efficient multi-component one pot synthesis under mild conditions. These compounds 1-20 were evaluated against human breast cancer cell lines (MCF-7) and human embryonic kidney cells (HEK293) for cytotoxic activities. Among them, compounds 6, 7, 15, 17 and 19 showed better anti-proliferative activities as (IC 50 value 48±1.70, 65±1.13, 92±1.18, 30±1.17 and 16±1.10µM) than curcumin drug (48±1.11µM). Molecular docking was also performed with active compounds 6, 7 and 15 against Bcl-2 protein which gave good binding affinity (ΔG=-9.08, -8.29 and -7.70kcal/mol) respectively. Furthermore, the structure-activity relationship (SAR) analysis revealed that the chromene and quinoline moieties, when attached with pyrimide and piperazine moieties, enhanced anti-proliferative activities. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Novel pyrrole derivatives bearing sulfonamide groups: Synthesis in vitro cytotoxicity evaluation, molecular docking and DFT study (United States)

    Bavadi, Masoumeh; Niknam, Khodabakhsh; Shahraki, Omolbanin


    The synthesis of new derivatives of pyrrole substituted sulfonamide groups is described. The in vitro anticancer activity of these pyrroles was evaluated against MCF7, MOLT-4 and HL-60 cells using MTT assay. The target compounds showed inhibitory activity against tested cell lines. Among the compounds, compound 1a exhibited good cytotoxic activity. The potential of this analog to induce apoptosis was confirmed in a nuclear morphological assay by Hoechst 33258 staining in the PC-12 cells. Finally, molecular docking was performed to determine the probable binding mode of the designed pyrrole derivatives into the active site of FGFR1 protein. DFT calculations were carried out at the B3LYP levels of theory with 6-31+G (d,p) basis set for compound 1a. The point group (C1) of it was obtained based on the optimized structures; the calculation of the FT-IR vibrational frequencies, 1H NMR and 13C NMR chemical shifts of the compound were carried out and compared with those obtained experimentally.

  14. Structural studies on Mycobacterium tuberculosis RecA: Molecular ...

    Indian Academy of Sciences (India)

    Structures of crystals of Mycobacterium tuberculosis RecA, grown and analysed under different conditions, provide insights into hitherto underappreciated details of molecular structure and plasticity. In particular, they yield information on the invariant and variable features of the geometry of the P-loop, whose binding to ATP ...

  15. Molecular dynamics of the structure and thermodynamics of dusty ...

    African Journals Online (AJOL)

    The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...

  16. Metal Oxide Nano structures: Synthesis, Properties, and Applications

    International Nuclear Information System (INIS)

    Xu, L. H.; Patil, D. S.; Yang, J.; Xiao, J.


    In recent years, nano structured materials have attracted wide attention due to their fascinating optical and electrical properties, which make these materials potentially suitable for applications in electronics, optics, photonics, and sensors. Some metal oxides show a wide variety of morphologies such as nano wires, nano rods, nano tubes, nano rings, and nano belts. Synthesis and investigation of these metal-oxide nano structures are beneficial not only for understanding the fundamental phenomena in low dimensional systems, but also for developing new-generation nano devices with high performance.

  17. Structure, Chemical Synthesis, and Biosynthesis of Prodiginine Natural Products. (United States)

    Hu, Dennis X; Withall, David M; Challis, Gregory L; Thomson, Regan J


    The prodiginine family of bacterial alkaloids is a diverse set of heterocyclic natural products that have likely been known to man since antiquity. In more recent times, these alkaloids have been discovered to span a wide range of chemical structures that possess a number of interesting biological activities. This review provides a comprehensive overview of research undertaken toward the isolation and structural elucidation of the prodiginine family of natural products. Additionally, research toward chemical synthesis of the prodiginine alkaloids over the last several decades is extensively reviewed. Finally, the current, evidence-based understanding of the various biosynthetic pathways employed by bacteria to produce prodiginine alkaloids is summarized.

  18. Synthesis of a Molecularly Imprinted Polymer for Dioxin

    Directory of Open Access Journals (Sweden)

    Magda Brattoli


    Full Text Available A molecularly imprinted polymer for recognising selectively 2,3,7,8-tetrachlorodibenzodioxin (TCDD was made by a new non-covalent method employing a“dummy” template. The proposed way represents a simplification of a synthetic schemeproposed by Lübke et al.[1] for covalent imprinting. Comparison of extraction yields of thenovel polymer, a non imprinted polymer and an imprinting polymer, prepared by theoriginal procedure demonstrates the binding capacity of the proposed polymer, which is inprinciple applicable to solid phase extraction (SPE of dioxin.

  19. Molecular Eigensolution Symmetry Analysis and Fine Structure

    Directory of Open Access Journals (Sweden)

    William G. Harter


    Full Text Available Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES. Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES used in Born-Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v, then applied to families of Oh clusters in SF6 spectra and to extreme clusters.

  20. New Hybrid Route to Biomimetic Synthesis

    National Research Council Canada - National Science Library

    Morse, Daniel


    To develop economical low-temperature routes to biomimetic synthesis of high-performance composite materials, with control of composition and structure based on the molecular mechanisms controlling...

  1. Structures of Life: The Role of Molecular Structures in Scientists' Work

    NARCIS (Netherlands)

    Vyas, Dhaval; Kulyk, Olga Anatoliyivna; van der Vet, P.E.; Nijholt, Antinus; van der Veer, Gerrit C.; Jorge, J


    The visual and multidimensional representations like images and graphical structures related to biology provide great insights into understanding the complexities of different organisms. Especially, life scientists use different representations of molecular structures to answer biological questions

  2. Synthesis and the crystal and molecular structures of (H3L . Cl)[CoCl4] and H2L[CuBr4] (L is 2,4,6-Tri(N,N-dimethylamino)methylphenol)

    International Nuclear Information System (INIS)

    Kovalchukova, O. V.; Stash, A. I.; Strashnova, S. B.; Romashkina, E. P.; Zaitsev, B. E.


    The complex compounds (H 3 L . Cl)[CoCl 4 ] (I) and H 2 L[CuBr 4 ] (II), where L is 2,4,6-tri(N,N-dimethylamino)methylphenol, were isolated in the crystalline state and studied by X-ray diffraction. The organic cations were found to be outer-sphere ligands. All three nitrogen atoms of the tertiary amino groups are protonated. In compound I, the H 3 L 3+ cation exists as the cis tautomer. In compound II, the H 2 L 2+ dication exists as the trans isomer. In the crystal structure, the dications are arranged in layers via hydrogen bonds.

  3. Ionization probes of molecular structure and chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, P.M. [State Univ. of New York, Stony Brook (United States)


    Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

  4. Synthesis, X-ray crystal structure and theoretical calculations of antileishmanial neolignan analogues

    International Nuclear Information System (INIS)

    Nascimento, Josenaide P. do; Santos, Lourivaldo S.; Carmo, Maria Carolina L. do; Brasil, Davi S.B.; Alves, Claudio N.; Santos, Regina Helena A.; Tozzo, Erica; Ferreira, Janaina G.


    The synthesis and X-ray crystal diffraction structure of two analogues of neolignans, 2-(4-chlorophenyl)-1-phenylethanone (20) and 2-[(4-chlorophenyl)thio]-1-(3,4-dimethoxyphenyl) propan-1-one (12) is described. The compound 12 presents activity against intracellular Leishmania donovani and Leishmania amazonensis amastigotes that cause cutaneous and visceral leishmaniasis. In addition, the density functional theory (DFT) with the B3LYP hybrid functional was employed to calculate a set of molecular descriptors for nineteen synthetic analogues of neolignans with antileishmanial activities. Afterwards, the stepwise discriminant analysis was performed to investigate possible relationship between the molecular descriptors and biological activities. Through this analysis the compounds were classified into two groups active and inactive according to their degree of biological activities, and the more important properties were charges on some key atoms, electronic affinity and ClogP. (author)

  5. Synthesis, X-ray crystal structure and theoretical calculations of antileishmanial neolignan analogues

    Energy Technology Data Exchange (ETDEWEB)

    Nascimento, Josenaide P. do; Santos, Lourivaldo S.; Carmo, Maria Carolina L. do; Brasil, Davi S.B.; Alves, Claudio N., E-mail: nahum@ufpa.b [Universidade Federal do Para (UFPA), Belem, PA (Brazil). Inst. de Ciencias Exatas e Naturais; Santos, Regina Helena A.; Tozzo, Erica; Ferreira, Janaina G. [Universidade de Sao Paulo (IQSC/USP), Sao Carlos, SP (Brazil). Inst. de Quimica


    The synthesis and X-ray crystal diffraction structure of two analogues of neolignans, 2-(4-chlorophenyl)-1-phenylethanone (20) and 2-[(4-chlorophenyl)thio]-1-(3,4-dimethoxyphenyl) propan-1-one (12) is described. The compound 12 presents activity against intracellular Leishmania donovani and Leishmania amazonensis amastigotes that cause cutaneous and visceral leishmaniasis. In addition, the density functional theory (DFT) with the B3LYP hybrid functional was employed to calculate a set of molecular descriptors for nineteen synthetic analogues of neolignans with antileishmanial activities. Afterwards, the stepwise discriminant analysis was performed to investigate possible relationship between the molecular descriptors and biological activities. Through this analysis the compounds were classified into two groups active and inactive according to their degree of biological activities, and the more important properties were charges on some key atoms, electronic affinity and ClogP. (author)

  6. Crystal and molecular structure of methyl l-glycero-α-d-manno-heptopyranoside, and synthesis of 1→7 linked l-glycero-d-manno-heptobiose and its methyl α-glycoside (United States)

    Artner, Daniel; Stanetty, Christian; Mereiter, Kurt; Zamyatina, Alla; Kosma, Paul


    Methyl l-glycero-α-d-manno-heptopyranoside was synthesized in good yield by a Fischer-type glycosylation of the heptopyranose with methanol in the presence of cation-exchange resin under reflux and microwave conditions, respectively. The compound crystallized from 2-propanol in an orthorhombic lattice of space group P21212 showing a comparatively porous structure with a 2-dimensional O–H⋯O hydrogen bond network. As model compounds for the side chain domains of the inner core structure of bacterial lipopolysaccharide, l-glycero-α-d-manno-heptopyranosyl-(1→7)-l-glycero-d-manno-heptopyranose and the corresponding disaccharide methyl α-glycoside were prepared. The former compound was generated via glycosylation of a benzyl 5,6-dideoxy-hept-5-enofuranoside intermediate followed by catalytic osmylation and deprotection. The latter disaccharide was efficiently synthesized in good yield by a straightforward coupling of an acetylated N-phenyltrifluoroacetimidate heptopyranosyl donor to a methyl 2,3,4,6-tetra-O-acetyl heptopyranoside acceptor derivative followed by Zemplén deacetylation. PMID:21741627

  7. Characterization structural and morphology ZSM-5 zeolite by hydrothermal synthesis

    International Nuclear Information System (INIS)

    Silva, V.J.; Crispim, A.C.; Queiroz, M.B.; Laborde, H.M.; Rodrigues, M.G.F.; Menezes, R.R.


    Solid acids are catalytic materials commonly used in the chemical industry. Among these zeolites are the most important business processes including water treatment, gas separation, and cracking long hydrocarbon chains to produce high octane gasoline. Its synthesis, characterization and applications have been widely studied. The objective this study was to synthesize the ZSM-5 zeolite for future use in separation processes and catalysis. The zeolite ZSM-5 was prepared by hydrothermal synthesis at 170°C, using silica, deionized water and the director of structures (TPABr - tetrapropylammonium bromide). The materials were characterized by X ray diffraction (XRD), scanning electron microscopy (SEM) and semiquantitative chemical analysis by X ray fluorescence (XRF). According to the XRD was possible to observe the formation of ZSM-5 zeolite, with peaks intense and well defined. The SEM showed the formation of individual particles, clean, rounded shapes. (author)

  8. Dihydroazulene Photochromism:Synthesis, Molecular Electronics and Hammett Correlations

    DEFF Research Database (Denmark)

    Broman, Søren Lindbæk

    This thesis describes the development of a versatile synthetic protocol for preparation of a large selection of dihydroazulenes (DHAs) with both electron withdrawing and donating groups. By UV-Vis and NMR spectroscopies and even in a single-molecule junction, their ability to undergo a light......-coupling reactions, systems with either one or two “molecular alligator clips” were prepared. These were studied in solution by UV-Vis absorption spectroscopy and in a single-molecule junction, the latter by the group of Danilov and Kubatkin at the Chalmers University of Technology. A single-molecule device......-reaction (VHF → DHA), studied by UV-Vis absorption spectroscopy. In seven different model systems, the rate of back-reaction was found to obey a Hammett correlation when plotting ln(k) against the appropriate σ-values. These plots were used to estimate the σ-value of substituents which have not yet been...

  9. Sequence-Specific β-Peptide Synthesis by a Rotaxane-Based Molecular Machine. (United States)

    De Bo, Guillaume; Gall, Malcolm A Y; Kitching, Matthew O; Kuschel, Sonja; Leigh, David A; Tetlow, Daniel J; Ward, John W


    We report on the synthesis and operation of a three-barrier, rotaxane-based, artificial molecular machine capable of sequence-specific β-homo (β 3 ) peptide synthesis. The machine utilizes nonproteinogenic β 3 -amino acids, a class of amino acids not generally accepted by the ribosome, particularly consecutively. Successful operation of the machine via native chemical ligation (NCL) demonstrates that even challenging 15- and 19-membered ligation transition states are suitable for information translation using this artificial molecular machine. The peptide-bond-forming catalyst region can be removed from the transcribed peptide by peptidases, artificial and biomachines working in concert to generate a product that cannot be made by either machine alone.

  10. 1-[(3-Aryloxy-3-aryl)propyl]-1H-imidazoles, new imidazoles with potent activity against Candida albicans and dermatophytes. Synthesis, structure-activity relationship, and molecular modeling studies. (United States)

    La Regina, Giuseppe; D'Auria, Felicia Diodata; Tafi, Andrea; Piscitelli, Francesco; Olla, Stefania; Caporuscio, Fabiana; Nencioni, Lucia; Cirilli, Roberto; La Torre, Francesco; De Melo, Nadja Rodrigues; Kelly, Steven L; Lamb, David C; Artico, Marino; Botta, Maurizio; Palamara, Anna Teresa; Silvestri, Romano


    New 1-[(3-aryloxy-3-aryl)propyl]-1 H-imidazoles were synthesized and evaluated against Candida albicans and dermatophytes in order to develop structure-activity relationships (SARs). Against C. albicans the new imidazoles showed minimal inhibitory concentrations (MICs) comparable to those of ketoconazole, miconazole, and econazole, and were more potent than fluconazole. Several derivatives ( 10, 12, 14, 18- 20, 24, 28, 29, 30, and 34) turned out to be potent inhibitors of C. albicans strains resistant to fluconazole, with MIC values less than 10 microg/mL. Against dermatophytes strains, compounds 20, 25, and 33 (MIC

  11. Thermal synthesis of oxide molecular sieve and Mn (K-OMS-2) from K-birnessite obtained from Sol-gel method

    International Nuclear Information System (INIS)

    Rezende, D.S.; Figueira, B.A.M.; Moraes, M.C. de; Silva, L.N. da; Mercury, J.M.R.; Figueiredo, G.P. de


    This study presents the thermal synthesis of molecular sieve with K-OMS2 structure from K-birnessite tunneling process, one Mn oxide with structure in layer. According X-Ray diffraction data it was possible to monitoring the conversion of the layered structure around 550 deg C for (K-OMS-2) tunnel with tetragonal system and I2/m space group. The FTIR main spectrum bands of K-OMS-2 was observed in 700, 525 e 470 cm-1 region and are related to elongation Mn 3+ -O e Mn 4+ -O in the tunnel structure. The product morphology identified by Scanning Electron Microscopy it was verified as pseudo tetragonal, reflecting externally the crystallographic system of cryptomelane structure. The results reveal one simple route for the Mn oxide molecular sieve with K-OMS-2 structure

  12. Synthesis and structural study of platinum group metal complexes ...

    Indian Academy of Sciences (India)

    )Cl]2, [CpRu(PPh3)2Cl] and [Cp∗M(-Cl)Cl]2, respectively, in the presence of NH4PF6. They were characterized by the following techniques viz. IR, NMR, mass spectrometry and UV-visible spectroscopy. The molecular structures of [2] and [7] ...

  13. Synthesis, biological evaluation and molecular docking studies of ...

    African Journals Online (AJOL)

    Compound 4, i.e., 1,3,4-oxadiazole-2-thione and its corresponding Mannich bases (5-17) were subjected to in silico screening as urease inhibitors, using crystal structure of urease (Protein Data Bank ID: 5FSE) as a model enzyme. Furthermore, the targeted compounds were evaluated for their in vitro urease inhibition and ...

  14. The synthesis of 2-iminochromenes using mesoporous molecular sieve MCM-41 as a heterogeneous and recyclable catalyst

    Directory of Open Access Journals (Sweden)

    Majid M. Heravi


    Full Text Available A highly efficient procedure for the synthesis of 2-iminochromenes via condensation of o-hydroxybenzaldehydes and malononitrile using a catalytic amount of mesoporous molecular sieve MCM-41 in good yields is achieved.

  15. A new copper(II) chelate complex with tridentate ligand: Synthesis, crystal and molecular electronic structure of aqua-(diethylenetriamine-N, N‧, N‧‧)-copper(II) sulfate monohydrate and its fire retardant properties (United States)

    Lavrenyuk, H.; Mykhalichko, O.; Zarychta, B.; Olijnyk, V.; Mykhalichko, B.


    The crystals of a new aqua-(diethylenetriamine-N, N‧, N‧‧)-copper(II) sulfate monohydrate have been synthesized by direct interaction of solid copper(II) sulfate pentahydrate with diethylenetriamine (deta). The crystal structure of [Cu(deta)H2O]SO4ṡH2O (1) has been determined by X-ray diffraction methods at 100 K and characterized using X-ray powder diffraction pattern: space group P 1 bar, a = 7.2819(4), b = 8.4669(4), c = 8.7020(3) Å, α = 83.590(3), β = 89.620(4), γ = 84.946(4)°, Z = 2. The environment of the Cu(II) atom is a distorted, elongated square pyramid which consists of three nitrogen atoms of the deta molecule and oxygen atom of the water molecule in the basal plane of the square pyramid (the average lengths of the in-plane Cu-N and Cu-O bonds are 2.00 Å). The apical position of the coordination polyhedron is occupied by complementary oxygen atom of the sulfate anion (the length of the axial Cu-O bond is 2.421(1) Å). The crystal packing is governed by strong hydrogen bonds of O-H⋯O and N-H⋯O types. The ab initio quantum-chemical calculations have been performed by the restricted Hartree-Fock method with a basis set 6-31∗G using the structural data of [Cu(deta)H2O]SO4ṡH2O. It has been ascertained that the degenerate d-orbitals of the Cu2+ ion split under the co-action of both the square-pyramidal coordination and the chelation. It is significant that visually observed crystals color (blue-violet) of the [Cu(deta)H2O]SO4ṡH2O complex is in good agreement with the calculated value of wavelength of visible light (λ = 5735 Å) which is closely related to the energy of the absorbed photon (Δ = 2.161 eV). Furthermore, the stereo-chemical aspect of influence of the CuSO4 upon combustibility of modified epoxy-amine polymers has been scrutinized.

  16. MOSBY: a molecular structure viewer program with portability and extensibility. (United States)

    Ueno, Yutaka; Asai, Kiyoshi


    A molecular structure viewer program, MOSBY has been developed for studies that use atomic coordinates to understand the structures of protein molecules. The program is designed to be portable with a comprehensive user interface by our high-throughput graphics library. In addition, it cooperates with extension modules customized for individual research topics and analysis. For example, an electron density module loads and displays electron density maps derived in X-ray crystallographic analysis superimposed to an atomic model. A molecular dynamics module reads a trajectory file of the results of molecular dynamics calculations and animates the structure. These plug-in modules are devised to function without modification to the MOSBY program. For variations of analysis and calculations with atomic coordinates, the portability and extensibility illustrated by MOSBY play an important rule in scientific computational tools with active software development.

  17. Synthesis and Molecular Structure of the 5-Methoxycarbonylpentyl α-Glycoside of the Upstream, Terminal Moiety of the O-Specific Polysaccharide of Vibrio cholerae O1, Serotype Inaba

    Directory of Open Access Journals (Sweden)

    Peng Xu


    Full Text Available The trimethylsilyl trifluoromethanesulfonate (TMSOTf-catalyzed reaction of methyl 6-hydroxyhexanoate with 3-O-benzyl-4-(2,4-di-O-acetyl-3-deoxy-L-glycero-tetronamido-4,6-dideoxy-2-O-levulinoyl-α-d-mannopyranosyl trichloroacetimidate followed by a two-step deprotection (hydrogenolysis over Pd/C catalyst and Zemplén deacylation, to simultaneously remove the acetyl and levulinoyl groups gave 5-(methoxycarbonylpentyl 4-(3-deoxy-L-glycero-tetronamido-4,6-dideoxy-α-D-mannopyranoside. The structure of the latter, for which crystals were obtained in the analytically pure state for the first time, followed from its NMR and high-resolution mass spectra and was confirmed by X-ray crystallography. The molecule has two approximately linear components; a line through the aglycon intersects a line through the mannosyl and tetronylamido groups at 120°. The crystal packing separates the aglycon groups from the tetronylamido and mannosyl groups, with only C-H…O hydrogen bonding among the aglycon groups and N-H…O, O-H…O and C-H…O links among the tetronylamido and mannosyl groups. A carbonyl oxygen atom accepts the strongest O-H…O hydrogen bond and two strong C-H…O hydrogen bonds. The geometric properties were compared with those of related molecules.

  18. Molecular structures guide the engineering of chromatin. (United States)

    Tekel, Stefan J; Haynes, Karmella A


    Chromatin is a system of proteins, RNA, and DNA that interact with each other to organize and regulate genetic information within eukaryotic nuclei. Chromatin proteins carry out essential functions: packing DNA during cell division, partitioning DNA into sub-regions within the nucleus, and controlling levels of gene expression. There is a growing interest in manipulating chromatin dynamics for applications in medicine and agriculture. Progress in this area requires the identification of design rules for the chromatin system. Here, we focus on the relationship between the physical structure and function of chromatin proteins. We discuss key research that has elucidated the intrinsic properties of chromatin proteins and how this information informs design rules for synthetic systems. Recent work demonstrates that chromatin-derived peptide motifs are portable and in some cases can be customized to alter their function. Finally, we present a workflow for fusion protein design and discuss best practices for engineering chromatin to assist scientists in advancing the field of synthetic epigenetics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Structural and molecular hair abnormalities in trichothiodystrophy. (United States)

    Liang, Christine; Morris, Andrea; Schlücker, Sebastian; Imoto, Kyoko; Price, Vera H; Menefee, Emory; Wincovitch, Stephen M; Levin, Ira W; Tamura, Deborah; Strehle, Katrin R; Kraemer, Kenneth H; DiGiovanna, John J


    We examined hair from 15 patients with trichothiodystrophy (TTD), a rare inherited disorder with brittle, cystine-deficient hair. They had a wide variety of phenotypes, from brittle hair only to severe intellectual impairment and developmental delay. Polarizing light microscopic examination showed alternating light and dark (tiger tail) bands under polarizing microscopy. Confocal microscopy captured structural features of breaks in intact TTD hairs. The autofluorescent appearance was regular and smooth in normal donors and markedly irregular in sections of TTD hairs possibly reflecting abnormalities in melanin distribution. Scanning electron microscopy revealed numerous surface irregularities. All TTD hair samples had reduced sulfur content. We observed an inverse correlation (R(val)=0.9) between sulfur content and percent of hairs with shaft abnormalities (trichoschisis, trichorrhexis nodosa, or ribbon/twist). There was no association between clinical disease severity and percent of abnormal hairs. Raman spectra of hairs from TTD patients and normal donors revealed a larger contribution of energetically less favored disulfide conformers in TTD hairs. Our data indicate that the brittleness of the TTD hair is dependent upon abnormalities at several levels of organization. These changes make TTD hairs excessively prone to breakage and weathering.

  20. RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity. (United States)

    Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng


    Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via:

  1. Electronic structure of molecular Rydberg states of some small molecules and molecular ion

    International Nuclear Information System (INIS)

    Sun Biao; Li Jiaming


    Based on an independent-particle-approximation (i.e. the multiple scattering self-consistent-field theory), the electronic structures of Rydberg states of the small diatomic molecules H 2 , He 2 and the He 2 + molecular ion were studied. The principal quantum number of the first state of the Rydberg series is determined from a convention of the limit of the molecular electronic configuration. The dynamics of the excited molecules and molecular ion has been elucidated. The theoretical results are in fair agreement with the existing experimental measurements, thus they can serve as a reliable basis for future refined treatment such as the configuration interaction calculation

  2. Nonlinear excitations in two-dimensional molecular structures with impurities

    DEFF Research Database (Denmark)

    Gaididei, Yuri Borisovich; Rasmussen, Kim; Christiansen, Peter Leth


    We study the nonlinear dynamics of electronic excitations interacting with acoustic phonons in two-dimensional molecular structures with impurities. We show that the problem is reduced to the nonlinear Schrodinger equation with a varying coefficient. The latter represents the influence of the imp......We study the nonlinear dynamics of electronic excitations interacting with acoustic phonons in two-dimensional molecular structures with impurities. We show that the problem is reduced to the nonlinear Schrodinger equation with a varying coefficient. The latter represents the influence...... excitations. Analytical results are in good agreement with numerical simulations of the nonlinear Schrodinger equation....

  3. Synthesis of carbon nano structures by plasma discharge

    International Nuclear Information System (INIS)

    Jimenez L, M.L.


    Due to the great quantity of applications of carbon neocarcinostatin (NEC) in diverse areas like: synthesis of super-resistant materials, hydrogen storage, nano sensors generation and nano catalysts, one has seen the necessity to generate new synthesis processes of these materials as well as to already improve those existent. The present work has as objective to optimize the NEC synthesis process by means of the electric arc method which uses alternating current to high frequencies (HF), obtaining relatively clean products; that is to say, it hardly presents amorphous material neither impurities. They stand out the obtaining of carbon nano fibers (NFC) by means of a luminescent-arc discharge, in a gas mixture He-CH 4 with 34% at.Ni/10.32%at.Y like catalyst; to a frequency of 42 k Hz and low power (300 W). This method benefits the agglomeration of the particles in both electrodes due to the high frequencies. The time of duration of the process oscillates between 5 and 20 minutes. The obtained product was characterized by scanning electron microscopy (MEB), transmission electron microscopy (MET) to determine the type of obtained NEC and by X-ray diffraction analysis and Raman spectroscopy to determine the purity of the samples. The NFC are relatively free of amorphous coal. The surface and structural analysis indicates that the fibers have a half diameter of 80 nm. It is also made, a study by optical emission spectroscopy of the plasma using the Swan band to determine the temperature. (Author)

  4. Molecular structure of dextran sulphate sodium in aqueous environment (United States)

    Yu, Miao; Every, Hayley A.; Jiskoot, Wim; Witkamp, Geert-Jan; Buijs, Wim


    Here we propose a 3D-molecular structural model for dextran sulphate sodium (DSS) in a neutral aqueous environment based on the results of a molecular modelling study. The DSS structure is dominated by the stereochemistry of the 1,6-linked α-glucose units and the presence of two sulphate groups on each α-glucose unit. The structure of DSS can be best described as a helix with various patterns of di-sulphate substitution on the glucose rings. The presence of a side chain does not alter the 3D-structure of the linear main chain much, but affects the overall spatial dimension of the polymer. The simulated polymers have a diameter similar to or in some cases even larger than model α-hemolysin nano-pores for macromolecule transport in many biological processes, indicating a size-limited translocation through such pores. All results of the molecular modelling study are in line with previously reported experimental data. This study establishes the three-dimensional structure of DSS and summarizes the spatial dimension of the polymer, serving as the basis for a better understanding on the molecular level of DSS-involved electrostatic interaction processes with biological components like proteins and cell pores.

  5. The extended evolutionary synthesis: its structure, assumptions and predictions. (United States)

    Laland, Kevin N; Uller, Tobias; Feldman, Marcus W; Sterelny, Kim; Müller, Gerd B; Moczek, Armin; Jablonka, Eva; Odling-Smee, John


    Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology. © 2015 The Author(s).

  6. The extended evolutionary synthesis: its structure, assumptions and predictions (United States)

    Laland, Kevin N.; Uller, Tobias; Feldman, Marcus W.; Sterelny, Kim; Müller, Gerd B.; Moczek, Armin; Jablonka, Eva; Odling-Smee, John


    Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology. PMID:26246559

  7. Nanohashtag structures based on carbon nanotubes and molecular linkers (United States)

    Frye, Connor W.; Rybolt, Thomas R.


    Molecular mechanics was used to study the noncovalent interactions between single-walled carbon nanotubes and molecular linkers. Groups of nanotubes have the tendency to form tight, parallel bundles (||||). Molecular linkers were introduced into our models to stabilize nanostructures with carbon nanotubes held in perpendicular orientations. Molecular mechanics makes it possible to estimate the strength of noncovalent interactions holding these structures together and to calculate the overall binding energy of the structures. A set of linkers were designed and built around a 1,3,5,7-cyclooctatetraene tether with two corannulene containing pincers that extend in opposite directions from the central cyclooctatetraene portion. Each pincer consists of a pairs of "arms." These molecular linkers were modified so that the "hand" portions of each pair of "arms" could close together to grab and hold two carbon nanotubes in a perpendicular arrangement. To illustrate the possibility of more complicated and open perpendicular CNTs structures, our primary goal was to create a model of a nanohashtag (#) CNT conformation that is more stable than any parallel CNT arrangements with bound linker molecules forming clumps of CNTs and linkers in non-hashtag arrangements. This goal was achieved using a molecular linker (C280H96) that utilizes van der Waals interactions to two perpendicular oriented CNTs. Hydrogen bonding was then added between linker molecules to augment the stability of the hashtag structure. In the hashtag structure with hydrogen bonding, four (5,5) CNTs of length 4.46 nm (18 rings) and four linkers (C276H92N8O8) stabilized the hashtag so that the average binding energy per pincer was 118 kcal/mol.

  8. A General Chemistry Experiment Incorporating Synthesis and Structural Determination (United States)

    van Ryswyk, Hal


    An experiment for the general chemistry laboratory is described wherein gas chromatography-mass spectroscopy (GC-MS) and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) are used to characterize the products of a series of microscale reactions on vanillin. A single sophisticated instrument can be incorporated into the laboratory given sufficient attention to the use of sampling accessories and software macros. Synthetic experiments coupled with modern instrumental techniques can be used in the general chemistry laboratory to illustrate the concepts of synthesis, structure, bonding, and spectroscopy.

  9. Synthesis and Structural Analysis of Polyester Prodrugs of Norfloxacin

    Directory of Open Access Journals (Sweden)

    Waclaw Kolodziejski


    Full Text Available Two-, three- and four-arm, star-shaped poly(ε-caprolactone andpoly(D,L-lactide homopolymers, and copolymers of ε-caprolactone with D,L-lactide weresynthesized via ring-opening polymerization of cyclic esters in the presence of glycerol,penthaerythritol and poly(ethylene glycol as initiators and stannous octoate as a catalyst.Thus obtained oligomers were successfully used in the synthesis of novel macromolecularprodrugs of norfloxacin. The structures of the polymers and prodrugs were elucidated bymeans of MALDI-TOF MS, NMR and IR studies.

  10. Synthesis of resorcinolic lipids bearing structural similarities to cytosporone A

    Directory of Open Access Journals (Sweden)

    Edson dos Anjos dos Santos


    Full Text Available Inspired by the structure and biological activities of resorcinolic lipids and, particularly cytosporone A- a potent inhibitor of plantule germination and growth, we have performed the synthesis of the analogs 3-heptyl-3-hydroxy-5,7-dimethoxy-2-benzofuran-1(3H-one (1 and 3-heptyl-3-hydroxy-4,6-dimethoxy-2-benzofuran-1(3H-one (2. The intermediates and products were submitted to allelopathic test using Lactuca sativa L. seeds. Target compound 1 showed an inhibitory effect on germination and growth of hypocotyl and radicle in milimolar range.

  11. Synthesis of resorcinolic lipids bearing structural similarities to cytosporone A

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Edson dos Anjos dos; Beatriz, Adilson; Lima, Denis Pires de [Universidade Federal Mato Grosso do Sul (UFMS), Campo Grande, MS (Brazil). Centro de Ciencias Exatas e Tecnologia. Dept. de Quimica], e-mail:; Marques, Maria Rita; Leite, Carla Braga [Universidade Federal Mato Grosso do Sul (UFMS), Campo Grande, MS (Brazil). Centro de Ciencias Biologicas. Dept. de Morfofisiologia


    Inspired by the structure and biological activities of resorcinolic lipids and, particularly cytosporone A- a potent inhibitor of plantule germination and growth, we have performed the synthesis of the analogs 3-heptyl-3-hydroxy-5,7-dimethoxy-2-benzofuran-1(3H)-one (1) and 3-heptyl-3-hydroxy-4,6-dimethoxy-2-benzofuran-1(3H)-one (2). The intermediates and products were submitted to allelopathic test using Lactuca sativa L. seeds. Target compound 1 showed an inhibitory effect on germination and growth of hypocotyl and radicle in millimolar range. (author)

  12. Synthesis of gold nanoparticles with different atomistic structural characteristics

    International Nuclear Information System (INIS)

    Esparza, R.; Rosas, G.; Lopez Fuentes, M.; Sanchez Ramirez, J.F.; Pal, U.; Ascencio, J.A.; Perez, R.


    A chemical reduction method was used to produce nanometric gold particles. Depending on the concentration of the main reactant compound different nanometric sizes and consequently different atomic structural configurations of the particles are obtained. Insights on the structural nature of the gold nanoparticles are obtained through a comparison between digitally-processed experimental high-resolution electron microscopy images and theoretically-simulated images obtained with a multislice approach of the dynamical theory of electron diffraction. Quantum molecular mechanical calculations, based on density functional theory, are carried out to explain the relationships between the stability of the gold nanoparticles, the atomic structural configurations and the size of nanoparticles

  13. Synthesis and reforming of high molecular-weigth compounds by the utilization of radiation

    International Nuclear Information System (INIS)

    Machi, Sueo


    Radiation effects on the synthesis are reforming of high molecular-weight compounds are reviewed. The report is divided into four main parts. The first part deals with the characteristics of the radiation processing. The reaction can be started in a wide range of temperature including very low temperature. Catalysts are unnecessary. The reaction velocity is fast, and the reaction in solid phase can be started uniformly. And the quality of products is well controllable. The second part deals with the synthesis of high molecular-weight compounds by radiation polymerization. Radical polymerization and ionizing polymerization, gas phase and liquid phase polymerization, the polymerization and copolymerization of fluorine-containing monomers, and solid phase polymerization and low temperature polymerization are included in this part. Attention is directed to the continuous production system for the radiation polymerization of ethylene developed by Japan Atomic Energy Research Institute. The third part deals with the reforming of high molecular-weight compounds by radiation graft polymerization. The combination of backbone polymers and monomers for reforming plastics and fibers, the membranes for reverse osmosis, porous membranes, and ion exchange membranes are included. The fourth part deals with the reforming of high molecular-weight compounds by the cross-linking. Polyethylene, PVC, ethyl acrylate copolymer and the like are included. (Iwakiri, K.)

  14. Synthesis, biological activity and solution structure of new analogues of the antimicrobial Gramicidin S. (United States)

    Kamysz, Elżbieta; Mickiewicz, Beata; Kamysz, Wojciech; Bielińska, Sylwia; Rodziewicz-Motowidło, Sylwia; Ciarkowski, Jerzy


    Gramicidin S (GS) is a cyclo-decapeptide antibiotic isolated from Bacillus brevis. The structural studies have shown that GS forms a two-stranded antiparallel β-sheet imposed by two II' β-turns. Despite its wide Gram+ and Gram- antimicrobial spectrum, GS is useless in therapy because of its high hemotoxicity in humans. It was found, however, that the analogues of GS-14 (GS with 14 amino acid residues) attained a better antimicrobial selectivity when their amphipatic moments were perturbed. In this study, we report effects of similar perturbations imposed on GS cyclo-decapeptide analogues. Having solved their structures by NMR/molecular dynamics and having tested their activities/selectivities, we have concluded that the idea of perturbation of the amphipatic moment does not work for GS-10_0 analogues. An innovative approach to the synthesis of head-to-tail cyclopeptides was used. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.

  15. Design, synthesis, and cocrystal structure of a nonpeptide Src SH2 domain ligand. (United States)

    Plummer, M S; Holland, D R; Shahripour, A; Lunney, E A; Fergus, J H; Marks, J S; McConnell, P; Mueller, W T; Sawyer, T K


    The specific association of an SH2 domain with a phosphotyrosine (pTyr)-containing sequence of another protein precipitates a cascade of intracellular molecular interactions (signals) which effect a wide range of intracellular processes. The nonreceptor tyrosine kinase Src, which has been associated with breast cancer and osteoporosis, contains an SH2 domain. Inhibition of Src SH2-phosphoprotein interactions by small molecules will aid biological proof-of-concept studies which may lead to the development of novel therapeutic agents. Structure-based design efforts have focused on reducing the size and charge of Src SH2 ligands while increasing their ability to penetrate cells and reach the intracellular Src SH2 domain target. In this report we describe the synthesis, binding affinity, and Src SH2 cocrystal structure of a small, novel, nonpeptide, urea-containing SH2 domain ligand.

  16. Synthesis and structural determination of twisted MoS2 nanotubes

    International Nuclear Information System (INIS)

    Santiago, P.; Schabes-Retchkiman, P.; Ascencio, J.A.; Mendoza, D.; Perez-Alvarez, M.; Espinosa, A.; Reza-SanGerman, C.; Camacho-Bragado, G.A.; Jose-Yacaman, M.


    In the present work we report the synthesis of MoS 2 nanotubes with diameters greater than 10 nm using a template method. The length and properties of these nanotubes are a direct result of the preparation method. High-resolution transmission electron microscopy is used to study the structure of these highly curved entities. Molecular dynamics simulations of MoS 2 nanotubes reveal that one of the stable forms of the nanotubes is a twisted one. The twisting of the nanotubes produces a characteristic contrast in the images, which is also studied using simulation methods. The analysis of the local contrast close to the perpendicular orientation shows geometrical arrays of dots in domain-like structures, which are demonstrated to be a product of the atomic overlapping of irregular curvatures in the nanotubes. The configuration of some of the experimentally obtained nanotubes is demonstrated to be twisted with a behavior suggesting partial plasticity. (orig.)

  17. Molecular structure and elastic properties of thermotropic liquid crystals: Integrated molecular dynamics—Statistical mechanical theory vs molecular field approach (United States)

    Capar, M. Ilk; Nar, A.; Ferrarini, A.; Frezza, E.; Greco, C.; Zakharov, A. V.; Vakulenko, A. A.


    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

  18. Structural Sizing of the EDIN0620 Body Components Using the APAS Structural Synthesis Computer Program (United States)

    Nolte, W. E.


    The use of a structural synthesis computer program to design components for a heavy lift launch vehicle is defined. A loads program was used to determine the vehicle shears, bending moments, and axial loads at two design loading conditions. A comparison was made between results from the structures program and the results of a weight estimating program which used historical data in determining component weights.

  19. Fluid structure and molecular interaction of acetophenone derivatives

    Indian Academy of Sciences (India)

    pp. 1129-1137. Fluid structure and molecular interaction of acetophenone derivatives. K K GUPTA and P J sINGH. Department of Physics, Government MSJ (PG) College, Bharatpur 321 001, India. E-mail: MS received 4 June 2003; revised 2 January 2004; accepted 2 January 2004. Abstract.

  20. Molecular cloning, sequence analysis and structure prediction of the ...

    African Journals Online (AJOL)

    Molecular cloning, sequence analysis and structure prediction of the related to b 0,+ amino acid transporter (rBAT) in Cyprinus carpio L. ... The amplified product was 2370 bp, including a 42 bp 5'-untranslated region, a 288 bp 3'-untranslated region, and a 2040 bp open reading frame (ORF), which encoded 679 amino acids ...

  1. Molecular conformation and liquid structure of 2-propanol through ...

    Indian Academy of Sciences (India)

    neutron diffraction data [12]. 3. Method of analysis. 3.1 General background. In the following paragraph we present the extraction of total neutron molecular structure .... carbon and oxygen contributions and important information about the hydrogen positions ... the hydroxyl group OD1 is at a staggered position, as expected.

  2. Molecular structure and DFT investigations on new cobalt(II ...

    Indian Academy of Sciences (India)

    Sci. Vol. 127, No. 12, December 2015, pp. 2137–2149. c Indian Academy of Sciences. DOI 10.1007/s12039-015-0976-x. Molecular structure and DFT investigations on new cobalt(II) chloride complex with superbase guanidine type ligand. SAIED M SOLIMANa,b,∗, MORSY A M ABU-YOUSSEFb,∗. , JΦRG ALBERINGc and.

  3. Variational cellular model of the molecular and crystal electronic structure

    International Nuclear Information System (INIS)

    Ferreira, L.G.; Leite, J.R.


    A variational version of the cellular method is developed to calculate the electronic structure of molecules and crystals. Due to the simplicity of the secular equation, the method is easy to be implemented. Preliminary calculations on the hydrogen molecular ion suggest that it is also accurate and of fast convergence [pt

  4. Molecular tailoring approach for exploring structures, energetics and ...

    Indian Academy of Sciences (India)


    4,5 proposed a density matrix divide-and-conquer (DC) method for electronic structure calculation of large molecules. The method is based on partitioning the density matrix and is applicable to both HF and DFT level of theories. Subsequently, Gadre et al. 6 formulated the. Molecular Tailoring Approach (MTA) for evaluating.

  5. Learning Molecular Structures in a Tangible Augmented Reality Environment (United States)

    Asai, Kikuo; Takase, Norio


    This article presents the characteristics of using a tangible table top environment produced by augmented reality (AR), aimed at improving the environment in which learners observe three-dimensional molecular structures. The authors perform two evaluation experiments. A performance test for a user interface demonstrates that learners with a…

  6. Molecular epidemiology and population structure of bovine Streptococcus uberis

    DEFF Research Database (Denmark)

    Rato, M G; Bexiga, R; Nunes, S F


    The molecular epidemiology and population structure of 30 bovine subclinical mastitis field isolates of Streptococcus uberis, collected from 6 Portuguese herds (among 12 farms screened) during 2002 and 2003, were examined by using pulsed-field gel electrophoresis (PFGE) for clustering of the isol...

  7. Molecular conformation and liquid structure of 2-propanol through ...

    Indian Academy of Sciences (India)

    The neutron diffraction data analysis of deuterated liquid 2-propanol at room temperature to define its molecular conformation is presented. 2-Propanol being a large molecule with twelve atomic sites, the conformation analysis is tricky and an improved method of data analysis is given. The intermolecular structural ...

  8. Density functional studies of molecular structures of N-methyl ...

    Indian Academy of Sciences (India)

    Density functional theory was applied to the calculation of molecular structures of N-methyl formamide (NMF), N,N-dimethyl formamide (DMF), and N,Ndimethyl acetamide (DMA). DFT calculations on NMF, DMF, and DMA were performed using a combination of the local functional of Vosko, Wilk, and Nusair (VWN) with the ...

  9. Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

    DEFF Research Database (Denmark)

    Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens


    2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v anthr...

  10. Structural changes in polytetrafluoroethylene molecular chains upon sliding against steel

    NARCIS (Netherlands)

    Shen, J.T.; Pei, Y.T.; Hosson, J.Th.M. De

    In this work, the influence of dry sliding between a steel counterpart ball and polytetrafluoroethylene (PTFE) plate sample on the transformation of PTFE molecular structure is investigated. With X-ray diffraction, differential scanning calorimetry, Fourier transform infrared (FT-IR) spectroscopy

  11. Structure of hydrogenated amorphous silicon from ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Buda, F. (Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, Ohio (USA)); Chiarotti, G.L. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Laboratorio Tecnologie Avanzate Superfici e Catalisi del Consorzio Interuniversitario Nazionale di Fisica della Materia, Padriciano 99, I-34012 Trieste (Italy)); Car, R. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Institut Romard de Recherche Numerique en Physique des Materiaux, CH-1015 Lausanne, Switzerland Department of Condensed Matter Physics, University of Geneva, CH-1211 Geneva (Switzerland)); Parrinello, M. (IBM Research Division, Zurich Research Laboratory, CH-8803 Rueschlikon (Switzerland))


    We have generated a model of hydrogenated amorphous silicon by first-principles molecular dynamics. Our results are in good agreement with the available experimental data and provide new insight into the microscopic structure of this material. The calculation lends support to models in which monohydride complexes are prevalent, and indicates a strong tendency of hydrogen to form small clusters.

  12. Exploring antioxidant reactivity and molecular structure of phenols ...

    Indian Academy of Sciences (India)



    Jul 11, 2017 ... Abstract. Phenolic compounds can be considered as the most important bioactive compounds in Mediterranean diet. However, many of the complex connections between phenols antioxidant reactivity and their molecular structure remain unsolved. To shine light on these issues, the antioxidant reactivity of ...

  13. Exploring antioxidant reactivity and molecular structure of phenols ...

    Indian Academy of Sciences (India)

    Phenolic compounds can be considered as themost important bioactive compounds in Mediterranean diet. However, many of the complex connections between phenols antioxidant reactivity and their molecular structure remain unsolved. To shine light on these issues, the antioxidant reactivity of 15 relevant phenolic ...

  14. Synthesis of Carbon nano structures by plasma discharge

    International Nuclear Information System (INIS)

    Jimenez L, M.L.


    Due to the great quantity of applications of the carbon nano structures (NEC) in diverse areas like: synthesis of super-resistant materials, hydrogen storage, nano sensors generation and nano catalysts, it has seen the necessity to generate new processes of synthesis of this materials as well as to already improve those existent. The present work has as objective to optimize the NEC synthesis process by means of the electric arc method which uses alternating current to high frequencies (HF), obtaining relatively clean products; that is to say, it hardly presents amorphous material neither sludges. They stand out the obtaining of carbon nano fibers (NFC) by means of a luminescent-arch discharge, in a gas mixture of He-CH 4 with 34% at. Ni/10.32% at.Y like catalyst; at a frequency of 42 kHz and low power (300 W). This method benefits the amass of the particles in both electrodes due to the high frequencies. The time of duration of the process oscillates between 5 and 20 minutes. The obtained product was characterized by scanning electron microscopy (MEB), transmission electron microscopy (MET) to determine the NEC type obtained and by X-ray diffraction analysis and Raman spectroscopy for determining the purity of the samples. The NFC is relatively free of amorphous coal. The surface and structural analysis indicates that the fibers have a half diameter of 80 nm. It is also made, a study by optical emission spectroscopy of plasma using the Swan band for determining the temperature. (Author)

  15. A diversity oriented synthesis of natural product inspired molecular libraries. (United States)

    Chauhan, Jyoti; Luthra, Tania; Gundla, Rambabu; Ferraro, Antonio; Holzgrabe, Ulrike; Sen, Subhabrata


    Natural products are the source of innumerable pharmaceutical drug candidates and also form an important aspect of herbal remedies. They are also a source of various bioactive compounds. Herein we have leveraged the structural attributes of several natural products in building a library of architecturally diverse chiral molecules by harnessing R-tryptophan as the chiral auxiliary. It is converted to its corresponding methyl ester 1 which in turn provided a bevy of 1-aryl-tetrahydro-β-carbolines 2a-d, which were then converted to chiral compounds via a diversity oriented synthetic strategy (DOS). In general, intermolecular and intramolecular ring rearrangements facilitated the formation of the final compounds. Four different classes of molecules with distinct architectures were generated, adding up to nearly twenty-two individual molecules. Phenotypic screening of a representative section of the library revealed two molecules that selectively inhibit MCF7 breast cancer cells with IC 50 of ∼5 μg mL -1 potency.

  16. Cambridge Structural Database as a tool for studies of general structural features of organic molecular crystals

    International Nuclear Information System (INIS)

    Kuleshova, Lyudmila N; Antipin, Mikhail Yu


    The review surveys and generalises data on the use of the Cambridge Structural Database (CSD) for studying and revealing general structural features of organic molecular crystals. It is demonstrated that software and facilities of the CSD allow one to test the applicability of a number of known concepts of organic crystal chemistry (the principle of close packing, the frequency of occurrence of space groups, the preferred formation of centrosymmetrical molecular crystals, etc.) on the basis of abundant statistical data. Examples of the use of the Cambridge Structural Database in engineering of molecular crystals and in the systematic search for compounds with specified properties are given. The bibliography includes 122 references.

  17. Synthesis and molecular structure of manganese complexes with ...

    Indian Academy of Sciences (India)


    bResearch Laboratory of Resources Utilization, Tokyo Institute of. Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226 8503, Japan. Manganese-dioxygen complexes are assumed to play significant roles in physiologically important enzymatic reactions including superoxide dismutation, decomposition of hydrogen ...

  18. Synthesis, structure and biological properties of active spirohydantoin derivatives

    Directory of Open Access Journals (Sweden)

    Lazić Anita M.


    Full Text Available Spirohidantoins represent an pharmacologically important class of heterocycles since many derivatives have been recognized that display interesting activities against a wide range of biological targets. First synthesis of cycloalkanespiro-5-hydantoins was performed by Bucherer and Lieb 1934 by the reaction of cycloalkanone, potassium cyanide and ammonium-carbonate at reflux in a mixture of ethanol and water. QSAR (Quantitative Structure-Activity Relationship studies showed that a wide range of biological activities of spirohydantoin derivatives strongly depend upon their structure. This paper describes different methods of synthesis of spirohydantoin derivatives, their physico-chemical properties and biological activity. It emphasizes the importance of cycloalkanespiro-5-hydantoins with anticonvulsant, antiproliferative, antipsychotic, antimicrobial and antiinflammatory properties as well as their importance in the treatment of diabetes. Numerous spirohydantoin compounds exhibit physiological activity such as serotonin and fibrinogen antagonist, inhibitors of the glycine binding site of the NMDA receptor also, antagonist of leukocyte cell adhesion, acting as allosteric inhibitors of the protein-protein interactions. Some spirohydantoin derivatives have been identified as antitumor agents. Their activity depends on the substituent presented at position N-3 of the hydantoin ring and increases in order alkene > ester > ether. Besides that, compounds that contain two electron withdrawing groups (e.g. fluorine or chlorine on the third and fourth position of the phenyl ring are better antitumor agents than compounds with a single electron withdrawing group. [Projekat Ministarstva nauke Republike Srbije, br. 172013

  19. Synthesis, Structure, and Properties of Refractory Hard-Metal Borides (United States)

    Lech, Andrew Thomas

    As the limits of what can be achieved with conventional hard compounds, such as tungsten carbide, are nearing reach, super-hard materials are an area of increasing industrial interest. The refractory hard metal borides, such as ReB2 and WB4, offer an increasingly attractive alternative to diamond and cubic boron nitride as a next-generation tool material. In this Thesis, a thorough discussion is made of the progress achieved by our laboratory towards understanding the synthesis, structure, and properties of these extremely hard compounds. Particular emphasis is placed on structural manipulation, solid solution formation, and the unique crystallographic manifestations of what might also be called "super-hard metals".

  20. Physiochemical Characteristics and Molecular Structures for Digestible Carbohydrates of Silages. (United States)

    Refat, Basim; Prates, Luciana L; Khan, Nazir A; Lei, Yaogeng; Christensen, David A; McKinnon, John J; Yu, Peiqiang


    The main objectives of this study were (1) to assess the magnitude of differences among new barley silage varieties (BS) selected for varying rates of in vitro neutral detergent fiber (NDF) digestibility (ivNDFD; Cowboy BS with higher ivNDFD, Copeland BS with intermediate ivNDFD, and Xena BS with lower ivNDFD) with regard to their carbohydrate (CHO) molecular makeup, CHO chemical fractions, and rumen degradability in dairy cows in comparison with a new corn silage hybrid (Pioneer 7213R) and (2) to quantify the strength and pattern of association between the molecular structures and digestibility of carbohydrates. The carbohydrate-related molecular structure spectral data was measured using advanced vibrational molecular spectroscopy (FT/IR). In comparison to BS, corn silage showed a significantly (P carbohydrates were significantly (P carbohydrate content of the silages. In conclusion, the univariate approach with only one-factor consideration (ivNDFD) might not be a satisfactory method for evaluating and ranking BS quality. FT/IR molecular spectroscopy can be used to evaluate silage quality rapidly, particularly the digestible fiber content.

  1. A Scalable Synthesis Pathway to Nanoporous Metal Structures. (United States)

    Coaty, Christopher; Zhou, Hongyao; Liu, Haodong; Liu, Ping


    A variety of nanoporous transition metals, Fe, Co, Au, Cu, and others, have been readily formed by a scalable, room-temperature synthesis process. Metal halide compounds are reacted with organolithium reductants in a nonpolar solvent to form metal/lithium halide nanocomposites. The lithium halide is then dissolved out of the nanocomposite with a common organic solvent, leaving behind a continuous, three-dimensional network of metal filaments that form a nanoporous structure. This approach is applicable to both noble metals (Cu, Au, Ag) and less-noble transition metals (Co, Fe, Ni). The microstructures of these nanoporous transition metals are tunable, as controlling the formation of the metal structure in the nanocomposite dictates the final metal structure. Microscopy studies and nitrogen adsorption analysis show these materials form pores ranging from 2 to 50 nm with specific surface areas from 1.0 m 2 /g to 160 m 2 /g. Our analysis also shows that pore size, pore volume, and filament size of the nanoporous metal networks depend on the mobility of target metal and the amount of lithium halide produced by the conversion reaction. Further, it has been demonstrated that hybrid nanoporous structures of two or more metals could be synthesized by performing the same process on mixtures of precursor compounds. Metals (e.g., Co and Cu) have been found to stabilize each other in nanoporous forms, resulting in smaller pore sizes and higher surface areas than each element in their pure forms. This scalable and versatile synthesis pathway greatly expands our access to additional compositions and microstructures of nanoporous metals.

  2. Molecular Cloud Structures and Massive Star Formation in N159 (United States)

    Nayak, O.; Meixner, M.; Fukui, Y.; Tachihara, K.; Onishi, T.; Saigo, K.; Tokuda, K.; Harada, R.


    The N159 star-forming region is one of the most massive giant molecular clouds (GMCs) in the Large Magellanic Cloud (LMC). We show the 12CO, 13CO, CS molecular gas lines observed with ALMA in N159 west (N159W) and N159 east (N159E). We relate the structure of the gas clumps to the properties of 24 massive young stellar objects (YSOs) that include 10 newly identified YSOs based on our search. We use dendrogram analysis to identify properties of the molecular clumps, such as flux, mass, linewidth, size, and virial parameter. We relate the YSO properties to the molecular gas properties. We find that the CS gas clumps have a steeper size–linewidth relation than the 12CO or 13CO gas clumps. This larger slope could potentially occur if the CS gas is tracing shocks. The virial parameters of the 13CO gas clumps in N159W and N159E are low (energy distribution type in comparison to the YSO candidates in N159W. These differences lead us to conclude that the giant molecular cloud complex in N159E is more evolved than the giant molecular cloud complex in N159W.

  3. Extracting Structure Parameters of Dimers for Molecular Tunneling Ionization Model (United States)

    Zhao, Song-Feng; Huang, Fang; Wang, Guo-Li; Zhou, Xiao-Xin


    We determine structure parameters of the highest occupied molecular orbital (HOMO) of 27 dimers for the molecular tunneling ionization (so called MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402]. The molecular wave functions with correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials which are numerically created using the density functional theory. We examine the alignment-dependent tunneling ionization probabilities from MO-ADK model for several molecules by comparing with the molecular strong-field approximation (MO-SFA) calculations. We show the molecular Perelomov–Popov–Terent'ev (MO-PPT) can successfully give the laser wavelength dependence of ionization rates (or probabilities). Based on the MO-PPT model, two diatomic molecules having valence orbital with antibonding systems (i.e., Cl2, Ne2) show strong ionization suppression when compared with their corresponding closest companion atoms. Supported by National Natural Science Foundation of China under Grant Nos. 11164025, 11264036, 11465016, 11364038, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001, and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  4. Synthesis, characterization, x-ray structure and antimicrobial activity ...

    African Journals Online (AJOL)

    intermolecular N3—H1N1•••O1 hydrogen bonds. (Table 2), resulting in the formation of zigzag layers lying parallel to (100) (Fig. 2b). The existence of π•••π interactions involving the centroid of the N4/C9-C13 pyridine ring (π•••π distance = 3.5108(18) Å) further stabilize the molecular packing. The structure of compound 2.

  5. Template-directed synthesis of kinetically and thermodynamically stable molecular necklace using ring closing metathesis. (United States)

    Dasgupta, Suvankar; Wu, Jishan


    We report the template-directed synthesis of a well-defined, kinetically stable [5]molecular necklace with dialkylammonium ion (R(2)NH(2)(+)) as recognition site and DB24C8 as macrocycle. A thread containing four dialkylammonium ions with olefin at both ends was first synthesized and then subjected to threading with an excess amount of DB24C8 to form pseudo[5]rotaxane, which in situ undergoes ring closing metathesis at the termini with second generation Grubbs catalyst to yield the desired [5]molecular necklace. The successful synthesis of [5]molecular necklace is mainly attributed to the self-assembly and dynamic covalent chemistry which allows the formation of thermodynamically most stable product. The self-assembly of the DB24C8 ring onto the recognition site known as templating effect was driven by noncovalent stabilizing interactions like [N(+)-H···O], [C-H···O] hydrogen bonds as well as [π···π] interactions which is facilitated in non-polar solvents. The reversible nature of olefin metathesis reaction makes it suitable for dynamic covalent chemistry since proof-reading and error-checking operates until it generates thermodynamically the most stable interlocked molecule. Riding on the success of [5]molecular necklace, we went a step further and attempted to synthesize [7]molecular necklace using the same protocol. This led to the synthesis of another thread with olefin at both ends but having six dibenzylammonium ions along the thread. However, the extremely poor solubility of this thread containing six secondary ammonium ions limits the self-assembly process even after we replaced the typical PF(6)(-) counter anion with a more lipophilic BPh(4)(-) anion. Although the poor solubility of the thread remains the bottleneck for making higher order molecular necklaces yet this approach of "threading-followed-by-ring-closing-metathesis" for the first time produces kinetically and thermodynamically stable, well-defined, homogeneous molecular necklace which

  6. Building bridges between cellular and molecular structural biology. (United States)

    Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J


    The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

  7. Design of Carborane Molecular Architectures via Electronic Structure Computations

    International Nuclear Information System (INIS)

    Oliva, J.M.; Serrano-Andres, L.; Klein, D.J.; Schleyer, P.V.R.; Mich, J.


    Quantum-mechanical electronic structure computations were employed to explore initial steps towards a comprehensive design of poly carborane architectures through assembly of molecular units. Aspects considered were (i) the striking modification of geometrical parameters through substitution, (ii) endohedral carboranes and proposed ejection mechanisms for energy/ion/atom/energy storage/transport, (iii) the excited state character in single and dimeric molecular units, and (iv) higher architectural constructs. A goal of this work is to find optimal architectures where atom/ion/energy/spin transport within carborane superclusters is feasible in order to modernize and improve future photo energy processes.

  8. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron. (United States)

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip


    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons.

  9. Biomimetic synthesis of ordered silica structures mediated by block copolypeptides. (United States)

    Cha, J N; Stucky, G D; Morse, D E; Deming, T J


    In biological systems such as diatoms and sponges, the formation of solid silica structures with precisely controlled morphologies is directed by proteins and polysaccharides and occurs in water at neutral pH and ambient temperature. Laboratory methods, in contrast, have to rely on extreme pH conditions and/or surfactants to induce the condensation of silica precursors into specific morphologies or patterned structures. This contrast in processing conditions and the growing demand for benign synthesis methods that minimize adverse environmental effects have spurred much interest in biomimetic approaches in materials science. The recent demonstration that silicatein-a protein found in the silica spicules of the sponge Tethya aurantia--can hydrolyse and condense the precursor molecule tetraethoxysilane to form silica structures with controlled shapes at ambient conditions seems particularly promising in this context. Here we describe synthetic cysteine-lysine block copolypeptides that mimic the properties of silicatein: the copolypeptides self-assemble into structured aggregates that hydrolyse tetraethoxysilane while simultaneously directing the formation of ordered silica morphologies. We find that oxidation of the cysteine sulphydryl groups, which is known to affect the assembly of the block copolypeptide, allows us to produce different structures: hard silica spheres and well-defined columns of amorphous silica are produced using the fully reduced and the oxidized forms of the copolymer, respectively.

  10. Photocatalytic Properties of Nb/MCM-41 Molecular Sieves: Effect of the Synthesis Conditions

    Directory of Open Access Journals (Sweden)

    Caterine Daza Gomez


    Full Text Available The effect of synthesis conditions and niobium incorporation levels on the photocatalytic properties of Nb/MCM-41 molecular sieves was assessed. Niobium pentoxide supported on MCM-41 mesoporous silica was obtained using two methods: sol-gel and incipient impregnation, in each case also varying the percentage of niobium incorporation. The synthesized Nb-MCM-41 ceramic powders were characterized using the spectroscopic techniques of infrared spectroscopy (IR, Raman spectroscopy, X-ray diffraction (XRD, and transmission electron microscopy (TEM. The photodegradation capacity of the powders was studied using the organic molecule, methylene blue. The effect of both the method of synthesis and the percentage of niobium present in the sample on the photodegradation action of the solids was determined. The mesoporous Nb-MCM-41 that produced the greatest photodegradation response was obtained using the sol-gel method and 20% niobium incorporation.

  11. Optimisation of the synthesis of vancomycin-selective molecularly imprinted polymer nanoparticles using automatic photoreactor (United States)

    Muzyka, Kateryna; Karim, Khalku; Guerreiro, Antonio; Poma, Alessandro; Piletsky, Sergey


    A novel optimized protocol for solid-state synthesis of molecularly imprinted polymer nanoparticles (nanoMIPs) with specificity for antibiotic vancomycin is described. The experimental objective was optimization of the synthesis parameters (factors) affecting the yield of obtained nanoparticles which have been synthesized using the first prototype of an automated solid-phase synthesizer. Applications of experimental design (or design of experiments) in optimization of nanoMIP yield were carried out using MODDE 9.0 software. The factors chosen in the model were the amount of functional monomers in the polymerization mixture, irradiation time, temperature during polymerization, and elution temperature. In general, it could be concluded that the irradiation time is the most important and the temperature was the least important factor which influences the yield of nanoparticles. Overall, the response surface methodology proved to be an effective tool in reducing time required for optimization of complex experimental conditions.

  12. Molecular cloning and expression of Corynebacterium glutamicum genes for amino acid synthesis in Escherichia coli cells

    International Nuclear Information System (INIS)

    Beskrovnaya, O.Yu.; Fonshtein, M.Yu.; Kolibaba, L.G.; Yankovskii, N.K.; Debabov, V.G.


    Molecular cloning of Corynebacterium glutamicum genes for threonine and lysine synthesis has been done in Escherichia coli cells. The clonal library of EcoRI fragments of chromosomal DNA of C. glutamicum was constructed on the plasmid vector λpSL5. The genes for threonine and lysine synthesis were identified by complementation of E. coli mutations in thrB and lysA genes, respectively. Recombinant plasmids, isolated from independent ThrB + clone have a common 4.1-kb long EcoRI DNA fragment. Hybrid plasmids isolated from LysA + transductants of E. coli have common 2.2 and 3.3 kb long EcoRI fragments of C. glutamicum DNA. The hybrid plasmids consistently transduced the markers thrB + and lysA + . The Southern hybridization analysis showed that the cloned DNA fragments hybridized with the fragments of identical length in C. glutamicum chromosomes

  13. Synthesis and application of magnetic molecularly imprinted polymers in sample preparation. (United States)

    Huang, Shuyao; Xu, Jianqiao; Zheng, Jiating; Zhu, Fang; Xie, Lijun; Ouyang, Gangfeng


    Magnetic molecularly imprinted polymers (MMIPs) have superior advantages in sample pretreatment because of their high selectivity for target analytes and the fast and easy isolation from samples. To meet the demand of both good magnetic property and good extraction performance, MMIPs with various structures, from traditional core-shell structures to novel composite structures with a larger specific surface area and more accessible binding sites, are fabricated by different preparation technologies. Moreover, as the molecularly imprinted polymer (MIP) layers determine the affinity, selectivity, and saturated adsorption amount of MMIPs, the development and innovation of the MIP layer are attracting attention and are reviewed here. Many studies that used MMIPs as sorbents in dispersive solid-phase extraction of complex samples, including environmental, food, and biofluid samples, are summarized. Graphical abstract The application of magnetic molecularly imprinted polymers (MIPs) in the sample preparation procedure improves the analytical performances for complex samples. MITs molecular imprinting technologies.

  14. Analysis of molecular mechanisms of ATP synthesis from the standpoint of the principle of electrical neutrality. (United States)

    Nath, Sunil


    Theories of biological energy coupling in oxidative phosphorylation (OX PHOS) and photophosphorylation (PHOTO PHOS) are reviewed and applied to ATP synthesis by an experimental system containing purified ATP synthase reconstituted into liposomes. The theories are critically evaluated from the standpoint of the principle of electrical neutrality. It is shown that the obligatory requirement to maintain overall electroneutrality of bulk aqueous phases imposes strong constraints on possible theories of energy coupling and molecular mechanisms of ATP synthesis. Mitchell's chemiosmotic theory is found to violate the electroneutrality of bulk aqueous phases and is shown to be untenable on these grounds. Purely electroneutral mechanisms or mechanisms where the anion/countercation gradient is dissipated or simply flows through the lipid bilayer are also shown to be inadequate. A dynamically electrogenic but overall electroneutral mode of ion transport postulated by Nath's torsional mechanism of energy transduction and ATP synthesis is shown to be consistent both with the experimental findings and the principle of electrical neutrality. It is concluded that the ATP synthase functions as a proton-dicarboxylic acid anion cotransporter in OX PHOS or PHOTO PHOS. A logical chemical explanation for the selection of dicarboxylic acids as intermediates in OX PHOS and PHOTO PHOS is suggested based on the pioneering classical thermodynamic work of Christensen, Izatt, and Hansen. The nonequilibrium thermodynamic consequences for theories in which the protons originate from water vis-a-vis weak organic acids are compared and contrasted, and several new mechanistic and thermodynamic insights into biological energy transduction by ATP synthase are offered. These considerations make the new theory of energy coupling more complete, and lead to a deeper understanding of the molecular mechanism of ATP synthesis. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Control of molecular weight distribution in synthesis of poly(2-hydroxyethyl methacrylate) using ultrasonic irradiation. (United States)

    Kubo, Masaki; Kondo, Takayuki; Matsui, Hideki; Shibasaki-Kitakawa, Naomi; Yonemoto, Toshikuni


    Poly(2-hydroxyethyl methacrylate) (PHEMA) was synthesized using ultrasonic irradiation without any chemical initiator. The effect of the ultrasonic power intensity on the time course of the conversion to polymer, the number average molecular weight, and the polydispersity were investigated in order to synthesize a polymer with a low molecular weight distribution (i.e., low polydispersity). The conversion to polymer increased with time. A higher ultrasonic power intensity resulted in a faster reaction rate. The number average molecular weight increased during the early stage of the reaction and then gradually decreased with time. A higher ultrasonic intensity resulted in a faster degradation rate of the polymer. The polydispersity decreased with time. This was because the degradation rate of a polymer with a higher molecular weight was faster than that of a polymer with a lower molecular weight. A polydispersity below 1.3 was obtained under ultrasonic irradiation. By changing the ultrasonic power intensity during the reaction, the number average molecular weight can be controlled while maintaining low polydispersity. When the ultrasonic irradiation was halted, the reactions stopped and the number average molecular weight and polydispersity did not change. On the basis of the experimental results, a kinetic model for synthesis of PHEMA under ultrasonic irradiation was constructed considering both polymerization and polymer degradation. The kinetic model was in good agreement with the experimental results for the time courses of the conversion to polymer, the number average molecular weight, and the polydispersity for various ultrasonic power intensities. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Facile synthesis of gold nanomaterials with unusual crystal structures. (United States)

    Fan, Zhanxi; Huang, Xiao; Chen, Ye; Huang, Wei; Zhang, Hua


    Gold (Au) nanomaterials have attracted wide research attention, owing to their high chemical stability, promising catalytic properties, excellent biocompatibility, unique electronic structure and outstanding localized surface plasmon resonance (LSPR) absorption properties; all of which are closely related to their size and shape. Recently, crystal-phase-controlled synthesis of noble metal nanomaterials has emerged as a promising strategy to tune their physicochemical properties. This protocol describes the detailed experimental procedures for the crystal-phase-controlled syntheses of Au nanomaterials with unusual crystal structures under mild conditions. Briefly, pure hexagonal close-packed (hcp) Au square sheets (AuSSs) with a thickness of ∼2.4 nm are synthesized using a graphene-oxide-assisted method in which HAuCl 4 is reduced by oleylamine in a mixture of hexane and ethanol. By using pure hexane as the solvent, well-dispersed ultrathin hcp/face-centered cubic (fcc) Au nanowires with a diameter of ∼1.6 nm on graphene oxide can be obtained. Meanwhile, hcp/fcc Au square-like plates with a side length of 200-400 nm are prepared via the secondary growth of Au on the hcp AuSSs. Remarkably, hexagonal (4H) Au nanoribbons with a thickness of 2.0-6.0 nm can be synthesized with a one-pot colloidal method in which HAuCl 4 is reduced by oleylamine in a mixed solvent of hexane and 1,2-dichloropropane. It takes 17-37 h for the synthesis of these Au nanomaterials with unusual crystal structures. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) are used to characterize the resultant Au nanomaterials, which could have many promising applications, such as biosensing, near-IR photothermal therapy, catalysis and surface-enhanced Raman scattering (SERS).

  17. Structural and Molecular Modeling Features of P2X Receptors

    Directory of Open Access Journals (Sweden)

    Luiz Anastacio Alves


    Full Text Available Currently, adenosine 5'-triphosphate (ATP is recognized as the extracellular messenger that acts through P2 receptors. P2 receptors are divided into two subtypes: P2Y metabotropic receptors and P2X ionotropic receptors, both of which are found in virtually all mammalian cell types studied. Due to the difficulty in studying membrane protein structures by X-ray crystallography or NMR techniques, there is little information about these structures available in the literature. Two structures of the P2X4 receptor in truncated form have been solved by crystallography. Molecular modeling has proven to be an excellent tool for studying ionotropic receptors. Recently, modeling studies carried out on P2X receptors have advanced our knowledge of the P2X receptor structure-function relationships. This review presents a brief history of ion channel structural studies and shows how modeling approaches can be used to address relevant questions about P2X receptors.

  18. Synthesis and crystal structure of chromium-bearing anhydrous wadsleyite (United States)

    Sirotkina, E. A.; Bindi, L.; Bobrov, A. V.; Aksenov, S. M.; Irifune, T.


    A chromium-bearing wadsleyite (Cr- Wad) was synthesized in the model system Mg2SiO4-MgCr2O4 at 14 GPa and 1600 °C and studied from the chemical and structural point of views. Microprobe data gave the formula Mg1.930Cr0.120Si0.945O4, on the basis of 4 oxygen atoms. The crystal structure has been studied by single-crystal X-ray diffraction. The orthorhombic unit-cell parameters are: a = 5.6909(5) Å, b = 11.4640(10) Å, c = 8.2406(9) Å, V = 537.62(9) Å3, Z = 8. The structure, space group Imma, was refined to R 1 = 5.99% in anisotropic approximation using 1135 reflections with F o > 4σ( F o) and 43 parameters. Chromium was found to substitute for both Mg at the octahedral sites and Si at the tetrahedral site, according to the reaction VIMg2+ + IVSi4+ = VICr3+ + IVCr3+. On the whole, the structural topology is nearly identical to that of pure wadsleyite. The successful synthesis of Cr- Wad may be important for the thermobarometry of mantle phase associations.

  19. Catalytic Synthesis of n-Butyl Oleate by Cerium Complex Doped Y/SBA-15 Composite Molecular Sieve (United States)

    Shi, Chunwei; Bian, Xue; Wu, Yongfu; Cong, Yufeng; Pei, Mingyuan


    Cerium ion was successfully incorporated into Y/SBA-15 micro-mesoporous molecular sieves via the hydrothermal synthesis method to give a series of composite materials. The prepared materials were thoroughly characterized using Fourier transform infrared spectroscopy (FT-IR), X-ray fluorescence spectroscopy (XRF), scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS) and differential thermo gravimetric analysis (TG-DTG). The results showed that the prepared composite materials retained the highly ordered mesoporous two-dimensional hexagonal structure of SBA-15 and the octagonal structure of Y. The catalyst Ce-Y/SBA-15 was prepared and characterized, then the esterification of n-butanol and oleic acid was studied with bismuth phosphotungstate as a catalyst. Using this model reaction, the effects of Ce-HY/SBA-15, molar ratio of alcohol to oleic acid, amount of catalysts, reaction time and reaction temperature were investigated. The experimental results show that the optimal reaction conditions were: 1.8:1 molar ratio of alcohol to acid, 5 % catalyst amount (based on weight of oleic acid), 4 h reaction time and reflux conditions. Under these conditions, the yield of esterification was 90.6 %. The results suggest that the addition of Ce can effectively improve the catalytic properties of composite molecular sieves.

  20. Library synthesis, screening, and discovery of modified Zinc(II)-Bis(dipicolylamine) probe for enhanced molecular imaging of cell death. (United States)

    Plaunt, Adam J; Harmatys, Kara M; Wolter, William R; Suckow, Mark A; Smith, Bradley D


    Zinc(II)-bis(dipicolylamine) (Zn-BDPA) coordination complexes selectively target the surfaces of dead and dying mammalian cells, and they have promise as molecular probes for imaging cell death. A necessary step toward eventual clinical imaging applications is the development of next-generation Zn-BDPA complexes with enhanced affinity for the cell death membrane biomarker, phosphatidylserine (PS). This study employed an iterative cycle of library synthesis and screening, using a novel rapid equilibrium dialysis assay, to discover a modified Zn-BDPA structure with high and selective affinity for vesicles containing PS. The lead structure was converted into a deep-red fluorescent probe and its targeting and imaging performance was compared with an unmodified control Zn-BDPA probe. The evaluation process included a series of FRET-based vesicle titration studies, cell microscopy experiments, and rat tumor biodistribution measurements. In all cases, the modified probe exhibited comparatively higher affinity and selectivity for the target membranes of dead and dying cells. The results show that this next-generation deep-red fluorescent Zn-BDPA probe is well suited for preclinical molecular imaging of cell death in cell cultures and animal models. Furthermore, it should be possible to substitute the deep-red fluorophore with alternative reporter groups that enable clinically useful, deep-tissue imaging modalities, such as MRI and nuclear imaging.

  1. Molecular modeling of nucleic Acid structure: electrostatics and solvation. (United States)

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E


    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. Copyright © 2014 John Wiley & Sons, Inc.

  2. Molecular Differentiated Initiator Reactivity in the Synthesis of Poly(caprolactone-Based Hydrophobic Homopolymer and Amphiphilic Core Corona Star Polymers

    Directory of Open Access Journals (Sweden)

    Eileen Deng


    Full Text Available Macromolecules that possess three-dimensional, branched molecular structures are of great interest because they exhibit significantly differentiated application performance compared to conventional linear (straight chain polymers. This paper reports the synthesis of 3- and 4-arm star branched polymers via ring opening polymerisation (ROP utilising multi-functional hydroxyl initiators and Sn(Oct2 as precatalyst. The structures produced include mono-functional hydrophobic and multi-functional amphiphilic core corona stars. The characteristics of the synthetic process were shown to be principally dependent upon the physical/dielectric properties of the initiators used. ROP’s using initiators that were more available to become directly involved with the Sn(Oct2 in the “in-situ” formation of the true catalytic species were observed to require shorter reaction times. Use of microwave heating (MWH in homopolymer star synthesis reduced reaction times compared to conventional heating (CH equivalents, this was attributed to an increased rate of “in-situ” catalyst formation. However, in amphiphilic core corona star formation, the MWH polymerisations exhibited slower propagation rates than CH equivalents. This was attributed to macro-structuring within the reaction medium, which reduced the potential for reaction. It was concluded that CH experiments were less affected by this macro-structuring because it was disrupted by the thermal currents/gradients caused by the conductive/convective heating mechanisms. These gradients are much reduced/absent with MWH because it selectively heats specific species simultaneously throughout the entire volume of the reaction medium. These partitioning problems were overcome by introducing additional quantities of the species that had been determined to selectively heat.

  3. Molecular Differentiated Initiator Reactivity in the Synthesis of Poly(caprolactone)-Based Hydrophobic Homopolymer and Amphiphilic Core Corona Star Polymers. (United States)

    Deng, Eileen; Nguyen, Nam T; Hild, Frédéric; Hamilton, Ian E; Dimitrakis, Georgios; Kingman, Samuel W; Lau, Phei-Li; Irvine, Derek J


    Macromolecules that possess three-dimensional, branched molecular structures are of great interest because they exhibit significantly differentiated application performance compared to conventional linear (straight chain) polymers. This paper reports the synthesis of 3- and 4-arm star branched polymers via ring opening polymerisation (ROP) utilising multi-functional hydroxyl initiators and Sn(Oct)2 as precatalyst. The structures produced include mono-functional hydrophobic and multi-functional amphiphilic core corona stars. The characteristics of the synthetic process were shown to be principally dependent upon the physical/dielectric properties of the initiators used. ROP's using initiators that were more available to become directly involved with the Sn(Oct)₂ in the "in-situ" formation of the true catalytic species were observed to require shorter reaction times. Use of microwave heating (MWH) in homopolymer star synthesis reduced reaction times compared to conventional heating (CH) equivalents, this was attributed to an increased rate of "in-situ" catalyst formation. However, in amphiphilic core corona star formation, the MWH polymerisations exhibited slower propagation rates than CH equivalents. This was attributed to macro-structuring within the reaction medium, which reduced the potential for reaction. It was concluded that CH experiments were less affected by this macro-structuring because it was disrupted by the thermal currents/gradients caused by the conductive/convective heating mechanisms. These gradients are much reduced/absent with MWH because it selectively heats specific species simultaneously throughout the entire volume of the reaction medium. These partitioning problems were overcome by introducing additional quantities of the species that had been determined to selectively heat.

  4. Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

    DEFF Research Database (Denmark)

    Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens


    2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v...... anthralin, the description of the vibrational structure of the compound is thus complicated by the circumstance that moment directions for transitions polarized perpendicular to the C2 axis (z) are not uniquely determined by symmetry, but can take any direction in the xy plane. The molecular vibrations...... of DHBP were investigated by IR polarization spectroscopy on samples aligned in stretched polyethylene. The observed Linear Dichroic (LD) absorbance curves, corresponding to absorbance measured with the electric vector of the sample beam parallel (U) and perpendicular (V) to the stretching direction, were...

  5. VPAC receptors: structure, molecular pharmacology and interaction with accessory proteins. (United States)

    Couvineau, Alain; Laburthe, Marc


    The vasoactive intestinal peptide (VIP) is a neuropeptide with wide distribution in both central and peripheral nervous systems, where it plays important regulatory role in many physiological processes. VIP displays a large biological functions including regulation of exocrine secretions, hormone release, fetal development, immune responses, etc. VIP appears to exert beneficial effect in neuro-degenerative and inflammatory diseases. The mechanism of action of VIP implicates two subtypes of receptors (VPAC1 and VPAC2), which are members of class B receptors belonging to the super-family of GPCR. This article reviews the current knowledge regarding the structure and molecular pharmacology of VPAC receptors. The structure-function relationship of VPAC1 receptor has been extensively studied, allowing to understand the molecular basis for receptor affinity, specificity, desensitization and coupling to adenylyl cyclase. Those studies have clearly demonstrated the crucial role of the N-terminal ectodomain (N-ted) of VPAC1 receptor in VIP recognition. By using different approaches including directed mutagenesis, photoaffinity labelling, NMR, molecular modelling and molecular dynamic simulation, it has been shown that the VIP molecule interacts with the N-ted of VPAC1 receptor, which is itself structured as a 'Sushi' domain. VPAC1 receptor also interacts with a few accessory proteins that play a role in cell signalling of receptors. Recent advances in the structural characterization of VPAC receptor and more generally of class B GPCRs will lead to the design of new molecules, which could have considerable interest for the treatment of inflammatory and neuro-degenerative diseases. © 2011 The Authors. British Journal of Pharmacology © 2011 The British Pharmacological Society.

  6. Exponential Repulsion Improves Structural Predictability of Molecular Docking

    Czech Academy of Sciences Publication Activity Database

    Bazgier, Václav; Berka, K.; Otyepka, M.; Banáš, P.


    Roč. 37, č. 28 (2016), s. 2485-2494 ISSN 0192-8651 Institutional support: RVO:61389030 Keywords : cyclin-dependent kinases * structure-based design * scoring functions * cdk2 inhibitors * force-field * ligand interactions * drug discovery * purine * potent * protein-kinase-2 * molecular docking * dock 6.6 * drug design * cyclin-dependent kinase 2 * directory of decoys Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.229, year: 2016

  7. Invariant molecular-dynamics approach to structural phase transitions

    International Nuclear Information System (INIS)

    Wentzcovitch, R.M.


    Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

  8. Theoretical study on the molecular and crystal structures of nitrogen ...

    Indian Academy of Sciences (India)

    The molecular and crystal structure of the adduct NF3·BF3 was studied computationally using density functional theory. It shows that the adduct exists in the form of a complex but is not ionic. The heats of formation in the gas and the condensed phase of the adduct are −1266.09 and −1276.37 kJ·mol−1, respectively, which ...

  9. Fused 1,2,3-Dithiazoles: Convenient Synthesis, Structural Characterization, and Electrochemical Properties

    Directory of Open Access Journals (Sweden)

    Lidia S. Konstantinova


    Full Text Available A new general protocol for synthesis of fused 1,2,3-dithiazoles by the reaction of cyclic oximes with S2Cl2 and pyridine in acetonitrile has been developed. The target 1,2,3-dithiazoles fused with various carbocycles, such as indene, naphthalenone, cyclohexadienone, cyclopentadiene, and benzoannulene, were selectively obtained in low to high yields. In most cases, the hetero ring-closure was accompanied by chlorination of the carbocyclic moieties. With naphthalenone derivatives, a novel dithiazole rearrangement (15→13 featuring unexpected movement of the dithiazole ring from α- to β-position, with respect to keto group, was discovered. Molecular structure of 4-chloro-5H-naphtho[1,2-d][1,2,3]dithiazol-5-one 13 was confirmed by single-crystal X-ray diffraction. Electrochemical properties of 13 were studied by cyclic voltammetry and a complex behavior was observed, most likely including hydrodechlorination at a low potential.

  10. Synthesis and evaluation of molecular rotors with large and bulky tert-butyldiphenylsilyloxy-substituted trityl stators. (United States)

    Arcos-Ramos, Rafael; Rodríguez-Molina, Braulio; Romero, Margarita; Méndez-Stivalet, J Manuel; Ochoa, María Eugenia; Ramírez-Montes, Pedro I; Santillan, Rosa; Garcia-Garibay, Miguel A; Farfán, Norberto


    The search for voluminous stators that may accommodate large rotator units and speed rotational dynamics in the solid state led us to investigate a simple and efficient method for the synthesis of molecular rotors with tert-butyldiphenylsilyl-protected (TBDPS) triphenylmethyl stators. Additionally, solid state characterization of these systems with two-, four-, and six-TBDPS groups provided us with a description of their crystallinity and thermal stability. Among them, molecular rotor 7c with the largest and most symmetric stator resulting from six peripheral silyl groups showed the best tendency to crystallize, and the study of its isotopologue 7c-d(4) by solid state (2)H NMR revealed a 2-fold motion of the 1,4-diethynylphenylene-d(4) rotator in the kHz regime.

  11. Using photoelectron diffraction to determine complex molecular adsorption structures

    International Nuclear Information System (INIS)

    Woodruff, D P


    Backscattering photoelectron diffraction, particularly in the energy-scan mode, is now an established technique for determining in a quantitative fashion the local structure of adsorbates on surfaces, and has been used successfully for ∼100 adsorbate phases. The elemental and chemical-state specificity afforded by the characteristic core level photoelectron binding energies means that it has particular advantages for molecular adsorbates, as the local geometry of inequivalent atoms in the molecule can be determined in a largely independent fashion. On the other hand, polyatomic molecules present a general problem for all methods of surface structure determination in that a mismatch of intramolecular distances with interatomic distances on the substrate surface means that the atoms in the adsorbed molecule are generally in low-symmetry sites. The quantities measured experimentally then represent an incoherent sum of the properties of each structural domain that is inequivalent with respect to the substrate point group symmetry. This typically leads to greater ambiguity or precision in the structural solutions. The basic principles of the method are described and illustrated with a simple example involving molecule/substrate bonding through only one constituent atom (TiO 2 -(110)/H 2 O). This example demonstrates the importance of obtaining quantitative local structural information. Further examples illustrate both the successes and the problems of this approach when applied to somewhat more complex molecular adsorbates.

  12. Synthesis and structural studies of copper sulfide nanocrystals

    Directory of Open Access Journals (Sweden)

    Peter A. Ajibade

    Full Text Available We report the synthesis and structural studies of copper sulfide nanocrystals from copper(II dithiocarbamate single molecule precursors. The optical studies of the as-prepared copper sulfide nanoparticles were carried out using UV–Visible and photoluminescence spectroscopy. The absorption spectra show absorption band edges at 287 nm and exhibit considerable blue shift that could be ascribed to the quantum confinement effects as a result of the small crystallite sizes of the nanoparticles and the photoluminescence spectra show emission curves that are red shifted with respect to the absorption band edges. The structural studies were carried out using powder X-ray diffraction, transmission electron microscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy and atomic force microscopy. The XRD patterns revealed the formation of hexagonal structure of covellite CuS with estimated crystallite sizes of 17.3–18.6 nm. The TEM images showed particles with almost spherical or rod shapes with average crystallite sizes of 3–9.8 nm. SEM images showed morphology with ball-like microsphere on the surfaces and EDS spectra confirmed the presence of CuS nanoparticles. Keywords: CuS, Dithiocarbamate, Nanoparticles, Electron microscopy, AFM

  13. Structural modeling and molecular dynamics simulation of the actin filament. (United States)

    Splettstoesser, Thomas; Holmes, Kenneth C; Noé, Frank; Smith, Jeremy C


    Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized. Copyright © 2011 Wiley-Liss, Inc.

  14. Synthesis, Structure, Stability and Redispersion of Gold-based Nanoparticles (United States)

    Tiruvalam, Ram Chandra

    Nanoscale gold has been shown to possess an intriguing combination of unexpected optical, photochemical and catalytic properties. The ability to control the size, shape, morphology, composition and dispersion of gold-based nanostructures is key to optimizing their performance for nanotechnology applications. The advanced electron microscopy studies described in this thesis analyze three important aspects of gold and gold-palladium alloy nanoparticles: namely, (i) the ability to synthesize gold nanoparticles of controlled size and shape in an aqueous medium; (ii) the colloidal preparation of designer gold-palladium alloys for selective oxidation catalysis; and (iii) the ability to disperse gold as finely and homogeneously as possible on a metal oxide or carbon support. The ability to exploit the nanoscale properties of gold for various engineering applications often depends on our ability to control size and shape of the nanoscale entity by careful manipulation of the synthesis parameters. We have explored an aqueous based synthesis route, using oleylamine as both a reductant and surfactant, for preparing gold nanostructures. By systematically varying synthesis parameters such as oleylamine concentration, reaction temperature, and aging time it is possible to identify processing regimens that generate Au nanostructures having either pseudo-spherical, faceted polyhedral, nanostar or wire shaped morphologies. Furthermore, by quenching the reaction partway through it is possible to create a class of metastable Au-containing structures such as nanocubes, nanoboxes and nanowires. Possible formation mechanisms for these gold based nano-objects are discussed. There is a growing interest in using supported bimetallic AuPd alloy nanoparticles for selective oxidation reactions. In this study, a systematic series of size controlled AuPd bimetallic particles have been prepared by colloidal synthesis methods. Particles having random alloy structures, as well as `designer

  15. Synthesis and Binding Ability of Molecular Probes Based on a Phenanthroline Derivative: Theory and Experiment

    Directory of Open Access Journals (Sweden)

    Xuefang Shang


    Full Text Available A fluorescent and colorimetric molecular probe containing phenol groups has been designed and synthesized. The anion binding ability was evaluated for biolgically important anions (F−, Cl−, Br−, I−, AcO− and H2PO4− by theoretical investigation, UV-Vis and fluorescence spectroscopy and 1H-NMR titration experiments. Results indicated the probe showed strong binding ability for H2PO4− without the interference of other anions tested and the interaction process was accompanied by color changes. Theoretical investigation analysis revealed that intramolecular hydrogen bonds existed in the structure of the probe and the roles of molecular frontier orbitals in molecular interplay were determined.

  16. Solid-Phase Synthesis of Molecularly Imprinted Polymer Nanoparticles with a Reusable Template - "Plastic Antibodies". (United States)

    Poma, Alessandro; Guerreiro, Antonio; Whitcombe, Michael J; Piletska, Elena V; Turner, Anthony P F; Piletsky, Sergey A


    Molecularly Imprinted Polymers (MIPs) are generic alternatives to antibodies in sensors, diagnostics and separations. To displace biomolecules without radical changes in infrastructure in device manufacture, MIPs should share their characteristics (solubility, size, specificity and affinity, localized binding domain) whilst maintaining the advantages of MIPs (low-cost, short development time and high stability) hence the interest in MIP nanoparticles. Herein we report a reusable solid-phase template approach (fully compatible with automation) for the synthesis of MIP nanoparticles and their precise manufacture using a prototype automated UV photochemical reactor. Batches of nanoparticles (30-400 nm) with narrow size distributions imprinted with: melamine (d = 60 nm, K d = 6.3 × 10 -8 m), vancomycin (d = 250 nm, K d = 3.4 × 10 -9 m), a peptide (d = 350 nm, K d = 4.8 × 10 -8 m) and proteins have been produced. Our instrument uses a column packed with glass beads, bearing the template. Process parameters are under computer control, requiring minimal manual intervention. For the first time we demonstrate the reliable re-use of molecular templates in the synthesis of MIPs (≥ 30 batches of nanoMIPs without loss of performance). NanoMIPs are produced template-free and the solid-phase acts both as template and affinity separation medium.

  17. Synthesis of Disentangled Ultra-High Molecular Weight Polyethylene: Influence of Reaction Medium on Material Properties

    Directory of Open Access Journals (Sweden)

    Giuseppe Forte


    Full Text Available The polymerization of ethylene to Ultra-High Molecular Weight Polyethylene (UHMWPE in certain reaction conditions allows synthesis of nascent powders with a considerably lower amount of entanglements: the material obtained is of great interest from both academic and industrial viewpoints. From an academic point of view, it is interesting to follow the evolution of the metastable melt state with the progressive entanglements formation. Industrially, it is valuable to have a solvent-free processing route for the production of high modulus, high strength tapes. Since the polymer synthesis is performed in the presence of a solvent, it is interesting to investigate the influence that the reaction medium can have on the catalyst activity, resultant molecular characteristics, and polymer morphology at the macroscopic as wells as microscopic level. In this paper, we present the effect that two typical polymerization solvents, toluene and heptane, and mixtures of them, have on the catalytic performance and on the polymer properties. The observations are that an unexpected increase of catalyst activity, accompanied by a significant improvement in mechanical properties, is found when using a carefully chosen mixture of solvents. A tentative explanation is given on the basis of the presented results.

  18. Synthesis of cerium oxide catalysts supported on MCM-41 molecular sieve

    International Nuclear Information System (INIS)

    Souza, E.L.S.; Barros, T.R.B.; Sousa, B.V. de


    Porous materials have been widely studied as catalysts and catalyst support. The MCM-41 structure is the one that has been most studied because of its application possibilities in chemical processes. This work aimed to obtain and characterize cerium oxide catalysts supported on MCM-41 molecular sieve. The molecular sieve was synthesized by the conventional method with the following molar composition: 1 SiO2: 0.30 CTABr: NH3 11: 144 H2O. Then, 25% w/w cerium was incorporated into the MCM-41 using the wet impregnation process and the material obtained was activated by calcination. From the XRD patterns was confirmed the structure of the molecular sieve, and were identified the cerium oxide phases in its structure. The textural catalysts characteristics were investigated by isotherms of N2 adsorption/desorption (BET method). (author)

  19. Estrogen Regulates Protein Synthesis and Actin Polymerization in Hippocampal Neurons through Different Molecular Mechanisms (United States)

    Briz, Victor; Baudry, Michel


    Estrogen rapidly modulates hippocampal synaptic plasticity by activating selective membrane-associated receptors. Reorganization of the actin cytoskeleton and stimulation of mammalian target of rapamycin (mTOR)-mediated protein synthesis are two major events required for the consolidation of hippocampal long-term potentiation and memory. Estradiol regulates synaptic plasticity by interacting with both processes, but the underlying molecular mechanisms are not yet fully understood. Here, we used acute rat hippocampal slices to analyze the mechanisms underlying rapid changes in mTOR activity and actin polymerization elicited by estradiol. Estradiol-induced mTOR phosphorylation was preceded by rapid and transient activation of both extracellular signal-regulated kinase (ERK) and protein kinase B (Akt) and by phosphatase and tensin homolog (PTEN) degradation. These effects were prevented by calpain and ERK inhibitors. Estradiol-induced mTOR stimulation did not require activation of classical estrogen receptors (ER), as specific ERα and ERβ agonists (PPT and DPN, respectively) failed to mimic this effect, and ER antagonists could not block it. Estradiol rapidly activated both RhoA and p21-activated kinase (PAK). Furthermore, a specific inhibitor of RhoA kinase (ROCK), H1152, and a potent and specific PAK inhibitor, PF-3758309, blocked estradiol-induced cofilin phosphorylation and actin polymerization. ER antagonists also blocked these effects of estrogen. Consistently, both PPT and DPN stimulated PAK and cofilin phosphorylation as well as actin polymerization. Finally, the effects of estradiol on actin polymerization were insensitive to protein synthesis inhibitors, but its stimulation of mTOR activity was impaired by latrunculin A, a drug that disrupts actin filaments. Taken together, our results indicate that estradiol regulates local protein synthesis and cytoskeletal reorganization via different molecular mechanisms and signaling pathways. PMID:24611062

  20. Synthesis and structural characterization of coaxial nano tubes intercalated of molybdenum disulfide with carbon

    International Nuclear Information System (INIS)

    Reza San German, C.M.


    In this work the study of some fundamental aspects in the growth of unidimensional systems of coaxial nano tubes from the mold method is approached. This method is an inclusion technique of a precursor reagent into oxide nano porous alumina film (mold), and later applying some processes of synthesis it is gotten to obtain the wished material. The synthesized structures are identified later because they take place by means of the initial formation of nano tubes of MoS 2 , enclosing to carbon nano tubes by the same method, with propylene flow which generates a graphitization process that 'copy' the mold through as it flows. Binary phase MoS 2 + C nano tubes were synthesized by propylene pyrolysis inside MoS 2 nano tubes prepared by template assisted technique. The large coaxial nano tubes constituted of graphite sheets inserted between the MoS 2 layers forming the outer part, and coaxial multi wall carbon nano tubes (MWCNT) intercalated with MoS 2 inside. High resolution electron microscopy (HRTEM), electron energy loss spectroscopy (EELS), high angle annular dark field (HAADF), gatan image filter (GIF), nano beam electron diffraction patterns (NBEDP), along with molecular dynamics simulation and quantum mechanical calculations were used to characterize the samples. The one-dimensional structures exhibit diverse morphologies such as long straight and twisted nano tubes with several structural irregularities. The inter-planar spacing between MoS 2 layers was found to increase from 6.3 to 7.4 A due to intercalation with carbon. Simulated HREM images revealed the presence of these twisted nano structures, with mechanical stretch into intercalate carbon between MoS 2 layers. Our results open up the possibility of using MoS 2 nano tubes as templates for the synthesis of new one- dimensional binary phase systems. (Author)

  1. Ultrafast electron diffraction: oriented molecular structures in space and time. (United States)

    Baskin, J Spencer; Zewail, Ahmed H


    The technique of ultrafast electron diffraction allows direct measurement of changes which occur in the molecular structures of isolated molecules upon excitation by femtosecond laser pulses. The vectorial nature of the molecule-radiation interaction also ensures that the orientation of the transient populations created by the laser excitation is not isotropic. Here, we examine the influence on electron diffraction measurements--on the femtosecond and picosecond timescales--of this induced initial anisotropy and subsequent inertial (collision-free) molecular reorientation, accounting for the geometry and dynamics of a laser-induced reaction (dissociation). The orientations of both the residual ground-state population and the excited- or product-state populations evolve in time, with different characteristic rotational dephasing and recurrence times due to differing moments of inertia. This purely orientational evolution imposes a corresponding evolution on the electron scattering pattern, which we show may be similar to evolution due to intrinsic structural changes in the molecule, and thus potentially subject to misinterpretation. The contribution of each internuclear separation is shown to depend on its orientation in the molecular frame relative to the transition dipole for the photoexcitation; thus not only bond lengths, but also bond angles leave a characteristic imprint on the diffraction. Of particular note is the fact that the influence of anisotropy persists at all times, producing distinct differences between the asymptotic "static" diffraction image and the predictions of isotropic diffraction theory.

  2. Large Molecule Structures by Broadband Fourier Transform Molecular Rotational Spectroscopy (United States)

    Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks


    Fourier transform molecular rotational resonance spectroscopy (FT-MRR) using pulsed jet molecular beam sources is a high-resolution spectroscopy technique that can be used for chiral analysis of molecules with multiple chiral centers. The sensitivity of the molecular rotational spectrum pattern to small changes in the three dimensional structure makes it possible to identify diastereomers without prior chemical separation. For larger molecules, there is the additional challenge that different conformations of each diastereomer may be present and these need to be differentiated from the diastereomers in the spectral analysis. Broadband rotational spectra of several larger molecules have been measured using a chirped-pulse FT-MRR spectrometer. Measurements of nootkatone (C15H22O), cedrol (C15H26O), ambroxide (C16H28O) and sclareolide (C16H26O2) are presented. These spectra are measured with high sensitivity (signal-to-noise ratio near 1,000:1) and permit structure determination of the most populated isomers using isotopic analysis of the 13C and 18O isotopologues in natural abundance. The accuracy of quantum chemistry calculations to identify diastereomers and conformers and to predict the dipole moment properties needed for three wave mixing measurements is examined.

  3. Molecular tailoring approach for exploring structures, energetics and ...

    Indian Academy of Sciences (India)

    Keywords. Molecular clusters; linear scaling methods; molecular tailoring approach (MTA); Hartree-Fock (HF) method; density functional theory (DFT); Møller-Plesset second order (MP2) method; molecular electron density (MED); molecular electrostatic potential.

  4. Relationship between molecular structure and Raman spectra of quinolines (United States)

    Frosch, Torsten; Popp, Jürgen


    DFT calculations were applied to investigate the relationship between the molecular structure and the Raman spectra of quinolines. A variety of different quinolines with increasing complexity was investigated and an aminoquinoline nucleus was found that describes the Raman spectrum of protonated chloroquine. It was discovered that the biological important, rigid C7-chloro group and C4-side chain of chloroquine significantly disturb certain molecular vibrations. The protonation at the N1 position causes dramatic changes of the Raman bands in the wavenumber region between 1500 cm -1 and 1650 cm -1. These bands are putative marker bands of the aminoquinoline drugs for π-π interactions to the hematin targets in malaria infected cells. The calculation of the normal modes and the illustration of the associated atomic displacements are very valuable for a deeper understanding of the associated bands in the Raman spectra.

  5. Green synthesis of mesoporous molecular sieve incorporated monoliths using room temperature ionic liquid and deep eutectic solvents. (United States)

    Zhang, Li-Shun; Zhao, Qing-Li; Li, Xin-Xin; Li, Xi-Xi; Huang, Yan-Ping; Liu, Zhao-Sheng


    A hybrid monolith incorporated with mesoporous molecular sieve MCM-41 of uniform pore structure and high surface area was prepared with binary green porogens in the first time. With a mixture of room temperature ionic liquids and deep eutectic solvents as porogens, MCM-41 was modified with 3-(trimethoxysilyl) propyl methacrylate (γ-MPS) and the resulting MCM-41-MPS was incorporated into poly (BMA-co-EDMA) monoliths covalently. Because of good dispersibility of MCM-41-MPS in the green solvent-based polymerization system, high permeability and homogeneity for the resultant hybrid monolithic columns was achieved. The MCM-41-MPS grafted monolith was characterized by scanning electron microscopy, energy dispersive spectrometer area scanning, transmission electron microscopy, FT-IR spectra and nitrogen adsorption tests. Chromatographic performance of MCM-41-MPS grafted monolith was characterized by separating small molecules in capillary electrochromatography, including phenol series, naphthyl substitutes, aniline series and alkyl benzenes. The maximum column efficiency of MCM-41-MPS grafted monolith reached 209,000 plates/m, which was twice higher than the corresponding MCM-41-MPS free monolith. Moreover, successful separation of non-steroidal anti-inflammatory drugs and polycyclic aromatic hydrocarbons demonstrated the capacity in broad-spectrum application of the MCM-41-MPS incorporated monolith. The results indicated that green synthesis using room temperature ionic liquid and deep eutectic solvents is an effective method to prepare molecular sieve-incorporated monolithic column. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Synthesis and application of a novel molecularly imprinted polymer-coated stir bar for microextraction of triazole fungicides in soil. (United States)

    Hu, Yuling; Li, Jiawei; Li, Gongke


    The preparation, characteristics and application of a sorptive stir bar coated with molecularly imprinted polymer (MIP) using triadimefon as the template molecule are described here. Raw glass capillary was coated with MIP through chemical bonding. The synthesis method was effective and reproducible with the batch-to-batch RSD within 7.8%. Scanning electron micrographs of the stir bar revealed a highly porous coating with average thickness of 15 μm. The synthesized stir bar was proved to be highly stable in most of the solvent for use. Extraction performance showed the fabricated stir bar has excellent molecular recognition abilities for triadimefon and the structure-related compounds, such as triadimenol, diniconazole, flutriafol, hexaconazole, tebuconazole, paclobutrazol and uniconazole, and thus can be applied for simultaneous determination of these triazole fungicides from complex samples by coupling with high-performance liquid chromatography. The variables that influence extraction were optimized with 10.0 μg/L standard solutions of triazole fungicides, and the analytical method was established for the determination of triazole fungicides in soil. The detection limits were in the range of 0.14-0.34 μg/L, and the recoveries were from 86.7 to 114.6% for spiked soil sample. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Corrigendum to "Synthesis, crystal structure and electrochemical and DNA binding studies of oxygen bridged-copper(II) carboxylate" [J. Mol. Struct. 1093 (2015) 135-143 (United States)

    Iqbal, Muhammad; Ali, Saqib; Tahir, Muhammad Nawaz; Muhammad, Niaz; Shah, Naseer Ali; Sohail, Manzar; Pandarinathan, Vedapriya


    The authors regret to inform that Scheme 1 in the article titled 'Synthesis, crystal structure and electrochemical and DNA binding studies of oxygen bridged-copper(II) carboxylate' in vol. 1093 of the Journal of Molecular Structure is incorrect. The corrected scheme is as shown in this correction. This is purely a copy error. The error does not affect the conclusion in paper. The authors would like to apologize for any inconvenience caused.

  8. III - V semiconductor structures for biosensor and molecular electronics applications

    Energy Technology Data Exchange (ETDEWEB)

    Luber, S.M.


    The present work reports on the employment of III-V semiconductor structures to biosensor and molecular electronics applications. In the first part a sensor based on a surface-near two dimensional electron gas for a use in biological environment is studied. Such a two dimensional electron gas inherently forms in a molecular beam epitaxy (MBE) grown, doped aluminum gallium arsenide - gallium arsenide (AlGaAs-GaAs) heterostructure. Due to the intrinsic instability of GaAs in aqueous solutions the device is passivated by deposition of a monolayer of 4'-substituted mercaptobiphenyl molecules. The influence of these molecules which bind to the GaAs via a sulfur group is investigated by Kelvin probe measurements in air. They reveal a dependence of GaAs electron affinity on the intrinsic molecular dipole moment of the mercaptobiphenyls. Furthermore, transient surface photovoltage measurements are presented which demonstrate an additional influence of mercaptobiphenyl chemisorption on surface carrier recombination rates. As a next step, the influence of pH-value and salt concentration upon the sensor device is discussed based on the results obtained from sensor conductance measurements in physiological solutions. A dependence of the device surface potential on both parameters due to surface charging is deduced. Model calculations applying Poisson-Boltzmann theory reveal as possible surface charging mechanisms either the adsorption of OH- ions on the surface, or the dissociation of OH groups in surface oxides. A comparison between simulation settings and physical device properties indicate the OH- adsorption as the most probable mechanism. In the second part of the present study the suitability of MBE grown III-V semiconductor structures for molecular electronics applications is examined. In doing so, a method to fabricate nanometer separated, coplanar, metallic electrodes based on the cleavage of a supporting AlGaAs-GaAs heterostructure is presented. This is followed

  9. Chemistry and structure of giant molecular clouds in energetic environments (United States)

    Anderson, Crystal Nicole


    Throughout the years many studies on Galactic star formation have been conducted. This resulted in the idea that giant molecular clouds (GMCs) are hierarchical in nature with substructures spanning a large range of sizes. The physical processes that determine how molecular clouds fragment, form clumps/cores and then stars depends strongly on both recent radiative and mechanical feed- back from massive stars and, on longer term, from enhanced cooling due to the buildup of metals. Radiative and mechanical energy input from stellar populations can alter subsequent star formation over a large part of a galaxy and hence is relevant to the evolution of galaxies. Much of our knowledge of star formation on galaxy wide scales is based on scaling laws and other parametric descriptions. But to understand the overall evolution of star formation in galaxies we need to watch the feedback processes at work on giant molecular cloud (GMC) scales. By doing this we can begin to answer how strong feedback environments change the properties of the substructure in GMCs. Tests of Galactic star formation theory to other galaxies has been a challenging process due to the lack of resolution with current instruments. Thus, only the nearest galaxies allow us to resolve GMCs and their substructures. The Large Magellanic Cloud (LMC), is one of the closest low metallicity dwarf galaxies (D˜ 50 kpc) and is close enough that current instruments can resolve the sub- structure of its GMCs to gas tracers (e.g. HCO+, HCN, HNC, CS, C2H, N2H+) detected in the LMC at 1.5-40 pc scales and in NGC 5253 at 40 pc scales. I then compare the molecular gas detections to the Central Molecular Zone in our Galaxy. Dense molecular gas was detected in all of the sources. For the regions in the LMC, molecular lines of CS, N2H+, C 2H, HNC, HCO+ and HCN were all detected in N159W and N113 while only HCN, HCO+, HNC, and C2H were detected in 30Dor-10. Toward NGC 5253 only HCO+, HCN, C2H and CS were detected. I observe

  10. Close-packed (polytypic) structures in molecular-dynamics simulations

    International Nuclear Information System (INIS)

    Moody, M.; Ray, J.R.; Rahman, A.


    Molecular-dynamics (MD) computer-simulation studies are used to study close-packed structures found in solid-phase atomic systems interacting via a Morse potential (parametrized to model Ni). A graphical display of particle positions [a (112-bar0) projection] within the parallelepiped forming the MD cell is illustrated. Such a graphic projection allows accurate, complete, and readily visual recognition of the stacking order of close-packed planes and is a much more effective way of identifying polytypes than a study of the pair-distribution function for the structure. These illustrations demonstrate the polytypic nature of previously and newly recognized MD close-packed structures. When assuming compatibility with periodic boundary conditions, as is conventional in MD, only certain polytypes are allowed for an MD simulation system. A discussion of compatibility between close-packed structures and the periodic boundary conditions is presented. The pair coordination numbers, geometrical structure-factor intensities, and potential-energy lattice sums are then calculated for some of these compatible structures. This paper concludes that, through careful consideration, a considerable variety of close-packed physical systems may be appropriately modeled with use of MD computer simulation. Conversely, proper interpretation of the data obtained during such studies may require awareness of the findings presented here

  11. Molecular structure of a tolyl derivative of γ-pyrone (United States)

    Tranfić Bakić, Marina; Cetina, Mario; Mazalović, Sanja


    A study of the molecular structure of a new derivative of γ-pyrone, which is assumed to be of biological and pharmacological importance, has been carried out. The detailed insight into the structure of the γ-pyrone derivative was obtained by 1H NMR, 13C NMR, IR and Raman spectroscopy. Furthermore, its crystal structure was determined by single crystal X-ray diffraction method and its behavior in solutions was examined by UV/Vis and fluorescence spectroscopy. Assignment of the vibrational spectra of the studied compound is presented and correlated to some structural parameters. DFT calculations, namely geometry optimization, frequency calculations, and NBO population analysis, were performed at B3LYP/6-311G++(d,p) level of theory and the obtained data was compared to the experimental results to further elucidate the structural details. In addition, energies of the electronic transitions were estimated using DFT calculations at the same level of theory, and the calculated results showed good agreement with experimental data. It was shown that longer Csbnd C and shorter Cdbnd C bonds alternate in the pyrone ring and that the structure of the studied γ-pyrone derivative comprises two intramolecular Csbnd H⋯O bonds. All the results pointed to relatively weak π-electron delocalization inside the pyrone moiety and significantly stronger π-electron delocalization through tolyl substituents.

  12. Structuration, space and time: the reconstruction of Anthony Giddens’ «structure-agency» synthesis theory

    Directory of Open Access Journals (Sweden)

    A. D. Osypchuk


    Full Text Available The article presents a theoretical and analytical reconstruction of A.Giddens’ Structuration theory as an attempt of ‘structure-agency’ synthesis in sociology. The concept of structuration is introduced by Giddens to solve the problem of duality of structure and agency where the former is defined as rules and resources. Structuration can’t be understood without reference to Giddens’ use of ‘time-space’ concept and related locality and regionalization concepts. Article analyses in details which theoretical and methodological possibilities and limitations comes out of defining structuration as constant flux of conducts in time-space, especially in regard to snapshots of previous conditions of system or structure and memories about them. The article also deals with the concepts of presence, locality, and regionalization that are the result of critical development of time geography approach and are based on combining time and space into one inseparable dimension. The main types and modes of regionalization are reviewed. It is emphasized that through regionalization, locality, and forms of presence and of routine practices Giddens defines not only social institutions but also social system. There is a brief theoretical and methodological discussion of correlation between social structure and social system and of the potential application of Structuration theory to analysis of social change.

  13. Ligand-protected gold clusters: the structure, synthesis and applications (United States)

    Pichugina, D. A.; Kuz'menko, N. E.; Shestakov, A. F.


    Modern concepts of the structure and properties of atomic gold clusters protected by thiolate, selenolate, phosphine and phenylacetylene ligands are analyzed. Within the framework of the superatom theory, the 'divide and protect' approach and the structure rule, the stability and composition of a cluster are determined by the structure of the cluster core, the type of ligands and the total number of valence electrons. Methods of selective synthesis of gold clusters in solution and on the surface of inorganic composites based, in particular, on the reaction of Aun with RS, RSe, PhC≡C, Hal ligands or functional groups of proteins, on stabilization of clusters in cavities of the α-, β and γ-cyclodextrin molecules (Au15 and Au25) and on anchorage to a support surface (Au25/SiO2, Au20/C, Au10/FeOx) are reviewed. Problems in this field are also discussed. Among the methods for cluster structure prediction, particular attention is given to the theoretical approaches based on the density functional theory (DFT). The structures of a number of synthesized clusters are described using the results obtained by X-ray diffraction analysis and DFT calculations. A possible mechanism of formation of the SR(AuSR)n 'staple' units in the cluster shell is proposed. The structure and properties of bimetallic clusters MxAunLm (M=Pd, Pt, Ag, Cu) are discussed. The Pd or Pt atom is located at the centre of the cluster, whereas Ag and Cu atoms form bimetallic compounds in which the heteroatom is located on the surface of the cluster core or in the 'staple' units. The optical properties, fluorescence and luminescence of ligand-protected gold clusters originate from the quantum effects of the Au atoms in the cluster core and in the oligomeric SR(AuSR)x units in the cluster shell. Homogeneous and heterogeneous reactions catalyzed by atomic gold clusters are discussed in the context of the reaction mechanism and the nature of the active sites. The bibliography includes 345 references.

  14. Methanol synthesis on ZnO(0001¯). IV. Reaction mechanisms and electronic structure

    International Nuclear Information System (INIS)

    Frenzel, Johannes; Marx, Dominik


    Methanol synthesis from CO and H 2 over ZnO, which requires high temperatures and high pressures giving rise to a complex interplay of physical and chemical processes over this heterogeneous catalyst surface, is investigated using ab initio simulations. The redox properties of the surrounding gas phase are known to directly impact on the catalyst properties and thus, set the overall catalytic reactivity of this easily reducible oxide material. In Paper III of our series [J. Kiss, J. Frenzel, N. N. Nair, B. Meyer, and D. Marx, J. Chem. Phys. 134, 064710 (2011)] we have qualitatively shown that for the partially hydroxylated and defective ZnO(0001 ¯ ) surface there exists an intricate network of surface chemical reactions. In the present study, we employ advanced molecular dynamics techniques to resolve in detail this reaction network in terms of elementary steps on the defective surface, which is in stepwise equilibrium with the gas phase. The two individual reduction steps were investigated by ab initio metadynamics sampling of free energy landscapes in three-dimensional reaction subspaces. By also sampling adsorption and desorption processes and thus molecular species that are in the gas phase but close to the surface, our approach successfully generated several alternative pathways of methanol synthesis. The obtained results suggest an Eley-Rideal mechanism for both reduction steps, thus involving “near-surface” molecules from the gas phase, to give methanol preferentially over a strongly reduced catalyst surface, while important side reactions are of Langmuir-Hinshelwood type. Catalyst re-reduction by H 2 stemming from the gas phase is a crucial process after each reduction step in order to maintain the catalyst's activity toward methanol formation and to close the catalytic cycle in some reaction channels. Furthermore, the role of oxygen vacancies, side reactions, and spectator species is investigated and mechanistic details are discussed based on

  15. Contributions to Advances in Blend Pellet Products (BPP) Research on Molecular Structure and Molecular Nutrition Interaction by Advanced Synchrotron and Globar Molecular (Micro)Spectroscopy. (United States)

    Guevara-Oquendo, VÍctor H; Yu, Peiqiang


    To date, advanced synchrotron-based and globar-sourced techniques are almost unknown to food and feed scientists. There has been little application of these advanced techniques to study blend pellet products at a molecular level. This article aims to provide recent research on advanced synchrotron and globar vibrational molecular spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction. How processing induced molecular structure changes in relation to nutrient availability and utilization of the blend pellet products. The study reviews Utilization of co-product components for blend pellet product in North America; Utilization and benefits of inclusion of pulse screenings; Utilization of additives in blend pellet products; Application of pellet processing in blend pellet products; Conventional evaluation techniques and methods for blend pellet products. The study focus on recent applications of cutting-edge vibrational molecular spectroscopy for molecular structure and molecular structure association with nutrient utilization in blend pellet products. The information described in this article gives better insight on how advanced molecular (micro)spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction.

  16. Some problems of synthesis of coordination compounds - the molecular predecessors of metal sulfides

    International Nuclear Information System (INIS)

    Larionov, S.V.


    Processes of metal sulfide preparations which require preliminary synthesis of coordination compounds o the metals (Cd, In, etc.) with organic sulfur-containing ligands have been considered. The promising trends in the synthesis are as follows: synthesis of chelate compounds and salts with rationally selected anions; synthesis of different-ligand compounds; synthesis of precursors for complex sulfides preparation. 14 refs

  17. Coalescence of silver unidimensional structures by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G.; Arenas, J.


    The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)

  18. Halogen derivatives of benzo- and dibenzocrown ethers: synthesis, structure, properties and application

    International Nuclear Information System (INIS)

    Pluzhnik-Gladyr, S M


    Methods of synthesis of halogenated benzo- and dibenzocrown ether derivatives are surveyed: halogenation of benzo- and dibenzocrown ethers with molecular halogens, N-halosuccinimides in the solid phase and different media (water, ethanol, halohydrocarbons) and hypohalites in water, as well as the 'assembly' method. Reactions of these compounds are considered: synthesis of phosphorus-containing crown ethers, organometallic synthesis, the Heck and Sonogashira reactions, synthesis of acetylene derivatives and other reactions. Special attention is focused on the complexing properties of halogenated benzocrown ethers with respect to ionic guests and neutral organic molecules. The possibility of synthesis of complexes of such compounds in the solid phase is demonstrated. The extraction and sorption properties of halogenated benzo- and dibenzocrown ethers are considered. Examples of practical use of these compounds are presented. The bibliography includes 203 references

  19. The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Bianchi, L.


    Neutron diffraction (ND) measurements on liquid methanol (CD 3 OD, CD 3 O(H/D), CD 3 OH) under ambient conditions were performed to obtain the distinct (intra- + inter-molecular), G dist (r) and inter-molecular, G inter (r) radial distribution functions (rdfs) for the three samples. The H/D substitution on hydroxyl-hydrogen (Ho) has been used to extract the partial distribution functions, G XHo (r) (X=C, O, and H - a methyl hydrogen) and G XX (r) at both the distinct and inter-molecular levels from the difference techniques of ND. The O-Ho bond length, which has been the subject of controversy in the past, is found purely from the distinct partial distribution function, G XHo (r) to be 0.98 ± 0.01 A. The C-H distance obtained from the distinct G XX (r) partial is 1.08 ± 0.01 A. These distances determined by fitting an intra-molecular model to the total distinct structure functions are 0.961 ± 0.001 A and 1.096 ± 0.001 A, respectively. The inter-molecular G XX (r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho-Ho partial pair distribution function (pdf), g HoHo (r), determined from the second order difference, shows that only one other Ho atom can be found within a mean Ho-Ho separation of 2.36 A. The average position of the O-Ho hydrogen bond determined for the first time purely from experimental inter-molecular G XHo (r) partial distribution function is found to be at 1.75 ± 0.03 A. The experimental structural results at the partial distribution level are compared with those obtained from molecular dynamics (MD) simulations performed in NVE ensemble by using both 3- and 6-site force field models for the first time in this study. The MD simulations with both the models reproduce the ND rdfs rather well. However, discrepancies begin to appear between the simulated and the experimental partial

  20. Synthesis of 4-aminophenyl substituted indole derivatives for the instrumental analysis and molecular docking evaluation studies (United States)

    Singh, Navneet; Kumar, Keshav


    The Indole has been known to maintain celebrity status since so many decades and has been a centre point at the spectrum of pharmacological research. The present work stimulates an idea of generating a pool of library of lead compounds. The data collected can be used for the mapping of biologically active compounds. The reported derivatives of 4-aminophenyl substituted Indole were prepared by the methods of Fischer Indole synthesis and Vilsemeier reaction followed by screening for instrumental analysis and molecular docking studies. The synthesized compounds 4-(1-(2-phenylhydrazono)ethyl)aniline, 1, 4-(1H-indol-2-yl)aniline, 2 and 2-(4-aminophenyl)-1H-indole-3-carbaldehyde, 3 were found to have remarkable yield and instrumental data analysis and also showed remarkable docked characteristic. The molecular docking studies revealed that ligand (amino acids) of comp. 1, 2 and 3 had been docked successfully on the binding site of the 3JUS protein selected from PDB with H bonding. The molecular docking data showed that compound 1, would possess remarkable biological activity and compd. 2 and 3 would possess mild to moderate biological activity. Thus this research work paves the way to synthesize new derivatives and thus to develop new compounds in future with accurate prediction.

  1. Conception and synthesis of new molecular cages for xenon MRI applications

    International Nuclear Information System (INIS)

    Delacour, L.


    Non-invasive proton magnetic resonance imaging ( 1 H MRI) is a powerful clinical tool for the detection of numerous diseases. Although MRI contrast agents are often used to improve diagnostic specificity, this technique has limited applications in molecular imaging because of its inherently low sensitivity when compared to nuclear medicine or fluorescence imaging. Laser-polarized 129 Xe NMR spectroscopy is a promising tool to circumvent sensitivity limitations. Indeed, optical pumping increases the nuclear spin polarization of xenon by several orders of magnitude (10 4 to 10 5 ), thus small amounts of gas dissolved in biological tissues (blood, lungs...) can be rapidly detected with an excellent signal-to-noise ratio. In addition, the high polarizability of the xenon electron cloud, which induces a very high sensitivity to its environment, makes this nucleus very attractive for molecular imaging. Detection of biomolecules can be achieved by biosensors, which encapsulate xenon atoms in molecular cages that have been functionalized to bind the desired biological target. Cage molecules such as cryptophanes have high affinity for xenon and thus appear as ideal candidates for its encapsulation. During this PhD thesis we worked on the synthesis and the functionalization of new cryptophanes. (author) [fr

  2. Imaging molecular structure and dynamics using laser driven recollisions

    International Nuclear Information System (INIS)

    Marangos, J.P.; Baker, S.; Torres, R.; Kajumba, N.; Haworth, C.; Robinson, J.; Tisch, J.W.G.; Lein, M.; Chirila, C.; Vozzi, C.


    Complete test of publication follows. Laser driven electron recollision provides a unique tool for measuring the structure and dynamics of matter. We illustrate this with experiments that use HHG to measure molecular structure with sub-Angstrom spatial and sub-femtosecond temporal resolution. Our recent work has looked in particular at the signal from high order harmonic generation which contains rich information about the structure and intra-molecular dynamics of small molecules. This we will illustrate by two types of experiment; (a) measurements of HHG from aligned molecular samples to observe two-centre recombination interference and electronic structure dependence of the angle dependent yield, (b) reconstruction of intra-molecular proton dynamics from the spectral dependence of the HHG using the intrinsic chirp of recolliding electrons. We experimentally investigate the process of intramolecular quantum interference in high-order harmonic generation in impulsively aligned CO 2 molecules. The recombination interference effect is clearly seen through the order dependence of the harmonic yield in an aligned sample. This confirms that the effective de Broglie wavelength of the returning electron wave is not significantly altered by acceleration in the Coulomb field of the molecular ion. For the first time, to our knowledge, we demonstrate that such interference effects can be effectively controlled by changing the ellipticity of the driving laser field. Here we also report the results of angular dependence measurements of high order harmonics (17 tt h - 27 th ) from impulsively aligned organic molecules: Acetylene, Ethylene, and Allene. Since these molecules have a relatively low I p an appropriately short pulse is required to produce as many harmonic orders as possible. This was provided by the ∼ 10 fs beam line of the ASTRA laser at Rutherford Appleton Laboratory whilst a somewhat longer pulse, properly forwarded with respect to the driving pulse, induced the

  3. DFT charge transfer of hybrid molecular ferrocene/Si structures

    International Nuclear Information System (INIS)

    Calborean, Adrian; Buimaga-Iarinca, Luiza; Graur, Florin


    The electrochemical behavior and electronic properties of redox-active ferrocenes grafted onto semiconductor Si(100) substrate were investigated theoretically by first-principles calculations. Organic molecules were attached via the formation of Si-C covalent bonds through two different linkers: vinyl (direct grafting), and N 3 (CH 2 ) 11 (indirect grafting). Redox energies and the electronic properties relating to different spacers in hybrid ferrocene Fc/Si and ferrocenium Fc + /Si structures were theoretically extracted and compared with experimental cyclic voltametry data. Electronic charge transfers are discussed through the alignment positions of the frontier orbitals of the molecule with respect to the Si substrate gap. Periodic boundary conditions were used to investigate the Si(100) as a slab surface and hybrid Fc/Si structures. The resulting projected density of states (PDOS) were compared with molecular results and discussed in the light of experimental data. (paper)

  4. Surfaces of Microparticles in Colloids: Structure and Molecular Adsorption Kinetics (United States)

    Dai, Hai-Lung


    Surfaces of micron and sub-micron size particles in liquid solution are probed by second harmonic generation (SHG) facilitated with femtosecond laser pulses. The particles probed include inorganic objects such as carbon black and color pigments, polymeric species like polystyrene beads, and biological systems such as blood cells and ecoli. In the experiments, dye molecules are first adsorbed onto the particle surface to allow generation of second harmonics upon light irradiation. Competition for adsorption between these surface dye molecules and the molecules of interest in the solution is then monitored by the SHG signal to reveal the molecular adsorption kinetics and surface structure. Specifically, surfactant adsorption on polymer surfaces, the structure of carbon black surface, and protein adsorption on biological surfaces, monitored by this technique, will be discussed.

  5. Structural versatility of Metal-organic frameworks: Synthesis and Characterization

    KAUST Repository

    Alsadun, Norah S.


    Metal-Organic Frameworks (MOFs), an emerging class of porous crystalline materials, have shown promising properties for diverse applications such as catalysis, gas storage and separation. The high degree of tunability of MOFs vs other solid materials enable the assembly of advanced materials with fascinating properties for specific applications. Nevertheless, the precise control in the construction of MOFs at the molecular level remains challenging. Particularly, the formation of pre-targeted multi-nuclear Molecular Building Block (MBB) precursors to unveil materials with targeted structural characteristics is captivating. The aim of my master project in the continuous quest of the group of Prof. Eddaoudi in exploring different synthetic pathways to control the assembly of Rare Earth (RE) based MOF. After giving a general overview about MOFs, I will discuss in this thesis the results of my work on the use of tri-topic oriented organic carboxylate building units with the aim to explore the assembly/construction of new porous RE based MOFs. In chapter 2 will discuss the assembly of 3-c linkers with RE metals was then evaluated based on symmetry and angularity of the three connected linkers. The focus of chapter 3 is cerium based MOFs and heterometallic system, based on 3-c ligands with different length and symmetry. Overall, the incompatibility of 3-c ligands with the 12-c cuo MBB did not allow to any formation of higher neuclearity (˃6), but it has resulted in affecting the connectivity of the cluster.

  6. Synthesis by irradiation and mechanism and structural characterization study of high melt strength polypropylene

    International Nuclear Information System (INIS)

    Lugao, Ademar Benevolo


    Polypropylene molecular structure is made only by linear molecules interacting by weak forces. The resulting PP has very low melt strength (MS). MS is important to make feasible to process PP by all the transformation technologies based on the free expansion of the melt. The aim of this work was to develop a new process to synthesize PP with crosslinks and/or long chain branches, known as High Melt Strength Polypropylene (HMSPP) and to characterize its structure and synthesis mechanism. HMSPP was obtained by the irradiation of PP under a crosslinking (acetylene) atmosphere or inert or oxidative one, followed by thermal treatment for radical recombination and thermal treatment for annihilation of the remaining radicals under reactive or inert atmosphere. The results from rheological characterization showed that the highest levels of MS were obtained by conducting irradiation and thermal treatments under crosslinking atmospheres. The results for the elucidation of reaction mechanism by electron spin resonance (ESR) showed that acetylene irradiation is effective in promoting the creation of double bonds, based on the formation of polyenil radicals. The results of structural unraveling showed that radiation promotes predominantly the degradation of atactic molecules or molecules with atactic defects. These results support the hypothesis of formation of branched PP molecules based on the reaction of those fragments with the double bonds created in the PP molecules. (author)

  7. Structures and physicochemical properties of molecular aggregates of lipids

    International Nuclear Information System (INIS)

    Iwahashi, Makio


    Structures and physicochemical properties of lipids such as fatty acids, alcohols, acylglycerols and steroids in their two- or three-dimensional states were studied through the measurements of surface pressure (π), surface-molecular area (A), vapor-pressure osmosis, radioactivity (R), self-diffusion coefficient (D), density, viscosity, near-infrared spectroscopy (NIR), 13 C-NMR spin-lattice relaxation time (T 1 ), ESR, SEM, DSC, X-ray diffraction and small-angle neutron scattering (SANS). Following results are obtained: (1) π-A and R-A relationships indicate that the explanation, being widely believed, of the reaction occurred in the oleic acid or the trioleylglycerol monolayer on the aqueous KMnO 4 solution is incorrect. (2) By using the LB film of 3 H-labelled fatty acid, the upper limit of the neutrino mass was determined. In addition, by using the LB film of 14 C-labelled fatty acid, a new type of crystal-transformation process was found, in which fatty-acid crystal transforms from its unstable state to its stable one by the transfer of the fatty acid molecules through the vapor phase. (3) Fatty acids always exist as their dimers in their liquid state and mostly in non-polar solvents; the dimers are the units of the molecular movements in the molten liquid and in solvents. T 1 results clearly showed the internal molecular movements of the dimers. In addition, D and SANS results indicated that two different kinds of fatty acids in their binary mixture make only each homodimers. (4) Furthermore, the study on the liquid structure of fatty acids such as cis-6-, cis-9-, cis-11-, trans-9-octadecenoic acids and stearic acid indicated that these fatty-acid dimers construct the clusters resemble to the smectic-liquid crystal in the liquid state. The clusters determine the physicochemical properties of the liquid of the fatty acid. (author)

  8. Equilibrium theory of molecular fluids: Structure and freezing transitions (United States)

    Ram, Jokhan


    In this article we review equilibrium theory of molecular fluids which includes structure and freezing transitions. The application of the theory to evaluate the pair correlation functions using Integral Equation methods and Computer Simulations have been discussed. Freezing of classical complex fluids based on the density functional approach is also discussed and compare a variety of its versions. Transitions discussed are sensitive to the value of direct correlation functions of the effective liquid which is required as an input information in the theory. Accurate evaluation of pair correlation functions is emphasized. Calculation of these correlation functions which pose problems in the case of ordered phases is discussed. The pair correlation functions of the ordered phase, which are supposed to be made up of two contributions, one that preserves the symmetry of the isotropic phase and a second that breaks it, are discussed. A new free-energy functional developed for an inhomogeneous system that contains both symmetry conserved and symmetry broken parts of the direct pair correlation function is discussed. The most useful three dimensional reference interaction site model (3D-RISM) and its extension done recently by many workers is discussed. Application of this theory to a large variety of complex systems in combination with the density functional theory method implemented in the Amsterdam density functional software package is discussed. Coupling of the 3D-RISM salvation theory with molecular dynamics in the Amber molecular dynamics package is also given. The importance of the density functional theory for the study of the structure and phase behaviour of hard polyhedral is also discussed. The dynamical density functional and its generalized form applied for many important class of problems such as binary mixture, anisotropic particles dynamics of freezing and wetting, colloidal samples, particle self diffusion in complex environment, colloidal sedimentation

  9. Micro structure processing on plastics by accelerated hydrogen molecular ions (United States)

    Hayashi, H.; Hayakawa, S.; Nishikawa, H.


    A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.

  10. Total synthesis of marinomycin A using salicylate as a molecular switch to mediate dimerization (United States)

    Evans, P. Andrew; Huang, Mu-Hua; Lawler, Michael J.; Maroto, Sergio


    Antibiotics play a significant role in human health because of their ability to treat life-threatening bacterial infections. The growing problems with antibiotic resistance have made the development of new antibiotics a World Health Organization priority. Marinomycin A is a member of a new class of bis-salicylate-containing polyene macrodiolides, which have potent antibiotic activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. Herein, we describe a triply convergent synthesis of this agent using the salicylate as a novel molecular switch for the chemoselective construction of the macrodiolide. This strategy raises new questions regarding the biosynthetic role of the salicylate and its potential impact on the mechanism of action of these types of agents. For instance, in contrast to penicillin, which enhances the electrophilicity of the cyclic amide through ring strain, salicylates reduce the electrophilicity of the aryl ester through an intramolecular resonance-assisted hydrogen bond to provide an amide surrogate.

  11. Synthesis and Bioconjugation of Gold Nanoparticles as Potential Molecular Probes for Light-Based Imaging Techniques

    Directory of Open Access Journals (Sweden)

    Raja Gopal Rayavarapu


    Full Text Available We have synthesized and characterized gold nanoparticles (spheres and rods with optical extinction bands within the “optical imaging window.” The intense plasmon resonant driven absorption and scattering peaks of these nanoparticles make them suitable as contrast agents for optical imaging techniques. Further, we have conjugated these gold nanoparticles to a mouse monoclonal antibody specific to HER2 overexpressing SKBR3 breast carcinoma cells. The bioconjugation protocol uses noncovalent modes of binding based on a combination of electrostatic and hydrophobic interactions of the antibody and the gold surface. We discuss various aspects of the synthesis and bioconjugation protocols and the characterization results of the functionalized nanoparticles. Some proposed applications of these potential molecular probes in the field of biomedical imaging are also discussed.

  12. Synthesis and analytical applications of molecularly imprinted polymers on the surface of carbon nanotubes: a review

    International Nuclear Information System (INIS)

    Dai, Hao; Xiao, Deli; Li, Hui; Yuan, Danhua; Zhang, Chan; He, Hua


    This review (with 142 references) summarize the state of the art in molecularly imprinting technology as applied to the surface of carbon nanotubes (CNTs) which result in so-called CNTs-MIPs. These nanomaterials offer a remedy to the flaws of traditional MIPs, such as poor site accessibility for templates, slow mass transfer and template leakage. They also are flexible in that different materials can be integrated with CNTs. Given the advantages of using CNT-MIPs, this technology has experienced rapid expansion, not the least because CNT-MIPs can be produced at low cost and by a variety of synthetic approaches. We summarize methods of, and recent advances in the synthesis of CNT-MIPs, and then highlight some representative applications. We also comment on their potential future developments and research directions. (author)

  13. The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Jianjun [University of South Florida, Tampa (USF); Cheng, Xiaolin [ORNL; Monticelli, Luca [Institut National de la Santé et de la Recherche Médicale (INSERM) and INTS, France; Heberle, Frederick A [ORNL; Kucerka, Norbert [Atomic Energy of Canada Limited (AECL), Canadian Neutron Beam Centre (CNBC) and Comenius University,; Tieleman, D. Peter [University of Calgary, ALberta, Canada; Katsaras, John [ORNL


    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.

  14. Molecular hijacking of siroheme for the synthesis of heme and d1 heme. (United States)

    Bali, Shilpa; Lawrence, Andrew D; Lobo, Susana A; Saraiva, Lígia M; Golding, Bernard T; Palmer, David J; Howard, Mark J; Ferguson, Stuart J; Warren, Martin J


    Modified tetrapyrroles such as chlorophyll, heme, siroheme, vitamin B(12), coenzyme F(430), and heme d(1) underpin a wide range of essential biological functions in all domains of life, and it is therefore surprising that the syntheses of many of these life pigments remain poorly understood. It is known that the construction of the central molecular framework of modified tetrapyrroles is mediated via a common, core pathway. Herein a further branch of the modified tetrapyrrole biosynthesis pathway is described in denitrifying and sulfate-reducing bacteria as well as the Archaea. This process entails the hijacking of siroheme, the prosthetic group of sulfite and nitrite reductase, and its processing into heme and d(1) heme. The initial step in these transformations involves the decarboxylation of siroheme to give didecarboxysiroheme. For d(1) heme synthesis this intermediate has to undergo the replacement of two propionate side chains with oxygen functionalities and the introduction of a double bond into a further peripheral side chain. For heme synthesis didecarboxysiroheme is converted into Fe-coproporphyrin by oxidative loss of two acetic acid side chains. Fe-coproporphyrin is then transformed into heme by the oxidative decarboxylation of two propionate side chains. The mechanisms of these reactions are discussed and the evolutionary significance of another role for siroheme is examined.

  15. Molecular Design of Bioinspired Nanostructures for Biomedical Applications: Synthesis, Self-Assembly and Functional Properties (United States)

    Xu, Hesheng Victor; Zheng, Xin Ting; Mok, Beverly Yin Leng; Ibrahim, Salwa Ali; Yu, Yong; Tan, Yen Nee


    Biomolecules are the nanoscale building blocks of cells, which play multifaceted roles in the critical biological processes such as biomineralization in a living organism. In these processes, the biological molecules such as protein and nucleic acids use their exclusive biorecognition properties enabled from their unique chemical composition, shape and function to initiate a cascade of cellular events. The exceptional features of these biomolecules, coupled with the recent advancement in nanotechnology, have led to the emergence of a new research field that focuses on the molecular design of bioinspired nanostructures that inherit the extraordinary function of natural biomaterials. These “bioinspired” nanostructures could be formulated by biomimetic approaches through either self-assembling of biomolecules or acting as a biomolecular template/precursor to direct the synthesis of nanocomposite. In either situation, the resulting nanomaterials exhibit phenomenal biocompatibility, superb aqueous solubility and excellent colloidal stability, branding them exceptionally desirable for both in vitro and in vivo biomedical applications. In this review, we will present the recent developments in the preparation of “bioinspired” nanostructures through biomimetic self-assembly and biotemplating synthesis, as well as highlight their functional properties and potential applications in biomedical diagnostics and therapeutic delivery. Lastly, we will conclude this topic with some personal perspective on the challenges and future outlooks of the “bioinspired” nanostructures for nanomedicine.

  16. Synthesis and Electrical Characterization of Metal-Molecule-Metal Nanowires for Nanoscale and Molecular Electronics (United States)

    Mayer, Theresa


    Considerable attention has been devoted to developing molecular-scale devices that function as nonlinear circuit elements and nanowires that interconnect these circuit elements. In this talk, we will present an overview of our research on the electrical characterization of metal-molecule-metal nanowires fabricated by template-directed synthesis. Polycarbonate membranes were used for the electrochemical preparation of nanowires with diameter of 30 - 40 nm and length of 2 - 4 microns. Functionalized dithioacetyl-molecules were adsorbed to the tips of the first Au or Pd segment of the nanowire using a potential-assisted assembly method, which resulted in ordered and uniform self-assembled monolayers (SAMs). A thin layer of seed metal was then deposited on top of the SAM by reduction of metal ions to form Ag or Pd nanoparticles prior to growing the second Au or Pd metal nanowire segment. The resulting in-wire devices were aligned and attached to pairs of large-area Au electrodes using an electrofluidic assembly technique. Electrical measurements were conducted at room temperature for nanowires with SAMs of C12, oligo (phenylene ethynylene) (OPE), and oligo(phenylene vinylene) (OPV) molecules, and with Pd and Au metal contacts. For biases between +/-1 V, the OPV molecular junctions had higher conductance than the OPE junctions. Both of these molecular wire junctions had current that was several orders of magnitude higher than the insulating C12 molecular junction. Comparison of OPE junctions formed with Au-Pd, Ag-Pd, and Pd-Pd contacts showed that the conductance of the Pd-Pd contact was the largest of the three investigated.

  17. Some new methyl-8-methoxypsoralens: synthesis, photobinding to DNA, photobiological properties and molecular modelling. (United States)

    Gia, O; Anselmo, A; Pozzan, A; Antonello, C; Magno, S M; Uriarte, E


    The tricyclic structure of known natural photochemotherapeutic drugs such as 8-methoxypsoralen and 5-methoxypsoralen is often taken as a model in the search of new photosensitizer agents with less phototoxic and mutagenic effects. This paper describes the synthesis, characterization, photobinding to DNA, photobiological properties and computational chemistry of some 8-methoxypsoralen derivatives bearing two or three methyl groups at the key positions of the two photoactive double bonds. Results showed that photoreactivity and photobiological behaviour depend on the pattern of methyl substitutions. Antiproliferative activity in cell lines shows good correlation with DNA interaction data.

  18. Synthesis, structural, DFT studies, docking and antibacterial activity of a xanthene based hydrazone ligand (United States)

    Naseem, Saira; Khalid, Muhammad; Tahir, Muhammad Nawaz; Halim, Mohammad A.; Braga, Ataualpa A. C.; Naseer, Muhammad Moazzam; Shafiq, Zahid


    Herein, we present the synthesis of novel xanthene-based hydrazone (1). The chemical structure of 1 was resolved using spectroscopic techniques such as NMR, FT-IR, UV-VIS and X-ray crystallographic approaches. X-ray diffraction analysis shows that the compound (1) crystallizes in triclinic crystal lattice with the Pbar1 space group and diffused to form multi-layered structure due to non-covalent interactions such as intramolecular hydrogen bonding (H.B). In addition to experimental investigation, density functional theory (DFT) calculation with M06-2X/6-31G(d,p) and B3LYP/6-31G(d,p) level of theories was performed on compound (1) to obtain optimized geometry, spectroscopic and electronic properties. DFT optimized geometry shows good agreement with the experimental XRD structure. The hyper conjugative interactions and hydrogen bonding network are responsible for the stability of compound (1) as revealed by natural bond orbital (NBO) calculation. Moreover, hydrogen bonding network in the dimer is confirmed by FT-IR and thermodynamic studies showing excellent agreement with XRD and NBO findings. TD-DFT/UV-VIS analysis provides insight that maximum excitation is found in 1 which shows good agreement with experimental UV-VIS result. The global reactivity parameters are calculated using the energies of frontier molecular orbitals also disclosed that the compound is more stable might be due to hydrogen bonding network. Experimental and molecular docking studies indicated that this compound has anti-bacterial and anti-diabetic properties. The binding affinity of this compound against the multidrug efflux pump subunit AcrB OS=Escherichia coli (strain K12) and Human Pancreatic Alpha-Amylase is -9.2 and -10.00 kcal/mol which are higher than the control drugs. Pi-Pi, Pi-anaion, amide-pi and pi-alkyl bonds play key role in drug-protein complexes.

  19. Drug Repositioning by Kernel-Based Integration of Molecular Structure, Molecular Activity, and Phenotype Data (United States)

    Wang, Yongcui; Chen, Shilong; Deng, Naiyang; Wang, Yong


    Computational inference of novel therapeutic values for existing drugs, i.e., drug repositioning, offers the great prospect for faster and low-risk drug development. Previous researches have indicated that chemical structures, target proteins, and side-effects could provide rich information in drug similarity assessment and further disease similarity. However, each single data source is important in its own way and data integration holds the great promise to reposition drug more accurately. Here, we propose a new method for drug repositioning, PreDR (Predict Drug Repositioning), to integrate molecular structure, molecular activity, and phenotype data. Specifically, we characterize drug by profiling in chemical structure, target protein, and side-effects space, and define a kernel function to correlate drugs with diseases. Then we train a support vector machine (SVM) to computationally predict novel drug-disease interactions. PreDR is validated on a well-established drug-disease network with 1,933 interactions among 593 drugs and 313 diseases. By cross-validation, we find that chemical structure, drug target, and side-effects information are all predictive for drug-disease relationships. More experimentally observed drug-disease interactions can be revealed by integrating these three data sources. Comparison with existing methods demonstrates that PreDR is competitive both in accuracy and coverage. Follow-up database search and pathway analysis indicate that our new predictions are worthy of further experimental validation. Particularly several novel predictions are supported by clinical trials databases and this shows the significant prospects of PreDR in future drug treatment. In conclusion, our new method, PreDR, can serve as a useful tool in drug discovery to efficiently identify novel drug-disease interactions. In addition, our heterogeneous data integration framework can be applied to other problems. PMID:24244318

  20. Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

    Directory of Open Access Journals (Sweden)

    Aparecido R. Silva


    Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

  1. Molecular manipulation of solid state structure: influences of organic components on vanadium oxide architectures (United States)

    Hagrman, Pamela J.; Finn, Robert C.; Zubieta, Jon


    Among the inorganic materials enjoying widespread contemporary interest, the metal oxide based solid phases occupy a prominent position by virtue of their applications to catalysis, sorption, molecular electronics, energy storage, optical materials and ceramics. The diversity of properties associated with these materials reflects the chemical composition, which allows variations in covalency, geometry and oxidation states, and the crystalline architecture, which may provide different pore structures, coordination sites, or juxtapositions of functional groups. Despite such fundamental and practical significance, the design of the structure of such materials remains a challenge in solid state chemistry. While organic materials have been synthesized which self-assemble into ordered arrays at low temperature and which exhibit molecular recognition and biomimetic activity, the ability to synthesize inorganic materials by rational design remains elusive. Small, soluble molecular building blocks with well-defined reaction chemistries which allow their low-temperature assembly into crystalline solid state inorganic materials are not well known. However, the existence of naturally occurring, structurally complex minerals establishes that hydrothermal synthesis can provide a low temperature pathway to produce open-framework and layered metastable structures utilizing inorganic starting materials. Thus, hydrothermal conditions have been used to prepare microporous tetrahedral framework solids that are capable of shape-selective absorption, like zeolites and aluminophosphates, and more recently in the preparation of complex solid arrays of the M/O/PO 3-4 and M/O/RPO 2-3 systems (M=V and Mo). The hydrothermal technique may be combined with the introduction of organic components which may act as charge compensating groups, space-filling units, structure directing agents, templates, tethers between functional groups, or conventional ligands in the preparation of inorganic

  2. Mathematical analysis of compressive/tensile molecular and nuclear structures (United States)

    Wang, Dayu

    Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

  3. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity ...

    Indian Academy of Sciences (India)

    s12039-016-1125-x. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity of lanthanide(III) complexes of 2-benzoylpyridine acetylhydrazone. KARREDDULA RAJA, AKKILI SUSEELAMMA and KATREDDI HUSSAIN REDDY. ∗.

  4. Using Combustion Synthesis to Reinforce Berms and Other Regolith Structures (United States)

    Rodriquez, Gary


    The Moonraker Excavator and other tools under development for use on the Moon, Mars, and asteroids will be employed to construct a number of civil engineering projects and to mine the soil. Mounds of loose soil will be subject to the local transport mechanisms plus artificial mechanisms such as blast effects from landers and erosion from surface vehicles. Some of these structures will require some permanence, with a minimum of maintenance and upkeep. Combustion Synthesis (CS) is a family of processes and techniques whereby chemistry is used to transform materials, often creating flame in a hard vacuum. CS can be used to stabilize civil engineering works such as berms, habitat shielding, ramps, pads, roadways, and the like. The method is to unroll thin sheets of CS fabric between layers of regolith and then fire the fabric, creating a continuous sheet of crusty material to be interposed among layers of loose regolith. The combination of low-energy processes, ISRU (in situ resource utilization) excavator, and CS fabrics, seems compelling as a general method for establishing structures of some permanence and utility, especially in the role of robotic missions as precursors to manned exploration and settlement. In robotic precursory missions, excavator/ mobility ensembles mine the Lunar surface, erect constructions of soil, and dispense sheets of CS fabrics that are covered with layers of soil, fired, and then again covered with layers of soil, iterating until the desired dimensions and forms are achieved. At the base of each berm, for example, is a shallow trench lined with CS fabric, fired and filled, mounded, and then covered and fired, iteratively to provide a footing against lateral shear. A larger trench is host to a habitat module, backfilled, covered with fabric, covered with soil, and fired. Covering the applied CS fabric with layers of soil before firing allows the resulting matrix to incorporate soil both above and below the fabric ply into the fused layer

  5. Structural archetypes in nickel(II) hybrid vanadates. Towards a directed hydrothermal synthesis

    International Nuclear Information System (INIS)

    Luis, R. Fernandez de; Urtiaga, M.K.; Mesa, J.L.; Rojo, T.; Arriortua, M.I.


    In the present work, we relate the modifications of the initial synthesis parameters (pH value, stoichiometry and concentration) with the different structural archetypes obtained in the {Ni/Bpy/VO} and {Ni/Bpe/VO} systems (4,4'-bipyridine (Bpy), 1,2-di(4-pyridyl) ethylene (Bpe)). The vanadium coordination is partially controlled by the hydrothermal synthesis conditions, and the final crystal structures depend on the synergetic interaction between the metal-organic subnets and the vanadium oxide subunits.

  6. Total synthesis, structure, and oral absorption of a thiazole cyclic peptide, sanguinamide A

    DEFF Research Database (Denmark)

    Nielsen, Daniel S; Hoang, Huy N; Lohman, Rink-Jan


    The first total synthesis and three-dimensional solution structure are reported for sanguinamide A, a thiazole-containing cyclic peptide from the sea slug H. sanguineus. Solution phase fragment synthesis, solid phase fragment assembly, and solution macrocyclization were combined to give (1) in 10......% yield. Spectral properties were identical for the natural product, requiring revision of its structure from (2) to (1). Intramolecular transannular hydrogen bonds help to bury polar atoms, which enables oral absorption from the gut....

  7. A bipyridyl thorium metallocene: synthesis, structure and reactivity. (United States)

    Ren, Wenshan; Song, Haibin; Zi, Guofu; Walter, Marc D


    The synthesis, structure and reactivity of a new bipy thorium metallocene have been studied. The reduction of the thorium chloride metallocene [η(5)-1,3-(Me(3)C)(2)C(5)H(3)](2)ThCl(2) (1) with potassium graphite in the presence of 2,2'-bipyridine gives the purple bipy metallocene [η(5)-1,3-(Me(3)C)(2)C(5)H(3)](2)Th(bipy) (2) in good yield. Complex 2 has been fully characterized by various spectroscopic techniques, elemental analysis and X-ray diffraction analysis. Complex 2 reacts cleanly with trityl chloride, silver halides and diphenyl diselenide, leading to the halide metallocenes [η(5)-1,3-(Me(3)C)(2)C(5)H(3)](2)ThX(2) (X = Cl (1), Br (3), I (4)) and [η(5)-1,3-(Me(3)C)(2)C(5)H(3)](2)Th(F)(μ-F)(3)Th[η(5)-1,3-(Me(3)C)(2)C(5)H(3)](F)(bipy) (5), and selenido metallocene [η(5)-1,3-(Me(3)C)(2)C(5)H(3)](2)Th(SePh)(2) (6), in good conversions. In addition, 2 cleaves the C[double bond, length as m-dash]S bond of CS(2) to give the sulfido complex, [η(5)-1,3-(Me(3)C)(2)C(5)H(3)](2)ThS (7), which further undergoes an irreversible dimerization or nucleophilic addition with CS(2), leading to the dimeric sulfido complex {[η(5)-1,3-(Me(3)C)(2)C(5)H(3)](2)Th}(μ-S)(2) (8) and dimeric trithiocarbonate complex {[η(5)-1,3-(Me(3)C)(2)C(5)H(3)](2)Th}(μ-CS(3))(2) (10) in good yields, respectively.

  8. Constitutional Isomers of Dendrimer-like Star Polymers: Design, Synthesis and Conformational and Structural Properties

    Energy Technology Data Exchange (ETDEWEB)

    Pople, John A


    The design, synthesis and solution properties of six constitutional isomers of dendrimer-like star polymers is described. Each of the polymers have comparable molecular weights ({approx} 80,000 g/mol), narrow polydispersities (< 1.19) and an identical number of branching junctures (45) and surface hydroxyl functionalities (48). The only difference in the six isomers is the placement of the branching junctures. The polymers are constructed from high molecular weight poly(e-caprolactone) with branching junctures derived from 2,2'-bis(hydroxylmethyl) propionic acid (bis-MPA) emanating from a central core. The use of various generations of dendritic initiators and dendrons coupled with the ring opening polymerization of e-caprolactones allowed a modular approach to the dendrimer-like star polymer isomers. The most pronounced effects on the physical properties/morphology and hydrodynamic volume was for those polymers in which the branching was distributed throughout the sample in a dendrimer-like fashion. The versatility of this approach has provided the possibility of understanding the relationship between architecture and physical properties. Dynamic light scattering and small angle X-ray scattering techniques were used to determine the hydrodynamic radius Rh and radius of gyration Rg respectively. The relationship between Rg and molecular weight was indicative of a compact star-like structure, and did not show advanced bias towards either the dense core or dense shell models. The radial density distribution of the isomers was therefore modeled according to a many arm star polymer, and good agreement was found with experimental measures of Rh/Rg.

  9. Exploring astrobiology using in silico molecular structure generation (United States)

    Meringer, Markus; Cleaves, H. James


    The origin of life is typically understood as a transition from inanimate or disorganized matter to self-organized, `animate' matter. This transition probably took place largely in the context of organic compounds, and most approaches, to date, have focused on using the organic chemical composition of modern organisms as the main guide for understanding this process. However, it has gradually come to be appreciated that biochemistry, as we know it, occupies a minute volume of the possible organic `chemical space'. As the majority of abiotic syntheses appear to make a large set of compounds not found in biochemistry, as well as an incomplete subset of those that are, it is possible that life began with a significantly different set of components. Chemical graph-based structure generation methods allow for exhaustive in silico enumeration of different compound types and different types of `chemical spaces' beyond those used by biochemistry, which can be explored to help understand the types of compounds biology uses, as well as to understand the nature of abiotic synthesis, and potentially design novel types of living systems. This article is part of the themed issue 'Reconceptualizing the origins of life'.

  10. Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Mehere, P.; Robinson, H.; Han, Q.; Lemkul, J. A.; Vavricka, C. J.; Bevan, D. R.; Li, J.


    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  11. Tyrosine Aminotransferase: Biochemical and Structural Properties and Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    P Mehere; Q Han; J Lemkul; C Vavricka; H Robinson; D Bevan; J Li


    Tyrosine aminotransferase (TAT) catalyzes the transamination of tyrosine and other aromatic amino acids. The enzyme is thought to play a role in tyrosinemia type II, hepatitis and hepatic carcinoma recovery. The objective of this study is to investigate its biochemical and structural characteristics and substrate specificity in order to provide insight regarding its involvement in these diseases. Mouse TAT (mTAT) was cloned from a mouse cDNA library, and its recombinant protein was produced using Escherichia coli cells and purified using various chromatographic techniques. The recombinant mTAT is able to catalyze the transamination of tyrosine using {alpha}-ketoglutaric acid as an amino group acceptor at neutral pH. The enzyme also can use glutamate and phenylalanine as amino group donors and p-hydroxy-phenylpyruvate, phenylpyruvate and alpha-ketocaproic acid as amino group acceptors. Through macromolecular crystallography we have determined the mTAT crystal structure at 2.9 {angstrom} resolution. The crystal structure revealed the interaction between the pyridoxal-5'-phosphate cofactor and the enzyme, as well as the formation of a disulphide bond. The detection of disulphide bond provides some rational explanation regarding previously observed TAT inactivation under oxidative conditions and reactivation of the inactive TAT in the presence of a reducing agent. Molecular dynamics simulations using the crystal structures of Trypanosoma cruzi TAT and human TAT provided further insight regarding the substrate-enzyme interactions and substrate specificity. The biochemical and structural properties of TAT and the binding of its cofactor and the substrate may help in elucidation of the mechanism of TAT inhibition and activation.

  12. Synthesis and properties of aqueous polyurethane dispersions: Influence of molecular weight of polyethylene glycol

    Energy Technology Data Exchange (ETDEWEB)

    Mumtaz, Fatima; Zuber, Mohammad; Zia, Khalid Mahmood [Government College University, Faisalabad (Pakistan); Jamil, Tahir [University of the Punjab, Lahore (Pakistan); Hussain, Rizwan [National Engineering and Scientific Commission (NESCOM), Islamabad (Pakistan)


    Aqueous polyurethane dispersions (PUDs) have recently emerged as important alternatives to their solvent-based counterparts for various applications due to increasing health and environmental awareness. A series of aqueous polyurethane dispersions containing carboxylate anion as hydrophilic pendant groups were synthesized through step growth polymerization reaction using hexamethylene diisocyanate (HDI), 1,4-butanediol (1,4-BDO), dimethylol propionic acid (DMPA) and polyethylene glycol (PEG) of different molecular weight. Effect of PEG molecular weight was investigated on molecular structure, contact angle measurement, and physical and adhesive properties of PU emulsions. Fourier transform infrared spectroscopy (FT-IR) was used to check the completion of polymerization reaction. Contact angle measurement indicated that the hydrophilicity of polymer increases by increasing molecular weight of PEG with a corresponding decrease in contact angle. Results of T-peel test showed a decrease in peel strength by increasing molecular weight of PEG. Moreover, solid contents%, drying time and storage stability suggested fast drying properties and greater stability of aqueous PU dispersions.

  13. Isotope chemistry and molecular structure. Carbon and oxygen isotope chemistry

    International Nuclear Information System (INIS)

    Bigeleisen, J.; Hom, R.C.; Ishida, T.


    The relationships between force constants and the isotope chemistry of carbon and oxygen are calculated for H 2 O, CO 2 , CH 2 O, CH 4 , C 2 H 4 , C 2 H 6 , and C 6 H 6 . Significant differences are found from the general features of protium--deuterium isotope chemistry. These are shown to be associated with a structural effect. Hydrogen is always an end atom except for hydrogen bonded moleules. Carbon is generally tetrahedrally bonded and its isotope chemistry shows significant contributions from the interaction between stretching and bending modes. These interactions lead to deviations in additivity of the total isotope effect from the contributions of the individual force constants. Stretching forces dominate the isotope chemistry of carbon and oxygen as they do in hydrogen. They account for 70%--90% of the reduced partition function ratios. Correlations are made between the stretching force contributions and molecular structure. It is shown that while significant differences exist between the specific contributions calculated from different force fields for methane, ethane, and benzene, the absolute value of ln(s/s') f is rather insensitive to the detailed structures of the F matrices studied

  14. Transmission electron microscopy and the molecular structure of icosahedral viruses. (United States)

    San Martín, Carmen


    The field of structural virology developed in parallel with methodological advances in X-ray crystallography and cryo-electron microscopy. At the end of the 1970s, crystallography yielded the first high resolution structure of an icosahedral virus, the T=3 tomato bushy stunt virus at 2.9Å. It took longer to reach near-atomic resolution in three-dimensional virus maps derived from electron microscopy data, but this was finally achieved, with the solution of complex icosahedral capsids such as the T=25 human adenovirus at ∼3.5Å. Both techniques now work hand-in-hand to determine those aspects of virus assembly and biology that remain unclear. This review examines the trajectory followed by EM imaging techniques in showing the molecular structure of icosahedral viruses, from the first two-dimensional negative staining images of capsids to the latest sophisticated techniques that provide high resolution three-dimensional data, or snapshots of the conformational changes necessary to complete the infectious cycle. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Controlling molecular deposition and layer structure with supramolecular surface assemblies (United States)

    Theobald, James A.; Oxtoby, Neil S.; Phillips, Michael A.; Champness, Neil R.; Beton, Peter H.


    Selective non-covalent interactions have been widely exploited in solution-based chemistry to direct the assembly of molecules into nanometre-sized functional structures such as capsules, switches and prototype machines. More recently, the concepts of supramolecular organization have also been applied to two-dimensional assemblies on surfaces stabilized by hydrogen bonding, dipolar coupling or metal co-ordination. Structures realized to date include isolated rows, clusters and extended networks, as well as more complex multi-component arrangements. Another approach to controlling surface structures uses adsorbed molecular monolayers to create preferential binding sites that accommodate individual target molecules. Here we combine these approaches, by using hydrogen bonding to guide the assembly of two types of molecules into a two-dimensional open honeycomb network that then controls and templates new surface phases formed by subsequently deposited fullerene molecules. We find that the open network acts as a two-dimensional array of large pores of sufficient capacity to accommodate several large guest molecules, with the network itself also serving as a template for the formation of a fullerene layer.

  16. Transmission electron microscopy in molecular structural biology: A historical survey. (United States)

    Harris, J Robin


    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. Solving structures of protein complexes by molecular replacement with Phaser

    International Nuclear Information System (INIS)

    McCoy, Airlie J.


    Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described. Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ‘tree search with pruning’ approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ‘automated MR’ mode and two case studies are used to show how to modify the automated search strategy for problematic cases

  18. Effect of processing on carbon molecular sieve structure and performance

    KAUST Repository

    Das, Mita


    Sub-micron sized carbon molecular sieve (CMS) materials were produced via ball milling for subsequent use in hybrid material formation. A detailed analysis of the effects of the milling process in the presence of different milling environments is reported. The milling process apparently alters the molecular scale structure and properties of the carbon material. Three cases: unmilled, air milled and nitrogen milled, were analyzed in this work. The property changes were probed using equilibrium sorption experiments with different gases. Furthermore, WAXD and BET results also showed differences between milling processes. Finally in order to improve the interfacial polymer-sieve region of hybrid membranes, the CMS surface was chemically modified with a linkage unit capable of covalently bonding the polymer to the sieve. A published single-wall carbon nanotube (SWCNTs) modification method was adopted to attach a primary aromatic amine to the surface. Several aspects including rigidity, chemical composition, bulky groups and length were considered in selecting the preferred linkage unit. Fortunately kinetic and equilibrium sorption properties of the modified sieves showed very little difference from unmodified samples, suggesting that the linkage unit is not excessively filling or obstructing access to the pores of the CMSs during the modification process. © 2010 Elsevier Ltd. All rights reserved.

  19. Introductory group theory and its application to molecular structure

    CERN Document Server

    Ferraro, John R


    The success of the first edition of this book has encouraged us to revise and update it. In the second edition we have attempted to further clarify por­ tions of the text in reference to point symmetry, keeping certain sections and removing others. The ever-expanding interest in solids necessitates some discussion on space symmetry. In this edition we have expanded the discus­ sion on point symmetry to include space symmetry. The selection rules in­ clude space group selection rules (for k = 0). Numerous examples are pro­ vided to acquaint the reader with the procedure necessary to accomplish this. Recent examples from the literature are given to illustrate the use of group theory in the interpretation of molecular spectra and in the determination of molecular structure. The text is intended for scientists and students with only a limited theoretical background in spectroscopy. For this reason we have presented detailed procedures for carrying out the selection rules and normal coor­ dinate treatment of ...

  20. Total Synthesis of (-)-Doliculide, Structure-Activity Relationship Studies and Its Binding to F-Actin

    NARCIS (Netherlands)

    Matcha, Kiran; Madduri, Ashoka V. R.; Roy, Sayantani; Ziegler, Slava; Waldmann, Herbert; Hirsch, Anna K. H.; Minnaard, Adriaan J.


    Actin, an abundant protein in most eukaryotic cells, is one of the targets in cancer research. Recently, a great deal of attention has been paid to the synthesis and function of actin-targeting compounds and their use as effective molecular probes in chemical biology. In this study, we have

  1. Influence of the molecular structure on hydrolyzability of epoxy resins

    International Nuclear Information System (INIS)

    Pays, M.F.


    EDF has decided to use glass reinforced composites for certain pipework in Pressurized Water Reactors (service water, emergency-supplied service water, fine pipe works, etc...) as a replacement for traditional materials. In practice, steel is prone to rapid corrosion in these circuits; introducing composites could prove economically viable if their long term behaviour can be demonstrated. However, composite materials can undergo deterioration in service through hydrolysis of the resin or the fibre-matrix interface. Different resins can be chosen depending on the programmed use. A first study has covered the hydrolyzability of polyester and vinyl ester resins. The present document undertakes the resistance to hydrolysis of epoxy resins, concentrating on those reputed to withstand high temperatures. This research uses model monomer, linking the molecular structure of the materials to their resistance to hydrolysis. (author)

  2. Calculations of optical rotation: Influence of molecular structure

    Directory of Open Access Journals (Sweden)

    Yu Jia


    Full Text Available Ab initio Hartree-Fock (HF method and Density Functional Theory (DFT were used to calculate the optical rotation of 26 chiral compounds. The effects of theory and basis sets used for calculation, solvents influence on the geometry and values of calculated optical rotation were all discussed. The polarizable continuum model, included in the calculation, did not improve the accuracy effectively, but it was superior to γs. Optical rotation of five or sixmembered of cyclic compound has been calculated and 17 pyrrolidine or piperidine derivatives which were calculated by HF and DFT methods gave acceptable predictions. The nitrogen atom affects the calculation results dramatically, and it is necessary in the molecular structure in order to get an accurate computation result. Namely, when the nitrogen atom was substituted by oxygen atom in the ring, the calculation result deteriorated.

  3. Hamiltonian flow over saddles for exploring molecular phase space structures (United States)

    Farantos, Stavros C.


    Despite using potential energy surfaces, multivariable functions on molecular configuration space, to comprehend chemical dynamics for decades, the real happenings in molecules occur in phase space, in which the states of a classical dynamical system are completely determined by the coordinates and their conjugate momenta. Theoretical and numerical results are presented, employing alanine dipeptide as a model system, to support the view that geometrical structures in phase space dictate the dynamics of molecules, the fingerprints of which are traced by following the Hamiltonian flow above saddles. By properly selecting initial conditions in alanine dipeptide, we have found internally free rotor trajectories the existence of which can only be justified in a phase space perspective. This article is part of the theme issue `Modern theoretical chemistry'.

  4. Coding considerations for standalone molecular dynamics simulations of atomistic structures (United States)

    Ocaya, R. O.; Terblans, J. J.


    The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

  5. Synthesis, structure and electronic structure of a new polymorph of CaGe2

    International Nuclear Information System (INIS)

    Tobash, Paul H.; Bobev, Svilen


    Reported are the flux synthesis, the crystal structure determination, the properties and the band structure calculations of a new polymorph of CaGe 2 , which crystallizes with the hexagonal space group P6 3 mc (no. 186) with cell parameters of a=3.9966(9) and c=10.211(4)A (Z=2; Pearson's code hP6). The structure can be viewed as puckered layers of three-bonded germanium atoms, ∼ 2 [Ge 2 ] 2- , which are stacked along the direction of the c-axis in an ABAB-fashion. The germanium polyanionic layers are separated by the Ca cations. As such, this structure is closely related to the structure of the other CaGe 2 polymorph, which crystallizes with the rhombohedral CaSi 2 type in the R3-bar m space group (No. 166), where the ∼ 2 [Ge 2 ] 2- layers are arranged in an AA'BB'CC'-fashion, and are also interspaced by Ca 2+ cations. LMTO calculations suggest that in spite of the formal closed-shell configuration for all atoms and the apparent adherence to the Zintl rules for electron counting, i.e., Ca 2+ [3b-Ge 1- ] 2 ), the phase will be a poor metal due to a small Ca-3d-Ge-4p band overlap. Magnetic susceptibility measurements as a function of the temperature indicate that the new CaGe 2 polymorph exhibits weak, temperature independent, Pauli-paramagnetism

  6. Synthesis of C-di-saccharidic compounds by radical cyclisation. Study of biological, structural and dynamic properties

    International Nuclear Information System (INIS)

    Rubinstenn, Gilles


    The synthesis of carbohydrate mimics and particularly of C-disaccharides, molecules in which the inter-glycosidic oxygen atom has been replaced by a methylene group, has become, this past two decades, an important challenge in organic chemistry. In the first chapter we present the synthesis of C-disaccharides from the neutral series by a silaketal tethering. The key step of this C-glycosylation is a radical macro-cyclisation. This strategy is applied to the synthesis of two analogues of natural, biologically active, products, the lactose and the Lewis x tri-saccharide. The biological activity of this mimetics is then evaluated. A new tethering strategy, based on the use of phosphorus III compounds, is applied, in the second chapter, to the building of C-disaccharides of the 2'-amino 2'- deoxy series. The third chapter deals with the structural and dynamics study of the C-glycosides prepared in chapter 1 by Nuclear Magnetic Resonance. A new methodology, studying the dipolar relaxation along an effective field, generated through an off-resonance RF field, allowed the precise measurement of longitudinal and transverse cross-relaxation rates. Structural and dynamics parameter thus derived are used as restraints for molecular modeling. The results of this study are then compared to those of the biological tests. (author) [fr

  7. Total chemical synthesis, refolding, and crystallographic structure of fully active immunophilin calstabin 2 (FKBP12.6). (United States)

    Bacchi, Marine; Jullian, Magali; Sirigu, Serena; Fould, Benjamin; Huet, Tiphaine; Bruyand, Lisa; Antoine, Mathias; Vuillard, Laurent; Ronga, Luisa; Chavas, Leonard M G; Nosjean, Olivier; Ferry, Gilles; Puget, Karine; Boutin, Jean A


    Synthetic biology (or chemical biology) is a growing field to which the chemical synthesis of proteins, particularly enzymes, makes a fundamental contribution. However, the chemical synthesis of catalytically active proteins (enzymes) remains poorly documented because it is difficult to obtain enough material for biochemical experiments. We chose calstabin, a 107-amino-acid proline isomerase, as a model. We synthesized the enzyme using the native chemical ligation approach and obtained several tens of milligrams. The polypeptide was refolded properly, and we characterized its biophysical properties, measured its catalytic activity, and then crystallized it in order to obtain its tridimensional structure after X-ray diffraction. The refolded enzyme was compared to the recombinant, wild-type enzyme. In addition, as a first step of validating the whole process, we incorporated exotic amino acids into the N-terminus. Surprisingly, none of the changes altered the catalytic activities of the corresponding mutants. Using this body of techniques, avenues are now open to further obtain enzymes modified with exotic amino acids in a way that is only barely accessible by molecular biology, obtaining detailed information on the structure-function relationship of enzymes reachable by complete chemical synthesis. © 2016 The Protein Society.

  8. Synthesis and structure of bis(β-dibenzoyl methanato -O,O') (aquo-O ...

    Indian Academy of Sciences (India)

    Synthesis and structure of bis(β-dibenzoyl methanato -O,O') (aquo-O) dioxouranium (VI) compound ... Keywords. β-diketonates; uranyl ion; adduct compound; crystal structure; hydrogen bonding. 1. Introduction. Structural studies on uranyl ... crystalline product obtained was filtered, washed with ether and dried. The crystal ...

  9. Molecular crowding of collagen: a pathway to produce highly-organized collagenous structures. (United States)

    Saeidi, Nima; Karmelek, Kathryn P; Paten, Jeffrey A; Zareian, Ramin; DiMasi, Elaine; Ruberti, Jeffrey W


    Collagen in vertebrate animals is often arranged in alternating lamellae or in bundles of aligned fibrils which are designed to withstand in vivo mechanical loads. The formation of these organized structures is thought to result from a complex, large-area integration of individual cell motion and locally-controlled synthesis of fibrillar arrays via cell-surface fibripositors (direct matrix printing). The difficulty of reproducing such a process in vitro has prevented tissue engineers from constructing clinically useful load-bearing connective tissue directly from collagen. However, we and others have taken the view that long-range organizational information is potentially encoded into the structure of the collagen molecule itself, allowing the control of fibril organization to extend far from cell (or bounding) surfaces. We here demonstrate a simple, fast, cell-free method capable of producing highly-organized, anistropic collagen fibrillar lamellae de novo which persist over relatively long-distances (tens to hundreds of microns). Our approach to nanoscale organizational control takes advantage of the intrinsic physiochemical properties of collagen molecules by inducing collagen association through molecular crowding and geometric confinement. To mimic biological tissues which comprise planar, aligned collagen lamellae (e.g. cornea, lamellar bone or annulus fibrosus), type I collagen was confined to a thin, planar geometry, concentrated through molecular crowding and polymerized. The resulting fibrillar lamellae show a striking resemblance to native load-bearing lamellae in that the fibrils are small, generally aligned in the plane of the confining space and change direction en masse throughout the thickness of the construct. The process of organizational control is consistent with embryonic development where the bounded planar cell sheets produced by fibroblasts suggest a similar confinement/concentration strategy. Such a simple approach to nanoscale

  10. Determining the stereochemical structures of molecular ions by ''Coulomb-explosion'' techniques with fast (MeV) molecular ion beams

    International Nuclear Information System (INIS)

    Gemmell, D.S.


    Recent studies on the dissociation of fast (MeV) molecular ion beams in thin foils suggest a novel alternative approach to the determination of molecular ion structures. In this article we review some recent high-resolution studies on the interactions of fast molecular ion beams with solid and gaseous targets and indicate how such studies may be applied to the problem of determining molecular ion structures. The main features of the Coulomb explosion of fast-moving molecular ion projectiles and the manner in which Coulomb-explosion techniques may be applied to the problem (difficult to attack by more conventional means) of determining the stereochemical structures of molecular ions has been described in this paper. Examples have been given of early experiments designed to elicit structure information. The techniques are still in their infancy, and it is to be expected that as both the technology and the analysis are refined, the method will make valuable contributions to the determination of molecular ion structures

  11. Molecular structure and exciton dynamics in organic conjugated polymers (United States)

    Thomas, Alan K.

    , quenchable, isolated singlet excitations. The structure of J aggregates which leads to isolated excitations, and the role which inter-chain contact sites play in triplet formation from these singlet excitations is revealed. New structure-function relationships were uncovered in poly (3-alkyl-thienylenevinylene) (P3ATV) derivatives using resonance Raman and photocurrent spectroscopies. Time-dependent spectroscopic theory was used to interpret experimental Raman and absorption spectra that revealed the presence of structural polymorphs. These polymorphs provide an explanation of the spectroscopic evidence without presumption of a deactivating dark state in this unusually non-fluorescence material. Photovoltaic devices constructed from blends of poly (2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT) and PCBM blends were examined using Raman and photocurrent imaging techniques. These techniques were used to identify different packing states in blended thin films and correlate photocurrent production with local order. Intensity modulated spectroscopic techniques (IMPS) were then used to locate regions of non-geminate charge recombination at interfaces between amorphous and crystalline regions in working devices. Next, P3HT/PCBM OPV devices were exposed to ionizing radiation in a vacuum chamber. These devices were characterized before and after exposure, using standardized solar cell tests, Raman imaging, wide-field IMPS, and IMVS spectroscopies. An analysis of the spectroscopic data determined that the donor polymer is highly resistant to radiation damage, and that the degradation of device performance is due to an effect (cross-linking or degradation) within aggregates of the acceptor. This dissertation concludes with an interpretation of the significance of the findings contained herein to organic electronics, followed by a brief outlook for future work in these fields. Potential theories to describe and predict molecular interactions for organic polymers in

  12. Synthesis and the crystal and molecular structure of the silver(I)–germanium(IV) polymeric complex with citrate anions ([Ag{sub 2}Ge(HCit){sub 2}(H{sub 2}O){sub 2}] ∙ 2H{sub 2}O){sub n}

    Energy Technology Data Exchange (ETDEWEB)

    Sergienko, V. S., E-mail: [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation); Martsinko, E. E.; Seifullina, I. I. [Mechnikov Odessa National University (Ukraine); Churakov, A. V. [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation); Chebanenko, E. A. [Mechnikov Odessa National University (Ukraine)


    The synthesis and X-ray diffraction study of compound ([Ag{sub 2}Ge(HCit){sub 2}(H{sub 2}O){sub 2}] ∙ 2H{sub 2}O){sub n}, where H{sub 4}Cit is the citric acid, are performed. In the polymeric structure, the HCit{sup 3–} ligand fulfils the tetradentate chelate–μ{sub 4}-bridging (3Ag, Ge) function (tridentate with respect to Ge and Ag atoms). The Ge atom is octahedrally coordinated by six O atoms of two HCit{sup 3–}ligands. The coordination polyhedron of the Ag atom is an irregular five-vertex polyhedron [four O atoms of four HCit{sup 3–} ligands and the O(H{sub 2}O) atom]. An extended system of O–H···O hydrogen bonds connects complex molecules into a supramolecular 3D-framework.

  13. Local Synthesis of Carbon Nanotubes in Silicon Microsystems: The Effect of Temperature Distribution on Growth Structure

    Directory of Open Access Journals (Sweden)

    Knut E. Aasmundtveit


    Full Text Available Local synthesis and direct integration of carbon nanotubes (CNTs into microsystems is a promising method for producing CNT-based devices in a single step, low-cost, and wafer-level, CMOS/MEMS-compatible process. In this report, the structure of the locally grown CNTs are studied by transmission imaging in scanning electron microscopy—S(TEM. The characterization is performed directly on the microsystem, without any post-synthesis processing required. The results show an effect of temperature on the structure of CNTs: high temperature favors thin and regular structures, whereas low temperature favors “bamboo-like” structures.

  14. Molecular structure of tetramethylgermane from gas electron diffraction (United States)

    Csákvári, Éva; Rozsondai, Béla; Hargittai, István


    The molecular structure of Ge(CH 3) 4 has been determined from gas-phase electron diffraction augmented by a normal coordinate analysis. Assuming tetrahedral symmetry for the germanium bond configuration, the following structural parameters are found: rg(GeC) = 1.958 ± 0.004 Å, rg(CH) = 1.111 ± 0.003 Å and ∠(GeCH) = 110.7 ± 0.2° ( R=4.0%). The methyl torsional barrier V 0 is estimated to be 1.3 kJ mol -1 on the basis of an effective angle of torsion 23.0 ± 1.5°, from the staggered form, yielded directly by the analysis. The GeC bond length of Ge(CH 3) 4 is the same, within experimental error, as that of Ge(C 6H 5) 4 and is in agreement with the prediction of a modified Schomaker-Stevenson relationship.

  15. Molecular structure-adsorption study on current textile dyes. (United States)

    Örücü, E; Tugcu, G; Saçan, M T


    This study was performed to investigate the adsorption of a diverse set of textile dyes onto granulated activated carbon (GAC). The adsorption experiments were carried out in a batch system. The Langmuir and Freundlich isotherm models were applied to experimental data and the isotherm constants were calculated for 33 anthraquinone and azo dyes. The adsorption equilibrium data fitted more adequately to the Langmuir isotherm model than the Freundlich isotherm model. Added to a qualitative analysis of experimental results, multiple linear regression (MLR), support vector regression (SVR) and back propagation neural network (BPNN) methods were used to develop quantitative structure-property relationship (QSPR) models with the novel adsorption data. The data were divided randomly into training and test sets. The predictive ability of all models was evaluated using the test set. Descriptors were selected with a genetic algorithm (GA) using QSARINS software. Results related to QSPR models on the adsorption capacity of GAC showed that molecular structure of dyes was represented by ionization potential based on two-dimensional topological distances, chromophoric features and a property filter index. Comparison of the performance of the models demonstrated the superiority of the BPNN over GA-MLR and SVR models.

  16. Bonding and structure in dense multi-component molecular mixtures. (United States)

    Meyer, Edmund R; Ticknor, Christopher; Bethkenhagen, Mandy; Hamel, Sebastien; Redmer, Ronald; Kress, Joel D; Collins, Lee A


    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10,000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systems engendered by variations in the concentration ratios. A basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers.

  17. Green synthesis and structural control of metal and mineral nanostructures

    DEFF Research Database (Denmark)

    Engelbrekt, Christian

    nanomaterials. In the first approach, time-resolved chronopotentiometry, pH, conductivity and turbidity, and ultraviolet-visible light spectroscopy were employed to follow the green synthesis of gold nanoparticles. Several distinct phases were observed with all techniques providing a broad picture....... Detailed crystallographic characterization was obtained by combining X-ray diffraction and infrared spectroscopy. The synthesis of CuO was further optimized and the flat, rod-shaped nanostructures applied as heterogeneous catalysts for oxidative dehydrogenation reactions. High activity and good reusability...

  18. Retinal structure, function, and molecular pathologic features in gyrate atrophy. (United States)

    Sergouniotis, Panagiotis I; Davidson, Alice E; Lenassi, Eva; Devery, Sophie R; Moore, Anthony T; Webster, Andrew R


    To describe phenotypic variability and to report novel mutational data in patients with gyrate atrophy. Retrospective case series. Seven unrelated patients (10 to 52 years of age) with clinical and biochemical evidence of gyrate atrophy. Detailed ophthalmologic examination, fundus photography, fundus autofluorescence (FAF) imaging, spectral-domain optical coherence tomography, and microperimetry testing were performed. The coding region and intron-exon boundaries of ornithine aminotransferase (OAT) were analyzed. OAT mRNA was isolated from peripheral blood leucocytes of 1 patient and analyzed. OAT mutation status and resultant clinical, structural, and functional characteristics. Funduscopy revealed circular areas of chorioretinal atrophy, and FAF imaging showed sharply demarcated areas of increased or preserved signal in all 7 patients. Spectral-domain optical coherence tomography revealed multiple intraretinal cystic spaces and hyperreflective deposit in the ganglion cell layer of all study subjects. Round tubular, rosette-like structures located in the outer nuclear layer of the retinae of the 4 older patients were observed (termed outer retinal tubulation). Thickening was evident in the foveolae of younger patients, despite the posterior pole appearing relatively preserved. Macular function, assessed by microperimetry, was preserved over areas of normal or increased autofluorescence. However, sensitivity was reduced even in structurally intact parts of the retina. The molecular pathologic features were determined in all study subjects: 9 mutations, 4 novel, were detected in the OAT gene. OAT mRNA was isolated from blood leukocytes, and monoallelic expression of a mutated allele was demonstrated in 1 patient. Fundus autofluorescence imaging can reveal the extent of neurosensory dysfunction in gyrate atrophy patients. Macular edema is a uniform finding; the fovea is relatively thick in early stages of disease and retinal tubulation is present in advanced disease

  19. A Chemical Template for Synthesis of Molecular Sheets of Calcium Carbonate (United States)

    Rianasari, Ina; Benyettou, Farah; Sharma, Sudhir Kumar; Blanton, Thomas; Kirmizialtin, Serdal; Jagannathan, Ramesh


    Inspired by the discovery of graphene and its unique properties, we focused our research to develop a scheme to create nacre like lamellar structures of molecular sheets of CaCO3 interleaved with an organic material, namely carbon. We developed a facile, chemical template technique, using a formulation of poly(acrylic) acid (PAA) and calcium acetate to create lamellar stacks of single crystal sheets of CaCO3, with a nominal thickness of 17 Å, the same as a unit-cell dimension for calcite (c-axis = 17.062 Å), interleaved with amorphous carbon with a nominal thickness of 8 Å. The strong binding affinity between carboxylate anions and calcium cations in the formulation was used as a molecular template to guide CaCO3 crystallization. Computational modeling of the FTIR spectra showed good agreement with experimental data and confirmed that calcium ions are bridged between polymer chains, resulting in a net-like polymer structure. The process readily lends itself to explore the feasibility of creating molecular sheets of other important inorganic materials and potentially find applications in many fields such as super capacitors and “low k di-electric” systems.

  20. Total synthesis based on the originally claimed structure of mucosin. (United States)

    Gallantree-Smith, Harrison C; Antonsen, Simen G; Görbitz, Carl H; Hansen, Trond V; Nolsøe, Jens M J; Stenstrøm, Yngve H


    The first total synthesis aimed at the naturally occurring eicosanoid bicycle mucosin is reported. A practical route has been devised allowing the issues relating to the previous assignment of stereochemistry to be examined. X-ray crystallography was performed on a late stage intermediate to pinpoint the topological relationship displayed by the featured bicyclo[4.3.0]non-3-ene scaffold.

  1. Synthesis, characterization and crystal structure of new nickel ...

    Indian Academy of Sciences (India)

    School of Chemistry, University College of Science, University of Tehran, Tehran, Iran. Email: ... nation polymers and coordination complexes, is a suit- able building block for supramolecular ..... Kianpour G, Salavati-Niasari M and Emadi H 2013. Precipitation synthesis and characterization of cobalt.

  2. Synthesis and structure of copper(II) complexes: Potential cyanide ...

    Indian Academy of Sciences (India)

    ing the oxidase models. The necessity to make progress in developing copper oxidase models requires synthesis of appropriate copper complexes to rationalize the func- tions of such oxidases unequivocally.46–52 Therefore, to study the coordination chemistry of Cu(II) incorpo- rating the new azo ligands,53 HLa and HLb, ...

  3. Synthesis, characterization, crystal structure and DNA-binding study ...

    Indian Academy of Sciences (India)


    SYNOPSIS. Synthesis and characterization of four mononuclear eight coordinated cadmium(II) complexes with newly explored carboxamide derivatives and study of interaction with calf-thymus DNA are reported. The results suggest that neutral complexes 2a and 2b bind to DNA in an intercalative mode. On the other hand, ...

  4. synthesis and structural studies of first row transition metal ...

    African Journals Online (AJOL)


    deals with the synthesis and characterization of NBHQO and its complexes with chromium(III), manganese(II), iron(III), cobalt(II), nickel(II) and copper(II). EXPERIMENTAL. All the chemicals used were either of AR or chemically pure grade. Mass spectra were recorded on a Perkin-Elmer Hitachi-6L spectrometer and 1H NMR ...

  5. Synthesis, structural characterization and biological activity of a ...

    Indian Academy of Sciences (India)

    3.1 Synthesis and formulation. Schiff base ligand H2L was synthesized by 1:1 conden- sation of O-aminophenol and O-vanillin in dehydrated alcohol. 1 was prepared using reaction among Zn(II) salt and the ligand in methanol. Coordination geo- metry of 1 was determined by different spectroscopic characterization.

  6. High-fidelity de novo synthesis of pathways using microchip-synthesized oligonucleotides and general molecular biology equipment. (United States)

    Wan, Wen; Lu, Min; Wang, Dongmei; Gao, Xiaolian; Hong, Jiong


    Engineering and evaluation of synthetic routes for generating valuable compounds require accurate and cost-effective de novo synthesis of genetic pathways. Here, we present an economical and streamlined de novo DNA synthesis approach for engineering a synthetic pathway with microchip-synthesized oligonucleotides (oligo). The process integrates entire oligo pool amplification, error-removal, and assembly of long DNA molecules. We utilized this method to construct a functional lycopene biosynthetic pathway (11.9 kb encoding 10 genes) in Escherichia coli using a highly error-prone microchip-synthesized oligo pool (479 oligos) without pre-purification, and the error-frequency was reduced from 14.25/kb to 0.53/kb. This low-equipment-dependent and cost-effective method can be widely applied for rapid synthesis of biosynthetic pathways in general molecular biology laboratories.

  7. X-ray diffraction, neutron diffraction and analysis of molecular structures

    International Nuclear Information System (INIS)

    Fontecilla-Camps, J.C.


    The only method that is capable to show the atomic structure of most of macromolecules is the X ray diffraction; neutron diffraction is mostly used for the localization of hydrogen atoms, too light to be detected by X ray diffraction. With the growing number of known structures, the molecular crystallographic study may combine the molecular replacement technique and the co-crystallization method, or use the new Laue method, and leads to the functional and topological analysis of biological molecular structures

  8. Synthesis and Characterization of Magnetic-Graphene Molecularly Imprinted Polymers for Selective Recognition of Ltryptophan

    Directory of Open Access Journals (Sweden)

    Zhang Yi


    Full Text Available In this paper, a novel molecular imprinted polymer using L-tryptophan(L-Trp as the template, dopamine(DA as both functional monomer and cross linking agent, magnetic graphene as the supporting matrix was synthesized. The prepared magnetic-graphene molecularly imprinted polymers(Fe3O4@GO-MIPs were characterized by Fourier transform infrared spectrometer(FT-IR, transmission electron microscopy (TEM, vibrating sample magnetometer (VSM, respectively. The results showed that when the molar ratio of L- tryptophan and dopamine was 1:4 and the reaction temperature was 60 °C, Fe3O4@GO-MIPs had the best adsorption quantity of 31.9 mg/g. The rebinding experiments indicated that Fe3O4@GO-MIPs not only have outstanding affinity and selectivity towards L-Trp over structurally related compounds but also easily reach the magnetic separation under an external magnetic field.

  9. The Role of Template Structure and Synergism between Inorganic and Organic Structure Directing Agents in the Synthesis of UTL Zeolite

    Czech Academy of Sciences Publication Activity Database

    Shvets, O. V.; Kasian, N.; Zukal, Arnošt; Pinkas, Jiří; Čejka, Jiří


    Roč. 22, č. 11 (2010), s. 3482-3495 ISSN 0897-4756 R&D Projects: GA ČR GA203/08/0604; GA ČR GA104/07/0383 Institutional research plan: CEZ:AV0Z40400503 Keywords : UTL zeolite * synthesis * zeolite molecular sietes Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.400, year: 2010

  10. Structural design, synthesis and structure-activity relationships of thiazolidinones with enhanced anti-Trypanosoma cruzi activity. (United States)

    Moreira, Diogo Rodrigo Magalhães; Leite, Ana Cristina Lima; Cardoso, Marcos Verissimo Oliveira; Srivastava, Rajendra Mohan; Hernandes, Marcelo Zaldini; Rabello, Marcelo Montenegro; da Cruz, Luana Faria; Ferreira, Rafaela Salgado; de Simone, Carlos Alberto; Meira, Cássio Santana; Guimaraes, Elisalva Teixeira; da Silva, Aline Caroline; dos Santos, Thiago André Ramos; Pereira, Valéria Rêgo Alves; Soares, Milena Botelho Pereira


    Pharmacological treatment of Chagas disease is based on benznidazole, which displays poor efficacy when administered during the chronic phase of infection. Therefore, the development of new therapeutic options is needed. This study reports on the structural design and synthesis of a new class of anti-Trypanosoma cruzi thiazolidinones (4 a-p). (2-[2-Phenoxy-1-(4-bromophenyl)ethylidene)hydrazono]-5-ethylthiazolidin-4-one (4 h) and (2-[2-phenoxy-1-(4-phenylphenyl)ethylidene)hydrazono]-5-ethylthiazolidin-4-one (4 l) were the most potent compounds, resulting in reduced epimastigote proliferation and were toxic for trypomastigotes at concentrations below 10 μM, while they did not display host cell toxicity up to 200 μM. Thiazolidinone 4 h was able to reduce the in vitro parasite burden and the blood parasitemia in mice with similar potency to benznidazole. More importantly, T. cruzi infection reduction was achieved without exhibiting mouse toxicity. Regarding the molecular mechanism of action, these thiazolidinones did not inhibit cruzain activity, which is the major trypanosomal protease. However, investigating the cellular mechanism of action, thiazolidinones altered Golgi complex and endoplasmic reticulum (ER) morphology, produced atypical cytosolic vacuoles, as well as induced necrotic parasite death. This structural design employed for the new anti-T. cruzi thiazolidinones (4 a-p) led to the identification of compounds with enhanced potency and selectivity compared to first-generation thiazolidinones. These compounds did not inhibit cruzain activity, but exhibited strong antiparasitic activity by acting as parasiticidal agents and inducing a necrotic parasite cell death. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Light-operated machines based on threaded molecular structures. (United States)

    Credi, Alberto; Silvi, Serena; Venturi, Margherita


    Rotaxanes and related species represent the most common implementation of the concept of artificial molecular machines, because the supramolecular nature of the interactions between the components and their interlocked architecture allow a precise control on the position and movement of the molecular units. The use of light to power artificial molecular machines is particularly valuable because it can play the dual role of "writing" and "reading" the system. Moreover, light-driven machines can operate without accumulation of waste products, and photons are the ideal inputs to enable autonomous operation mechanisms. In appropriately designed molecular machines, light can be used to control not only the stability of the system, which affects the relative position of the molecular components but also the kinetics of the mechanical processes, thereby enabling control on the direction of the movements. This step forward is necessary in order to make a leap from molecular machines to molecular motors.

  12. Synthesis, structural, spectroscopic and biological studies of Schiff base complexes (United States)

    Diab, M. A.; El-Sonbati, A. Z.; Shoair, A. F.; Eldesoky, A. M.; El-Far, N. M.


    Schiff base ligand 4-((pyridin-2- yl)methyleneamino)-1,2-dihydro-2,3-dimethyl-1-phenylpyrazol-5-one (PDMP) and its complexes were prepared and characterized on the basis of elemental analysis, IR, mass spectra and thermogravimetric analysis. All results confirm that the complexes have 1:1 (M: PMDP) stoichiometric formula [M(PMDP)Cl2H2O ] (M = Cu(II), Co(II), Ni(II) and Mn(II)), [Cd(PMDP)Cl2] and the ligand behaves as a bi/tridentate forming five-membered chelating ring towards the metal ions, bonding through azomethine nitrogen/exocyclic carbonyl oxygen, azomethine pyridine nitrogen and exocyclic carbonyl oxygen. The shift in the band positions of the groups involved in coordination has been utilized to estimate the metal-nitrogen and/or oxygen bond lengths. The complexes of Co(II), Ni(II) and Cu(II) are paramagnetic and the magnetic as well as spectral data suggest octahedral geometry, whereas the Cd(II) complex is tetrahedral. The XRD studies show that both the ligand and its metal complexes (1 and 3) show polycrystalline with crystal structure. Molecular docking was used to predict the binding between PMDP ligand and the receptors. The corrosion inhibition of mild steel in 2 M HCl solution by PDMP was explored utilizing potentiodynamic polarization, electrochemical impedance spectroscopy (EIS) and (EFM) electrochemical frequency modulation method. Potentiodynamic polarization demonstrated that PDMP compound is mixed-type inhibitor. EIS spectra exhibit one capacitive loop and confirm the protective ability. The percentage of inhibition efficiency was found to increase with increasing the inhibitor concentration.

  13. Sound Synthesis and Musical Composition by Physical Modelling of Self-Sustained Oscillating Structures


    Poyer, François; Cadoz, Claude


    Paper 3 - Audio Synthesis (Oral Presentations); International audience; In this paper, we present the first results of a study that is carried out with the sound synthesis and musical creation environment GENESIS on self-sustained oscillating structures models. Based on the mass-interaction CORDIS-ANIMA physical modelling formalism, GENESIS has got the noteworthy property that it allows to work both on sound itself and on musical composition in a single coherent environment. By taking as a st...

  14. Synthesis and Structural Studies of Nanocrystalline Cd 0.3 Zn 0.7 Fe ...

    African Journals Online (AJOL)

    Synthesis and Structural Studies of Nanocrystalline Cd 0.3 Zn 0.7 Fe 2 O 4. ... South African Journal of Chemistry ... The synthesis of Cd0.3Zn0.7Fe2O4 nanoparticles has been achieved by a simple thermal decomposition method from the inorganic precursor, Cdd0.3Zn0.7Fe2(cin)3(N2H4)2, which was obtained by a novel ...

  15. Uranium hetero-bimetallic complexes: synthesis, structure and magnetic properties

    International Nuclear Information System (INIS)

    Le Borgne, Th.


    The aim of this thesis is to synthesize molecular complexes with uranium and transition metal ions in close proximity, to determine the nature of the magnetic interaction between them. We decided to use Schiff bases as assembling ligands, which are unusual for uranium (IV). Although the simplest Schiff bases, such as H 2 Salen, lead to ligand exchange reactions, the bi-compartmental Schiff base H 4 L 6 (bis(3-hydroxy-salicylidene) - 2,2-dimethyl-propylene) allows the crystal structure determination of the complex [L 6 Cu(pyr)]U[L 6 Cu].2pyr, obtained by reaction of the metallo-ligand H 2 L 6 Cu with U(acac) 4 . In this manner, the complexes [L 6 Co(pyr)] 2 U and [L 6 Ni(pyr)] 2 U.pyr were also isolated, as well as the compounds in which the paramagnetic ions have been exchanged by the diamagnetic ions Zn II , Zr IV and Th IV ': [L 6 Zn(pyr)] 2 U, [L 6 Cu] 2 Zr and [L 6 Cu(pyr)]Th[L 6 Cu].2pyr. These complexes are the first which involve three metallic centres assembling by the means of a hexa-dentate Schiff base. The crystalline structures show, for all these complexes, the outstanding orthogonal arrangement of the two fragments L 6 M around the central atom which is in a dodecahedral environment of eight oxygen atoms of two Schiff bases. The syntheses of the isostructural complexes Cu2 II and Zn 2 U in which the uranium (IV) ion is close, in the first one, to the paramagnetic ion Cu II and, in the second one, to the diamagnetic ion Zn II , has allowed the use of the empiric method to determine the nature of the magnetic interaction between an f element and a transition metal. The comparison of the magnetic behaviour of two complexes Cu 2 U and Zn 2 U, expressed by the variation of χT vs T, reveals the ferromagnetic interaction in the heart of the triad Cu-U-Cu. The magnetic behaviour of the complexes Cu 2 Th et Cu 2 Zr which does not show any coupling between the two copper (II) ions and the weak antiferromagnetic interaction in the Ni 2 U compound, favour the

  16. MWW-type titanosilicate synthesis, structural modification and catalytic applications to green oxidations

    CERN Document Server

    Wu, Peng; Xu, Le; Liu, Yueming; He, Mingyuan


    This book provides a comprehensive review of a new generation of selective oxidation titanosilicate catalysts with the MWW topology (Ti-MWW) based on the research achievements of the past 12 years. It gives an overview of the synthesis, structure modification and catalytic properties of Ti-MWW. Ti-MWW can readily be prepared by means of direct hydrothermal synthesis with crystallization-supporting agents, using dual-structure-directing agents and a dry-gel conversion technique. It also can be post-synthesized through unique reversible structure transformation and liquid-phase isomorphous subst

  17. Merremoside D: de novo synthesis of the purported structure, NMR analysis, and comparison of spectral data. (United States)

    Sharif, Ehesan U; Wang, Hua-Yu Leo; Akhmedov, Novruz G; O'Doherty, George A


    The first synthesis of the purported structure of Merremoside D has been achieved in 22 longest linear steps. The de novo asymmetric synthesis relied on the use of asymmetric catalysis to selectively install all 21 stereocenters in the final compounds from commercially available achiral starting materials. Adiabatic gradient 2D NMR techniques (gHSQCAD, gHMBCAD, gH2BCAD, gHSQCTOXYAD, ROESYAD) were used to completely assign the structure of synthetic Merremoside D. Comparison of our assignments with the limited NMR data reported for natural Merremoside D allows for the tentative confirmation of its structure.

  18. Influence of the synthesis conditions of gold nanoparticles on the structure and architectonics of dipeptide composites

    Energy Technology Data Exchange (ETDEWEB)

    Loskutov, Alexander I., E-mail: [Moscow State Technological University STANKIN (Russian Federation); Guskova, Olga A. [Leibniz Institute of Polymer Research Dresden (Germany); Grigoriev, Sergey N.; Oshurko, Vadim B. [Moscow State Technological University STANKIN (Russian Federation); Tarasiuk, Aleksei V. [Russian Academy of Medical Sciences, FSBI “Zakusov Institute of Pharmacology” (Russian Federation); Uryupina, Olga Ya. [Russian Academy of Sciences, Frumkin Institute of Physical Chemistry and Electrochemistry (Russian Federation)


    A wide variety of peptides and their natural ability to self-assemble makes them very promising candidates for the fabrication of solid-state devices based on nano- and mesocrystals. In this work, we demonstrate an approach to form peptide composite layers with gold nanoparticles through in situ reduction of chloroauric acid trihydrate by dipeptide and/or dipeptide/formaldehyde mixture in the presence of potassium carbonate at different ratios of components. Appropriate composition of components for the synthesis of highly stable gold colloidal dispersion with particle size of 34–36 nm in dipeptide/formaldehyde solution is formulated. Infrared spectroscopy results indicate that dipeptide participates in the reduction process, conjugation with gold nanoparticles and the self-assembly in 2D, which accompanied by changing peptide chain conformations. The structure and morphology of the peptide composite solid layers with gold nanoparticles on gold, mica and silica surfaces are characterized by atomic force microscopy. In these experiments, the flat particles, dendrites, chains, mesocrystals and Janus particles are observed depending on the solution composition and the substrate/interface used. The latter aspect is studied on the molecular level using computer simulations of individual peptide chains on gold, mica and silica surfaces.

  19. Synthesis, photodynamic activity, and quantitative structure-activity relationship modelling of a series of BODIPYs. (United States)

    Caruso, Enrico; Gariboldi, Marzia; Sangion, Alessandro; Gramatica, Paola; Banfi, Stefano


    Here we report the synthesis of eleven new BODIPYs (14-24) characterized by the presence of an aromatic ring on the 8 (meso) position and of iodine atoms on the pyrrolic 2,6 positions. These molecules, together with twelve BODIPYs already reported by us (1-12), represent a large panel of BODIPYs showing different atoms or groups as substituent of the aromatic moiety. Two physico-chemical features ( 1 O 2 generation rate and lipophilicity), which can play a fundamental role in the outcome as photosensitizers, have been studied. The in vitro photo-induced cell-killing efficacy of 23 PSs was studied on the SKOV3 cell line treating the cells for 24h in the dark then irradiating for 2h with a green LED device (fluence 25.2J/cm 2 ). The cell-killing efficacy was assessed with the MTT test and compared with that one of meso un-substituted compound (13). In order to understand the possible effect of the substituents, a predictive quantitative structure-activity relationship (QSAR) regression model, based on theoretical holistic molecular descriptors, was developed. The results clearly indicate that the presence of an aromatic ring is fundamental for an excellent photodynamic response, whereas the electronic effects and the position of the substituents on the aromatic ring do not influence the photodynamic efficacy. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Synthesis, Crystal Structure and in vitro DNA Binding Studies of Combretastatin A-4 Analogue

    Directory of Open Access Journals (Sweden)

    Masood Ahmad Rizvi


    Full Text Available Synthesis of a novel Combretastatin A-4 analogue using Schiff’s reaction of benzil and 4-aminoantipyrine has been achieved under solvent free conditions. The structure of compound was examined spectroscopically and confirmed from single crystal diffraction studies. The synthesized Combretastatin A-4 analogue was investigated for its DNA binding ability as the plausible mechanism for its antitumor activity. The binding propensity of the synthesized compound with calf-thymus (CT DNA was monitored with absorption and emission spectrophotometric titrations. The calculations predict a binding constant of 7.24×104 for the complex of the synthesized compound with CT DNA which is comparable in magnitude to that of DNA binding of bactericidal drug enoxacin and typical intercalation indicator ethidium bromide (EB. Competitive binding studies of the synthesized compound with EB using fluorescence titration reveal that it displaces the DNA-bound EB and binds in intercalative mode which was further supported by circular dichroism (CD spectroscopy. The probable site and binding energy of the compound with DNA was further theoretically investigated by molecular docking studies. The significant DNA binding ability of the synthesized Combretastatin A4 analogue as revealed from this study could be related to the anticancer activity of the Combretastatin A4.

  1. Influence of arsenic stress on synthesis and localization of low-molecular-weight thiols in Pteris vittata

    Energy Technology Data Exchange (ETDEWEB)

    Sakai, Yuki [Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kitaku, Sapporo 060-8589 (Japan); Watanabe, Toshihiro, E-mail: [Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kitaku, Sapporo 060-8589 (Japan); Wasaki, Jun [Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-7-1, Higashi-Hiroshima 739-8521 (Japan); Senoura, Takeshi [Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Shinano, Takuro [National Agricultural Research Center for Hokkaido Region, Sapporo 062-8555 (Japan); Osaki, Mitsuru [Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kitaku, Sapporo 060-8589 (Japan)


    The roles of low-molecular-weight thiols (LMWTs), such as glutathione and phytochelatins, in arsenic (As) tolerance and hyperaccumulation in Pteris vittata an As-hyperaccumulator fern remain to be better understood. This study aimed to thoroughly characterize LMWT synthesis in P. vittata to understand the roles played by LMWTs in As tolerance and hyperaccumulation. LMWT synthesis in P. vittata was induced directly by As, and not by As-mediated oxidative stress. Expression of PvECS2, one of the putative genes of {gamma}-glutamylcysteine synthetase ({gamma}ECS), increases in P. vittata shoots at 48 h after the onset of As exposure, almost corresponding to the increase in the concentrations of {gamma}-glutamylcysteine and glutathione. Furthermore, localization of As showed similar trends to those of LMWTs in fronds at both whole-frond and cellular levels. This study thus indicates the specific contribution of LMWTs to As tolerance in P. vittata. {gamma}ECS may be responsible for the As-induced enhancement of LMWT synthesis. - Pteris vittata specifically enhances low-molecular-weight thiol synthesis against arsenic toxicities

  2. New biosourced chiral molecularly imprinted polymer: Synthesis, characterization, and evaluation of the recognition capacity of methyltestosterone. (United States)

    Saadaoui, Asma; Sanglar, Corinne; Medimagh, Raouf; Bonhomme, Anne; Baudot, Robert; Chatti, Saber; Marque, Sylvain; Prim, Damien; Zina, Mongia Saïd; Casabianca, Herve


    New biosourced chiral cross-linkers were reported for the first time in the synthesis of methyltestosterone (MT) chiral molecularly imprinted polymers (cMIPs). Isosorbide and isomannide, known as 1,4:3,6-dianhydrohexitols, were selected as starting diols. The cMIPs were synthesized following a noncovalent approach via thermal radical polymerization and monitored by Raman spectroscopy. These cross-linkers were fully characterized by 1 H and 13 C nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry. The cross-polarization magic angle spinning 13 C NMR, Fourier transform infrared spectroscopy, scanning electron microscopy, and specific surface areas following the Brunauer-Emmett-Teller (BET) method were used to characterize the cMIPs. The effect of stereochemistry of cross-linkers on the reactivity of polymerization, morphology, and adsorption-recognition properties of the MIP was evaluated. The results showed that the cMIP exhibited an obvious improvement in terms of rebinding capacity for MT as compared with the nonimprinted polymer (NIP). The highest binding capacity was observed for cMIP-Is (27.298 mg g -1 ) for high concentrations (500 mg L -1 ). However, the isomannide homologue cMIP-Im showed higher recovery-up to 65% and capacity for low concentrations (15 mg L -1 ). The experimental data were properly fitted by the Freundlich adsorption isothermal model. Copyright © 2016 John Wiley & Sons, Ltd.

  3. Synthesis, Biological Evaluation, and Molecular Modeling Studies of New Oxadiazole-Stilbene Hybrids against Phytopathogenic Fungi (United States)

    Jian, Weilin; He, Daohang; Song, Shaoyun


    Natural stilbenes (especially resveratrol) play important roles in plant protection by acting as both constitutive and inducible defenses. However, their exogenous applications on crops as fungicidal agents are challenged by their oxidative degradation and limited availability. In this study, a new class of resveratrol-inspired oxadiazole-stilbene hybrids was synthesized via Wittig-Horner reaction. Bioassay results indicated that some of the compounds exhibited potent fungicidal activity against Botrytis cinerea in vitro. Among these stilbene hybrids, compounds 11 showed promising inhibitory activity with the EC50 value of 144.6 μg/mL, which was superior to that of resveratrol (315.6 μg/mL). Remarkably, the considerably abnormal mycelial morphology was observed in the presence of compound 11. The inhibitory profile was further proposed by homology modeling and molecular docking studies, which showed the possible interaction of resveratrol and oxadiazole-stilbene hybrids with the cytochrome P450-dependent sterol 14α-demethylase from B. cinerea (BcCYP51) for the first time. Taken together, these results would provide new insights into the fungicidal mechanism of stilbenes, as well as an important clue for biology-oriented synthesis of stilbene hybrids with improved bioactivity against plant pathogenic fungi in crop protection.

  4. Epoxy resin synthesis using low molecular weight lignin separated from various lignocellulosic materials. (United States)

    Asada, Chikako; Basnet, Sunita; Otsuka, Masaya; Sasaki, Chizuru; Nakamura, Yoshitoshi


    A low molecular weight lignin from various lignocellulosic materials was used for the synthesis of bio-based epoxy resins. The lignin extracted with methanol from steam-exploded samples (steaming time of 5 min at steam pressure of 3.5 MPa) from different biomasses (i.e., cedar, eucalyptus, and bamboo) were functionalized by the reaction with epichlorohydrin, catalyzed by a water-soluble phase transfer catalyst tetramethylammonium chloride, which was further reacted with 30 wt% aqueous NaOH for ring closure using methyl ethyl ketone as a solvent. The glycidylated products of the lignin with good yields were cured to epoxy polymer networks with bio-based curing agents i.e., lignin itself and a commercial curing agent TD2131. Relatively good thermal properties of the bio-based epoxy network was obtained and thermal decomposition temperature at 5% weight loss (Td5) of cedar-derived epoxy resin was higher than that derived from eucalyptus and bamboo. The bio-based resin satisfies the stability requirement of epoxy resin applicable for electric circuit boards. The methanol-insoluble residues were enzymatically hydrolyzed to produce glucose. This study indicated that the biomass-derived methanol-soluble lignin may be a promising candidate to be used as a substitute for petroleum-based epoxy resin derived from bisphenol A, while insoluble residues may be processed to give a bioethanol precursor i.e., glucose. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Novel synthesis and structural analysis of zinc oxide nanoparticles for the non enzymatic glucose biosensor. (United States)

    Dayakar, T; Venkateswara Rao, K; Bikshalu, K; Rajendar, V; Park, Si-Hyun


    A non-enzymatic glucose biosensor was developed by utilizing the zinc oxide nanoparticles (ZnO NPs) synthesized by a novel green method using the leaf extract of Ocimum tenuiflorum. The structural, optical and morphological properties of ZnO NPs characterized by means of X-ray diffraction (XRD), ultraviolet-visible (UV-vis) spectroscopy, Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), energy-dispersive X-ray (EDAX) spectroscopy, and transmission electron microscopy (TEM). The XRD analysis revealed that the ZnO NPs were crystalline and had a hexagonal wurtzite structure. The crystallite size measured by XRD was the same as that measured using SEM and TEM. The UV-vis absorption spectrum estimates the band gap of ZnO NPs present in the range of 2.82 to 3.45eV. The reduction and formation of ZnO NPs mainly due to the involvement of leaf extract bio-molecular compounds analyzed from the FTIR spectra. The SEM result confirms the morphology of the NPs responsible from the various concentration of leaf extract in the synthesis process. HRTEM analysis depicts the spherical structure of ZnO NPs. The synthesized NPs have the average size ranges from 10 to 20nm. The fabricated GCE/ZnO glucose sensor represents superior electro catalytic activity that has been observed for ZnO NPs with a reproducible sensitivity of 631.30μAmM -1 cm -2 , correlation coefficient of R=0.998, linear dynamic range from 1-8.6mM, low detection limit of 0.043μM (S/N=3) and response time<4s. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure

    Directory of Open Access Journals (Sweden)

    Wouter A. A. de Steenhuijsen Piters


    Full Text Available The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem—also called “microbiome”—is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1:e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting.

  7. Synthesis, structure and photocatalytic properties of β-ZrMo2O8

    Indian Academy of Sciences (India)


    Synthesis, structure and photocatalytic properties of β-ZrMo2O8. PRANGYA PARIMITA SAHOO, S SUMITHRA, GIRIDHAR MADRAS and. T N GURU ROW*. Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India. Abstract. Monoclinic ZrMo2O8 was synthesized via solid state method ...

  8. Solvent-free synthesis of nanosized hierarchical sodalite zeolite with a multi-hollow polycrystalline structure

    KAUST Repository

    Zeng, Shangjing


    A solvent-free route is developed for preparing nanoscale sodalite zeolite with a multi-hollow structure. Furthermore, the synthesis of nanosized hollow sodalite polycrystalline aggregates with a mesoporous structure and high crystallinity is investigated by adding an organosilane surfactant as a mesopore-generating agent.

  9. Synthesis, structural and ferromagnetic properties of La1–x Kx ...

    Indian Academy of Sciences (India)


    Aug 26, 2016 ... Synthesis, structural and ferromagnetic properties of La1–KMnO3 (0.0≤ 0.25) phases by solution combustion method ... Structural parameters were determined by the Rietveld refinement method using powder XRD data. Parent ... The ratio of the Mn3+/Mn4+ was determined by the iodometric titration.

  10. A Network of AOPs for reduced thyroid hormone synthesis derived from inhibition of Thyroperoxidase - A common Molecular Initiating Event Leading to Species-Specific Indices of Adversity. (United States)

    This collection of 3 AOPs describe varying outcomes of adversity dependent upon species in response to inhibition of thyroperoxidase (TPO) during development. Chemical inhibition of TPO, the molecular-initiating event (MIE), results in decreased thyroid hormone (TH) synthesis, a...

  11. Molecular dynamics approaches to the design and synthesis of PCB targeting molecularly imprinted polymers: interference to monomer-template interactions in imprinting of 1,2,3-trichlorobenzene. (United States)

    Cleland, Dougal; Olsson, Gustaf D; Karlsson, Björn C G; Nicholls, Ian A; McCluskey, Adam


    The interactions between each component of the pre-polymerisation mixtures used in the synthesis of molecularly imprinted polymers (MIP) specific for 1,2,3,4,5-pentachlorobenzene (1) and 1,2,3-trichlorobenzene (2) were examined in four molecular dynamics simulations. These simulations revealed that the relative frequency of functional monomer-template (FM-T) interactions was consistent with results obtained by the synthesis and evaluation of the actual MIPs. The higher frequency of 1 interaction with trimethylstyrene (TMS; 54.7%) than 1 interaction with pentafluorostyrene (PFS; 44.7%) correlated with a higher imprinting factor (IF) of 2.1 vs. 1.7 for each functional monomer respectively. The higher frequency of PFS interactions with 2 (29.6%) than TMS interactions with 2 (1.9%) also correlated well with the observed differences in IF (3.7) of 2 MIPs imprinted using PFS as the FM than the IF (2.8) of 2 MIPs imprinted using TMS as the FM. The TMS-1 interaction dominated the molecular simulation due to high interaction energies, but the weaker TMS-2 resulted in low interaction maintenance, and thus lower IF values. Examination of the other pre-polymerisation mixture components revealed that the low levels of TMS-2 interaction was, in part, due to interference caused by the cross linker (CL) ethyleneglycol dimethylacrylate (EGDMA) interactions with TMS. The main reason was, however, attributed to MeOH interactions with TMS in both a hydrogen bond and perpendicular configuration. This positioned a MeOH directly above the π-orbital of all TMS for an average of 63.8% of MD2 creating significant interference to π-π stacking interactions between 2 and TMS. These findings are consistent with the deviation from the 'normal' molecularly imprinted polymer synthesis ratio of 1 : 4 : 20 (T : FM : CL) of 20 : 1 : 29 and 15 : 6 : 29 observed with 2 and TMS and PFS respectively. Our molecular dynamics simulations correctly predicted the high level

  12. Death Associated Protein Kinases: Molecular Structure and Brain Injury

    Directory of Open Access Journals (Sweden)

    Claire Thornton


    Full Text Available Perinatal brain damage underlies an important share of motor and neurodevelopmental disabilities, such as cerebral palsy, cognitive impairment, visual dysfunction and epilepsy. Clinical, epidemiological, and experimental studies have revealed that factors such as inflammation, excitotoxicity and oxidative stress contribute considerably to both white and grey matter injury in the immature brain. A member of the death associated protein kinase (DAPk family, DAPk1, has been implicated in cerebral ischemic damage, whereby DAPk1 potentiates NMDA receptor-mediated excitotoxicity through interaction with the NR2BR subunit. DAPk1 also mediate a range of activities from autophagy, membrane blebbing and DNA fragmentation ultimately leading to cell death. DAPk mRNA levels are particularly highly expressed in the developing brain and thus, we hypothesize that DAPk1 may play a role in perinatal brain injury. In addition to reviewing current knowledge, we present new aspects of the molecular structure of DAPk domains, and relate these findings to interacting partners of DAPk1, DAPk-regulation in NMDA-induced cerebral injury and novel approaches to blocking the injurious effects of DAPk1.

  13. Modeling Carbon and Hydrocarbon Molecular Structures in EZTB (United States)

    Lee, Seungwon; vonAllmen, Paul


    A software module that models the electronic and mechanical aspects of hydrocarbon molecules and carbon molecular structures on the basis of first principles has been written for incorporation into, and execution within, the Easy (Modular) Tight-Binding (EZTB) software infrastructure, which is summarized briefly in the immediately preceding article. Of particular interest, this module can model carbon crystals and nanotubes characterized by various coordinates and containing defects, without need to adjust parameters of the physical model. The module has been used to study the changes in electronic properties of carbon nanotubes, caused by bending of the nanotubes, for potential utility as the basis of a nonvolatile, electriccharge- free memory devices. For example, in one application of the module, it was found that an initially 50-nmlong carbon, (10,10)-chirality nanotube, which is a metallic conductor when straight, becomes a semiconductor with an energy gap of .3 meV when bent to a lateral displacement of 4 nm at the middle.

  14. Synthesis and characterization of sugar based low molecular weight gelators and the preparation of chiral sulfinamides (United States)

    Mangunuru, Hari Prasad Reddy

    Low molecular weight gelators (LMWGs) have received considerable attention in the field of chemistry from last few decades. These compounds form self-assembled fibrous networks like micelles, cylindrical, sheets, fibers, layers and so on. The fibrous network entraps the solvent and forms gel, because of the self-assembly phenomenon and their demonstrated potential uses in a variety of areas, ranging from environmental to medicinal applications. Sugars are good starting materials to synthesize the new class of LMWG's, because these are different from some expensive materials, these are natural products. We have synthesized and characterized the LMGS's based on D-glucose and D-glucosamine. D-glucosamine is the versatile starting material to make different peptoids and triazoles. Several series of compounds were synthesized using compounds 1-3 as starting material and studied the gelation behavior all the compounds. We have studied the self-assembling properties of a new class of tripeptoids, synthesized by one-pot Ugi reaction from simple starting materials. Among the focused library of tripeptoids synthesized, we found that several efficient low molecular weight organogelators were obtained for aqueous DMSO and ethanol mixtures. We have also synthesized and characterized a series of monosaccharide triazole derivatives. These compounds were synthesized from N-acetyl glucosamine and D-glucose via a Cu(I) catalyzed azide/alkyne cycloaddition reaction (CuAAc). The compounds have been screened for their gelation properties and several efficient low molecular weight organo/hydro gelators were obtained, among these compounds, five per-acetyl glucosamine derivatives and one peracetyl glucose derivative were able to form gels in water. These new molecules are expected to be useful in drug delivery and tissue engineering.*. Asymmetric synthesis of chiral amines is a challenging in synthetic organic chemistry. The development of new catalysts for asymmetric organic

  15. Methodology in structural determination and synthesis of insect pheromone

    Directory of Open Access Journals (Sweden)

    Guo-Qiang Lin


    Full Text Available By means of ethereal washing of insect pheromone glands of female moths, GC-MS detection along with microchemical reactions and electroantennogram (EAG survey, six economically important insect species were targeted for pheromone identification. The discovery of a natural pheromone inhibitor, chemo-selectivity and species isolation by pheromone will be described. The modified triple bond migration and triethylamine liganded vinyl cuprate were applied for achiral pheromone synthesis in double bond formation. Some optically active pheromones and their stereoisomers were synthesized through chiral pool or asymmetric synthesis. Some examples of chiral recognition of insects towards their chiral pheromones will be discussed. A CaH2 and silica gel catalyzed Sharpless Expoxidation Reaction was found in shortening the reaction time.

  16. New data structures and algorithms for logic synthesis and verification

    CERN Document Server

    Amaru, Luca Gaetano


    This book introduces new logic primitives for electronic design automation tools. The author approaches fundamental EDA problems from a different, unconventional perspective, in order to demonstrate the key role of rethinking EDA solutions in overcoming technological limitations of present and future technologies. The author discusses techniques that improve the efficiency of logic representation, manipulation and optimization tasks by taking advantage of majority and biconditional logic primitives. Readers will be enabled to accelerate formal methods by studying core properties of logic circuits and developing new frameworks for logic reasoning engines. · Provides a comprehensive, theoretical study on majority and biconditional logic for logic synthesis; · Updates the current scenario in synthesis and verification – especially in light of emerging technologies; · Demonstrates applications to CMOS technology and emerging technologies.

  17. The synthesis and structure of new vinylogous carbamates of sparteine (United States)

    Włodarczak, Jacek; Wysocka, Waleria; Katrusiak, Andrzej


    Synthesis of new ( E)-(-)-[2-methyl ( 2), ethyl ( 3), isopropyl ( 4), benzyl ( 5) and phenyl ( 6)] carbonylmethylideno-17-oxosparteine by the Eschenmoser coupling reaction has been described. Stereochemistry of these compounds has been determined by 13C and 1H NMR and that of compound 2 additionally by X-ray analysis. The Haasnoot equation has been used to determine the HCCH dihedral angle in ( E)-(-)-2-methyl-(methylcarbonylomethylideno)-17-oxosparteine on the basis of NMR spectroscopy.

  18. Optimized Solid Phase-Assisted Synthesis of Dendrons Applicable as Scaffolds for Radiolabeled Bioactive Multivalent Compounds Intended for Molecular Imaging

    Directory of Open Access Journals (Sweden)

    Gabriel Fischer


    Full Text Available Dendritic structures, being highly homogeneous and symmetric, represent ideal scaffolds for the multimerization of bioactive molecules and thus enable the synthesis of compounds of high valency which are e.g., applicable in radiolabeled form as multivalent radiotracers for in vivo imaging. As the commonly applied solution phase synthesis of dendritic scaffolds is cumbersome and time-consuming, a synthesis strategy was developed that allows for the efficient assembly of acid amide bond-based highly modular dendrons on solid support via standard Fmoc solid phase peptide synthesis protocols. The obtained dendritic structures comprised up to 16 maleimide functionalities and were derivatized on solid support with the chelating agent DOTA. The functionalized dendrons furthermore could be efficiently reacted with structurally variable model thiol-bearing bioactive molecules via click chemistry and finally radiolabeled with 68Ga. Thus, this solid phase-assisted dendron synthesis approach enables the fast and straightforward assembly of bioactive multivalent constructs for example applicable as radiotracers for in vivo imaging with Positron Emission Tomography (PET.

  19. Pathways to Structure-Property Relationships of Peptide-Materials Interfaces: Challenges in Predicting Molecular Structures. (United States)

    Walsh, Tiffany R


    An in-depth appreciation of how to manipulate the molecular-level recognition between peptides and aqueous materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomolecules is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomolecule onto one materials composition over another, one surface facet over another, or one crystalline polymorph over another. Deeper knowledge of the aqueous abiotic-biotic interface, to establish clear structure-property relationships in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relationships but can often be challenging to accomplish via experimental approaches alone. In addition to myriad existing challenges associated with determining the detailed molecular structure of any molecule adsorbed at an aqueous interface, experimental characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to experimental techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with experiment, molecular simulations at the atomistic level can bring complementary and critical insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, molecular simulation approaches also face


    Directory of Open Access Journals (Sweden)

    N. Yu. Abramycheva


    Full Text Available Materials and methods. 285 Russian patients with amyotrophic lateral sclerosis (ALS including 260 patients with a sporadic form and 25 with a familial form were examined for mutations in SOD1, C9orf72, TARDBP,  ANG and other genes and the presence of associations among polymorphic sites in ATXN2 (polyCAG and VEGF (-2578С/А genes.Molecular genetic analysis was performed using direct sequencing, fragment analysis and real-time polymerase chain reaction. On the last stage, rare ALS candidate genes were evaluated using a next generation sequencing (NGS panel.Results. Total rate of the identified mutations in the examined ALS cohort was 9.5 %. The most frequently observed defects were mutations in the SOD1 (24.0 % in familial ALS and 4.6 % in sporadic ALS and C9orf72 (pathological hexanucleotide repeat expansion was identified in 1.8 % cases of ALS, all sporadic genes. The TARDBP gene didn’t contain any mutations, though in the ALS group deletion c.715-126delG located in intron 5 of the TARDBP gene was significantly over-represented – 38.0 % vs. 26.6 % (χ2 = 13.17; р = 0.002. Mutations in the ANG gene were identified in 1.05 % of ALS patients (all cases were sporadic. In 1 (0.35 % sporadic case a G1082A mutation in the DCTN1 gene was identified. The examined group significantly more frequently carried a risk allele of the ATXN2 gene with an “intermediate” (28–33  number of CAG repeats – 5.0 % vs. 1.7 % in the control group (χ2 = 3.89; р = 0.0486. In Russian ALS patients, an association between the disease and the presence of a risk А-allele and homozygote genotype А/А of -2578С/А polymorphism in the VEGF gene was identified (χ2 = 7.14; р = 0.008 and χ2 = 13.46; р = 0.001 for the rates in the ALS population and in the control population, respectively, which is confirmed by the odds ratio.Conclusion. In the current article, molecular structure of ALS in the Russian population was examined, rates of individual genetic forms

  1. Synthesis and characterization of montmorillonite clay intercalated with molecular magnetic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Martins, Marcel G.; Martins, Daniel O.T.A.; Carvalho, Beatriz L.C. de [Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24.020–150 (Brazil); Mercante, Luiza A. [Laboratório Nacional de Nanotecnologia para o Agronegócio (LNNA), Embrapa Instrumentação, São Carlos, SP 13560 970 (Brazil); Soriano, Stéphane [Instituto de Física, Universidade Federal Fluminense, Niterói, RJ 24.210 346 (Brazil); Andruh, Marius [Inorganic Chemistry Laboratory, Faculty of Chemistry, University of Bucharest, Str. Dumbrava Rosie nr. 23, Bucharest (Romania); Vieira, Méri D., E-mail: [Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24.020–150 (Brazil); Vaz, Maria G.F., E-mail: [Instituto de Química, Universidade Federal Fluminense, Niterói, RJ 24.020–150 (Brazil)


    In this work montmorillonite (MMT) clay, whose matrix was modified with an ammonium salt (hexadecyltrimethylammonium bromide – CTAB), was employed as an inorganic host for the intercalation of three different molecular magnetic compounds through ion exchange: a nitronyl nitroxide derivative 2-[4-(N-ethyl)-pyridinium]-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (p-EtRad{sup +}) and two binuclear coordination compounds, [Ni(valpn)Ln]{sup 3+}, where H{sub 2}valpn stands for 1,3-propanediyl-bis(2-iminomethylene-6-methoxy-phenol), and Ln=Gd{sup III}; Dy{sup III}. The pristine MMT and the intercalated materials were characterized by X-ray powder diffraction (XRD), infrared spectroscopy (IR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA) and magnetic measurements. The X-ray diffraction data analysis showed an increase of the interlamellar space of the intercalated MMT, indicating the intercalation of the magnetic compounds. Furthermore, the magnetic properties of the hybrid compounds were investigated, showing similar behavior as the pure magnetic guest species. - Graphical abstract: Montmorillonite clay was employed as inorganic host for the intercalation of three different molecular magnetic compounds through ion exchange - Highlights: • Montmorillonite was employed as a host material. • Three molecular magnetic compounds were intercalated through ion exchange. • The compounds were successful intercalated maintaining the layered structure. • The hybrid materials exhibited similar magnetic behavior as the pure magnetic guest.

  2. Comparison between 5,10,15,20-tetraaryl- and 5,15-diarylporphyrins as photosensitizers: synthesis, photodynamic activity, and quantitative structure-activity relationship modeling. (United States)

    Banfi, Stefano; Caruso, Enrico; Buccafurni, Loredana; Murano, Roberto; Monti, Elena; Gariboldi, Marzia; Papa, Ester; Gramatica, Paola


    The synthesis of a panel of seven nonsymmetric 5,10,15,20-tetraarylporphyrins, 13 symmetric and nonsymmetric 5,15-diarylporphyrins, and one 5,15-diarylchlorin is described. In vitro photodynamic activities on HCT116 human colon adenocarcinoma cells were evaluated by standard cytotoxicity assays. A predictive quantitative structure-activity relationship (QSAR) regression model, based on theoretical holistic molecular descriptors, of a series of 34 tetrapyrrolic photosensitizers (PSs), including the 24 compounds synthesized in this work, was developed to describe the relationship between structural features and photodynamic activity. The present study demonstrates that structural features significantly influence the photodynamic activity of tetrapyrrolic derivatives: diaryl compounds were more active with respect to the tetraarylporphyrins, and among the diaryl derivatives, hydroxy-substituted compounds were more effective than the corresponding methoxy-substituted ones. Furthermore, three monoarylporphyrins, isolated as byproducts during diarylporphyrin synthesis, were considered for both photodynamic and QSAR studies; surprisingly they were found to be particularly active photosensitizers.

  3. Novel α, β-Unsaturated Sophoridinic Derivatives: Design, Synthesis, Molecular Docking and Anti-Cancer Activities

    Directory of Open Access Journals (Sweden)

    Yiming Xu


    Full Text Available Using sophoridine 1 and chalcone 3 as the lead compounds, a series of novel α, β-unsaturated sophoridinic derivatives were designed, synthesized, and evaluated for their in vitro cytotoxicity. Structure-activity relationship (SAR analysis indicated that introduction of α, β-unsaturated ketone moiety and heterocyclic group might significantly enhance anticancer activity. Among the compounds, 2f and 2m exhibited potential effects against HepG-2 and CNE-2 human cancer cell lines. Furthermore, molecular docking studies were performed to understand possible docking sites of the molecules on the target proteins and the mode of binding. This work provides a theoretical basis for structural optimizations and exploring anticancer pathways of this kind of compound.

  4. Synthesis, In Vitro Biological Evaluation, and Molecular Docking of New Triazoles as Potent Antifungal Agents. (United States)

    Li, Xiang; Liu, Chao; Tang, Sheng; Wu, Qiuye; Hu, Honggang; Zhao, Qingjie; Zou, Yan


    Based on the structure of the active site of CYP51 and the structure-activity relationships of azole antifungal compounds that we designed in a previous study, a series of 1-{1-[2-(substitutedbenzyloxy)ethyl]-1H-1,2,3-triazol-4-yl}-2-(2,4-difluorophenyl)-3-(1H-1,2,4-triazol-1-yl)propan-2-ols (6a-n) were designed and synthesized utilizing copper-catalyzed azide-alkyne cycloaddition. Preliminary antifungal tests against eight human pathogenic fungi in vitro showed that all the title compounds exhibited excellent antifungal activities with a broad spectrum in vitro. Molecular docking results indicated that the interaction between the title compounds and CYP51 comprised π-π interactions, hydrophobic interactions, and the narrow hydrophobic cleft. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Structure sensitivity of Cu and CuZn catalysts relevant to industrial methanol synthesis (United States)

    van den Berg, Roy; Prieto, Gonzalo; Korpershoek, Gerda; van der Wal, Lars I.; van Bunningen, Arnoldus J.; Lægsgaard-Jørgensen, Susanne; de Jongh, Petra E.; de Jong, Krijn P.


    For decades it has been debated whether the conversion of synthesis gas to methanol over copper catalysts is sensitive or insensitive to the structure of the copper surface. Here we have systematically investigated the effect of the copper particle size in the range where changes in surface structure occur, that is, below 10 nm, for catalysts with and without zinc promotor at industrially relevant conditions for methanol synthesis. Regardless of the presence or absence of a zinc promotor in the form of zinc oxide or zinc silicate, the surface-specific activity decreases significantly for copper particles smaller than 8 nm, thus revealing structure sensitivity. In view of recent theoretical studies we propose that the methanol synthesis reaction takes place at copper surface sites with a unique configuration of atoms such as step-edge sites, which smaller particles cannot accommodate. PMID:27703166

  6. Molecular structure investigation and tautomerism aspects of (E)-3 ...

    Indian Academy of Sciences (India)

    calculations. The effect of the intermolecular N-H—. O H-bonding interactions on the calculated geometric parameters has been tested. The electronic spectra were assigned with the aid of the TD-DFT calculations. 2. Experimental. 2.1 Synthesis and spectral investigations. A mixture of indolin-2-one 1 (1.5 mmol, 200 mg), ...

  7. Antimicrobial profile of some novel keto esters: Synthesis, crystal structures and structure-activity relationship studies. (United States)

    Khan, Imtiaz; Saeed, Aamer; Arshad, Mohammad Ifzan; White, Jonathan Michael


    Rapid increase in bacterial resistance has become a major public concern by escalating alongside a lack of development of new anti-infective drugs. Novel remedies in the battle against multidrug-resistant bacterial strains are urgently needed. So, in this context, the present work is towards the investigation of antimicrobial efficacy of some novel keto ester derivatives, which are prepared by the condensation of substituted benzoic acids with various substituted phenacyl bromides in dimethylformamide at room temperature using triethylamine as a catalyst. The structural build-up of the target compounds was accomplished by spectroscopic techniques including FTIR, (1)H and (13)C NMR spectroscopy and mass spectrometry. The purity of the synthesized compounds was ascertained by elemental analysis. The molecular structures of compounds (4b) and (4l) were established by X-ray crystallographic analysis. The prepared analogues were evaluated for their antimicrobial activity against Gram-positive (Staphylococcus aureus, Micrococcus leuteus) and Gram-negative (Pseudomonas picketti, Salmonella setuball) bacteria and two fungal pathogenic strains (Aspergillus niger, Aspergillus flavus), respectively. Among the screened derivatives, several compounds were found to possess significant activity but (4b) and (4l) turned out to be lead molecules with remarkable antimicrobial efficacy. The structure-activity relationship analysis of this study also revealed that structural modifications on the basic skeleton affected the antimicrobial activity of the synthesized compounds.

  8. Synthesis of Triptycene-Based Molecular Rotors for Langmuir-Blodgett Monolayers. (United States)

    Kaleta, Jiří; Kaletová, Eva; Císařová, Ivana; Teat, Simon J; Michl, Josef


    We describe syntheses of six triptycene-containing molecular rotors with several single-crystal X-ray diffraction analyses. These rod-shaped molecules carrying an axial rotator are designed to interleave on an aqueous surface into Langmuir-Blodgett (LB) monolayers containing a two-dimensional trigonal array of dipoles rotatable about an axis normal to the surface. Monolayer formation was verified with the simplest of the rotor structures. On an aqueous subphase containing divalent cations (Mg(2+), Ca(2+), Zn(2+), Sr(2+), or Cd(2+)), the LB isotherm yielded an area of 53 ± 3 Å(2)/molecule (monolayer of type A), compatible with the anticipated triangular packing of axes normal to the surface. On pure water, the area is 30 ± 3 Å(2)/molecule, and it is proposed that in this monolayer (type B), the molecular axes are tilted by 40-45° to a structure similar to those observed in single crystals of related triptycenes. After transfer to a gold surface, ellipsometry and PM IRRAS yield tilt angles of 29 ± 4° (monolayers of type A) and 38 ± 4° (type B). A full-scale examination of monolayers from all the rotors on a subphase and after transfer is underway and will be reported separately.

  9. Molecular mechanism and structure of Trigger Factor bound to the translating ribosome (United States)

    Merz, Frieder; Boehringer, Daniel; Schaffitzel, Christiane; Preissler, Steffen; Hoffmann, Anja; Maier, Timm; Rutkowska, Anna; Lozza, Jasmin; Ban, Nenad; Bukau, Bernd; Deuerling, Elke


    Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions of Escherichia coli TF and nascent chains during translation. Furthermore, we provide the first full-length structure of TF associated with ribosome–nascent chain complexes by using cryo-electron microscopy. In its active state, TF arches over the ribosomal exit tunnel accepting nascent chains in a protective void. The growing nascent chain initially follows a predefined path through the entire interior of TF in an unfolded conformation, and even after folding into a domain it remains accommodated inside the protective cavity of ribosome-bound TF. The adaptability to accept nascent chains of different length and folding states may explain how TF is able to assist co-translational folding of all kinds of nascent polypeptides during ongoing synthesis. Moreover, we suggest a model of how TF's chaperoning function can be coordinated with the co-translational processing and membrane targeting of nascent polypeptides by other ribosome-associated factors. PMID:18497744

  10. Synthesis and structure of two-dimensional transition-metal dichalcogenides

    KAUST Repository

    Shi, Yumeng


    Two-dimensional (2D) transition-metal dichalcogenides (TMDCs) exhibit unique electrical, optical, thermal, and mechanical properties, which enable them to be used as building blocks in compact and lightweight integrated electronic systems. The controllable and reliable synthesis of atomically thin TMDCs is essential for their practical application. Recent progress in large-area synthesis of monolayer TMDCs paves the way for practical production of various 2D TMDC layers. The intrinsic optical and electrical properties of monolayer TMDCs can be defined by stoichiometry during synthesis. By manipulating the lattice structure or layer stacking manner, it is possible to create atomically thin van der Waals materials with unique and unexplored physical properties. In this article, we review recent developments in the synthesis of TMDC monolayers, alloys, and heterostructures, which shine light on the design of novel TMDCs with desired functional properties.

  11. Synthesis of computational structures for analog signal processing

    CERN Document Server

    Popa, Cosmin Radu


    Presents the most important classes of computational structures for analog signal processing, including differential or multiplier structures, squaring or square-rooting circuits, exponential or Euclidean distance structures and active resistor circuitsIntroduces the original concept of the multifunctional circuit, an active structure that is able to implement, starting from the same circuit core, a multitude of continuous mathematical functionsCovers mathematical analysis, design and implementation of a multitude of function generator structures

  12. Synthesis, crystal structure, and spectra of 3,3- dimethyl-1-N-(1'-phenyl-2',3'-dimethyl-5'-oxo-3'- pyrazolin-4'-yl)imino-1,2,3,4-tetrahydroisoquinoline

    International Nuclear Information System (INIS)

    Sokol, V.I.; Ryabov, M.A.; Merkur'eva, N.Yu.; Davydov, V.V.; Zaitsev, B.E.; Shklyaev, Yu.V.; Sergienko, V.S.; Zaitsev, B.E.


    The synthesis and the crystal and molecular structure of 3,3-dimethyl-1-N-(1'-phenyl-2',3'- dimethyl-5'-oxo-3'-pyrazolin-4'-yl)imino-1,2,3,4-tetrahydroisoquinoline are reported. As is evidenced by the 1H NMR, IR, and electron spectra, the tautomeric form of the compounds observed in the crystal is also retained in solutions

  13. Molecular, structural, and phylogenetic analyses of Taxus chinensis JAZs. (United States)

    Zhang, Meng; Chen, Ying; Nie, Lin; Jin, Xiaofei; Fu, Chunhua; Yu, Longjiang


    Taxus spp. are ancient gymnosperms that produce a unique secondary metabolite, namely, taxol, an anticancer drug. JAZ proteins are key regulators of the JA signaling pathway, which control taxol biosynthesis. However, the JAZ proteins of Taxus spp. are poorly studied. In this work, nine JAZ genes from Taxus chinensis were identified using our previous transcriptome data and named as TcJAZ1-TcJAZ9. Of these nine TcJAZ proteins, eight contain Jas and TIFY domains, and the Jas domain of TcJAZ6 is incomplete. Most TcJAZs and PsJAZs are not related to AtJAZs and OsJAZs. Phylogenetic analysis divided all JAZ proteins from Arabidopsis thaliana, Oryza sativa, Picea sitchensis, and T. chinensis into eight subgroups; gymnosperms JAZs were classified into subgroups V-VIII, and angiosperm JAZs were categorized into subgroups I-V. Three motifs of subgroups VI-VIII were identified in gymnosperm JAZs, indicating that gymnosperm JAZ proteins exhibit a different evolutionary process from those of angiosperms. The expression patterns of nine TcJAZs showed that TcJAZ2/3/8 was a key regulator, indicating their important roles in T. chinensis. Results revealed that gymnosperm JAZs differ from angiosperm JAZs in terms of molecular structure. Three novel conserved motifs were found in TcJAZs and PsJAZs. This study provides a basis for research on JA regulatory system in Taxus spp. and for elucidating the significance of JA signaling pathway to land plants. Copyright © 2017. Published by Elsevier B.V.

  14. An Insight towards Conceptual Understanding: Looking into the Molecular Structures of Compounds (United States)

    Uyulgan, Melis Arzu; Akkuzu, Nalan


    The subject of molecular structures is one of the most important and complex subject in chemistry which a majority of the undergraduate students have difficulties to understand its concepts and characteristics correctly. To comprehend the molecular structures and their characteristics the students need to understand related subjects such as Lewis…

  15. Structural archetypes in nickel(II) hybrid vanadates. Towards a directed hydrothermal synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Luis, R. Fernandez de; Urtiaga, M.K. [Dpto. Mineralogia y Petrologia, Facultad de Ciencia y Tecnologia, Universidad del Pais Vasco/UPV/EHU, Apdo. 644, 48080 Bilbao (Spain); Mesa, J.L.; Rojo, T. [Dpto. Quimica Inorganica, Facultad de Ciencia y Tecnologia, Universidad del Pais Vasco UPV/EHU, Apdo. 644, 48080 Bilbao (Spain); Arriortua, M.I. [Dpto. Mineralogia y Petrologia, Facultad de Ciencia y Tecnologia, Universidad del Pais Vasco/UPV/EHU, Apdo. 644, 48080 Bilbao (Spain)], E-mail:


    In the present work, we relate the modifications of the initial synthesis parameters (pH value, stoichiometry and concentration) with the different structural archetypes obtained in the {l_brace}Ni/Bpy/VO{r_brace} and {l_brace}Ni/Bpe/VO{r_brace} systems (4,4'-bipyridine (Bpy), 1,2-di(4-pyridyl) ethylene (Bpe)). The vanadium coordination is partially controlled by the hydrothermal synthesis conditions, and the final crystal structures depend on the synergetic interaction between the metal-organic subnets and the vanadium oxide subunits.

  16. Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques. (United States)

    Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M; Prates, Luciana L; Yu, Peiqiang


    The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HED N/OM ), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques (United States)

    Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M.; Prates, Luciana L.; Yu, Peiqiang


    The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HEDN/OM), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions.

  18. Synthesis, biological evaluation, QSAR analysis, and molecular docking of chalcone derivatives for antimalarial activity

    Directory of Open Access Journals (Sweden)

    Jufrizal Syahri


    and DNA synthesis. The formed binding interaction (H-bond toward residues of Ala16, Ser108, and Ile164 also indicate the activity of 5c against chloroquine-resistance P. falciparum strain. Conclusions: We have successfully determined the effects of some chalcone derivatives on antimalarial activity against the chloroquine-sensitive Pf3D7 strain. Compound 5c and 10a were described a good antiplasmodial compounds. Interestingly, these in vitro results relevance with IC50 predicted QSAR studies. Moreover, molecular docking simulation provided insight into the binding modes of 5c into the anti-folate resistance from malarial P. falciparum.

  19. Solvent effect on the synthesis of clarithromycin: A molecular dynamics study (United States)

    Duran, Dilek; Aviyente, Viktorya; Baysal, Canan


    Clarithromycin (6- O-methylerythromycin A) is a 14-membered macrolide antibiotic which is active in vitro against clinically important gram-positive and gram-negative bacteria. The selectivity of the methylation of the C-6 OH group is studied on erythromycin A derivatives. To understand the effect of the solvent on the methylation process, detailed molecular dynamics (MD) simulations are performed in pure DMSO, pure THF and DMSO:THF (1:1) mixture by using the anions at the C-6, C-11 and C-12 positions of 2',4''-[ O-bis(TMS)]erythromycin A 9-[ O-(dimethylthexylsilyl)oxime] under the assumption that the anions are stable on the sub-nanosecond time scale. The conformations of the anions are not affected by the presence of the solvent mixture. The radial distribution functions are computed for the distribution of different solvent molecules around the `O-' of the anions. At distances shorter than 5 Å, DMSO molecules are found to cluster around the C-11 anion, whereas the anion at the C-12 position is surrounded by the THF molecules. The anion at the C-6 position is not blocked by the solvent molecules. The results are consistent with the experimental finding that the methylation yield at the latter position is increased in the presence of a DMSO:THF (1:1) solvent mixture. Thus, the effect of the solvent in enhancing the yield during the synthesis is not by changing the conformational properties of the anions, but rather by creating a suitable environment for methylation at the C-6 position.

  20. Synthesis and Evaluation of CO2 Thickeners Designed with Molecular Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Robert Enick; Erick Beckman; J. Karl Johnson


    The objective of this research was to use molecular modeling techniques, coupled with our prior experimental results, to design, synthesize and evaluate inexpensive, non-fluorous carbon dioxide thickening agents. The first type of thickener that was considered was associating polymers. Typically, these thickeners are copolymers that contain a highly CO{sub 2}-philic monomer, and a small concentration of a CO{sub 2}-phobic associating monomer. Yale University was solely responsible for the synthesis of a second type of thickener; small, hydrogen bonding compounds. These molecules have a core that contains one or more hydrogen-bonding groups, such as urea or amide groups. Non-fluorous, CO{sub 2}-philic functional groups were attached to the hydrogen bonding core of the compound to impart CO{sub 2} stability and macromolecular stability to the linear 'stack' of these compounds. The third type of compound initially considered for this investigation was CO{sub 2}-soluble surfactants. These surfactants contain conventional ionic head groups and composed of CO{sub 2}-philic oligomers (short polymers) or small compounds (sugar acetates) previously identified by our research team. Mobility reduction could occur as these surfactant solutions contacted reservoir brine and formed mobility control foams in-situ. The vast majority of the work conducted in this study was devoted to the copolymeric thickeners and the small hydrogen-bonding thickeners; these thickeners were intended to dissolve completely in CO{sub 2} and increase the fluid viscosity. A small but important amount of work was done establishing the groundwork for CO{sub 2}-soluble surfactants that reduced mobility by generating foams in-situ as the CO{sub 2}+surfactant solution mixed with in-situ brine.