Chemical Constituents of a Marine-Derived Endophytic Fungus Penicillium commune G2M

Cultivation of the endophytic fungus Penicillium commune, which was isolated from the semi-mangrove plant Hibiscus tiliaceus, afforded one new compound 1-O-(2,4-dihydroxy-6-methylbenzoyl)-glycerol (1) along with thirteen known products, including 1-O-acetylglycerol (2), N-acetyltryptophan (3), 3-indolylacetic acid methyl ester (4), 1-(2,4-dihydroxy-3,5-dimethylphenyl)ethanone (5), 2-(2,5-dihydroxyphenyl)acetic acid (6), (4R,5S)-5-hydroxyhexan-4-olide (7), thymidine (8), uracil (9), thymine (10), ergosterol (11), beta-sitosterol (12), beta-daucosterol (13), and ergosta-7,22-dien-3 beta,5 alpha,6 beta-triol (14). The structures of these compounds were established by detailed NMR spectroscopic analysis, as well as by comparison with literature data or with authentic samples.

Chemical constituents of marine medicinal mangrove plant Sonneratia caseolaris

Twenty-four compounds including eight steroids (1-8), nine triterpenoids (9-16, 24), three flavonoids (20-22), and four benzenecarboxylic derivatives (17-19, 23) were isolated and identified from stems and twigs of medicinal mangrove plant Sonneratia caseolaris. The structures of the isolated compounds were determined by extensive analysis of their spectroscopic data. Among these metabolites, compounds 1, 4-20 and 22-24 were isolated and identified for the first time from S. caseolaris. In the in vitro cytotoxic assay against SMMC-7721 human hepatoma cells, compound 21 (3',4',5,7-tetrahydroxyflavone) exhibited significant activity with IC50 2.8 mu g/mL, while oleanolic acid (14), 3,3'-di-O-methyl ether ellagic acid (18), and 3,3',4-O-tri-O-methyl ether ellagic acid (19) showed weak activity. None of these compounds displayed significant antibacterial activites.

The chemical constituents from red alga Gymnogongrus flabelliformis Harv.

Eight compounds were isolated from red alga Gymnogongrus flabelliformis Harv. In normal phase silica gel, Sephadex LH-20 gel column chromatography, reverse phase HPLC, and recrystallization. Based on MS and 1D NMR spectroscopic data, their structures were determined as: stigmast-4-en-3-one (I), cholest-4-en-3-one (II), cholesterol (III), uracil (IV), uridine (V), adenosine (VI), succinic acid (VII), and 5-hydroxy-4-methyl-5-pentyl-2,5-dihydro-furan-2-on (VIII). All of them were obtained from this species for the first time. Cytotoxicity of these compounds was screened using standard MTT method, but all the compounds were inactive (IC50 > 10 mu g/ml).

Electrochemical and quantum chemical study of purines as corrosion inhibitors for mild steel in 1 M HCl solution

The purines and its derivatives, such as, guanine, adenine, 2,6-diaminopurine, 6-thioguanine and 2,6-dithiopurine, were investigated as corrosion inhibitors for mild steel in 1 M HCl solution by weight loss measurements, electrochemical tests and quantum chemical calculations. The polarization curves of mild steel in the hydrochloric acid solutions of the purines showed that both cathodic and anodic processes of steel corrosion were suppressed. The Nyquist plots of impedance expressed mainly as a depressed capacitive loop with different compounds and concentrations. For all these purines, the inhibition efficiency increased by increasing the inhibitor concentration, and the inhibition efficiency orders are 2,6-dithiopurine > 6-thioguanine > 2,6-diaminopurine > adenine > guanine with the highest inhibiting efficiency of 88.0% for 10(-3) M 2,6-dithiopurine. The optimized structures of purines, the Mulliken charges, molecular orbital densities and relevant parameters were calculated by quantum chemical calculations. The quantum chemical calculation results inferred that the adsorption belong to physical adsorption, which might arise from the pi stacking between the pi electron of the purines and the metal surface. (C) 2008 Elsevier Ltd. All rights reserved.

Chemical Constituents of Nitraira tangutorum Seed from Qaidam Basin

Six compounds were isolated from the 75% ethanol extract of Nitraria tangutorum seed.On the basis of spectroscopic methods including 1H NMR,13C NMR and ESI-MS and comparison with literature,their structures were elucidated as daucosterol(1),4-hydroxypipecolic acid(2),quercetin(3),allantoin(4),1,2,3,4-tetrahydro-1-methyl-β-carboline-3-carboxylic acid(5) and L-tyrosine(6).Compounds 1,2,3,5 and 6 were isolated from Nitraria tangtorum for the first time.

Chemical constituents from the whole plant of Euphorbia altotibetic

Four new jatrophane diterpenoids, altotibetin A (1), altotibetin B (2), altotibetin C (3), altotibetin D (4), and nine known compounds, beta-sitosterol, cycloart-23-ene-3beta,25-diol, cycloart-25-ene-3beta,24-diol, lupeol acetate, scopoletin, kaempferol, uracil, uridine, astragalin, and daucosterol have been isolated from the whole plant of Euphorbia altotibetic PAULS. Their structures were established by spectral methods, and the configurations of 1 and 2 were confirmed by X-ray analysis.

Descriptive Simulation: Combining Symbolic and Numerical Methods in the Analysis of Chemical Reaction Mechanisms

The Kineticist's Workbench is a computer program currently under development whose purpose is to help chemists understand, analyze, and simplify complex chemical reaction mechanisms. This paper discusses one module of the program that numerically simulates mechanisms and constructs qualitative descriptions of the simulation results. These descriptions are given in terms that are meaningful to the working chemist (e.g., steady states, stable oscillations, and so on); and the descriptions (as well as the data structures used to construct them) are accessible as input to other programs.

Artificial opal photonic crystals and inverse opal structures - fundamentals and applications from optics to energy storage

Photonic crystals (PhCs) influence the propagation of light by their periodic variation in dielectric contrast or refractive index. This review outlines the attractive optical qualities inherent to most PhCs namely the presence of full or partial photonic band gaps and the possibilities they present towards the inhibition of spontaneous emission and the localization of light. Colloidal self-assembly of polymer or silica spheres is one of the most favoured and low cost methods for the formation of PhCs as artificial opals. The state of the art in growth methods currently used for colloidal self-assembly are discussed and the use of these structures for the formation of inverse opal architectures is then presented. Inverse opal structures with their porous and interconnected architecture span several technological arenas - optics and optoelectronics, energy storage, communications, sensor and biological applications. This review presents several of these applications and an accessible overview of the physics of photonic crystal optics that may be useful for opal and inverse opal researchers in general, with a particular emphasis on the recent use of these three-dimensional porous structures in electrochemical energy storage technology. Progress towards all-optical integrated circuits may lie with the concepts of the photonic crystal, but the unique optical and structural properties of these materials and the convergence of PhC and energy storage disciplines may facilitate further developments and non-destructive optical analysis capabilities for (electro)chemical processes that occur within a wide variety of materials in energy storage research.

NMR methods for characterizing the pore structures and hydrogen storage properties of microporous carbons.

(1)H NMR spectroscopy is used to investigate a series of microporous activated carbons derived from a poly(ether ether ketone) (PEEK) precursor with varying amounts of burnoff (BO). In particular, properties relevant to hydrogen storage are evaluated such as pore structure, average pore size, uptake, and binding energy. High-pressure NMR with in situ H(2) loading is employed with H(2) pressure ranging from 100 Pa to 10 MPa. An N(2)-cooled cryostat allows for NMR isotherm measurements at both room temperature ( approximately 290 K) and 100 K. Two distinct (1)H NMR peaks appear in the spectra which represent the gaseous H(2) in intergranular pores and the H(2) residing in micropores. The chemical shift of the micropore peak is observed to evolve with changing pressure, the magnitude of this effect being correlated to the amount of BO and therefore the structure. This is attributed to the different pressure dependence of the amount of adsorbed and non-adsorbed molecules within micropores, which experience significantly different chemical shifts due to the strong distance dependence of the ring current effect. In pores with a critical diameter of 1.2 nm or less, no pressure dependence is observed because they are not wide enough to host non-adsorbed molecules; this is the case for samples with less than 35% BO. The largest estimated pore size that can contribute to the micropore peak is estimated to be around 2.4 nm. The total H(2) uptake associated with pores of this size or smaller is evaluated via a calibration of the isotherms, with the highest amount being observed at 59% BO. Two binding energies are present in the micropores, with the lower, more dominant one being on the order of 5 kJ mol(-1) and the higher one ranging from 7 to 9 kJ mol(-1).

Comparison of the experimental, semi-experimental and ab initio equilibrium structures of acetylene: Influence of relativisitic effects and of the diagonal Born-Oppenheimer corrections

The equilibrium structure of acetylene (also named ethyne) has been reinvestigated to resolve the small discrepancies noted between different determinations. The size of the system as well as the large amount of available experimental data provides the quite unique opportunity to check the magnitude and relevance of various contributions to equilibrium structure as well as to verify the accuracy of experimental results. With respect to pure theoretical investigation, quantum-chemical calculations at the coupled-cluster level have been employed together with extrapolation to the basis set limit, consideration of higher excitations in the cluster operator, inclusion of core correlation effects as well as relativistic and diagonal Born-Oppenheimer corrections. In particular, it is found that the extrapolation to the complete basis set limit, the inclusion of higher excitations in the electronic-correlation treatment and the relativistic corrections are of the same order of magnitude. It also appears that a basis set as large as a core-valence quintuple-zeta set is required for accurately accounting for the inner-shell correlation contribution. From a pure experimental point of view, the equilibrium structure has been determined using very accurate rotational constants recently obtained by a global analysis (that is to say that all non-negligible interactions are explicitely included in the Hamiltonian matrix) of rovibrational spectra. Finally, a semi-experimental equilibrium structure (where the equilibrium rotational constants are obtained from the experimental ground state rotational constants and computed rovibrational corrections) has been obtained from the available experimental ground-state rotational constants for ten isotopic species corrected for computed vibrational corrections. Such a determination led to the revision of the ground-state rotational constants of two isotopologues, thus showing that structural determination is a good method to identify errors in experimental rotational constants. The three structures are found in a very good agreement, and our recommended values are rCC 120.2958(7) pm and rCH 106.164(1) pm. © 2011 American Institute of Physics.

Modelling of nano-imprint forming process for the production of miniaturised 3D structures

Nano-imprint forming (NIF) as manufacturing technology is ideally placed to enable high resolution, low-cost and high-throughput fabrication of three-dimensional fine structures and the packaging of heterogeneous micro-systems (S.Y. Chou and P.R. Krauss, 1997). This paper details a thermo-mechanical modelling methodology for optimising this process for different materials used in components such as mini-fluidics and bio-chemical systems, optoelectronics, photonics and health usage monitoring systems (HUMS). This work is part of a major UK Grand Challenge project - 3D-Mintegration - which is aiming to develop modelling and design technologies for the next generation of fabrication, assembly and test processes for 3D-miniaturised systems.

Low temperature crystal structures of two rhodanine derivatives, 3-amino rhodanine and 3-methyl rhodanine: geometry of the rhodanine ring

Rhodanines (2-thio-4-oxothiazolidines) are synthetic small molecular weight organic molecules with diverse applications in biochemistry, medicinal chemistry, photochemistry, coordination chemistry and industry. The X-ray crystal structure determination of two rhodanine derivatives, namely (I), 3-aminorhodanine [3-amino-2-thio-4-oxothiazolidine], C3H4N2OS2, and (II) 3-methylrhodanine [3-methyl-2-thio-4-oxothiazolidine], C4H5NOS2, have been conducted at 100 K. I crystallizes in the monoclinic space group P2(1)/n with unit cell parameters a = 9.662(2), b = 9.234(2), c = 13.384(2) angstrom, beta = 105.425(3)degrees, V = 1151.1(3) angstrom(3), Z = 8 (2 independent molecules per asymmetric unit), density (calculated) = 1.710 mg/m(3), absorption coefficient = 0.815 mm(-1). II crystallizes in the orthorhombic space group Iba2 with unit cell a = 20.117(4), b = 23.449(5), c = 7.852(2) angstrom, V = 3703.9(12) angstrom(3), Z = 24 (three independent molecules per asymmetric unit), density (calculated) = 1.584 mg/m(3), absorption coefficient 0.755 mm(-1). For I in the final refinement cycle the data/restraints/parameter ratios were 2639/0/161, goodness-of-fit on F-2 = 0.934, final R indices [I > 2sigma(I)] were R1 = 0.0299, wR2 = 0.0545 and R indices (all data) R1 = 0.0399, wR2 = 0.0568. The largest difference peak and hole were 0.402 and -0.259 e angstrom(-3). For II in the final refinement cycle the data/restraints/parameter ratios were 3372/1/221, goodness-of-fit on F(2) = 0.950, final R indices [I > 2sigma(I)] were R1 = 0.0407, wR2 = 0.1048 and R indices (all data) R1 = 0.0450, wR2 = 0.1088. The absolute structure parameter = 0.19(9) and largest difference peak and hole 0.934 and -0.301 e angstrom(-3). Details of the geometry of the five molecules (two for I and three for II) and the crystal structures are fully discussed. Corresponding features of the molecular geometry are highly consistent and firmly establish the geometry of the rhodanine

Central nervous system drugs: Low temperature X-ray structures of (I) the base 5-(2,3-dichlorophenyl)-2,4-diamino-6-fluoromethyl-pyrimidine (4030W92) and (II) 5-(2,6-dichlorophenyl)-1-H-2,4-diamino-6-methyl-pyrimidine methanesulphonic acid salt (227C89)

The X-ray crystal structures of (I), the base 4030W92, 5-(2,3-dichlorophenyl)-2,4-diamino-6-fluoromethyl-pyrimidine, C11H9Cl2FN4, and (II) 227C89, the methanesulphonic acid salt of 5-(2,6-dichlorophenyl)-1-H-2,4-diamino-6-methyl-pyrimidine, C11H11Cl2N4 center dot CH3O3S, have been carried out at low temperature. A detailed comparison of the two structures is given. Structure (I) is non-centrosymmetric, crystallizing in space group P2(1) with unit cell a = 10.821(3), b = 8.290(3), c = 13.819(4) angstrom, beta = 105.980(6)degrees, V = 1191.8(6) angstrom(3), Z = 4 (two molecules per asymmetric unit) and density (calculated) = 1.600 mg/m(3). Structure (II) crystallizes in the triclinic space group P (1) over bar with unit cell a = 7.686(2), b = 8.233(2), c = 12.234(2) angstrom, alpha = 78.379(4), beta = 87.195(4), gamma = 86.811(4)degrees, V = 756.6(2) angstrom(3), Z = 2, density (calculated) = 1.603 mg/m(3). Final R indices [I > 2sigma(I)] are R1 = 0.0572, wR2 = 0.1003 for (I) and R1 = 0.0558, wR2 = 0.0982 for (II). R indices (all data) are R1 = 0.0983, wR2 = 0.1116 for (I) and R1 = 0.1009, wR2 = 0.1117 for (II). 5- Phenyl-2,4 diaminopyrimidine and 6-phenyl-1,2,4 triazine derivatives, which include lamotrigine (3,5-diamino-6-(2,3-dichlorophenyl)-1,2,4-triazine), have been investigated for some time for their effects on the central nervous system. The three dimensional structures reported here form part of a newly developed data base for the detailed investigation of members of this structural series and their biological activities.

IR/Raman spectroscopy and DFT calculations of cyclic di-amino acid peptides. Part III: comparison of solid state and solution structures of cyclo(L-Ser-L-Ser)

B3-LYP/cc-pVDZ calculations of the gas-phase structure and vibrational spectra of the isolated molecule cyclo(L-Ser-L-Ser), a cyclic di-amino acid peptide (CDAP), were carried out by assuming C-2 symmetry. It is predicted that the minimum-energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L-Beryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol(-1)) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X-ray crystallographic structure of cyclo(L-Ser-L-Ser), shows that the DKP ring displays a near-planar conformation, with both the two L-Beryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier-transform infrared (FT-IR) spectra of solid state and aqueous solution samples of cyclo(L-Ser-L-Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid-state samples show characteristic amide I vibrations which are split (Raman:1661 and 1687 cm(-1), IR:1666 and 1680 cm(-1)), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of ~ 30 cm(-1), which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm(-1). The occurrence of this cis amide II mode at a wavenumber above 1500 cm(-1) concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C-alpha atoms, and is also indicative of a relatively unstrained DKP ring.