Synthetic Model Compounds Research Articles

The effect of lignin content and lignin modification on Norway spruce wood properties and decay resistance

This thesis describes studies with three different Norway spruce cutting clones in three growing environments differing in soil and climatic conditions within the boreal zone. The main aim was to follow variation in the radial growth rate, wood properties and lignin content and to modify wood lignin with a natural monolignol, coniferyl alcohol, by making use of inherent wood peroxidases. In addition, the incorporation of chlorinated anilines into lignin was studied with synthetic model compounds and synthetic lignin preparations to show whether unnatural compounds originating from pesticides could be bound in the lignin polymer. Annual ring width, latewood proportion and wood properties such as weight density, modulus of rupture (MOR) and modulus of elasticity (MOE) were determined. Fourier transform infrared (FTIR) spectroscopy was applied to the quantitative estimation of lignin in heartwood, sapwood and earlywood samples by using a principal component regression (PCR) technique. Wood blocks were treated with coniferyl alcohol by using a vacuum impregnation method. The effect of impregnation was assessed by FTIR and by a fungal decay test. Trees from a fertile site showed the highest growth rate and sapwood lignin content and the lowest latewood proportion, weight density and MOR. Trees from a medium fertile site had the lowest growth rate and the highest latewood proportion, weight density, MOE and MOR. The most rapidly growing clone showed the lowest latewood proportion, weight density, MOE and MOR. The slowest growing clone had the lowest sapwood lignin content and the highest latewood proportion, weight density, MOE and MOR. Fairly large variation was found between the individual trees and between the growing seasons but much less variation between the sites and between the clones. The coniferyl alcohol impregnation increased the content of different lignin-type phenolic compounds in the wood as well as wood decay resistance against a white-rot fungus, Coriolus versicolor. Also the incorporation of chlorinated anilines into lignin was shown to be possible and the intermediate quinone methide was seen to be trapped by 3,4-dichloroaniline during the dehydrogenative polymerization of coniferyl alcohol, which resulted in a dimer of coniferyl alcohol with a β-O-4 structure and with dichloroaniline bound by a benzylamine bond. In conclusion, in this thesis it was shown that the different Norway spruce cutting clones maintained clone-dependent wood properties in the different growing sites although variation between tree individuals was high and climatic factors affected growth. It was also shown that the natural monolignol, coniferyl alcohol, and chlorinated anilines could be incorporated into the lignin polymer in vivo and in vitro, respectively. The coniferyl alcohol impregnation experiment resulted in the improved resistance of the wood blocks to fungal decay, while chlorinated anilines were covalently bound into the lignin polymer and they could not be released by mild acid hydrolysis.

Catalysis by the Isolated Tryptophan Tryptophylquinone-Containing Subunit of Aromatic Amine Dehydrogenase Is Distinct from Native Enzyme and Synthetic Model Compounds and Allows Further Probing of TTQ Mechanism

Para-substituted benzylamines are poor reactivity probes for structure-reactivity studies with TTQ-dependent aromatic amine dehydrogenase (AADH). In this study, we combine kinetic isotope effects (KIEs) with structure-reactivity studies to show that para-substituted benzylamines are good reactivity probes of TTQ mechanism with the isolated TTQ-containing subunit of AADH. Contrary to the TTQ-containing subunit of methylamine dehydrogenase (MADH), which is catalytically inactive, the small subunit of AADH catalyzes the oxidative deamination of a variety of amine substrates. Observed rate constants are second order with respect to substrate and inhibitor (phenylhydrazine) concentration. Kinetic studies with para-substituted benzylamines and their dideuterated counterparts reveal KIEs (>6) larger than those observed with native AADH (KIEs approximately unity). This is attributed to formation of the benzylamine-derived iminoquinone requiring structural rearrangement of the benzyl side chain in the active site of the native enzyme. This structural reorganization requires motions from the side chains of adjacent residues (which are absent in the isolated small subunit). The position of Phealpha97 in particular is responsible for the conformational gating (and hence deflated KIEs) observed with para-substituted benzylamines in the native enzyme. Hammett plots for the small subunit exhibit a strong correlation of structure-reactivity data with electronic substituent effects for para-substituted benzylamines and phenethylamines, unlike native AADH for which a poor correlation is observed. TTQ reduction in the isolated subunit is enhanced by electron withdrawing substituents, contrary to structure-reactivity studies reported for synthetic TTQ model compounds in which rate constants are enhanced by electron donating substituents. We infer that para-substituted benzylamines are good reactivity probes of TTQ mechanism with the isolated small subunit. This is attributed to the absence of structural rearrangement prior to H-transfer that limits the rate of TTQ reduction by para-substituted benzylamines in native enzyme.

High‐spin versus broken symmetry—Effect of DFT spin density representation on the geometries of three diiron (III) model compounds

Unrestricted density functional theory calculations have been conducted on three diiron(III) synthetic model compounds containing antiferromagnetically coupled high-spin (HS) irons for which crystallographic structures and Raman spectral data are available. Three density functionals have been employed: BPW91, PWC, and BOP. The study compares the effects on optimized geometries and harmonic vibrational frequencies of spin-paired (SP) low-spin, HS, and broken symmetry antiferromagnetically coupled singlet representations of the spin density distribution. The geometries around the diiron centers in the HS and broken symmetry (BS) representations are found to be similar, both markedly different from those arising from the SP representation. Small differences between the HS and BS results are seen in bond lengths, angles, Raman frequencies, and spin densities associated with oxo and peroxo bridges between the irons.

Stereochemical analysis of α1, a mating hormone of the phytopathogen Phytophthora

The stereochemistry of α1, the first identified mating hormone of the plant pathogen Phytophthora, has been unknown due to its acyclic flexible nature. Here, two stereogenic centers of α1 are determined to be (3 RS,15 R)-configuration by NMR analysis of the Mosher’s esters of α1 and a synthetic model compound. The information obtained here will be helpful for reducing the burden of the researchers who are trying to synthesize all the possible stereoisomers of α1 to elucidate its full stereochemistry.

Mechanism of Nitrite Reduction at T2Cu Centers: Electronic Structure Calculations of Catalysis by Copper Nitrite Reductase and by Synthetic Model Compounds

The mechanism of nitrite reduction at the Cu(II) center of both copper nitrite reductase and a number of corresponding synthetic models has been investigated by using both QM/MM and cluster calculations employing density functional theory methods. The mechanism in both cases is found to be very similar. Initially nitrite is bound in a bidentate fashion to the Cu(II) center via the two oxygen atoms. Upon reduction of the copper center, the two possible coordination modes of the protonated nitrite, by either nitrogen or a single oxygen atom, are close in energy, with nitrogen coordination probably preferred. Further protonation of this species leads to N-O bond cleavage, and an electron transfer from the Cu(I) center to the N-O+ ligand, resulting in loss of NO and regeneration of the resting state of the enzyme having a bound water molecule.

Development of catalytic tar decomposition downstream from a dual fluidized bed biomass steam gasifier

Gasification of biomass is an attractive technology for combined heat and power production. Although a lot of research and development work has been carried out during the past decade the commercial breakthrough for this technology is still to come. One problem that has not been completely solved so far is the tar content in the product gas, which can cause plugging in the colder parts of the plant. Among the possible gas cleaning methods, catalytic hot gas cleaning is rather promising because of the complete destruction of the tars instead of creating a waste stream which is difficult to dispose. Different catalysts were measured in laboratory scale reactors fed by synthetic gas mixtures and tar model compounds. Commercial steam-reforming catalysts for heavy hydrocarbons (particularly naphthas) proved best as tar decomposing catalysts. Based on these results 3 nickel-based monolith type of catalyst were produced and afterwards tested in a laboratory scale reactor fed by slip streams taken from the 8 MW dual fluidized bed steam gasifier plant in Güssing, Austria. Almost complete tar and considerable ammonia decomposition could be achieved over this catalyst at temperatures above 850 °C and space velocities of about 1100 h − 1 .

Mycenarubins A and B, Red Pyrroloquinoline Alkaloids from the Mushroom Mycena rosea

AbstractTwo previously unknown red alkaloid pigments, mycenarubin A (1), and a dimer thereof, mycenarubin B (6), have been isolated from fruiting bodies of Mycena rosea and the structures of these pyrroloquinoline alkaloids have been established by 2D NMR and ESI‐MS methods. Their absoluteconfigurations were determined by comparison of their CD spectra with the CD spectrum of a synthetic model compound. The fungal pigments are structurally related to the damirones, isolated from a marine sponge, and may be biosynthetically derived from tryptophan and S‐adenosylmethionine.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)

Going forward

Since this is the founding issue of “Biopolymers,” we wish to set down our thoughts on the nature and scope of the new Journal. It will be a publication devoted to high quality original research in the field of biopolymers (proteins, nucleic acids, polysaccharides, etc.) and synthetic model compounds for such substances. The emphasis of the papers sought is to be on the polymeric nature of the materials and systems investigated This Journal will include both experimental and theoretical reports. Normal length papers and “Communications to the Editor” will be rigorously judged. The latter will be limited to reports of special timeliness and originality. Subjects such as structure and function of biopolymers are suitable, as are studies on synthetic analogs of biopolymers, genetic investigations, details of biological organization, and biosynthetic pathways of polymer formation. We believe that our undertaking represents a fusion of the macromolecular research in physics, chemistry, and biology of life processes. The editorial board shall strive to remain sensitive to the most modern and up-to-date reports and modify their thinking as this hybrid science grows. Biopolymers will continue to publish original research articles and reviews in the general area of macromolecular structure and function. Even 44 years ago, the editorial team recognized what s almost dogmatic today - the study of proteins, nucleic acids, and carbohydrates is truly a multidisciplinary endeavor. In this regard, the Journal will serve as a forum to present research that draws from multiple fields for the advancement of biopolymer science. In addition to review articles from leading authors on “hot” topics familiar to our readership, the Journal now will publish reviews that approach the study of biopolymers from new and, at times, unconventional perspectives. As practitioners in the field, our entire editorial team is sensitive to the constraints that today's research environment places on authors and referees. Therefore, there are no page or color charges associated with publication in Biopolymers and full papers can be of any length (both word count and artwork). The Journal will handle all papers expeditiously, taking full advantage of web technology in submission and review of manuscripts. All papers will appear on-line within a week of acceptance. The new editorial board is excited by the technical and conceptual changes to the Journal, as well as by the commitment that our publisher, John Wiley & Sons, has made to Biopolymers. We look forward to working with you to grow the Journal and invite your comments and feedback every step along the way. For the Associate Editors and Editorial Advisory Board, Gary D. Glick Ph.D. Editor-in-Chief*, * University of Michigan.

Revised Structure of Zamamistatin.

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Rearrangement of the Mo/Fe/S Cluster under the Reducing Conditions; Alternative Synthesis of MoFe4S6(PEt3)4Cl Cluster from [(Cl4-cat)Mo(MeCN)Fe3S4Cl3](Et4N)

Synthetic model compounds for FeMo-cofactor have been pursued persistently by synthetic inorganic chemists. Continuous efforts resulted in P-cluster analogs of [(Tp)2Mo2Fe6S9(SH)2] 3− and [(Fe4S3)2(μ6-S)] clusters, recently. Our ongoing efforts to synthesize FeMo-cofactor model compounds has produced many new Mo/Fe/S clusters, including (Cl4-cat)2Mo2Fe6S8(PR3)6 (R = Et, Pr, and Bu), Fe(DMF)Cl(Cl4-cat)2Mo2Fe2S4(PEt3)2ClFe4S4(PEt3)3(CO)6Cl, 4

Polypyrroles as Antioxidants: Kinetic Studies on Reactions of Bilirubin and Biliverdin Dimethyl Esters and Synthetic Model Compounds with Peroxyl Radicals in Solution. Chemical Calculations on Selected Typical Structures

[reaction: see text] Rate constants for hydrogen-atom transfer (HAT) from bilirubin dimethyl ester (BRDE) and biliverdin dimethyl ester (BVDE) to peroxyl radicals during inhibited autoxidation of styrene initiated by azo-bisisobutyronitrile (AIBN) were k(inh)(BRDE) = 22.5 x 10(4) and k(inh)(BVDE) = 10.2 x 10(4) M(-1) s(-1), and the stoichiometric factors (n) were 2.0 and 2.7, respectively. A synthetic tetrapyrrole (bis(dipyrromethene)) containing the alpha-central (2,2') CH2 linkage gave k(inh) = 39.9 x 10(4) M(-1) s(-1) and n = 2.3, whereas the beta-linked (3,3') isomer was not an active antioxidant. Several dipyrrinones were synthesized as mimics of the two outer heterocyclic rings of bilirubin and biliverdin. The dipyrrinones containing N-H groups in each ring were active antioxidants, whereas those lacking two such "free" N-H groups, such as N-CH3 dipyrrinones and dipyrromethenes, did not exhibit antioxidant activity. Overall, the relative k(inh) values compared to those of phenolic antioxidants, 2,6-di-tert-butyl-4-methoxyphenol (DBHA) and 2,6-di-tert-butyl-4-methylphenol (BHT), were 2,2'-bis(dipyrromethene) > BRDE > DBHA > dipyrrinones > BVDE > BHT. This general trend in antioxidant activities was also observed for the inhibited autoxidation of cumene initiated by AIBN. Chemical calculations of the N-H bond dissociation enthalpies (BDEs) of the typical structures support a HAT mechanism from N-H groups to trap peroxyl radicals. Intramolecular hydrogen bonding of intermediate nitrogen radicals has a major influence on the antioxidant activities of all compounds studied. Indeed, chemical calculations showed that the initial nitrogen radical from a dipyrrinone is stabilized by 9.0 kcal/mol because of H-bonding between the N-H remaining on one ring and the ground-state pyrrolyl radical of the adjacent ring in the natural zusammen structure. The calculated minimum structure of bilirubin shows strong intramolecular H-bonding of the N-H groups with carbonyl groups resulting in the known "ridge-tile" structure which is not an active HAT antioxidant. The calculated minimum structure of biliverdin is planar. BRDE is readily converted into BVDE by reaction with the electron-deficient DPPH* radical under argon in chlorobenzene. An electron-transfer mechanism is proposed for the initiating step in this reaction, and this is supported by the relatively low ionizing potential of a model dipyrrole representing the two central rings of bilirubin.

Revised structure of zamamistatin

The structure of zamamistatin, a novel bromotyrosine derivative from the Okinawan sponge Pseudoceratina sp. was revised by comparison of the 13C NMR data of zamamistatin with those of synthetic model compounds.

Configuration of the Psymberin Amide Side Chain

[structure: see text] The structure of the amide side chain of psymberin, a potent and selective cytotoxin, is proposed. Syn and anti models of the amide side chain were prepared, and the structural assignment was confirmed by X-ray crystallographic analysis of the anti isomer. Comparison of (1)H and (13)C NMR data establishes homology between the natural product and the synthetic model compound of anti configuration and not the corresponding syn isomer.

Identifying the Characteristic Secondary Ions of Lignin Polymer Using ToF−SIMS

The chemical structure of lignin, a complex, irregular polymer of phenylpropane units that occurs in plant cell walls, was investigated using time-of-flight secondary ion mass spectrometry (ToF-SIMS). The positive ToF-SIMS spectra of lignin isolated from pine and beech wood showed prominent secondary ions possessing guaiacyl (at m/z 137 and 151) or syringyl (at m/z 167 and 181) rings, which are the basic building units of lignin polymer. This shows that ToF-SIMS is a useful tool for lignin structural analysis. The peaks at m/z 137 and 167 were assigned as the C6-C1 ion, and the peaks at m/z 151 and 181 may be double-component, the C6-C1 ion and the C6-C2 ion. We confirmed the characteristic guaiacyl ions using a synthetic lignin model compound, dehydrogenation polymer (DHP), which was formed by polymerizing of unlabeled and deuterium-labeled coniferyl alcohols. The formation mechanism of the main secondary ions was deduced by labeling specific positions of coniferyl alcohols with a stable isotope to study the relationship between chemical structure and secondary ion formation in ToF-SIMS.

Absolute Stereo-structure of Kendarimide A, a Novel MDR Modulator, from a Marine Sponge

The absolute stereostructure of two N-methylcysteines in kendarimide A (1), a novel linear peptide reversing multidrug resistance (MDR) mediated by P-glycoprotein, was determined by comparison with synthetic model compounds. For this purpose, four diastereomers (17a-d) of the C-terminal tetrapeptides in kendarimide A (1), containing L,L-, L,D-, D,L-, D,D-N-methylcysteinyl-N-methylcysteine, were synthesized. The absolute configuration of both the two adjacent N-methylcysteines in 1, which form an eight-membered disulfide ring (ox-[MeCys-MeCys]), was elucidated to be L-configuration by comparison of the NMR spectral data of the four model tetrapeptides with that of kendarimide A (1).

Nematocidal thiocyanatins from a southern Australian marine sponge Oceanapia sp.

Investigations of a southern Australian marine sponge, Oceanapia sp., have yielded two new beta methyl branched bisthiocyanates, thiocyanatins D1 (3a) and D(2) (3b), along with two new thiocarbamate thiocyanates, thiocyanatins E1 (4a) and E2 (4b). The new thiocyanatins belong to a rare class of bioactive marine metabolite previously only represented by thiocyanatins A-C (1, 2a/b). Structures were assigned on the basis of detailed spectroscopic analysis, with comparisons to the known bisthiocyanate thiocyanatin A (1) and synthetic model compounds (5-7). The thiocyanatins exhibit potent nematocidal activity, and preliminary structure-activity relationship investigations have confirmed key characteristics of the thiocyanatin pharmacophore.

Hemodextrin: a self-assembled cyclodextrin–porphyrin construct that binds dioxygen

Synthetic hemoprotein model compounds are of great interest due to the vital roles and complexities of hemoproteins. This study reports a novel, self-assembled hemoprotein model, hemodextrin. The synthesis and characterization of py-PPCD (2 A-monopyridylmethyl-perPEGylated-β-cyclodextrin) ( 2) is described. The molecular design is based on a pegylated cyclodextrin scaffold that bears both a heme-binding pocket and an axial ligand that binds an iron porphyrin. The binding constant for Fe(III)TPPS [iron(III) meso-tetra(4-sulphonatophenyl)porphyrin] by py-PPCD ( 2) was determined to be 2×10 6 M −1 at pH 6.0 by observing characteristic changes in the UV–Vis spectrum of the porphyrin. The pyridyl nitrogen of py-PPCD ( 2) was shown to ligate to the iron center by observing signal changes in the Fe(II)-porphyrin 1H-NMR spectrum. This hemodextrin ensemble was shown to bind dioxygen reversibly and to form a stable ferryl species.

Synthesis and characterization of reduced heme and heme/copper carbonmonoxy species.

Carbon monoxide readily binds to heme and copper proteins, acting as a competitive inhibitor of dioxygen. As such, CO serves as a probe of protein metal active sites. In our ongoing efforts to mimic the active site of cytochrome c oxidase, reactivity toward carbon monoxide offers a unique opportunity to gain insight into the binding and spectroscopic characteristics of synthetic model compounds. In this paper, we report the synthesis and characterization of CO-adducts of ((5/6)L)Fe(II), [((5/6)L)Fe(II)...Cu(I)](B(C(6)F(5))(4)), and [(TMPA)Cu(I)(CH(3)CN)](B(C(6)F(5))(4)), where TMPA = tris(2-pyridylmethyl)amine and (5/6)L = a tetraarylporphyrinate tethered in either the 5-position ((5)L) or 6-position ((6)L) to a TMPA copper binding moiety. Reaction of ((5/6)L)Fe(II) [in THF (293 K): UV-vis 424 (Soret), 543-544 nm; (1)H NMR delta(pyrrole) 52-59 ppm (4 peaks); (2)H NMR (from ((5)L-d(8))Fe(II)) delta(pyrrole) 53.3, 54.5, 55.8, 56.4 ppm] with CO in solution at RT yielded ((5/6)L)Fe(II)-CO [in THF (293 K): UV-vis 413-414 (Soret), 532-533 nm; IR nu(CO)(Fe) 1976-1978 cm(-1); (1)H NMR delta(pyrrole) 8.8 ppm; (2)H NMR (from ((5)L-d(8))Fe(II)-CO) delta(pyrrole) 8.9 ppm; (13)C NMR delta((CO)Fe) 206.8-207.1 ppm (2 peaks)]. Experiments repeated in acetonitrile, acetone, toluene, and dichloromethane showed similar spectroscopic data. Binding of CO resulted in a change from five-coordinate, high-spin Fe(II) to six-coordinate, low-spin Fe(II), as evidenced by the upfield shift of the pyrrole resonances to the diamagnetic region ((1)H and (2)H NMR spectra). Addition of CO to [((5/6)L)Fe(II)...Cu(I)](B(C(6)F(5))(4)) [in THF (293 K): UV-vis ((6)L only) 424 (Soret), 546 nm; (1)H NMR delta(pyrrole) 54-59 ppm (multiple peaks); (2)H NMR (from [((5)L-d(8))Fe(II).Cu(I)](B(C(6)F(5))(4))) delta(pyrrole) 53.4 ppm (br)] gave the bis-carbonyl adduct [((5/6)L)Fe(II)-CO...Cu(I)-CO](B(C(6)F(5))(4)) [in THF (293 K): UV-vis ((6)L only) 413 (Soret), 532 nm; IR nu(CO)(Fe) 1971-1973 cm(-1), nu(CO)(Cu) 2091-2093 cm(-1), approximately 2070(sh) cm(-1); (1)H NMR delta(pyrrole) 8.7-8.9 ppm; (2)H NMR (from [((5)L-d(8))Fe(II)-CO...Cu(I)-CO](B(C(6)F(5))(4))) delta(pyrrole) 8.9 ppm; (13)C NMR delta((CO)Fe) 206.8-208.1 ppm (2 peaks), delta((CO)Cu) 172.4 ((5)L), 178.2 ((6)L) ppm]. Experiments in acetonitrile, acetone, and toluene exhibited spectral features similar to those reported. The [((5/6)L)Fe(II)-CO.Cu(I)-CO](B(C(6)F(5))(4)) compounds yielded (CO)(Fe) spectra analogous to those seen for ((5/6)L)Fe(II)-CO and (CO)(Cu) spectra similar to those seen for [(TMPA)Cu(I)-CO](B(C(6)F(5))(4)) [in THF (293 K): IR nu(CO)(Cu) 2091 cm(-1), approximately 2070(sh) cm(-1); (13)C NMR delta((CO)Cu) 180.3 ppm]. Additional IR studies were performed in which the [((5)L)Fe(II)-CO...Cu(I)-CO](B(C(6)F(5))(4)) in solution was bubbled with argon in an attempt to generate the iron-only mono-carbonyl [((5)L)Fe(II)-CO.Cu(I)](B(C(6)F(5))(4)) species; in coordinating solvent or with axial base present, decreases in characteristic IR-band intensities revealed complete loss of CO from copper and variable loss of CO from the heme.

Determination of the Absolute Configuration of Hydroxyiridals by Chiroptical and NMR Spectroscopic Methods

AbstractHydroxyiridals − monocyclic triterpenoids − are found abundantly in sword lilies. They feature a homofarnesyl side chain that is hydroxylated at one of the allylic methylene groups, which gives rise to a chiral carbon atom. The absolute configuration of six hydroxyiridals from different sources was determined by the exciton chirality method and by NMR spectroscopy of the diastereoisomeric MTPA and MPA esters. All three measurements gave consistent results, establishing the (R) configuration for all of the hydroxyiridals. The reliability of these methods for the stereochemical analysis of acyclic secondary allylic alcohols was confirmed by applying them to a synthetic model compound of known configuration. In the course of this study, two new iridals − 16,26‐dihydroxyiridal 7 and 18,19‐epoxyiridal 8 − were isolated from extracts of I. versicolor and the iridal fraction of I. missouriensis was analyzed thoroughly. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)

A study of 1,5-hydrogen shift and cyclization reactions of an alkali isomerized methyl linolenoate

Heating a mixture formed by alkali isomerization of methyl linolenoate ( 1 ) produces a complex mixture with the bicyclic hexahydroindenoic esters 4β-(7-methoxycarbonylheptyl)-5α-methyl-2,3,3aα,4,5,7aαhexahydroindene (CL5) and 4β-ethyl-5α-(6-methoxycarbonylhexyl)-2,3,3aα,4,5,7aα-hexahydroindene (CL6) as main components. Similar isomerization reactions of three synthetic model compounds, methyl 9 Z,13 E,15 Z-octadecatrienoate ( 2 ), 9 Z,14 E,16 E-octadecatrienoate ( 4 ) and 9 Z,11 E,15 Z-octadecatrienoate ( 5 ) corroborated the results obtained with alkali isomerized methyl linolenoate.