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  • Polymer and Materials Science  (112,478)
  • Biochemistry and Biotechnology  (16,218)
  • Nuclear reactions  (4,460)
  • Heterocycles
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  • 1
    Electronic Resource
    Electronic Resource
    The Effect of the Carbon Ligand on the Reaction of Organozinc Reagents in the Synthesis of Substituted 2,5-Dihydrofurans: A Rare Example of An Uncatalysed Allylic-Substitution Reaction Involving Alkyl Zinc Halides (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1711-1718 
    Details
    ISSN: 1434-193X
    Keywords: Heterocycles ; Zinc ; Palladium ; Catalysts ; Sulfur ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---Organozinc halides derived from Grignard reagents behave differently in their reaction with ethyl (±±)-(2RS,3SR)-tetrahydro-4-methylene-2-phenyl-3-(phenylsulfonyl)furan-3-carboxylate (3) according to the hybridisation of the carbon ligand. During the development of short multi-component reactions for the synthesis of diverse functionalized ethyl 2,5-dihydrofuran-3-carboxylates it was discovered that aryl and vinyl zinc halides undergo clean reaction with 3 in the presence of Pd(PPh3)4. In contrast, when alkyl zinc halides are reacted with 3 in the presence of Pd(PPh3)4, reductive desulfonation of 3 is observed. Remarkably, in the absence of a transition metal catalyst, the allylic substitution of 3 with alkyl zinc halides proceeds cleanly and in moderate to good yield.
    Additional Material: 2 Ill.
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  • 2
    Electronic Resource
    Electronic Resource
    1-Alkyl- and Azeto[1,2-a][1,5]benzodiazepine Derivatives in the Reaction of o-Phenylenediamine with 3-(Dimethylamino)propiophenones (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1973-1976 
    Details
    ISSN: 1434-193X
    Keywords: Benzodiazepines ; Heterocycles ; Azeto[1,2-a]-1,5-benzodiazepines ; Cyclizations ; Cycloadditions ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---The reaction of o-phenylenediamine (4) with one, two or three equivalents of p-substituted 3-dimethylaminopropiophenone hydrochlorides 5a-e was studied. 4-Aryl-2,3-dihydro-1H-1,5-benzodiazepine derivatives 6a-e were obtained in good yields, along with the 1:2-adducts 7c-e and the unexpected 1:3-adducts rac-8c-e. The type of adduct formed is determined by the molar ratio of the reactants 4 and 5 and by the nature of the substituent in the para position of the propiophenone 5.
    Additional Material: 1 Ill.
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  • 3
    Electronic Resource
    Electronic Resource
    Reaction of 1,3-Disubstituted Acetone Derivatives with Pseudohalides: A Simple Approach to Spiro[4.4]nonane-Type Bis-Oxazolidines and -Imidazolidines (Bicyclic Carbamates, Thiocarbamates, Ureas, and Thioureas) (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 205-209 
    Details
    ISSN: 1434-193X
    Keywords: Heterocycles ; Carbohydrates ; Imidazolidines ; Oxazolidines ; Spiro compounds ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---Prochiral 1,3-dihydroxyacetone forms racemic oxazolidine- and oxazoline-type spiro[4.4]nonanes upon reactions with potassium (thio)cyanate and cyanamide. In contrast, 1,3-diaminoacetone yields only the corresponding spiro-bisimidazolidinethione under similar conditions together with monocyclic by-products, but the spiro-bisimidazolidinone is accessible by reaction of 1,3-dichloroacetone with urea. The resolution of the racemic spiro-bisoxazolidinethione 2a was achieved by using brucine as the resolving agent.
    Additional Material: 1 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    Synthesis and Absolute Configuration of Hongoquercin A, an Antibacterial Sesquiterpene-Substituted Orsellinic Acid Isolated as a Fungal Metabolite (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 297-302 
    Details
    ISSN: 1434-193X
    Keywords: Antibiotics ; Configuration determination ; Heterocycles ; Hongoquercin A ; Terpenoids ; Total synthesis ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---(±)-Hongoquercin A (1), the racemate of an antibacterial fungal metabolite, has been synthesized starting from geranylacetone (2) and ethyl orsellinate (ethyl 2,4-dihydroxy-6-methylbenzoate, 5). The structure (±)-1 has been confirmed by X-ray analysis of its ethyl ester (±)-10. Synthesis of the naturally occurring (+)-hongoquercin A from (-)-sclareol (11) established its configuration as depicted in 1.
    Additional Material: 1 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    Proximate, syn-Periplanar Bisdiazene Skeletons: Syntheses, Structures, Homoconjugate Reactivity and Photochemistry (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 763-785 
    Details
    ISSN: 1434-193X
    Keywords: Bisdiazenes ; Homoconjugation ; Photochemistry ; Heterocycles ; Diazenes ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---Rigid N=N/N=N (diazene/diazene) systems (F) consisting of more or less alkylated DBH and DBO chromophoric units (1, 2, X-ray structures), with very short π,π distances [d = 2.849 (1a, av.), 2.822 Å (2)] and almost perfect syn-periplanar π,π alignments [ω = 168.6 (1a), 174.2° (2)] as well as the more flexible, less “proximate” metathesis isomers (3a,c, 27a,c, d 〉4.6 Å, ω = 90-100°) have been synthesized. Homoconjugate π,π interaction (in 1, 2, not in 3, 27) is deduced from UV spectroscopic measurements [π → π* maxima at 239 (234) nm (sh, 260)], while PE analyses furnished only small interaction parameters (1a: 〈0.3 eV). The potential of the novel syn-periplanar N=N/N=N motif in 1 and 2 for the synthesis of somewhat exotic polyheterocycles has been explored by calculation (B3LYP) as well as experimentally: i.a. kinetically stabilized, all-cis-peralkylated tetrazolidines (38, 44) and perhydro-1,2,4,5-tetrazines (41, 47) have become accessible (i.a. via novel azomethine/diazene and azomethine/azomethine cycloadditions). In 1a with its unreactive DBO chromophoric subunits, in the “buttressed” derivatives 1b-d, as well as in the DBH/DBO combination 2, and likewise in more ‘distant’ 27 (differently from the analogous C=C/C=C and N=N/C=C systems), irrespective of the excitation conditions employed (light of λ ≥≥ 280, 254 nm, low temperature matrix irradiation, acetone sensitization) no [2+2]photocycloaddition was observed. Instead exclusively N2-elimination took place. It is argued that unproductive N=N/N=N photocycloaddition would have become observable through metathesis isomerization of the respective tetrazetidines.
    Additional Material: 9 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    Proximate, syn-Periplanar Diazene/Diazene(di)oxy, Diazeneoxy/Diazene(di)oxy, and Diazenedioxy/Diazenedioxy Skeletons: Syntheses, [2+2]Photocycloadditions, Metathesis (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 787-806 
    Details
    ISSN: 1434-193X
    Keywords: Photochemistry ; Heterocycles ; Diazenes ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---Of two very proximate syn-periplanar bisdiazenes (1,2) mono-, di-, tri- and tetra-N-oxides were prepared, representing six combinations of the individual N=N/N=NO/ON=NO chromophores. According to DFT calculations (B3LYP/6-31G*), [2+2]photocycloaddition to the respective oxidized tetrazetidines is significantly to moderately endothermic. The metathesis isomerization of the oxidized tetrazetidines is generally highly exothermic and kinetically increasingly favorable with increasing oxidation state. In practice, four out of the six bichromophoric combinations undergo selectively, in competition with N2 elimination from a DBH unit (13) still partially, metathesis isomerization upon π → π* excitation (monochromatic 254 nm light). In the case of the syn-N=NO/N=NO combinations (5/6, 14), the photoaddition is thermally reversed. For a ON=NO/N=N combination (30), internal electron transfer is responsible for a complex reaction pattern. The preparative value of the metathesis reactions, though, is limited: The metathesis-derived bis[diazene mono(di)oxides] undergo relatively fast secondary photoreactions, while the tri(tetra)oxides undergo rapid thermal transformations. For the N=N/N=NO systems (12), of three potential pathways for its metathesis isomerization, the one that takes place via σ-symmetric intermediates (63, 64) is excluded by virtue of the retention of optical purity in the photometathesis of a highly enriched enantiomer [(-)-12]. Matrix irradiation experiments (12 K, IR control) with 12 result in the appearance of a kinetically highly labile transient. Supported by DFT calculations it is concluded that in the metathesis reactions, the respective tetrazetidine oxides (increasingly destabilized by interactions between oxygen lone pairs and NNσ* orbitals) function as vibrationally excited transients. That thermal reversion of these transients might be a general, nonproductive competition, is suggested by the experimental verification of a “reversed photometathesis” (51 → 15) and by the generally low rates in product formation upon irradiation. The question remains to be answered why in structurally analogous molecular skeletons, [2+2]photocycloaddition occurs in the C=C/N=N and variously oxidized N=N/N=N, and not, however, in the parent N=N/N=N combinations.
    Additional Material: 4 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    Synthesis of Ascididemine and an Isomer (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 849-855 
    Details
    ISSN: 1434-193X
    Keywords: Marine alkaloids ; Heterocycles ; Natural products ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---Ascididemine (9H-quino[4,3,2-de][1,10]phenanthrolin-9-one) (1) and an isomer (9H-quino[4,3,2-de][1,7]phenanthrolin-9-one) (4) have been synthesized starting from 1,4-dimethoxyacridone (7). The acridone was converted into 1,4-dimethoxy-9-ethynylacridine (11) by a triflate coupling. The ethynylacridine was converted in one-pot into 3H-6-methoxypyrido[2,3,4-kl]acridine (15) by reaction with sodium diformylamide; the mechanism of this key transformation is discussed. Conversion into 6H-4-bromopyrido[2,3,4-kl]acridin-6-one (19) and 6H-pyrido[2,3,4-kl]acridin-6-one (17), followed by reaction of each of these under high pressure conditions with acrolein N,N-dimethylhydrazone, gave ascididemine and its isomer, respectively.
    Additional Material: 2 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    Polyol Peptidomimetics (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1113-1120 
    Details
    ISSN: 1434-193X
    Keywords: Peptidomimetics ; Reverse turn mimetics ; Glycomimetics ; Heterocycles ; Lactams ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: -D-Glucurono-3,6-lactone and L-cysteine combine in a highly stereoselective manner to give the 7,5-bicyclic thiazolidinlactam 2. The α-hydroxy group of the D-glucurono-3,6-lactone was exchanged for an amino function (to give 13) and, after condensation with L-cysteine methyl ester, the polyol dipeptide 7 was obtained. Peptide couplings proceed without the need to protect the three secondary hydroxy groups of the seven-membered ring. The amino group of 7 was deprotected and selectively elongated to the pseudo-tripeptide 16. The depsipeptide 17 was obtained by condensation of Boc-Ala-OH with the polyol 2. Elongation at the carboxy terminus yielded 19 and 20. The bicyclic scaffold populates a well-defined solution conformation; the hydroxy groups mimic the side chains of hydrophilic amino acids and can be further functionalized.
    Additional Material: 1 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    Proximate, syn-Periplanar, Rigid Imine(Nitrone)/Ene-, and Diazene(Diazeneoxy)/Ene Systems: Syntheses, Homoconjugate Reactivity and Photochemistry (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 743-762 
    Details
    ISSN: 1434-193X
    Keywords: Chromophores ; Photochemistry ; Heterocycles ; Diazenes ; Imines ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---The chances for intramolecular imine/ene (→ azetidines), diazene/ene (→ 1,2-diazetidines), diazeneoxy/ene (→ 1,2-diazetidine oxides) and diazenedioxiene (→ 1,2-diazetidine dioxides) [2+2]photocycloadditions and for the isolation of the respective photoproducts, have been probed with specifically designed substrates. Upon direct or sensitized excitation, [2+2]cycloaddition was found to be the exclusive or at least dominant chemical process for the C=N/C=C, N=N/C=C and ON=N(O)/C=C systems featuring very small π,π-distances of 2.8-3.0 Å and large π,π-interorbital angles of 160-170° (7 → 51, 17 → 55, 33 → 58 (competing N2 elimination), 22 → 62). This is not the case, however, in ON=NO/C=C (23, where electron transfer is a possibility), or in the more flexible, less “proximate” C=N/C=N (57) and C=NO/C=N (63) systems (π,π-distances of 〉3.8 Å). While the corseted 1,2-diazetidine photoadducts (55, 58) proved to be thermally stable, their N-oxides (62, 65) were thermally too labile to be directly observable above -65 °C. For the latter's only fleeting existence, electronic rather than strain effects are held responsible (B3LYP/6-31G* calculations). Very facile C=NO/C=C (12 → 13) and N=NO/C=C (22 → 24) [3+2]cycloadditions, homoconjugate addition of H2 and of dienophiles ([2+2+2]) to the diazene/ene 17 (→ 39, 41, 45) are manifestations of “proximity” in these bichromophoric skeletons.
    Additional Material: 1 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    Oxidative Heterocyclization of 2-Alkynylbenzaldehydes with 1,2-Phenylenediamine (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1433-1441 
    Details
    ISSN: 1434-193X
    Keywords: Alkynes ; Annelation reactions ; Carbonyl compounds ; Heterocycles ; Polycycles ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---Upon condensation of ortho-phenylenediamine (2) with ortho-alkynylbenzaldehydes in nitrobenzene, oxidative cyclizations are observed, which result in benzimidazo[2,1-a]isoquinolines (8) or isoindolo[2,1-a]quinoxalines (9) depending on the influence of additional substituents at the alkyne.
    Additional Material: 1 Ill.
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  • 11
    Electronic Resource
    Electronic Resource
    Synthesis of 5-Methylbenzo[b]thieno[2,3-c]isoquinolines and5-Methylbenzo[b]seleno[2,3-c]isoquinolines (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1353-1357 
    Details
    ISSN: 1434-193X
    Keywords: Heterocycles ; Rearrangements ; C-C coupling ; C-C coupling ; Cyclizations ; Isoquinolines ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: -5-Methylbenzo[b]thieno[2,3-c]isoquinolines and 5-methylbenzo[b]seleno[2,3-c]isoquinolines 11b,c have been prepared by Bischler-Napieralski cyclization of 2-acetamido-3-phenylbenzo[b]heteroarenes.
    Additional Material: 4 Tab.
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  • 12
    Electronic Resource
    Electronic Resource
    Calculated Properties and Ring-Chain Rearrangements of Triphosphirane (P3H3) (2000)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 2000 (2000), S. 103-112 
    Details
    ISSN: 1434-1948
    Keywords: Ab initio calculations ; Ionization potentials ; Phosphorus ; Heterocycles ; Small ring systems ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ab initio quantum chemical calculations have been used to explore the P3H3 potential energy surface focussing on the ring-chain rearrangements of the three-membered ring in (PH)3 (1), the parent triphosphirane. Relative energies between stationary points were estimated using the QCISD(T)/6-311G(d,p) method based on MP2/6-31G(d,p) geometries and corrected for zero-point contributions. Ring strain, proton affinities, ionization and excitation energies and heats of formation have been evaluated using larger basis sets, e.g. 6-311++G(3df,2p). The cyclic trans-triphosphirane (1a) is the most stable P3H3 isomer and lies about 40 kJ/mol below the open-chain phosphanyldi-phosphene (H2P-P=PH). The decrease of ring strain in three-membered rings when CH2 is replaced by PH is confirmed. Triphosphirane 1a is a virtually strain-free ring and even gains some stabilization relative to three separate P-P single bonds. The reduced ring strain also helps diminish the phosphorus inversion barrier to 224 kJ/mol compared to the monocyclic isomers of (CH2)(PH)2 and (CH2)2(PH). Compound 1a follows a pure ring-opening or a 1,2-hydrogen shift rather than a combined motion pathway, in fundamental contrast with corresponding processes of diphosphirane and phosphirane. This is due to the existence of an open-chain P3H3 phosphorane intermediate stabilized by allylic conjugation. The pericyclic ring-opening of 1a is the most favored process but the energy barrier in the gas phase is about 180 kJ/mol high. Electron density is largely delocalized within the three-membered P3 ring not only in the C3v-symmetric 1b (all-cis) but also in 1a (Cs). The proton affinity of 1a is similar to that of PH3. The proton affinities decrease with n in cyclo-(CH3)3 -n(PH)n and their values were obtained: PA(1a) = 777 ±10, PA(diphosphirane) = 799 ±10 and PA(phosphirane) = 802 ±10 kJ/mol. Heats of formation are evaluated as follows (ΔH°f0 at 0 K in kJ/mol): 1a, 70 ±10; cyclo-(PH)2(PH2)+ (protonated 1a), 821 ±10; diphosphirane, 85 ±10; cyclo-(CH2)(PH)(PH2)+ (protonated diphosphirane), 814 ±10; phosphirane, 86 ±10; and protonated phosphirane, 812 ±10 kJ/mol. All P rings remain cyclic following ionization to the radical cations. Adiabatic ionization energies (IEa) are estimated as: 1a and diphosphirane, 9.3 ±0.3 eV and phosphirane 9.5 ±0.3 eV. The first UV absorption band shifts toward the longer wavelength region on going from phosphirane to 1a. The GIAO/B3LYP computed magnetic shieldings for 1a and related molecules reveal a clear relationship between the narrow bond angles in the rings and their unusually strong magnetic shielding. The similarity of the predicted 31P-NMR signals in 1a and its heteroanalog diphosphirane, (CH2)(PH)2, can be rationalized in terms of a compensation of the carbon-substituent effect (downfield shift) and the bond-bending effect imposed by the ring (upfield shift).
    Additional Material: 5 Ill.
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  • 13
    Electronic Resource
    Electronic Resource
    Novel Fluorescent Dyes by the Extension of the Core of Perylenetetracarboxylic Bisimides (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 365-380 
    Details
    ISSN: 1434-193X
    Keywords: Fluorescent dyes ; Perylenes ; Heterocycles ; NIR dyes ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---Core-extended perylenetetracarboxylic bisimides were prepared by Diels-Alder reaction followed by reduction, or by nitration followed by cyclisation. Highly fluorescent dyes were obtained with absorption regions from the visible to the NIR. Applications for solar energy harvesting, and quantum counters were suggested.
    Additional Material: 9 Ill.
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  • 14
    Electronic Resource
    Electronic Resource
    Preparation and Characterization of Cyanovinyl-Substituted 2-Aminothiophenes and 2-Aminothiazoles and Some of Their Heterooligomers (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1327-1334 
    Details
    ISSN: 1434-193X
    Keywords: Heterocycles ; Thiophenes ; Solvatochromism ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: -The reaction of 2,2-dicyanoethenyl- and 1,2,2-tricyanoethenyl-substituted bromoalkanes, bromomethyl benzenes, thiophenes, and furans 19-22 with 3-aminothioacrylamides and their 2-azaanalogues 23 and 24 gives a series of 5-dicyanoethenyl- and 5-tricyanoethenyl-substituted 2-aminothiophenes, 2-aminothiazoles and their (hetero)benzologous analogues 25-32. The solvatochromism, which is a characteristic feature of these donor-acceptor substituted heterocyclic compounds, was studied in detail and correlated with the Kamlet-Taft solvent parameters.
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  • 15
    Electronic Resource
    Electronic Resource
    Nucleophilic Substitution of 4H-Imidazoles - A Key Step in the Synthesis of Fused Imidazoles and New Chromophores (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1661-1668 
    Details
    ISSN: 1434-193X
    Keywords: Imidazoles ; Nucleophilic substitutions ; Fulvenes ; Pseudo-azulenes ; Heterocycles ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---The electrophilic properties of the 4H-imidazoles 1 and their protonated derivatives 2 permit the introduction of nucleophilic building blocks, as illustrated by reactions of 1 with selected amines. Depending on the nature of the amine and the substituents R1 on the heterocycle 1, single (3) or double (4) transamination is observed. The 1H-NMR spectra of the products, as well as X-ray structure analyses of compounds 3f and 4c, confirm that the residues at the 4- and/or 5-positions of 1 are exchanged. The tautomerism between 3e-h and 3e′-h′ seems to be central to the chemistry of these mixed substituted derivatives. Using orthoesters and acetophenone dimethylacetal as cyclization partners, the imidazo[4,5-d]imidazoles 5 and the 4H-imidazo[4,5-b]pyrazines 6 are obtained, respectively. Reduction of 3e with Zn/HCl or H2S leads to the air-sensitive, strongly fluorescent leuco compounds 8. Quenching of 8 by addition of aromatic aldehydes results in a condensation reaction and, coupled with the subsequent redox disproportionation, this conversion constitutes an alternative route to imidazo[4,5-d]imidazoles of type 11. The unexpected reaction of 3e-h with Lawesson's reagent allows synthesis of the 6-azapentafulvenes 14. The relevant spectral data show 14 to be members of a new chromophoric system, in which an electron-rich five-membered ring is coupled with an electron-deficient ring.
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  • 16
    Electronic Resource
    Electronic Resource
    A Simple Stereoselective Synthesis of Enantiopure 2-Substituted Pyrrolidines and Piperidines from Chiral (R)-Phenylglycinol-Derived Bicyclic 1,3-Oxazolidines (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1719-1726 
    Details
    ISSN: 1434-193X
    Keywords: Asymmetric synthesis ; Nitrogen heterocycles ; Heterocycles ; Pyrrolidines ; Piperidines ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---Chiral, nonracemic 2-substituted pyrrolidines and piperidines were prepared in high ee and moderate to good chemical yields in three steps from (R)-phenylglycinol and γ- or δ-chloroketones. The key step of the synthesis was the stereoselective reductive ring-opening of chiral bicyclic 1,3-oxazolidines prepared by condensation of (R)-phenylglycinol and the corresponding ketones.
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  • 17
    Electronic Resource
    Electronic Resource
    Substituted Tetraoxa[8]circulenes - New Members of the Liquid Crystal Family (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1637-1640 
    Details
    ISSN: 1434-193X
    Keywords: Circulenes ; Heterocycles ; Liquid crystals ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: ---A general method for the synthesis of substituted tetraoxa[8]circulenes based on alkylation of 2,3-bis(bromomethyl)-1,4-dimethoxybenzene with acetylides is reported. Four of the compounds shows LC behavior, and the tetraoxa[8]circulenes are thus new candidates for discotic mesogens.
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  • 18
    Electronic Resource
    Electronic Resource
    Syntheses of Batzelline A, Batzeline B, Isobatzelline A, and Isobatzelline B (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 1173-1183 
    Details
    ISSN: 1434-193X
    Keywords: Marine alkaloids ; Pyrroloquinoline ; Total synthesis ; Heterocycles ; Alkaloids ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: -Batzellines A and B (1a, b) and isobatzellines A and B (2a, b) are 1,3,4,5-tetrahydropyrrolo[4,3,2-de]quinoline-containing marine alkaloids characterized by the presence of a methylthio substituent at C-2 of the tricyclic system. We describe here the total synthesis of these natural compounds following the synthetic strategy that we have used previously for the synthesis of damirones A and B, batzelline C, isobatzelline C, discorhabdin C, and makaluvamines A, B, C, and D. The introduction of the methylthio group by electrophilic substitution of a pyrrolo[4,3,2-de]quinoline, appropriately substituted and in a suitable oxidation state, is the key step in the success of these syntheses.
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  • 19
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    Intramolecular Copper- and Rhodium-Mediated Carbenoid Reactions of α-(Propargyloxy)silyl-α-diazoacetates (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 1213-1221 
    Details
    ISSN: 1434-193X
    Keywords: Diazo compounds ; Carbenes ; Carbenoids ; Silicon ; Heterocycles ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: -Copper(I) triflate catalyzes the transformation of α-[(2-alkynyl)oxy]silyl-α-diazoacetates 1a-g into 1,2-bis(2,5-dihydro-1,2-oxasilol-4-yl)ethenes 2 and/or 2H-1,2-oxasilines 3. With rhodium(II) perfluorobutyrate as catalyst, 1a-e furnish only 3 but no 2. Bicyclic 2-methoxyfurans 6 are formed when 1a,c,e (containing terminal alkyne functions) are treated with catalytic amounts of copper(I) chloride. The experimental observations are explained in terms of metal-mediated intramolecular cyclopropenation and subsequent metal-assisted ring-opening of the strained bicyclic cyclopropene leading to vinylcarbene-metal complexes. An unusual autoxidation of 2H-1,2-oxasilines 3a,c,e is also described.
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  • 20
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    Electronic Resource
    The Preparation of 2,3,5-Tri- and 2,3-Disubstituted Furans by Regioselective Palladium(0)-Catalyzed Coupling Reactions: Application to the Syntheses of Rosefuran and the F5 Furan Fatty Acid (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2045-2057 
    Details
    ISSN: 1434-193X
    Keywords: Homogenous catalysis ; Palladium ; Cross-coupling ; Heterocycles ; Synthetic methods ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The 5-acceptor-substituted 2,3-dibromofurans 1 and 2 underwent a regioselective Pd0-catalyzed coupling reaction at the C-2 carbon atom. With alkynes the corresponding 2-alkynylfurans 4 and 5 were accessible (49-97% yield). Alkyl-, aryl-, and alkenylzinc reagents gave the 2-substituted furans 8 starting from compound 2 (66-84% yield). The 2-allylfurans 8e and 8f were obtained by a regioselective Stille coupling in 79% and 73% yield. The latter reaction was also applied to the parent 2,3-dibromofuran (27) and yielded the substitution product 28 (60% yield). Subsequent Pd0-catalyzed reactions to introduce a methyl group in 3-position by a methyldebromination were successfully conducted for 2-alkynyl-3-bromofurans with MeZnCl and PdCl2(PPh3)2 as the catalyst in THF (reflux) to yield compounds 13-16 and 24 (67-76%) and with SnMe4 and PdCl2[P(o-Tol)3]2 as the catalyst in DMA (90 °C) for the 2-allyl-3-bromofuran 8e to yield 18 (70%). The more facile reaction of the 2-alkynylfurans relative to those of furans bearing an sp3-carbon atom at C-2 appears to be due to steric reasons. Studies on the 2-alkyl-3-bromofuran 20 supported this notion. With the regioselective coupling methodology the terpene rosefuran (22) was prepared in four steps starting from furan 2 (35% yield overall). The F5 furan fatty acid (26) was synthesized from furan 1 in five steps (29% yield overall).
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  • 21
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    Synthesis of (-)-Cytoxazone, a Novel Cytokine Modulator Isolated from Streptomyces sp. (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2965-2967 
    Details
    ISSN: 1434-193X
    Keywords: Amino alcohol ; Asymmetric synthesis ; Cell signaling ; Dihydroxylations ; Heterocycles ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Cytoxazone [(4R,5R)-(-)-5-hydroxymethyl-4-(4-methoxyphenyl)-2-oxazolidinone, 1], a new immunosuppressant, was synthesized by starting from p-methoxycinnamyl alcohol (2) employing the Sharpless asymmetric dihydroxylation as the key reaction in 26% overall yield (7 steps).
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  • 22
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    Electronic Resource
    Borane Insertion into Group-4 Metal-to-Carbon Bonds: The Reaction of HB(C6F5)2 with (η2-Formaldehyde)zirconocene Dimer and with (Butadiene)zirconocene (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 2243-2247 
    Details
    ISSN: 1434-1948
    Keywords: Metallaoxirane ; HBR2 addition ; (Formaldehyde)zirconocene ; (Butadiene)zirconocene ; Heterocycles ; Boron ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: (η2-Formaldehyde)zirconocene dimer (8) cleanly adds one or two molar equivalents of the borane HB(C6F5)2 by insertion of the H-[B] unit into the zirconium-carbon bond of the metallaoxirane moieties to form the mono- and bis-insertion products 16 and 17, respectively. These systems contain five-membered heterocyclic rings that are built up by connecting five different elements, namely H, B, C, O, and Zr. The bis(borane) insertion product 17 was characterized by an X-ray crystal structure analysis. (Butadiene)zirconocene reacts with HB(C6F5)2 in a similar way by insertion of the H-[B] unit into the (butadiene)C4-Zr linkage to form the metallacycle 18.
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  • 23
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    Insights into the Staudinger Reaction: Experimental and Theoretical Studies on the Stabilization of cis-Phosphazides (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 1659-1664 
    Details
    ISSN: 1434-1948
    Keywords: Phosphorus ; Iminophosphorane ; Staudinger reaction ; Heterocycles ; Ab initio calculations ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Staudinger-model reaction H3P (1) + HN3 (2) → H3P=NH (5) + N2 (6) has been investigated at the CCSD(T)/6-31G**//MP2(Full)/6-31G* level. Primary products formed in this reaction are the phosphazides H3P=N-N=NH (3) which exist as trans and cis isomers. In contrast to some previous assumptions, cis -3is 8.2 kcal mol-1 more stable than trans -3 but decomposes rather easily into the expected products H3P=NH and N2. This decomposition can be effectively hampered by intramolecular donor-acceptor interactions as shown by calculations on model compounds as well as by experiments. Thus the reaction of a methylene-σ3,λ3-phosphanyl-σ5,λ5-phosphorane with PhN3 led to a new four-membered heterocycle containing a thermally remarkable stable cis-phosphazide moiety.
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  • 24
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    New Inorganic Metallacycles and the First Six-Membered Covalent “True” Heterocycle - Oxidation of RC(E)NHPPh2 (E = O or S; R = H2N, Ph, or Py) with O, S, or Se to Give RC(E)NHP(E′)Ph2 (E′ = O, S, Se) and Their Coordination Chemistry (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 1445-1452 
    Details
    ISSN: 1434-1948
    Keywords: Metallacycles ; Solid-state structures ; Heterocycles ; Oxidations ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Direct oxidation of PhC(O)NHPPh2, H2NC(S)NHPPh2, (C5H4N)C(S)NHPPh2 with O2, S8, or Se gives [PhC(O)NHP(O)Ph2] (1), [H2NC(S)NHP(S)Ph2] (2), [H2NC(O)NHP-(S)Ph2] (3), [PhC(O)NHP(S)Ph2] (4), [(C5H4N)C(S)NHP(S)Ph2] (5), and [H2NC(S)NHP(Se)Ph2] (6). Deprotonation of 1, 2, 4-6 with potassium tert-butoxide gives K[PhC(O)NP(O)Ph2] (7), K[H2NC(S)NP(S)Ph2] (8), K[PhC(O)NP(S)Ph2] (9), K[(C5H4N)C(S)NP(S)Ph2] (10), and K[H2NC(S)NP(Se)Ph2] (11). Reaction of 4with KOBu and [Cu(Ph3P)2][NO3] gives [Cu(Ph3P)(PhC(O)NP(S)Ph2)] (12) which is the first crystallographically characterised example of a non-ionic six-membered “true” heterocycle (i.e. a ring in which every heterocatom is different). 9 and 10 were treated with [PdCl2(COD)] to give [Pd{PhC(O)NP(S)Ph2}2] (13) and [Pd{(C5H4N)C(O)NP(S)Ph2}2] (14), respectively The anion of 8 coordinates to zinc forming [Zn{H2NC(S)NP(S)Ph2}2] (15). Treatment of 2 or 8 with [PtCl2(COD)] gives [Pt{H2NC(S)NP(S)Ph2}{H2NC(S)NHP(S)Ph2}]+Cl- (16) and [Pt{H2NC(S)NP(S)Ph2}2] (17), respectively. The X-ray structures of 12, 15-17are reported.
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    Syntheses, Structures, and Coordination of Diborylbipyridines and Bipyridinediborates (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 393-398 
    Details
    ISSN: 1434-1948
    Keywords: Boranes ; Bipyridine ; Crystal structures ; Donor-acceptor interaction ; Heterocycles ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 6,6′-Bis(diethylboryl)-2,2′-bipyridine (1a) was obtained in low yield by in situ deprotonation of 2,2′-bipyridine in the presence of diethyl(methoxy)borane. 6,6′-Dilithio-2,2′-bipyridine reacts with various alkoxyboranes leading to bipyridinediborates 2 in good yields. The derivatives 2b and 2c allow the formation of the free diborylbipyridines 1b and 1c. The coordination properties of the diboryl-bipyridines as tetrafunctional donor-acceptor compounds have been used for the formation of the copper complex 4 and of the adduct 5 which is built from diborylbipyridine and a dihydroxydiboroxan derivative. The composition of the products follows from spectroscopic data and from X-ray structure analyses for 2f, 4, and 5.
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    Synthesis and Structure of 2-Hydro-, 2-Alkyl-, 2-Alkynyl-, and 2-Stannyl-2,3-dihydro-1H-1,3,2-diazaboroles (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 491-497 
    Details
    ISSN: 1434-1948
    Keywords: Boron ; Diazaboroles ; Hydrides ; Tin ; Heterocycles ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 1,3-Di-tert-butyl-2,3-dihydro-1H-1,3,2-diazaborole (4a) and 1,3-bis(2,6-dimethylphenyl)-2,3-dihydro-1H-1,3,2-diazaborole (4b) were formed by the reaction of the corresponding 2-bromo or 2-iodo derivatives 1a and 2b with LiAlH4. Treatment of 1a with n-butyllithium afforded 2-n-butyl-1,3-di-tert-butyl-2,3-dihydro-1H-1,3,2-diazaborole (5a), whereas 1,3-di-tert-butyl-2-cyano-2,3-dihydro-1H-1,3,2-diazaborole (3a) was converted into the 2-tert-butyl derivative 6a or the 2-ethynyl-1,3,2-diazaborole 7a by means of tert-butyllithium or by the ethylenediamine adduct of lithium acetylide. Similarly, 1,3-di-tert-butyl-2-trimethylstannyl-2,3-dihydro-1H-1,3,2-diazaborole (8a) and 1,3-bis(2,6-dimethylphenyl)-2-trimethylstannyl-2,3-dihydro-1H-1,3,2-diazaborole (8b) were accessible from 1a or 2b and trimethylstannyllithium. In the complex 9a the compound 3a serves as an η1 ligand towards the [Cr(CO)5] unit via the cyano group. These novel compounds were characterized by 1H-, 11B-, 13C-, and 119Sn-NMR spectroscopy, as well as by X-ray structure analyses of 4b, 8a, and 9a.
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  • 27
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    Reactions of 1,8-Diheterocyclotetradeca-4,11-diynes with (η4-Cycloocta-1,5-diene)(η5-cyclopentadienyl)cobalt (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 499-504 
    Details
    ISSN: 1434-1948
    Keywords: Alkynes ; Heterocycles ; Cyclizations ; Cobalt ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The following monocyclic and bicyclic 14-membered diynes were treated with [CpCo(cod)]: 1-oxacyclotetradeca-4,11-diyne (2), 1,8-dioxacyclotetradeca-4,11-diyne (3), cyclotetradeca-4,11-diynone (4), cyclotetradeca-4,11-diyne-1,8-dione (5), 1,1,8,8-tetramethyl-1,8-disilacyclotetradeca-4,11-diyne (6), 1-allyl-1-azacyclotetradeca-4,11diyne (7), 1,8-dipropyl-1,8-diazacyclotetradeca-1,11-diyne (8), 1,8-diallyl-1,8-diazacyclotetradeca-4,11-diyne (9), 1,8-diazabicyclo[6.6.4]octadeca-4,11-diyne (10), 1,8-diazabicyclo[6.6.6]eicosa-4,11-diyne (11), 1,10-diazabicyclo[8.6.6]docosa-13,19-diyne (12) and 1,12-diazabicyclo[10.6.6]tetracosa-15,21-diyne (13). In all cases we obtained an intramolecular cyclobutadiene complex stabilized with a CpCo fragment (15-26). For 3 we could isolate, besides the cyclobutadiene complex 16, the trimerization product 28. In the cases of 15, 16, 18, 20, 23, 25, and 26 the structure of the cylobutadiene complexes could be confirmed by X-ray studies. Common to all structures is a boat-like conformation of the tricyclic unit containing the cyclobutadiene ring. The two cycloheptene units adopt a chair conformation in which the heteroatom is removed from the metal center.
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  • 28
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    Synthesis, X-ray Crystal Structures and Reactivity Towards Alkynes of Gold(I)-Phosphinine Complexes (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 2233-2241 
    Details
    ISSN: 1434-1948
    Keywords: Phosphorus ; Heterocycles ; Phosphinines ; Gold ; Cycloadditions ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The coordination behaviour of 2,6-disilyl-substituted phosphinines towards gold(I) has been examined. The reaction of the bis(trimethylsilyl)phosphinine 1 with [AuCl(SMe2)] gives the corresponding AuCl derivative 2. X-ray crystal structure analysis reveals that the aromaticity of the phosphinine ring is slightly reduced as a result of the poor π-back bonding ability of the AuCl fragment. The same phenomenon is observed in the cationic complex [Au(1)2][GaCl4] (3) which was readily prepared by reaction of two equivalents of 1 with [AuCl(SMe2)] followed by treatment with GaCl3 at low temperature. Reaction of 2,6-bis(phenylethynyldimethylsilyl)phosphinine (4) with the same precursor leads similarly to the complex [AuCl(4)] (5). Interestingly, this complex dimerizes upon crystallization to give the bis(phosphabarrelene) complex 6, also structurally characterized. The formation of 6 results from a [4 + 2] cycloaddition between one alkynyl group of each phosphinine with the other phosphinine subunit. The formation of the cationic complex [Au(4)][GaCl4] (8) occurs under classical conditions but it disproportionates to give the cationic complex [Au(4)2][GaCl4] (9) and colloidal gold deposition. The formation of 9 has been ascertained by treating 8 with one equivalent of ligand 4. Additionally, 9 can also be obtained in a straightforward fashion by treating two equivalents of 4 with [AuCl(SMe2)] followed by treatment with GaCl3 at low temperature. The structure of 9 has been elucidated. Despite a particular arrangement of the alkyne groups which encapsulate the gold coordination sphere, no gold-alkyne interactions are visible.
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  • 29
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    Intramolecular Donor-Assisted Cyclization of Organotin Compounds (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 887-898 
    Details
    ISSN: 1434-1948
    Keywords: Tin ; Phosphorus ; Intramolecular coordination ; O ligands ; Heterocycles ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: New intramolecularly coordinated organotin compounds containing the monoanionic O,C,O-coordinating ligand {4-tert-Bu-2,6-[P(O)(OEt)2]2C6H2}- have been synthesized by substitution reactions starting from organotin halides. In view of the enhanced reactivity of the intramolecularly coordinated compounds {4-tert-Bu-2,6-[P(O)(OEt)2]2C6H2}SnR2R′ (2, R = Ph, R′ = CH2SiMe3; 3, R = R′ = Ph; 6, R = R′ = Cl), cationic tin species are suggested to occur as intermediates in the formation of the heterocyclic compounds [1(Sn),3(P)-Ph2SnOP(O)(OEt)-5-tert-Bu-7-P(O)(OEt)2]C6H2 (8), [1(Sn), 3(P)-Ph(Me3SiCH2)SnOP(O)(OEt)-5-tert-Bu-7-P(O)(OEt)2]C6H2 (15), and {[1(Sn),3(P)-Cl2SnOP(O)(OEt)-5-tert-Bu-7-P(O)(OEt)]C6H2}2 (16). The latter compounds are formed by intramolecular cyclizations of pentacoordinate cationic tin species under elimination of ethyl halide. Furthermore, the synthesis of [1(Sn),3(P)-Ph2SnOP(O)(OH)-5-tert-Bu-7-P(O)(OH)2]C6H2 (13) is described. Reaction of 8 with an excess of Me3SiBr leads to the unexpected formation of {2-[P(O)(OEt)(OSiMe3)]-4-tert-Bu-6-[P(O)(OEt)2]C6H2}SnPhBr2 (9) as a result of an O-Sn bond cleavage initiated by Me3SiBr and subsequent reaction of the intermediate with further Me3SiBr under Sn-C bond cleavage. The high donor capacity and the rigidity of the new ligand {4-tert-Bu-2,6-[P(O)(OEt)2]2C6H2}- are demonstrated by X-ray diffraction analyses of the tetraorganotin compound 2 and the monoorganotin trichloride 6. Furthermore, the molecular structures of the 2,3,1-oxaphosphastannoles 8 and 16 are discussed.
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  • 30
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    Cyclic Ketiminoboranes (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 7-9 
    Details
    ISSN: 1434-1948
    Keywords: Boranes ; Diazaboroles ; Heterocycles ; Ketiminoboranes ; Crystal Structures ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The cyclocondensation reaction of benzil-bis(trimethylsilylimin) (3) and Cl2B-NiPr2 via silicon-boron exchangeresults in the solvent-dependent formation of the 1,3,2-diazaborole 1a or the 1,3,6,8,2,7-tetraazadiborecin 2a. Using the more rigid 9,10-bis(trimethylsilylimino)phenanthrene instead of 3 only the five-membered heterocycle 4,5-biphenylene-2-diisopropylamino-1,3,2-diazaborole (1b) is formed. The cyclic ketiminoboranes are characterized by NMR and X-ray diffraction data. The 1,3,2-diazaborole ring is almost planar, while the conformation of the 1,3,6,8,2,7-tetraazadiborecin has the shape of a figure-eight loop.
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  • 31
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    Synthesis and 1H-, 15N-, 31P-, 183W-Multinuclear Magnetic Resonance Study of the Cyclotriphosphazenes [N3P3(dobp)2(OC5H4N-4)2] and [N3P3(dobp)(OC5H4N-4)4] and Their W(CO)5 Complexes (dobp = 2,2′-dioxybiphenyl) (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 1015-1020 
    Details
    ISSN: 1434-1948
    Keywords: Cyclotriphosphazenes ; Oxypyridine ; Carbonyltungsten compounds ; NMR spectroscopy ; Heterocycles ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The reactions of [N3P3(dobp)2Cl2] and [N3P3(dobp)Cl4] with a mixture of HOC5H4N-4 and K2CO3 in acetone give the cyclotriphosphazenes [N3P3(dobp)2(OC5H4N-4)2] and [N3P3(dobp)(OC5H4N-4)4], respectively. These compounds react with [W(MeOH)(CO)5] in methanol to give mixtures of the polymetallic complexes [N3P3(dobp)2(OC5H4N-4)2{W(CO)5}x] (x = 1, 2) and [N3P3(dobp)(OC5H4N-4)4{W(CO)5}x] (x = 1-4), which are unstable in solution, slowly undergoing loss of the pentacarbonyl moiety. A complete characterization by multinuclear 1H, 15N, 31P, 183W magnetic resonance has revealed that the complexation of the N atom of one 4-oxypyridine ligand by the W(CO)5 fragment has a measurable effect on other parts of the phosphazene molecule very far away from the coordination site. The changes observed in δ183W have been used to identify the components in mixtures of compounds incorporating different numbers of tungsten atoms in the molecule. The characterization of less sensitive nuclei has been accomplished by means of indirect detection methods.
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  • 32
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    Novel Condensed Thionated Bis(phosphonic) Acid Salts with a Rigid Naphthalene-1,8-diyl Backbone (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 2327-2333 
    Details
    ISSN: 1434-1948
    Keywords: Heterocycles ; Organo-phosphorus compounds ; Dithiadiphosphetane disulfides ; Phosphonates ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: New salts of thionated (naphthalene-1,8-diyl)bis(phosphonic) acid monoanhydrides [PPh4+]2[C10H6PS2(μ-S)PS22-] (2) and [K+]2[C10H6PS2(μ-S)POS2-]·H2O (3) both containing the C3P2S ring, were prepared in high yields by the reaction of 2,4-(naphthalene-1,8-diyl)-1,3,2,4-dithiadiphosphetane 2,4-disulfide (1) with NaHS and PPh4Cl, or KOH, respectively, in water. The derivative 3, containing a P=O terminal bond as well as P-S-P bridge, undergoes, in acid conditions, a rearrangement reaction leading to the O,S-symmetrically substituted derivative [K+]2[C10H6PS2(μ-O)PS22-] (4) containing a C3P2O heterocycle. Dipotassium salt 4 was converted into the bis(tetraphenylphosphonium) salt 5 by the treating with PPh4Cl. Hydrolysis of [PyH+][C10H6P(S)(NHMe)(μ-S)PS22-] (15) led to [CH3NH3+][PyH+][C10H6POS(μ-O)POS2-]·1.5 Py (6). New compounds were characterised by 31P{1H}-, 1H- and 13C{1H}-NMR, FT-IR, ES-MS and in the cases 2-6 by X-ray structure determination. The 31P{1H}-NMR spectra of these mixed O,S-derivatives are briefly discussed.
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  • 33
    Electronic Resource
    Electronic Resource
    Synthesis, Structure and Reactivity of 3,4-Dihydro-2H-1,2,4,3-triazaboroles (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 1193-1198 
    Details
    ISSN: 1434-1948
    Keywords: Boron ; Triazaboroles ; Heterocycles ; Halogens ; Cyanides ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 3,4-Dihydro-2,4-diphenyl-2H-1,2,4,3-triazaboroles 3a, 3b, and 4 were synthesized by cyclocondensation of N1,N3-diphenylformamidrazone (1) with dibromophenylborane, dibromomethylborane, and boron trichloride. 3-Chloro-3,4-dihydro-2,4-diphenyl-2H-1,2,4,3-triazaborole (4) was converted into 3,4-dihydro-2,4-diphenyl-2H-1,2,4,3-triazaborole (5) by treatment with LiAlH4. The corresponding 3-cyanato and 3-cyano derivatives 6 and 7 resulted from the reaction of 4 with AgOCN and AgCN, respectively. Compound 7 was transformed into the bis(1,2,4,3-triazaborolyl)oxane 8 by silver oxide. Compounds 1-8 were characterized by elemental analyses and spectroscopic methods (1H, 11B, and 13C NMR; IR; MS). The molecular structure of 8 was established by single-crystal X-ray diffraction analysis.
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  • 34
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    Electronic Resource
    The Synthesis of Novel Cyclic β-Amino Acids as Intermediates for the Preparation of Bicyclic β-Lactams (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2433-2441 
    Details
    ISSN: 1434-193X
    Keywords: Amino acids ; Lactams ; Schiff bases ; Nitrogen heterocycles ; Heterocycles ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Several derivatives of homopipecolic acid are prepared by α-amino alkylation of malonic acid with cyclic imines 6 and 7. These are prepared on a large scale and with different substitution patterns. The β-amino acids 8 and 9 were formed in high yield and with remarkable diastereoselectivity if chiral imines are used as starting materials. The diastereoselectivity of the amino alkylation leading to homopipecolic acid analogues is compared to those of thiazolidineacetic acids by epimerisation experiments. A method for resolution of the obtained racemic β-amino acids by diastereomeric salt formation is described. The β-amino acids 9 and 15 were converted into their corresponding carbacepham analogues 14 and isopenam 16. The isopenam endo-16 was selectively epimerised by mild basic treatment of the N/S-acetal to give an exo-configured precursor of isopenicillin G.
    Additional Material: 2 Tab.
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  • 35
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    Electronic Resource
    Pd-Catalyzed Asymmetric Allylic Alkylation of 3-Acetoxy-N-(tert-butyloxycarbonyl)-1,2,3,6-tetrahydropyridine - Preparation of Key Intermediates for Natural Product Synthesis (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2515-2521 
    Details
    ISSN: 1434-193X
    Keywords: Asymmetric synthesis ; Heterocycles ; Palladium ; Alkylations ; Allyl complexes ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A convenient synthesis of racemic tetrahydropyridine 1 was developed. Pd-catalyzed allylic alkylation of 1 with malonate and dimethylacetoxymalonate as nucleophiles with the phosphanylcarboxylic acid L1 and the dihydrooxazol L2 as ligands, were carried out and gave enantiomeric excesses of up to 98%. Absolute configurations were determined for all compounds described. From the alkylation products (+)- and (-)-2a, and (+)- and (-)-2b a variety of versatile, nonracemic chiral intermediates were prepared.
    Additional Material: 1 Tab.
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  • 36
    Electronic Resource
    Electronic Resource
    Nucleophilic Substitution Reactions with the 3-Borane-1,4,5-trimethylimidazol-2-ylidene Anion. - Unexpected Formation of an Imidazabole Isomer (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 789-793 
    Details
    ISSN: 1434-1948
    Keywords: Boranes ; Carbenes ; Heterocycles ; Imidazoles ; X-ray structures ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The nucleophilic carbene 3-borane-1,4,5-trimethylimidazol-2-ylidene anion (1-) reacts with the electrophiles CH3I, (CH3)3SiCl, (CH3)3SnCl, and the bromodiazaboroline 7 to form the 2-substituted imidazoles 4, 5, 6, and 8. With triethylborane, the anionic carbene borane adduct 9- is obtained. An unexpected result was achieved when chlorodimethoxyborane and HBCl2 · S(CH3)2 were used as electrophiles. In both cases only the imidazabole 14a could be isolated. Imidazole 5, the imidazole borane adduct 3a and the imidazabole 14a were characterized by X-ray structure analyses.
    Additional Material: 3 Ill.
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  • 37
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    Electronic Resource
    Carbon=Carbon Hydrogenation of Silicon-Functionalized Silaheterocycles (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 1095-1102 
    Details
    ISSN: 1434-1948
    Keywords: Silanorbornenes ; Silanorbornanes ; Silicon-functionalized olefins ; Silacyclobutanes ; Hydrogenations ; Heterocycles ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Catalytic hydrogenation of olefins containing functionalized silicon groups affords the saturated products in good yields. Chloro and alkoxy substituents at the silicon atom remain unaffected and, in the case of heterocyclic compounds, the cyclic or bicyclic moieties remain intact. The 2-silanorbornanes 4, 5, and 6 were synthesized from the corresponding 2-silanorbornenes 1, 2, and 3, and organosilanes 13 and 14 possessing the cyclopentyl group, were prepared from the cyclopentenyl-substituted precursors 10 and 12. The 3-vinyl-substituted silacyclobutanes 15, 17, and 18 were also hydrogenated in a simple apparatus with diethyl ether or THF as solvent, and Pd/C as a recoverable catalyst system. A basic organosilicon compound, trichloro(vinyl)silane, is hydrogenated in a nearly quantitative yield to form the saturated trichloro(ethyl)silane; this emphasizes the general applicability of this method.
    Additional Material: 2 Ill.
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  • 38
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    Electronic Resource
    Synthesis of N-Acetylglucosaminyl and Diacetylchitobiosyl Amides of Heterocyclic Carboxylic Acids as Potential Chitinase Inhibitors (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2293-2297 
    Details
    ISSN: 1434-193X
    Keywords: Carboxylic acid amides ; Chitinase ; Chitobiose ; Heterocycles ; Enzyme inhibitors ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 2-(Dimethylamino)oxazoline-4-carboxylic acids 5 were prepared by condensation of binucleophilic amino acids 4and O-ethyl-N,N-dimethylisourea 3. New heterocyclic N-acetylglucosaminyl amides and chitobiosyl amides 8 were obtained by the coupling of tetraacetylglucosamine 6a or heptaacetylchitobiosylamine 6b with acid chlorides of heterocyclic carboxylic acids 2 or 5a and subsequent deacetylation. Based on their substitution patterns, compounds 8were expected to have inhibitory activity towards chitinases. Enzyme assays showed that glycosyl amides 8 indeed were moderate inhibitors of chitinases, the diacetylchitobiosyl amides 8d-f generally having higher inhibitory activities than the N-acetylglucosaminyl amide derivatives 8a-c. Inhibitory activities depended on the chitinase tested.
    Additional Material: 2 Tab.
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  • 39
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    Electronic Resource
    2-Substituted 5-Acetyl-4-Thiazolyl Triflates as Useful Building Blocks for the Preparation of Functionalized Thiazoles (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 3117-3126 
    Details
    ISSN: 1434-193X
    Keywords: Heterocycles ; Thiazoles ; Pyrido[3,4-c]thiazoles ; Triflates ; Palladium ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The readily available 2-substituted 5-acetyl-4-thiazolyl triflates 2are useful building blocks for the preparation of functionalised thiazoles by means of palladium-catalysed cross-coupling reactions with organometallic reagents and alkoxycarbonylation and deoxygenation reactions. The combination of palladium-catalysed coupling of 2 together with 1-alkynes/6-endo-dig annulation reactions in the presence of ammonia leads to functionalised pyrido[3,4-c]thiazoles in satisfactory yields. The utilisation of uncatalysed displacement reactions of the triflate group represents a very simple method for the synthesis of 4-N-,4-O-, and 4-S-substituted thiazoles.
    Additional Material: 2 Tab.
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  • 40
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    Electronic Resource
    Silicon-Oxygen Heterocycles from Thermal, Photochemical, and Transition-Metal-Catalyzed Decomposition of α-(Alkoxysilyl and Alkenyloxysilyl)-α-diazoacetates (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 1939-1946 
    Details
    ISSN: 1434-193X
    Keywords: Diazo compounds ; Carbenes ; Carbenoids ; Silicon ; Heterocycles ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Photolysis of (ethoxy)silyl-, (propyloxy)silyl-, and (isopro-pyloxy)silyl-substituted diazoacetates 1a-c leads to tetrahydro-1,2-oxasiloles 2a-c by intramolecular C-H insertion of a carbene intermediate. Photochemical or catalytic decomposition of (allyloxysilyl)diazoacetates 3a-e results in intramolecular cyclopropanation which provides 3-oxa-2-silabicyclo[3.1.0]hexane systems 5a-e. In contrast, the thermal reaction of 3b-d gives rise to 2,5-dihydro-1,2-oxasiloles 4b-d, which are likely to be formed on a pyrazoline rather than a carbene route. For (3-butenyloxysilyl)diazoacetate 3f, all modes of decomposition generate the 3-oxa-2-silabicyclo[4.1.0]heptane system 7. Fluoride-induced cleavage of the bicyclic systems 5b-d provides trans-2-hydroxyalkyl-1-cyclopropanecarboxylates 9 diastereospecifically.
    Additional Material: 1 Tab.
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  • 41
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    Electronic Resource
    An Easy Access to 1-Azaspiropentane-2-carboxamides - The First Derivatives of a New Type of Amino Acids (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2017-2024 
    Details
    ISSN: 1434-193X
    Keywords: Amino acids ; Azaspiropentanes ; Heterocycles ; Peptides ; Strained molecules ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Azaspiropentanecarboxamides 10 and 12 are formed with remarkable ease in two steps in a one-pot operation from methyl 2-chloro-2-cyclopropylideneacetate (4) by addition of a primary amine in tetrahydrofuran and subsequent treatment with sodium hydride/triethylamine in the presence of another equivalent of a primary amine or ammonia. Achievable yields of the amides 10, 12 were moderate to good (27-59%, 12-48%), while the corresponding esters 9 could only be obtained in poor yields (4-14%). The new α-amino acid amides are surprisingly stable, and they can be incorporated into small peptides as demonstrated with the preparation of the glycine 13e and the spirocyclopro-paneoxazoline derivative 14e.
    Additional Material: 2 Ill.
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  • 42
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    Electronic Resource
    New Heterocycles from the Reaction between Some Natural α-Amino Acid Hydrazides and Formaldehyde (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2943-2948 
    Details
    ISSN: 1434-193X
    Keywords: Amino acids ; α-Amino acid phenylhydrazides ; Heterocycles ; Cyclization reactions ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ring forming condensation between some natural α-amino acid phenylhydrazides (1) and aqueous formaldehyde (2) has opened a novel synthetic route to hexahydro-1,2,4-triazin-6-one derivatives (3). Polycyclic systems were obtained from the same reaction carried out with L-aspartic acid 1,4-bis(2-phenylhydrazide) (1d), L-histidine phenylhydrazide (1e) and L-tryptophan phenylhydrazide (1f) which gave perhydro-4,6-dioxo-2,8-diphenyl[1,2,4]triazino[4,5-d][1,2,4]triazepine (5) perhydro-1-oxo-3-phenylimidazo[5,4-d][1,2,4]triazino[4,5-a]pyridine (7) and 1,2,3-H-3-(2-phenylcarbazoyl)-β-carboline (8), respectively. Substrates 1 were conveniently obtained by direct reaction of phenylhydrazine with L-α-amino acid esters retaining the original chirality.
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  • 43
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    Electronic Resource
    Synthesis Mediated by Ring-Closing Metathesis - Applications in the Synthesis of Azasugars and Alkaloids (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 959-968 
    Details
    ISSN: 1434-193X
    Keywords: Heterocycles ; Alkaloids ; Castanospermine ; Metathesis ; Azasugars ; Manzamine A ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: -The application of the ring-closing metathesis (RCM) reaction to the construction of a wide variety of nitrogen-containing ring systems is described. The examples include pyrrolizidine, indolizidine, and quinolizidine derivatives related to azasugars. A formal total synthesis of castanospermine (5) is presented. The utilisation of two RCM steps in the synthetic sequence leading to the multicyclic ABCDE nucleus 7 of the complex alkaloid manzamine A (6) is discussed.
    Additional Material: 3 Ill.
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  • 44
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    Electronic Resource
    A New Strategy for the Asymmetric Synthesis of 1,3-Oxathiolane-Based Nucleoside Analogues (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 1455-1458 
    Details
    ISSN: 1434-193X
    Keywords: Nucleoside analogues ; 1,3-Oxathiolanes ; Chiral sulfoxides ; Heterocycles ; Antiviral agents ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: -A ready asymmetric synthesis of 3′-oxathionucleosides has been accomplished in three main steps from benzoyloxyethanal. The synthesis is characterized by high overall yield and considerable enantiomeric excesses. It represents a general synthetic path to prepare a wide range of heterosubstituted sulfur-containing nucleoside analogues.
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  • 45
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    Electronic Resource
    Novel Stereoelectronic Behavior of Bicyclic Glycosyl Donors: Application to the Synthesis of Both 2-Deoxy-α- and -β-Glycosides (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 1869-1874 
    Details
    ISSN: 1434-193X
    Keywords: Carbohydrates ; Heterocycles ; Electrostatic interactions ; Glycosylation ; Glycosides ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Two pairs of novel stereoisomeric, cyclic glycosyl donors exhibit different behaviors in glycosylation processes. In the pair of α-gluco (1) and β-manno (2), the former exhibits reversability with its glycoside product whereas the latter does not. In the α-gluco (3) and β-manno (4) set, the former undergoes glycosyl transfer via an isolable intermediate whereas the latter does not. The differing anomeric effects exerted in the ground states are proposed as the force which explains the differences in behavior.
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  • 46
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    Electronic Resource
    Synthesis of the Enantiomers of 2-sec-Butyl-4,5-dihydrothiazole and (1R,5S,7R)-3,4-Dehydro-exo-brevicomin, Pheromone Components of the Male Mouse, Mus musculus (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2167-2173 
    Details
    ISSN: 1434-193X
    Keywords: Acetals ; Heterocycles ; Mouse ; Mus musculus/ Pheromones ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Two components [2-sec-butyl-4,5-dihydrothiazole (1) and 3,4-dehydro-exo-brevicomin (2)] of a male-produced pheromone of the mouse Musmusculus have been synthesized in optically active forms. The enantiomers of 1 were obtained with an enantiomeric purity of ca. 92% ee and were found to be readily racemizable. Asymmetric dihydroxylation was employed as the key reaction (15→16) allowing the preparation of (1R,5S,7R)-2 with ca. 94% ee.
    Additional Material: 1 Tab.
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  • 47
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    Electronic Resource
    Umpolung of Reactivity of Lithium Trimethylsilyldiazomethane at the C-5 Position of 6-Substituted Uracil Derivatives (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2751-2755 
    Details
    ISSN: 1434-193X
    Keywords: Lithium ; Lithium trimethylsilyldiazomethane ; Heterocycles ; Uracil derivatives ; Pyrazolo[4,3-d]pyrimidindiones ; Pyrazolo[4,3-d]pyrimidindiones ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The nucleophilic addition of TMSC(Li)N2 at the low reactive C-5 position of the uracil ring of C-6 substituted uracil derivatives is reported. The ratio of C-5 versus C-6 nucleophilic addition of TMSC(Li)N2 dramatically depends on the stereoelectronic properties of the C-6 substituent. In particular, substituents characterized both by sterically bulky and/or electron-withdrawing (EWG) effects appear to direct the nucleophile mainly (methyl, chloromethyl or halogen) or completely (isopropyl) toward the C-5 position. The fine-tuned substituent selectivity found in the nucleophilic addition of TMSC(Li)N2 to C-6 substituted uracils plays a leading role in the synthesis of new trimethylsilyl-1H-[4,3-d]pyrimidin-5,7-dione derivatives, which can in turn be easily modified through known silicon chemistry.
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  • 48
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    Electronic Resource
    Mixing in Stars and the Evolution of the 3He Abundance (1998)
    Springer
    Space science reviews 84 (1998), S. 199-206 
    Details
    ISSN: 1572-9672
    Keywords: Nuclear reactions ; Nucleosynthesis ; Abundances ; Stars:Evolution ; Interior ; Rotation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract We first recall the observational and theoretical facts that constitute the so-called 3He problem. We then review the chemical anomalies that could be related to the destruction of 3He in red giants stars. We show how a simple consistent mechanism can lead to the destruction of 3He in low mass stars and simultaneously account for the low 12C/13C ratios and low lithium abundances observed in giant stars of different populations. This process should both naturally account for the recent measurements of 3He/H in galactic HII regions and allow for high values of 3He observed in some planetary nebulae. We propose a simple statistical estimation of the fraction of stars that may be affected by this process.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1005027519798
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  • 49
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    Folding type-specific secondary structure propensities of amino acids, derived from α-helical, β-sheet, α/β, and α+β proteins of known structures (1998)
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 35-49 
    Details
    ISSN: 0006-3525
    Keywords: folding type-specific secondary structure propensities ; amino acids ; α-helical proteins ; β sheet proteins ; α/β proteins ; α+β proteins ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Folding type-specific secondary structure propensities of 20 naturally occurring amino acids have been derived from α-helical, β-sheet, α/β, and α+β proteins of known structures. These data show that each residue type of amino acids has intrinsic propensities in different regions of secondary structures for different folding types of proteins. Each of the folding types shows markedly different rank ordering, indicating folding type-specific effects on the secondary structure propensities of amino acids. Rigorous statistical tests have been made to validate the folding type-specific effects. It should be noted that α and β proteins have relatively small α-helices and β-strands forming propensities respectively compared with those of α+β and α/β proteins. This may suggest that, with more complex architectures than α and β proteins, α+β and α/β proteins require larger propensities to distinguish from interacting α-helices and β-strands. Our finding of folding type-specific secondary structure propensities suggests that sequence space accessible to each folding type may have differing features. Differing sequence space features might be constrained by topological requirement for each of the folding types. Almost all strong β-sheet forming residues are hydrophobic in character regardless of folding types, thus suggesting the hydrophobicities of side chains as a key determinant of β-sheet structures. In contrast, conformational entropy of side chains is a major determinant of the helical propensities of amino acids, although other interactions such as hydrophobicities and charged interactions cannot be neglected. These results will be helpful to protein design, class-based secondary structure prediction, and protein folding. © 1998 John Wiley & Sons, Inc. Biopoly 45: 35-49, 1998
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  • 50
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    Electronic Resource
    Torsional control of double-stranded DNA branch migration (1998)
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 69-83 
    Details
    ISSN: 0006-3525
    Keywords: DNA branched junctions ; branch migration ; superhelical torque ; control of DNA structure ; endonuclease VII ; nanomechanical device ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: DNA branched junctions are analogues of Holliday junction recombination intermediates. Partially mobile junctions contain a limited amount of homology flanking the branch point. A partially mobile DNA branched junction has been incorporated into a synthetic double-stranded circular DNA molecule. The junction is flanked by four homologous nucleotide pairs, so that there are five possible locations for the branch point. Two opposite arms of the branched junction are joined to form the circular molecule, which contains 262 nucleotides to the base of the junction. This molecule represents a system whereby torque applied to the circular molecule can have an impact on the junction, by relocating its branch point. Ligation of the molecule produces two topoisomers; about 87% of the product is a relaxed molecule, and the rest is a molecule with one positive supercoil. The position of the branch point is assayed by cleaving the molecule with endonuclease VII. We find that the major site of the branch point in the relaxed topoisomer is at the maximally extruded position in the relaxed molecule. Upon the addition of ethidium, the major site of the branch point migrates to the minimally extruded position. © 1998 John Wiley & Sons, Inc. Biopoly 45: 69-83, 1998
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    Electronic Resource
    Conformational change and aggregation of κ-carrageenan studied by flow field-flow fractionation and multiangle light scattering (1998)
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 85-96 
    Details
    ISSN: 0006-3525
    Keywords: conformation ; aggregation ; κ-carrageenan ; flow field-flow fractionation ; multiangle light scattering ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relatively novel combination of flow field-flow fractionation (FFF) and multiangle light scattering (MALS) was employed to study a nondegraded κ-carrageenan in different 0.1M salt solutions. The applicability of the technique was tested, and the effects of salt type and salt composition on the molar mass and radius of gyration were studied. A conformational ordering was induced at room temperature by switching the solvent from 0.1M NaCl (coil form) to 0.1M NaI (helix form). An approximate doubling of the average molar mass and an increase in radius of gyration was then observed, in agreement with results obtained previously using size exclusion chromatography-MALS. This increase in size was attributed to conformational ordering and to the formation of double helices. Severe aggregation was observed above 40% CsI in the 0.1M mixed salt solution of CsI and NaI. This was ascribed to the association of helices into large aggregates. For these large associates, having molar masses of several millions, a reversal of the elution order in flow FFF was detected. © 1998 John Wiley & Sons, Inc. Biopoly 45: 85-96 1998
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  • 52
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    Electronic Resource
    Calculations on the low energy conformers of N-acetyl-D-alanyl-D-alanine (1998)
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 119-133 
    Details
    ISSN: 0006-3525
    Keywords: conformations of D-alanyl-D-alanine ; β-lactam ; structural overlay ; AMBER force field ; AM1 ; ab initio ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this article a conformational analysis of the D-alanyl-D-alanine dipeptide, both charged and neutral, has been carried out. The preferred conformations were determined by means of ab initio and semiempirical quantum, together with empirical force field calculations. The AMBER* force field and the 6-31 + G** and 6-31G** ab initio levels give rise to a coincident minimum energy structure, which, on the other hand, differs from that determined by AM1, 3-21 + G, and 3-21G. The solvent effect on the different charged and neutral conformations have been considered through the AMSOL semiempirical method. A quantification regarding the structural similarities between the different dipeptide conformations and the ampicillin has been performed. The results show that the best overlay is attained by the minimum structure energy obtained by using the 6-31 + G** methodology, which presents a planar amidic nitrogen. © 1998 John Wiley & Sons, Inc. Biopoly 45: 119-133, 1998
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    C6-oxidized cellulose: Ion interactions with mono- and divalent cations (1998)
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 157-163 
    Details
    ISSN: 0006-3525
    Keywords: chemical oxidation ; cellulose ; conformational transition ; capillary viscosity ; microcalorimetry ; calcium ions ; gels ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational behavior of different molecular weight fractions of a synthetic C6-oxidized derivative of cellulose were investigated by means of capillary viscometry, CD, and microcalorimetric measurements. Experiments were carried out in the presence of either monovalent or divalent counterions.The experimental data indicated that C6-oxidized cellulose can assume an ordered extended conformation at low ionic strength, induced by the intrachain repulsions of negative charges. This conformation was suggested to be very similar to the fully extended structure of cellulose. In addition to this, upon increasing the ionic strength, a conformational transition of the order-to-disorder type occurred. In fact, the screening of the electrostatic repulsions introduced a number of conformational kinks into the cellulosic backbone, which enabled the polymer to assume a more coiled conformation hence producing less viscous aqueous solutions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 157-163, 1998
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    Conformational stability of biological polyelectrolytes: Evaluation of enthalpy and entropy changes of conformational transitions (1998)
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 203-216 
    Details
    ISSN: 0006-3525
    Keywords: conformational stability ; biological polyelectrolytes ; enthalpy ; entropy ; conformational transitions ; carrageenan ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new method is proposed for the determination of the enthalpy and entropy changes of nonionic origin upon conformational transition of linear biopolyelectrolytes in solution. For all transition midpoints, defined by given temperature and ionic strength, the total free energy change of the system is zero, which means that the nonionic contribution to the free energy change is equal in value and opposite in sign to the polyelectrolytic one. The counterion condensation theory of linear polyelectrolytes provides for the appropriate analytical expression to be used in such calculations. Linear plots of the proper functions of the calculated free energy changes vs the proper functions of temperature allows for the determination of the enthalpic and entropic terms of the nonionic free energy change of transition.The method has been applied to the extensive available data of the ion-induced conformational change of κ-carrageenan, a linear sulfated galactan extracted from seaweeds. The method has proved very successful, with the results showing a remarkable convergency of the enthalpy values for different monovalent counterions. On the other hand, the above approach has made it possible to explain the known effect of counterion specificity on the transition by a small difference in the nonionic entropic contributions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 203-216, 1998
    Additional Material: 5 Ill.
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    UV resonance Raman spectroscopy of DNA and protein constituents of viruses: Assignments and cross sections for excitations at 257, 244, 238, and 229 nm (1998)
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 247-256 
    Details
    ISSN: 0006-3525
    Keywords: uv resonance Raman spectroscopy ; Raman cross section ; hypochromism ; DNA ; deoxynucleoside ; protein ; aromatic amino acid ; virus assembly ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ultraviolet resonance Raman (UVRR) spectra of H2O and D2O solutions of the nucleoside (dA, dG, dC, dT) and aromatic amino acid (Phe, Trp, Tyr) constituents of DNA viruses have been obtained with laser excitation wavelengths of 257, 244, 238, and 229 nm. Using the 981 cm-1 marker of Na2SO4 as an internal standard, Raman frequencies and scattering cross sections were evaluated for all prominent UVRR bands at each excitation wavelength. The results show that UVRR cross sections of both the nucleosides and amino acids are strongly dependent on excitation wavelength and constitute sensitive and selective probes of the residues. The results provide a library of UVRR marker bands for structural analysis of DNA viruses and other nucleoprotein assemblies. © 1998 John Wiley & Sons, Inc. Biopoly 45: 247-256, 1998
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    Lumbricus terrestris hemoglobin: A comparison of small-angle X-ray scattering and cryoelectron microscopy data (1998)
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 289-298 
    Details
    ISSN: 0006-3525
    Keywords: hemoglobin ; hexagonal bilayer ; Lumbricus ; electron microscopy ; three-dimensional reconstruction ; small-angle x-ray scattering ; three-dimensional models ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The quaternary structure of Lumbricus terrestris hemoglobin was investigated by small-angle x-ray scattering (SAXS). Based on the SAXS data from several independent experiments, a three-dimensional (3D) consensus model was established to simulate the solution structure of this complex protein at low resolution (about 3 nm) and to yield the particle dimensions. The model is built up from a large number of small spheres of different weights, a result of the two-step procedure used to calculate the SAXS model. It accounts for the arrangement of 12 subunits in a hexagonal bilayer structure and for an additional central unit of cylinder-like shape. This model provides an excellent fit of the experimental scattering curve of the protein up to h = 1 nm-1 and a nearly perfect fit of the experimental distance distribution function p(r) in the whole range. Scattering curves and p(r) functions were also calculated for low-resolution models based on 3D reconstructions obtained by cryoelectron microscopy (EM). The calculated functions of these models also provide a very good fit of the experimental scattering curve (even at h 〉 1 nm-1) and p(r) function, if hydration is taken into account and the original model coordinates are slightly rescaled. The comparison of models reveals that both the SAXS-based and the EM-based model lead to a similar simulation of the protein structure and to similar particle dimensions. The essential differences between the models concern the hexagonal bilayer arrangement (eclipsed in the SAXS model, one layer slightly rotated in the EM model), and the mass distribution, mainly on the surface and in the central part of the protein complex. © John Wiley & Sons, Inc. Biopoly 45: 289-298, 1998
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    Conformational changes due to vicinal glycosylation: The branched α-l-Rhap(1-2)[β-d-Galp(1-3)]-β-d-Glc1-OMe trisaccharide compared with its parent disaccharides* (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 417-432 
    Details
    ISSN: 0006-3525
    Keywords: conformational changes ; vicinal glycosylation ; branched α-l-Rhap(1-2)[β-d-Galp(1-3)]-β-d-Glc1-OMe trisaccharide ; parent disaccharides ; hydrogen bond ; isotope effect ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformations of the α-l-Rhap(1-2)-β-d-Glc1-OMe and β-d-Galp(1-3)-β-d-Glc1-OMe disaccharides and the branched title trisaccharide were examined in DMSO-d6 solution by 1H-nmr. The distance mapping procedure was based on rotating frame nuclear Overhauser effect (NOE) constraints involving C- and O-linked protons, and hydrogen-bond constraints manifested by the splitting of the OH nmr signals for partially deuteriated samples. An “isotopomer-selected NOE” method for the unequivocal identification of mutually hydrogen-bonded hydroxyl groups was suggested. The length of hydrogen bonds thus detected is considered the only one motionally nonaveraged nmr-derived constraint. Molecular mechanics and molecular dynamics methods were used to model the conformational properties of the studied oligosaccharides. Complex conformational search, relying on a regular Φ,Ψ-grid based scanning of the conformational space of the selected glycosidic linkage, combined with simultaneous modeling of different allowed orientations of the pendant groups and the third, neighboring sugar residue, has been carried out. Energy minimizations were performed for each member of the Φ,Ψ grid generated set of conformations. Conformational clustering has been done to group the minimized conformations into families with similar values of glycosidic torsion angles. Several stable syn and anti conformations were found for the 1→2 and 1→3 bonds in the studied disaccharides. Vicinal glycosylation affected strongly the occupancy of conformational states in both branches of the title trisaccharide. The preferred conformational family of the trisaccharide (with average Φ,Ψ values of 38°, 17° for the 1→2 and 48°, 1° for the 1→3 bond, respectively) was shown by nmr to be stabilized by intramolecular hydrogen bonding between the nonbonded Rha and Gal residues. © 1998 John Wiley & Sons, Inc. Biopoly 46: 417-432, 1998
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    Buffer dependence of refractive index increments of protein solutions (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 489-492 
    Details
    ISSN: 0006-3525
    Keywords: refractive index increment ; proteins ; solvent ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The refractive index increment of a protein solution is a property not only of the protein, but also of the solvent. This is demonstrated theoretically and confirmed experimentally using analytical interferometry. © 1998 John Wiley & Sons, Inc. Biopoly 46: 489-492, 1998
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    Editor's comments (1998)
    New York : Wiley-Blackwell
    Biopolymers 47 (1998), S. 1-1 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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    Conformational behavior of the HAV-VP3(110-121) peptidic sequence and synthetic analogs in membrane environments studied by CD and computational methods (1998)
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 479-492 
    Details
    ISSN: 0006-3525
    Keywords: hepatitis A ; synthetic peptides ; CD ; liposomes ; computational study ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The present study was undertaken to examine the structural features that may be important to explain the immunogenicity of the (110-121) peptide sequence (FWRGDLVFDFQV) of VP3 capsid protein of hepatitis A virus. A conformational analysis of the preferred conformations by CD and molecular mechanics was carried out. Present results suggest that the interaction with liposomes as biomembrane model induces and stabilizes the amphipathic β-structure of the peptide.To study the contribution of amino acid replacements at the RGD tripeptide as well as the influence of the peptide chain length on peptide conformation, solid-phase peptide synthesis of several peptide analogs was carried out and the peptide conformation was studied using CD spectroscopy. The results show that the RGD sequence is necessary to induce the β-structure in the presence of liposomes. © 1998 John Wiley & Sons, Inc. Biopoly 45: 479-492, 1998
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    Liquid crystal formation in DNA fragment solutions (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 31-37 
    Details
    ISSN: 0006-3525
    Keywords: DNA liquid crystals ; DNA fragments ; screened Coulomb interactions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The critical volume fractions pertaining to the formation of DNA liquid crystals were obtained from polarization microscopy, 31P-nmr, and phase separation experiments. The DNA length (approximately one to two times the persistence length 50 nm), ionic strength, and counterion variety dependencies are reported. The cholesteric-isotropic transition is interpreted in terms of the coexistence equations, which are derived from the solution free energy including orientational entropy and excluded volume effects. With the wormlike chain as reference system, the electrostatic contribution to the free energy is evaluated as a thermodynamic perturbation in the second virial approximation with a Debye-Hückel potential of mean force. The hard core contribution has been evaluated with scaled particle theory and/or a simple generalization of the Carnahan-Starling equation of state for hard spheres. For sufficiently high ionic strengths, the agreement is almost quantitative. At lower amounts of added salt deviations are observed, which are tentatively attributed to counterion screening effects. The contour length dependence agrees with a DNA persistence length 50 nm. © 1998 John Wiley & Sons, Inc. Biopoly 46: 31-37, 1998
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    Gelation of gelatin observation in the bulk and at the air-water interface (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 245-252 
    Details
    ISSN: 0006-3525
    Keywords: gelatin ; gelation ; atomic force microscopy ; interfacial rheology ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Gelation of gelatin under various conditions has been followed by atomic force microscopy (AFM) with the objective of understanding more fully the structure formed during the gelation process. AFM images were obtained of the structures formed from both the bulk sol and in surface films during the onset of gelation. While gelation occurred in the bulk sol, the extent of helix formation was monitored by measurements of optical rotation, and the molecular aggregation was imaged by AFM. Interfacial gelatin films formed at the air-water interface were also studied. Measurements of surface tension and surface rheology were made periodically and Langmuir-Blodgett films were drawn from the interface to allow AFM imaging of the structure of the interfacial layer as a function of time. Structural studies reveal that at low levels of helical content the gelatin molecules assemble into aggregates containing short segments of dimensions comparable to those expected for gelatin triple helices. With time larger fibrous structures appear whose dimensions suggest that they are bundles of triple helices. As gelation proceeds, the number density of fibers increases at the expense of the smaller aggregates, eventually assembling into a fibrous network. The gel structure appears to be sensitive to the thermal history, and this is particularly important in determining the structure and properties of the interfacial films. © 1998 John Wiley & Sons, Inc. Biopoly 46: 245-252, 1998
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    Ribozyme chemogenetics (1998)
    New York : Wiley-Blackwell
    Biopolymers 48 (1998), S. 65-81 
    Details
    ISSN: 0006-3525
    Keywords: nucleotide analogue interference mapping ; phosphorothioate ; group I intron ; interference suppression ; RNA ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this review I will outline several chemogenetic approaches used to determine the chemical basis of large ribozyme function and structure. The term chemogenetics was first used to describe site-specific functional group modification experiments in the analysis of DNA-protein interactions. Within the past few years equivalent experiments have been performed on large catalytic RNAs using both single-site substitution and interference mapping techniques with nucleotide analogues. While functional group mutagenesis is an important aspect of a chemogenetic approach, chemical correlates to genetic revertants and suppressors must also be realized for the genetic analogy to be intellectually valid and experimentally useful. Several examples of functional group revertants and suppressors have now been obtained within the Tetrahymena group I ribozyme. These experiments define an ensemble of tertiary hydrogen bonds that have made it possible to construct a detailed model of the ribozyme catalytic core. The model includes a functionally important monovalent metal ion binding site, a wobble-wobble receptor motif for helix-helix packing interactions, and a minor groove triple helix. © 1998 John Wiley & Sons, Inc. Biopoly 48: 65-81, 1998
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    Design, synthesis, and analysis of conformationally constrained nucleic acids (1998)
    New York : Wiley-Blackwell
    Biopolymers 48 (1998), S. 83-96 
    Details
    ISSN: 0006-3525
    Keywords: nucleic acid ; disulfide cross-link ; structure ; dynamics ; stability ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this review I discuss straightforward and general methods to modify nucleic acid structure with disulfide cross-links. A motivating factor in developing this chemistry was the notion that disulfide bonds would be excellent tools to probe the structure, dynamics, thermodynamics, folding, and function of DNA and RNA, much in the way that cystine cross-links have been used to study proteins. The chemistry described has been used to synthesize disulfide cross-linked hairpins and duplexes, higher order structures like triplexes, nonground-state conformations, and tRNAs. Since the cross-links form quantitatively by mild air oxidation and do not perturb either secondary or tertiary structure, this modification should prove quite useful for the study of nucleic acids. © 1998 John Wiley & Sons, Inc. Biopoly 48: 83-96, 1998
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    On the role of magnesium ions in RNA stability (1998)
    New York : Wiley-Blackwell
    Biopolymers 48 (1998), S. 113-135 
    Details
    ISSN: 0006-3525
    Keywords: divalent cations ; magnesium ; RNA ; ion binding ; RNA folding ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Divalent cations, like magnesium, are crucial for the structural integrity and biological activity of RNA. In this article, we present a picture of how magnesium stabilizes a particular folded form of RNA. The overall stabilization of RNA by Mg2+ is given by the free energy of transferring RNA from a reference univalent salt solution to a mixed salt solution. This term has favorable energetic contributions from two distinct modes of binding: diffuse binding and site binding. In diffuse binding, fully hydrated Mg ions interact with the RNA via nonspecific long-range electrostatic interactions. In site binding, dehydrated Mg2+ interacts with anionic ligands specifically arranged by the RNA fold to act as coordinating ligands for the metal ion. Each of these modes has a strong coulombic contribution to binding; however, site binding is also characterized by substantial changes in ion solvation and other nonelectrostatic contributions. We will show how these energetic differences can be exploited to experimentally distinguish between these two classes of ions using analyses of binding polynomials. We survey a number of specific systems in which Mg2+-RNA interactions have been studied. In well-characterized systems such as certain tRNAs and some rRNA fragments these studies show that site-bound ions can play an important role in RNA stability. However, the crucial role of diffusely bound ions is also evident. We emphasize that diffuse binding can only be described rigorously by a model that accounts for long-range electrostatic forces. To fully understand the role of magnesium ions in RNA stability, theoretical models describing electrostatic forces in systems with complicated structures must be developed. © 1999 John Wiley & Sons, Inc. Biopoly 48: 113-135, 1998
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    Three-dimensional structure of the ion-chanel forming peptide trichorzianin TA VII bound to sodium dodecyl sulfate micelles (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 75-88 
    Details
    ISSN: 0006-3525
    Keywords: 1H-nmr ; molecular modeling ; peptaibol ; peptide-lipid interaction ; sodium dodecyl sulfate micelles ; trichorzianin TA VII ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Trichorzianin TA VII, Ac0 U1 A2 A3 U4 J5 Q6 U7 U8 U9 S10 L11 U12 P13 V14 U15 I16 Q17 Q18 Fol19, is a nonadecapeptide member of the peptaibol antibiotics biosynthesized by Trichoderma soil fungi, which is characterized by a high proportion of the α,α-dialkylated amino acids, α-aminoisobutyric acid (Aib, U) and isovaline (Iva, J), an acetylated N-terminus and a C-terminal phenylalaninol (Pheol, Fol). The main interest in such peptides stems from their ability to interact with phospholipid bilayers and form voltage-dependent transmembrane channels in planar lipid bilayers. In order to provide insights into the lipid-peptide interaction promoting the voltage gating, the conformational study of TA VII in the presence of perdeuterated sodium dodecyl sulfate (SDS-d25) micelles has been carried out. 1H sequential assignments have been performed with the use of two-dimensional homo- and -heteronuclear nmr techniques including double quantum filtered correlated spectroscopy, homonuclear Hartmann-Hahn, nuclear Overhauser effect spectroscopy, 1H-13C heteronuclear single quantum correlation, and heteronuclear multiple bond correlation. Conformational parameters, such as 3JNHCαH coupling constants, temperature coefficients of amide protons (Δδ/ΔTNH) and quantitative nuclear Overhauser enhancement data, lead to detailed structural information. Ninety-eight three-dimensional structures consistent with the nmr data were generated from 231 interproton distances and six Φ dihedral angle restraints, using restrained molecular dynamics and energy minimization calculations. The average rms deviation between the 98 refined structures and the energy-minimized average structure is 0.59 Å for the backbone atoms. The structure of trichorzianin TA VII associated with SDS micelles, as determined by these methods, is characterized by two right-handed helical segments involving residues 1-8 and 11-19, linked by a β-turn that leads to an angle about 90°-100° between the two helix axes; residues 18 and 19 at the end of the C-terminal helix exhibit multiple conformations. © 1998 John Wiley & Sons, Inc. Biopoly 46: 75-88, 1998
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    Spectroscopic studies of 9-hydroxyellipticine binding to DNA (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 127-143 
    Details
    ISSN: 0006-3525
    Keywords: 9-hydroxyellipticine ; DNA ; CD ; linear dichroism ; resonance light scattering ; intercalation ; drug-drug interactions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The binding of 9-hydroxyellipticine to calf thymus DNA, poly[d(A-T)]2, and poly-[d(G-C)]2 has been studied in detail by means of CD, linear dichroism, resonance light scattering, and molecular dynamics. The transition moment polarizations of 9-hydroxyelliptiycine were determined in polyvinyl alcohol stretched film. Spectroscopic solution studies of the DNA/drug complex are combined with theoretical CD calculations using the final 50 ps of a series of molecular dynamics simulations as input. The spectroscopic data shows 9-hydroxyellipticine to adopt two main binding modes, one intercalative and the other a stacked binding mode involving the formation of drug oligomers in the DNA major groove. Analysis of the intercalated binding mode in poly[d(A-T)]2 suggests the 9-hydroxyellipticine hydroxyl group lies in the minor groove and hydrogen bonds to water with the pyridine ring protruding into the major groove. The stacked binding mode was examined using resonance light scattering and it was concluded that the drug was forming small oligomer stacks rather than extended aggregates. Reduced linear dichroism measurements suggested a binding geometry that precluded a minor groove binding mode where the plane of the drug makes a 45° angle with the plane of the bases. Thus it was concluded that the drug stacks in the major groove. No obvious differences in the mode of binding of 9-hydroxyellipticine were observed between different DNA sequences; however, the stacked binding mode appeared to be more favorable for calf thymus DNA and poly[d(G-C)]2 than for poly[d(A-T)]2, an observation that could be explained by the slightly greater steric hindrance of the poly[d(A-T)]2 major groove. A strong concentration dependence was observed for the two binding modes where intercalation is favored at very low drug load, with stacking interactions becoming more prominent as the drug concentration is increased. Even at DNA : drug mixing ratios of 70:1 the stacked binding mode was still important for GC-rich DNAs. © 1998 John Wiley & Sons, Inc. Biopoly 46: 127-143, 1998
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    Interaction of branched chain polymeric polypeptides with phospholipid model membranes (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 169-179 
    Details
    ISSN: 0006-3525
    Keywords: macromolecular carriers ; drug targeting and delivery ; branched chain synthetic polypeptides ; membrane-synthetic polypeptide interaction ; lipid monolayers/bilayers ; polymer therapeutics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The surface properties at the air/water interface and the interaction of branched chain polymeric polypeptides with a general formula poly[Lys-(DL-Alam-X1)], where X = Π (AK), Ser (SAK), or Glu (EAK), with phospholipids were investigated. Polylysine derivatives with polycationic (SAK, AK) or amphoteric (EAK) were capable to spread and form stable monomolecular layers. The stability of monolayers at the air/water interface was dependent on the side-chain terminal amino acid residue of polymers and can be described by SAK 〈 AK 〈 EAK order. The area per amino acid residue values calculated from compression isotherms were in the same range as compared to those of linear poly-α-amino acids and proteins. Moreover, these polymers interact with phospholipid monomolecular layers composed of dipalmitoyl phosphatidyl choline (DPPC) or DPPC/PG (PG: phosphatidyl glycerol; 95/5, mol/mol). Data obtained from compression isotherms of phospholipids spread on aqueous polymer solutions at different initial surface pressure indicated that insertion into lipid monolayers for SAK or AK is more pronounced than for EAK. The interaction between branched polypeptides and phospholipid membranes was further investigated using lipid bilayers with DPPC/PG and fluorescent probes located either at the polar surface [1-(4-trimethylammonium-phenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH) sodium anilino naphthalene sulfonate (ANS)] or within the hydrophobic core (DPH) of the liposome. Changes in fluorescence intensity and in polarization were observed when TMA-DPH or ANS, but not DPH were used. Comparative data also indicate that all three polymers interact only with the outer surface of the bilayer, but even the most marked penetration of polycationic polypeptide (SAK) did not result in alteration of the ordered state of the alkyl chains in the bilayer. Taken together, data obtained from mono- or bilayer experiments suggest that the interaction between branched polymers and phospholipids are highly dependent on the charge properties (Ser vs Glu) and on the identity (Ser vs Ala) of side-chain terminating amino acids. The binding of polymers to the model membranes could be mainly driven by electrostatic forces, but the significant role of hydrophilic properties in case of SAK cannot be excluded. © 1998 John Wiley & Sons, Inc. Biopoly 46: 169-179, 1998
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    Relationship between conformation and geometry as evidenced by molecular dynamics simulation of Cα,α-dialkylated glycines (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 239-244 
    Details
    ISSN: 0006-3525
    Keywords: Cα,α-dialkylated glycines ; molecular dynamics ; geometry and conformation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relationship between the local backbone conformation and bond angles at Cα of symmetrically substituted Cα,α-dialkylated glycines (Cα,α-dimethylglycine or α-aminoisobutyric acid, Aib; Cα,α-diethylglycine, Deg; Cα,α-di-n-propylglycine, Dpg) has been investigated by molecular dynamics (MD) simulation adopting flat bottom harmonic potentials, instead of the usual harmonic restraints, for the Cα bond angles. The MD simulations show that the Cα bond angles are related to the local backbone conformation, irrespectively of the side-chain length of Aib, Deg, and Dpg residues. Moreover, the N-Cα-C′ (τ) angle is the most sensitive conformational parameter and, in the folded form, is always larger and more flexible than in the extended one. © 1998 John Wiley & Sons, Inc. Biopoly 46: 239-244, 1998
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    Methionine ligation strategy in the biomimetic synthesis of parathyroid hormones (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 319-327 
    Details
    ISSN: 0006-3525
    Keywords: methionine ligation ; parathyroid hormones ; biomimetic ligation ; S-methylation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In biological systems, both proteolysis and aminolysis of amide bonds produce activated intermediates through acyl transfer reactions either inter- or intramolecularly. Protein splicing is an illustrative example that proceeds through a series of catalyzed acyl transfer reactions and culminates at an O- or S-acyl intermediate. This intermediate leads to an uncatalyzed acyl migration to form an amide bond in the spliced product. A ligation method mimicking the uncatalyzed final steps in protein splicing has been developed utilizing the acyl transfer amide-bond feature for the blockwise coupling of unprotected, free peptide segments at methionine (Met). The latent thiol moiety of Met can be exploited using homocysteine at the α-amino terminal position of a free peptide for transthioesterification with another free peptide containing an α-thioester to give an S-acyl intermediate. A subsequent, proximity-driven S- to N-acyl migration of this acyl intermediate spontaneously rearranges to form a homocysteinyl amide bond. S-methylation with excess p-nitrobenezensulfonate yields Met at the ligation site. The methionine ligation is selective and orthogonal, and is usually completed within 4 h when performed at slightly basic pH and under strongly reductive conditions. No side reactions due to acylation were observed with any other α-amines of both peptide segments as seen in the synthesis of parathyroid hormone peptides. Furthermore, cyclic peptide can also be obtained through the same strategy by placing both homocysteine at the amino terminus and the thioester at the carboxyl terminus in an unprotected peptide precursor. These biomimetic ligation strategies hold promise for engineering novel peptides and proteins. © 1998 John Wiley & Sons, Inc. Biopoly 46: 319-327, 1998
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    Modeling the free solution electrophoretic mobility of short DNA fragments (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 359-373 
    Details
    ISSN: 0006-3525
    Keywords: boundary element method ; DNA electrophoresis ; electrophoretic mobility of DNA ; free solution electrophoretic mobility of DNA ; ion relaxation, DNA electrophoresis ; modeling electrophoresis of polyions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Boundary element methods are used to model the free solution electrophoretic mobility of short DNA fragments. The Stern surfaces of the DNA fragments are modeled as plated cylinders that reproduce translational and rotational diffusion constants. The solvent-accessible and ion-accessible surfaces are taken to be coincident with the Stern surface. The mobilities are computed by solving simultaneously the coupled Navier-Stokes, Poisson, and ion-transport equations. The equilibrium electrostatics are treated at the level of the full Poisson-Boltzmann equation and ion relaxation is included. For polyions as highly charged as short DNA fragments, ion relaxation is substantial. At .11 M KCl, the simulated mobilities of a 20 base pair DNA fragment are in excellent agreement with experiment. At .04 M Tris acetate, pH = 8.0, the simulated mobilities are about 10-15% higher than experimental values and this discrepancy is attributed to the relatively large size of the Tris counterion. The length dependence of the mobility at .11 M KCl is also investigated. Earlier mobility studies on lysozyme are reexamined in view of the present findings. In addition to electrophoretic mobilities, the effective polyion charge measured in steady state electrophoresis and its relationship to the preferential interaction parameter γgG is briefly considered. © 1998 John Wiley & Sons, Inc. Biopoly 46: 359-373, 1998
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    Aggregation of dermorphin and L-Ala dermorphin examined by light scattering at sub-NMR concentrations (1998)
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 341-346 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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    Correlation between rate of enzyme-substrate diffusional encounter and average Boltzmann factor around active site (1998)
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 355-360 
    Details
    ISSN: 0006-3525
    Keywords: diffusional encounter ; Brownian dynamics ; average Boltzmann factor ; acetylcholinesterase ; Poisson-Boltzmann ; electrostatics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The utility of the average Boltzmann factor around the active site of an enzyme as the predictor of the electrostatic enhancement of the substrate binding rate is tested on a set of data on wild-type acetylcholinesterase and 18 charge mutants recently obtained by Brownian dynamics simulations. A good correlation between the average Boltzmann factors and the substrate binding rate constants is found. The effects of single charge mutations on both the Boltzmann factor and the substrate binding rate constant are modest, i.e., 〈5 fold increase or decrease. This is consistent with the experimental results of Shafferman et al. but does not support their suggestion that the overall rate of the catalytic reaction is not limited by the diffusional encounter of acetylcholinesterase and its substrate. © 1998 John Wiley & Sons, Inc. Biopoly 45: 355-360, 1998
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    Reconstructing the protein-water interface (1998)
    New York : Wiley-Blackwell
    Biopolymers 45 (1998), S. 469-478 
    Details
    ISSN: 0006-3525
    Keywords: molecular dynamics ; hydrated proteins ; crystal structures ; density distributions ; globular proteins ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using molecular dynamics simulations of fully hydrated proteins and analysis of crystal structures contained in the Protein Data Bank, we develop a transferable set of perpendicular radial distribution functions for water molecules around globular proteins. These universal functions may be used to reconstruct the unique three-dimensional solvent density distribution around every individual protein with a modest error. We discuss potential applications of this solvent treatment in protein x-ray crystallographic refinements and in theoretical modeling. We also present a fast, grid-based algorithm for construction of the perpendicular solvent density distributions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 469-478, 1998
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    Design strategies for the construction of independently folded polypeptide motifs (1998)
    New York : Wiley-Blackwell
    Biopolymers 47 (1998), S. 23-29 
    Details
    ISSN: 0006-3525
    Keywords: independently folded polypeptide motifs ; miniproteins ; natural target domains ; BBA motif ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this paper we present a redesign strategy for the development of uniquely folded polypeptide motifs of less than 40 residues. These mini proteins are based on natural target domains, including the zinc finger domains (BBA motif) Nomenclature corresponds to the defined elements of secondary structure, beginning at the N-terminus of the peptide. Roman lettering refers to a specific motif while Greek characters correspond to the elements of secondary structure within that motif. and the disulfide-rich snake and scorpion toxins (BBB motif). These motifs are designed to act as the molecular framework for the construction of novel functional polypeptides. We will explore the structural determinants of the folded BBA motif, inspired by the zinc finger peptides, in relation to the redesign process. © 1998 John Wiley & Sons, Inc. Biopoly 47: 23-29, 1998
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    Peptide ion channels: Design and creation of function (1998)
    New York : Wiley-Blackwell
    Biopolymers 47 (1998), S. 75-81 
    Details
    ISSN: 0006-3525
    Keywords: ion channel ; synthetic peptide ; de novo design ; template-assembled synthetic proteins ; supramolecular assembly ; membrane protein ; planer lipid bilayers ; amphiphilic peptide ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To create ion channel function by synthetic peptides is a challenge in the de novo design of artificial membrane proteins. Amphiphilic α-helical motifs of ∼ 20 amino acid residues to span lipid bilayers are most often used for the creation of peptide ion channels. Template molecules to tether helical peptides have been employed to obtain more organized pore structures. Approaches to form molecular assembly of peptides in the membranes by hydrogen bonding have been also investigated. We have developed approaches to assemble helices with individual amino acid sequences to construct artificial helical proteins. Using one of these approaches, four helices corresponding to the voltage sensor segments (S4 in repeat I-IV) of the sodium channel were assembled on a peptide template to give a protein having ion channel activity with rectification. © 1998 John Wiley & Sons, Inc. Biopoly 47: 75-81, 1998
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    Collagen mimetics (1998)
    New York : Wiley-Blackwell
    Biopolymers 47 (1998), S. 127-142 
    Details
    ISSN: 0006-3525
    Keywords: collagen mimetics ; triple helix ; peptoid ; template ; biophysics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Collagen peptidomimetics have been synthesized as an alternative to natural collagen. The incorporation of unnatural residues such as peptoids in the collagen sequences can demonstrate potent and specific biological activity and enhance the biostability against enzymatic degradation. Furthermore, the use of achiral peptoids simplifies synthetic strategies by reducing racemization problems. The peptoid residue N-isobutylglycine (Nleu) has been successfully incorporated into a series of collagen mimetics composed of Gly-Pro-Nleu, Gly-Nleu-Pro, and Gly-Nleu-Nleu. The discovery of template-assembled collagen mimetics and metal binding ability has laid the foundation for new opportunities in the design of novel collagen mimetic complexes. This review summarizes the synthesis and integrated biophysical analyses of the structures of these collagen mimetics. Solid phase segment condensation techniques have been utilized for the synthesis of the single chain and template-assembled analogues. The characterization of the collagen-like structures has been established by temperature-dependent optical rotation measurements, CD, NMR spectroscopy, and molecular modelling simulations. © 1998 John Wiley & Sons, Inc. Biopoly 47: 127-142, 1998
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    Syntheses of squarylium-substituted alanine and its peptide, and formation of their thin films onto a poly(3-methylthiophene)/Au electrode (1998)
    New York : Wiley-Blackwell
    Biopolymers 47 (1998), S. 179-183 
    Details
    ISSN: 0006-3525
    Keywords: non-natural amino acid ; peptide ; squarylium dye ; thin film ; poly(3-methylthiophene) ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We designed a polypeptide that behaves as a photodevice by using a non-natural amino acid with replacement of an α-hydrogen by a squarylium dye and succeeded in syntheses of the non-natural amino acid derivative containing a squarylium and its peptide with trialanine Ala-Ala-Ala. Strong dye-dye interactions were confirmed by absorption and CD spectra for the peptide in 2,2,2-trifluoroethanol solution and in water suspension. The non-natural amino acid derivative could be deposited onto a PMeT/Au electrode by the micelle disruption method. © 1998 John Wiley & Sons, Inc. Biopoly 47: 179-183, 1998
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    Editorial: Protein-protein interactions: Mimics and inhibitors (1998)
    New York : Wiley-Blackwell
    Biopolymers 47 (1998), S. 263-263 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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    New developments of the electrostatically driven monte carlo method: Test on the membrane-bound portion of melittin (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 117-126 
    Details
    ISSN: 0006-3525
    Keywords: electrostatically driven Monte Carlo method ; cluster analysis ; global energy minimum ; perturbed conformations ; conformational space ; lowest energy conformations ; polypeptide chain ; melittin, membrane-bound portion ; Empirical Conformational Energy Program for Peptides 3 ; annealing methods ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electrostatically driven Monte Carlo (EDMC) method has been greatly improved by adding a series of new features, including a procedure for cluster analysis of the accepted conformations. This information is used to guide the search for the global energy minimum. Alternative procedures for generating perturbed conformations to sample the conformational space were also included. These procedures enhance the efficiency of the method by generating a larger number of low-energy conformations.The improved EDMC method has been used to explore the conformational space of a 20-residue polypeptide chain whose sequence corresponds to the membrane-bound portion of melittin. The ECEPP/3 (Empirical Conformational Energy Program for Peptides) algorithm was used to describe the conformational energy of the chain. After an exhaustive search involving 14 independent runs, the lowest energy conformation (LEC) (-91.0 kcal/mol) of the entire study was encountered in four of the runs, while conformations higher in energy by no more than 1.8 kcal/mol were found in the remaining runs with the exception of one of them (run 8). The LEC is identical to the conformation found recently by J. Lee, H.A. Scheraga, and S. Rackovsky [(1998) “Conformational Analysis of the 20-Residue Membrane-Bound Portion of Melittin by Conformational Space Annealing,” Biopolymers, Vol. 46, pp. 103-115] as the lowest energy conformation obtained in their study using the conformational space annealing method. These results suggest that this conformation corresponds to the global energy minimum of the ECEPP/3 potential function for this specific sequence; it also appears to be the conformation of lowest free energy. © 1998 John Wiley & Sons, Inc. Biopoly 46: 117-126, 1998
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    Renaturation of condensed DNA studied through a decoupling scheme (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 195-200 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
    Additional Material: 3 Ill.
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    Band broadening in gel electrophoresis: Scaling laws for the dispersion coefficient measured by FRAP (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 201-214 
    Details
    ISSN: 0006-3525
    Keywords: band broadening ; dispersion ; DNA ; gels ; electrophoresis ; fluorescence recovery ; photobleaching ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We determined quantitatively the band broadening effect during gel electrophoresis by measuring the longitudinal dispersion coefficient Dx, with a fluorescence recovery after photobleaching setup, coupled to an electrophoretic cell. We carried out measurements as a function of the electric field, the average pore size, and the molecular length of DNA fragments. Our results are in good agreement with the predictions of the biased reptation model with fluctuations described by T. A. Duke et al. [(1992) Physics Review Letters, vol. 69, pp. 3260-3263]. This agreement is observed on single-stranded DNA [persistence length ≅ 4 nm; B. Tinland et al. (1997) Macromolecules, vol. 30, pp. 5763-5765] in polyacrylamide gels and on double-stranded DNA (persistence length ≅ 50 nm) in agarose gels, two systems where the ratio between the average pore size and the Kuhn length is larger than 1. © 1998 John Wiley & Sons, Inc. Biopoly 46: 201-214, 1998
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    Inherent DNA curvature and flexibility correlate with TATA box functionality (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 403-415 
    Details
    ISSN: 0006-3525
    Keywords: molecular dynamics ; DNA curvature ; DNA flexibility ; TATA box functionality ; TATA box binding protein (TBP) ; TBP recognition ; TBP binding ; TBP transcriptional activation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Four 1.5 ns molecular dynamics (MD) simulations were performed on the d(GCTATAAAAGGG) · d(CCCTTTTATAGC) double helix dodecamer bearing the Adenovirus major late promoter TATA element and three iso-composition mutants for which physical and biochemical data are available from the same laboratory. Three of these DNA sequences experimentally induce tight binding with the TATA box binding protein (TBP) and induce high transcription rates; the other DNA sequence induces much lower TBP binding and transcription. The x-ray crystal structures have previously shown that the duplex DNA in DNA-TBP complexes are highly bent. We performed and analyzed MD simulations for these four DNAs, whose experimental structures are not available, in order to address the issue of whether inherent DNA structure and flexibility play a role in establishing these observed preferences. A comparison of the experimental and simulated results demonstrated that DNA duplex sequence-dependent curvature and flexibility play a significant role in TBP recognition, binding, and transcriptional activation. © 1998 John Wiley & Sons, Inc. Biopoly 46: 403-415, 1998
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    The solution structure of small peptides: An IR CD study of aqueous solutions of (L-Ala)n [n = 3, 4, 5, 6] at different temperatures and ionic strengths (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 455-463 
    Details
    ISSN: 0006-3525
    Keywords: vibrational CD ; solution conformation ; alanine oligopeptides ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solution conformation of a number of small, linear alanine oligomers was investigated via ir (or vibrational) CD (VCD). We find that these oligopeptides assume distinct solution conformations that depend primarily on chain lengths, and to a lesser degree on temperature, ionic strength, and pH. As expected, the longer chain oligomers exhibit more distinct VCD features and, presumably, more stable solution structures. At the level of the hexamer, however, aggregation of the peptide occurs. The fast time scale of VCD allows solution structures to be detected that may not be observable using slower techniques such as various forms of nmr spectroscopy. The VCD results reported here confirm that it is generally possible to obtain conformational information for small, linear homo- and heterooligopeptides via VCD spectroscopy. In this respect, the sensitivity of VCD is similar to that of electronic CD. Furthermore, the temperature dependence of the VCD results indicate that at elevated temperatures, the increasing number of conformational states results in a loss of discernible conformers, and consequently, a broadening and weakening of the VCD features. © 1998 John Wiley & Sons, Inc. Biopoly 46: 455-463, 1998
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    Miniaturized hemoproteins (1998)
    New York : Wiley-Blackwell
    Biopolymers 47 (1998), S. 5-22 
    Details
    ISSN: 0006-3525
    Keywords: hemoproteins ; model systems ; miniaturized proteins ; mimochromes ; helix structures ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The present paper highlights and reviews current research in the field of hemoprotein models. Hemoproteins have been extensively studied in order to understand structure-function relationships, and to design new molecules with desired functions. A wide number of synthetic analogues have been developed, using quite different approaches. They differ in molecular structures, ranging from simple meso-substituted tetraaryl-metalloporphyrins and peptide-porphyrin conjugates.In this paper we summarize the state of the art on peptide based hemoprotein models. We also report here the approach used by us to develop a new class of molecules, named mimochromes. They can be regarded as miniaturized hemoproteins, because mimochromes are low molecular weight compounds with some structural and functional properties common to those of the parent high molecular weight protein. The basic structure of mimochromes is a deuteroporphyrin ring covalently linked to two helical peptide chains. Two molecules of this series have been fully characterized. All the information derived from their structural analysis has been applied to the design of new analogues with additional functions. © 1998 John Wiley & Sons, Inc. Biopoly 47: 5-22, 1998
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    An electrostatic model for the dielectric effects, the adsorption of multivalent ions, and the bending of B-DNA (1998)
    New York : Wiley-Blackwell
    Biopolymers 46 (1998), S. 503-516 
    Details
    ISSN: 0006-3525
    Keywords: discrete charge model of DNA ; dielectric cylinder in water ; effective dielectric constant ; salt effects ; Debye shielding factor ; potential variations in DNA surface ; Boltzmann averaged bending angles ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have studied electrostatic properties of DNA with a discrete charge model consisting of a cylindrical dielectric core with a radius of 8 Å and a dielectric constant Di = 4, surrounded by two helical strings of phosphate point charges at 10 Å from the axis, immersed in an aqueous medium with dielectric constant Dw = 78.54. Eliminating the dielectric core makes potentials in the phosphate surface less negative by about 0.5 kT/e. Salt effects are evaluated for the model without a dielectric core, using the shielded Coulomb potential. Smearing the phosphate charges increases their potential by about 2.5 kT/e, due mostly to the self-potential of the smeared charge. Potentials in the center of the minor and major grooves vary less than 0.02 kT/e along their helical path. The potential in the center of the minor groove is from 1.0 to 1.7 kT/e, more negative than in the center of the major groove, depending on dielectric core and salt concentration. So multivalent cations and also larger cationic ligands, such as some antibiotics, are likely to adsorb in the minor groove, in agreement with earlier computations by A. and B. Pullman. Dielectric effects on the surface potential and the local potential variations are found to be relatively small. Bending of DNA is studied by placing a multivalent cation, MZ+, in the center of the minor or major groove, curving DNA around it for a certain length, and calculating the free energy difference between the bent and the straight configuration. Boltzmann averaged bending angles, 〈β〉, are found to be maximal in 0.03M monovalent salt, for a length of about 50 or 25 Å of curved DNA when an MZ+ ion is adsorbed in the minor or the major groove, respectively. When the dielectric constant of water is used throughout the calculation, we find maximal bends of 〈β〉 = 11° for M2+ and 〈β〉 = 16° for M3+ in the minor groove, 〈β〉 = 13° for M3+ in the major groove. The absence of bends in DNA adsorbed to mica in the presence of Mg salts supports the role of Mg2+ in “ion bridging” between DNA and mica. The treatment of the effective dielectric constant between two points outside a dielectric cylinder in water is appended. © 1998 John Wiley & Sons, Inc. Biopoly 46: 503-516, 1998
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    Protein design: On the threshold of functional properties (1998)
    New York : Wiley-Blackwell
    Biopolymers 47 (1998), S. 63-73 
    Details
    ISSN: 0006-3525
    Keywords: protein de novo design ; novel macromolecules ; topological templates ; Template Assembled Synthetic Proteins (TASP) ; biosensors ; protein folding ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ultimate goal in protein de novo design is the creation of novel macromolecules with tailor-made receptor, sensory, and catalytic functions. Despite considerable progress in understanding basic rules of secondary structure formation and protein stability, the well-known protein folding problem is still far from being solved and, in general, only a limited number of designed proteins are folded uniquely. In this article the state-of-the-art in protein design is demonstrated on some selected examples, indicating that the construction of protein-like macromolecules mimicking some essential features of natural proteins seems to be within reach. Thus, protein design and mimicry has become an interdisciplinary challenge with most intriguing perspectives. © 1998 John Wiley & Sons, Inc. Biopoly 47: 63-73, 1998
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    Mode of action of linear amphipathic α-helical antimicrobial peptides (1998)
    New York : Wiley-Blackwell
    Biopolymers 47 (1998), S. 451-463 
    Details
    ISSN: 0006-3525
    Keywords: bacteria ; antibiotics ; linear amphipathic α-helical antimicrobial peptides ; peptide-lipid interactions ; membrane permeation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The increasing resistance of bacteria to conventional antibiotics resulted in a strong effort to develop antimicrobial compounds with new mechanisms of action. Antimicrobial peptides seem to be a promising solution to this problem. Many studies aimed at understanding their mode of action were described in the past few years. The most studied group includes the linear, mostly α-helical peptides. Although the exact mechanism by which they kill bacteria is not clearly understood, it has been shown that peptide-lipid interactions leading to membrane permeation play a role in their activity. Membrane permeation by amphipathic α-helical peptides can proceed via either one of the two mechanisms: (a) transmembrane pore formation via a “barrel-stave” mechanism; and (b) membrane destruction/solubilization via a “carpet-like” mechanism. The purpose of this review is to summarize recent studies aimed at understanding the mode of action of linear α-helical antimicrobial peptides. This review, which is focused on magainins, cecropins, and dermaseptins as representatives of the amphipathic α-helical antimicrobial peptides, supports the carpet-like rather the barrel-stave mechanism. That these peptides vary with regard to their length, amino acid composition, and net positive charge, but act via a common mechanism, may imply that other linear antimicrobial peptides that share the same properties also share the same mechanism. © 1999 John Wiley & Sons, Inc. Biopoly 47: 451-463, 1998
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    Modified oligoribonucleotides as site-specific probes of RNA structure and function (1998)
    New York : Wiley-Blackwell
    Biopolymers 48 (1998), S. 39-55 
    Details
    ISSN: 0006-3525
    Keywords: modified nucleotides ; site-specific probes ; RNA structure ; RNA function ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Modified nucleotides can be incorporated site specifically into RNA by the use of total chemical synthesis as well as by use of a variety of recombinant RNA techniques. The range of nucleotide analogues includes modifications to base, sugar, and phosphate for structure-function analysis and for cross-linking studies as well as to answer specific mechanistic questions in RNA catalysis. We describe how RNA containing site-specific modifications are prepared, concentrating in particular on routes involving chemically synthesized oligoribonucleotides, and give examples of their application in studies of the hammerhead and hairpin ribozymes. © 1998 John Wiley & Sons, Inc. Biopoly 48: 39-55, 1998
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    Dressed for success: Realizing the catalytic potential of RNA (1998)
    New York : Wiley-Blackwell
    Biopolymers 48 (1998), S. 29-37 
    Details
    ISSN: 0006-3525
    Keywords: amide synthase ; catalytic antibodies ; Diels-Alderase ; ideal catalyst platform ; in vitro selection ; Lewis acid ; modified uridines ; modified RNA ; ribozymes ; SELEX ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this manuscript the catalytic ability of RNA is examined and compared to other biopolymers. Despite having considerably fewer catalytically enabling properties when compared to proteins, the power of in vitro selection has allowed for RNA and DNA catalysts to be isolated. RNA catalysis has been expanded by incorporating modified bases to enrich the structural and functional diversity of RNA. Successful examples of new RNA chemistry using base modifications include carbon-carbon bond forming reactions and creation of highly specific active sites that are capable of recognizing small organic molecules without the need for nucleic acid templating or intercalation. In fact, the scope of functional modifications available for use in the RNA platform may eventually surpass those that are found in proteins and there are already hints that well chosen modifications allow nucleic acid catalysts to take advantage of mechanisms not available to selected protein catalysts for similar reactions. The chemical versatility of RNA is just emerging and future research directions will likely entail more creative methods for functional modification that will lead to new catalysts. © 1998 John Wiley & Sons, Inc. Biopoly 48: 29-37, 1998
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  • 91
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    Electronic Resource
    New developments in structure determination of pseudoknots (1998)
    New York : Wiley-Blackwell
    Biopolymers 48 (1998), S. 137-153 
    Details
    ISSN: 0006-3525
    Keywords: RNA ; pseudoknot ; Turnip Yellow Mosaic Virus ; Mouse Mammary Tumor Virus ; Beet Western Yellows Virus ; Simian Retrovirus type-1 ; Hepatitis Delta Virus ; translational frameshifting ; ribozyme ; nmr ; x-ray diffraction ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recently, several high-resolution structures of RNA pseudoknots have become available. Here we review the progress in this area. The majority of the structures obtained belong to the classical or H-type pseudoknot family. The most complicated pseudoknot structure elucidated so far is the Hepatitis Delta Virus ribozyme, which forms a nested double pseudoknot. In particular, the structure-function relationships of the H-type pseudoknots involved in translational frameshifting have received much attention. All molecules considered show interesting new structural motifs. © 1999 John Wiley & Sons, Inc. Biopoly 48: 137-153, 1998
    Additional Material: 13 Ill.
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  • 92
    Electronic Resource
    Electronic Resource
    Improved protein refolding using hollow-fibre membrane dialysis (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 57 (1998), S. 590-599 
    Details
    ISSN: 0006-3592
    Keywords: protein refolding ; hollow-fibre membrane ; dialysis ; carbonic anhydrase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: We have used a cellulose acetate, hollow-fibre (HF) ultrafiltration membrane to refold bovine carbonic anhydrase, loaded into the lumen space, by removing the denaturant through controlled dialysis via the shell side space. When challenged with GdnHCl-denatured carbonic anhydrase, 70% of the loaded protein reptated through the membrane into the circulating dialysis buffer. Reptation occurred because the protein, in its fully unfolded configuration, was able to pass through the pores. The loss of carbonic anhydrase through the membrane was controlled by the dialysis conditions. Dialysis against 0.05 M Tris-HCl for 30 min reduced the denaturant around the protein to a concentration that allowed the return of secondary structure, increasing the hydrodynamic radius, thus preventing protein transmission. Under these conditions a maximum of 42% of carbonic anhydrase was recovered (from a starting concentration of 5 mg/mL) with 94% activity. This is an improvement over refolding carbonic anhydrase by simple batch dilution, which gave a maximum reactivation of 85% with 35% soluble protein yield. The batch refolding of carbonic anhydrase is very sensitive to temperature; however, during HF refolding between 0 and 25°C the temperature sensitivity was considerably reduced. In order to reduce the convection forces that give rise to aggregation and promote refolding the dialyzate was slowly heated from 4 to 25°C. This slow, temperature-controlled refolding gave an improved soluble protein recovery of 55% with a reactivation yield of 90%. The effect of a number of additives on the refolding system performance were tested: the presence of PEG improved both the protein recovery and the recovered activity from the membrane, while the detergents Tween 20 and IGEPAL CA-630 increased only the refolding yield. ©1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 590-599, 1998.
    Additional Material: 8 Ill.
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  • 93
    Electronic Resource
    Electronic Resource
    Metabolic engineering (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 119-120 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: No abstract.
    Type of Medium: Electronic Resource
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  • 94
    Electronic Resource
    Electronic Resource
    Activity losses among T4 lysozyme variants after adsorption to colloidal silica (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 658-662 
    Details
    ISSN: 0006-3592
    Keywords: T4 lysozyme ; silica nanoparticles ; synthetic enzyme variants ; surface-induced conformational change ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Maintaining a specific molecular conformation is essential for the proper functioning of an enzyme. A substantial loss of catalytic activity can occur from the displacement caused by even a single amino acid substitution. Activity may also be lost as an enzyme undergoes a conformational change during adsorption. In this study, we investigated the effect of thermostability on the activities of three T4 lysozyme variants after adsorption to 9 nm colloidal silica particles. Less-stable T4 lysozyme variants lost more activity after adsorption than did more stable variants, apparently because they experienced more extensive structural alteration. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58: 658-662, 1998.
    Additional Material: 4 Ill.
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  • 95
    Electronic Resource
    Electronic Resource
    On-line metabolic pathway analysis based on metabolic signal flow diagram (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 139-148 
    Details
    ISSN: 0006-3592
    Keywords: metabolic engineering ; pathway analysis ; metabolic and energetic model ; physiological state ; Saccharomyces cerevisiae ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In this work, an integrated modeling approach based on a metabolic signal flow diagram and cellular energetics was used to model the metabolic pathway analysis for the cultivation of yeast on glucose. This approach enables us to make a clear analysis of the flow direction of the carbon fluxes in the metabolic pathways as well as of the degree of activation of a particular pathway for the synthesis of biomaterials for cell growth. The analyses demonstrate that the main metabolic pathways of Saccharomyces cerevisiae change significantly during batch culture. Carbon flow direction is toward glycolysis to satisfy the increase of requirement for precursors and energy. The enzymatic activation of TCA cycle seems to always be at normal level, which may result in the overflow of ethanol due to its limited capacity. The advantage of this approach is that it adopts both virtues of the metabolic signal flow diagram and the simple network analysis method, focusing on the investigation of the flow directions of carbon fluxes and the degree of activation of a particular pathway or reaction loop. All of the variables used in the model equations were determined on-line; the information obtained from the calculated metabolic coefficients may result in a better understanding of cell physiology and help to evaluate the state of the cell culture process. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:139-148, 1998.
    Additional Material: 9 Ill.
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  • 96
    Electronic Resource
    Electronic Resource
    Experimental determination of group flux control coefficients in metabolic networks (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 149-153 
    Details
    ISSN: 0006-3592
    Keywords: Metabolic Control Analysis ; flux control coefficients ; top down MCA ; metabolic engineering ; Corynebacterium glutamicum ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Grouping of reactions around key metabolite branch points can facilitate the study of metabolic control of complex metabolic networks. This top-down Metabolic Control Analysis is exemplified through the introduction of group (flux, as well as concentration) control coefficients whose magnitudes provide a measure of the relative impact of each reaction group on the overall network flux, as well as on the overall network stability, following enzymatic amplification. In this article, we demonstrate the application of previously developed theory to the determination of group flux control coefficients. Experimental data for the changes in metabolic fluxes obtained in response to the introduction of six different environmental perturbations are used to determine the group flux control coefficients for three reaction groups formed around the phosphoenolpyruvate/pyruvate branch point. The consistency of the obtained group flux control coefficient estimates is systematically analyzed to ensure that all necessary conditions are satisfied. The magnitudes of the determined control coefficients suggest that the control of lysine production flux in Corynebacterium glutamicum cells at a growth base state resides within the lysine biosynthetic pathway that begins with the PEP/PYR carboxylation anaplorotic pathway. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:149-153, 1998.
    Additional Material: 3 Ill.
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  • 97
    Electronic Resource
    Electronic Resource
    Application of mathematical tools for metabolic design of microbial ethanol production (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 154-161 
    Details
    ISSN: 0006-3592
    Keywords: central carbon pathways ; metabolic optimization ; ethanol production ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Many attempts to engineer cellular metabolism have failed due to the complexity of cellular functions. Mathematical and computational methods are needed that can organize the available experimental information, and provide insight and guidance for successful metabolic engineering. Two such methods are reviewed here. Both methods employ a (log)linear kinetic model of metabolism that is constructed based on enzyme kinetics characteristics. The first method allows the description of the dynamic responses of metabolic systems subject to spatiotemporal variations in their parameters. The second method considers the product-oriented, constrained optimization of metabolic reaction networks using mixed-integer linear programming methods. The optimization framework is used in order to identify the combinations of the metabolic characteristics of the glycolytic enzymes from yeast and bacteria that will maximize ethanol production. The methods are also applied to the design of microbial ethanol production metabolism. The results of the calculations are in qualitative agreement with experimental data presented here. Experiments and calculations suggest that, in resting Escherichia coli cells, ethanol production and glucose uptake rates can be increased by 30% and 20%, respectively, by overexpression of a deregulated pyruvate kinase, while increase in phosphofructokinase expression levels has no effect on ethanol production and glucose uptake rates. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:154-161, 1998.
    Additional Material: 7 Ill.
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  • 98
    Electronic Resource
    Electronic Resource
    Multiple mechanisms controlling carbon metabolism in bacteria (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 170-174 
    Details
    ISSN: 0006-3592
    Keywords: catabolite repression ; phosphotransferase system ; inducer exclusion ; inducer expulsion ; protein kinase ; transcriptional regulation ; transport regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Catabolite repression is a universal phenomenon, found in virtually all living organisms. These organisms range from the simplest bacteria to higher fungi, plants, and animals. A mechanism involving cyclic AMP and its receptor protein (CRP) in Escherichia coli was established years ago, and this mechanism has been assumed by many to serve as the prototype for catabolite repression in all organisms. However, recent studies have shown that this mechanism is restricted to enteric bacteria and their close relatives. Cyclic AMP-independent mechanisms of catabolite repression occur in other bacteria, yeast, plants, and even E. coli. In fact, single-celled organisms such as E. coli, Bacillus subtilis, and Saccharomyces cerevisiae exhibit multiple mechanisms of catabolite repression, and most of these are cyclic AMP-independent. The mechanistic features of the best of such characterized processes are briefly reviewed, and references are provided that will allow the reader to delve more deeply into these subjects. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:170-174, 1998.
    Additional Material: 2 Ill.
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  • 99
    Electronic Resource
    Electronic Resource
    How will bioinformatics influence metabolic engineering? (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 162-169 
    Details
    ISSN: 0006-3592
    Keywords: bioinformatics ; metabolic engineering ; genetic engineering ; mathematical analysis ; stoichiometry ; enzyme kinetics ; modal analysis ; genetic circuits ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Ten microbial genomes have been fully sequenced to date, and the sequencing of many more genomes is expected to be completed before the end of the century. The assignment of function to open reading frames (ORFs) is progressing, and for some genomes over 70% of functional assignments have been made. The majority of the assigned ORFs relate to metabolic functions. Thus, the complete genetic and biochemical functions of a number of microbial cells may be soon available. From a metabolic engineering standpoint, these developments open a new realm of possibilities. Metabolic analysis and engineering strategies can now be built on a sound genomic basis. An important question that now arises; how should these tasks be approached? Flux-balance analysis (FBA) has the potential to play an important role. It is based on the fundamental principle of mass conservation. It requires only the stoichiometric matrix, the metabolic demands, and some strain specific parameters. Importantly, no enzymatic kinetic data is required. In this article, we show how the genomically defined microbial metabolic genotypes can be analyzed by FBA. Fundamental concepts of metabolic genotype, metabolic phenotype, metabolic redundancy and robustness are defined and examples of their use given. We discuss the advantage of this approach, and how FBA is expected to find uses in the near future. FBA is likely to become an important analysis tool for genomically based approaches to metabolic engineering, strain design, and development. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:162-169, 1998.
    Additional Material: 4 Ill.
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  • 100
    Electronic Resource
    Electronic Resource
    Artificial promoters for metabolic optimization (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 191-195 
    Details
    ISSN: 0006-3592
    Keywords: control analysis ; Lactococcus lactis ; gene expression ; flux ; oligonucleotide ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In this article, we review some of the expression systems that are available for Metabolic Control Analysis and Metabolic Engineering, and examine their advantages and disadvantages in different contexts. In a recent approach, artificial promoters for modulating gene expression in micro-organisms were constructed using synthetic degenerated oligonucleotides. From this work, a promoter library was obtained for Lactococcus lactis, containing numerous individual promoters and covering a wide range of promoter activities. Importantly, the range of promoter activities was covered in small steps of activity change. Promoter libraries generated by this approach allow for optimization of gene expression and for experimental control analysis in a wide range of biological systems by choosing from the promoter library promoters giving, e.g., 25%, 50%, 200%, and 400% of the normal expression level of the gene in question. If the relevant variable (e.g., the flux or yield) is then measured with each of these constructs, then one can calculate the control coefficient and determine the optimal expression level. One advantage of the method is that the construct which is found to have the optimal expression level is then, in principle, ready for use in the industrial fermentation process; another advantage is that the system can be used to optimize the expression of different enzymes within the same cell. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:191-195, 1998.
    Additional Material: 3 Ill.
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