Total synthesis of 2',3',4',5',5' '-(2)h(5)-ribonucleosides: the key building blocks for NMR structure elucidation of large RNA

The diastereospecific chemical syntheses of uridine-2',3',4',5',5' '-(2)H(5) (21a), adenosine-2',3',4',5',5' '-(2)H(5) (21b), cytidine-2',3',4',5',5' '-(2)H(5)(2)H(5) (21c), and guanosine-2',3',4',5',5' '-(2)H(5) (21d) (>97 atom % (2)H at C2', C3', C4', and C5'/C5' ') have been achieved for their use in the solution NMR structure determination of oligo-RNA by the Uppsala "NMR-window" concept (refs 4a-c, 5a, 6), in which a small (1)H segment is NMR-visible, while the rest is made NMR-invisible by incorporation of the deuterated blocks 21a-d. The deuterated ribonucleosides 21a-d have been prepared by the condensation of appropriately protected aglycone with 1-O-acetyl-2,3,5-tri-O-(4-toluoyl)-alpha/beta-D-ribofuranose-2,3,4,5,5'-(2)H(5) (19), which has been obtained via diastereospecific deuterium incorporation at the C2 center of appropriate D-ribose-(2)H(4) derivatives either through an oxidation-reduction-inversion sequence or a one-step deuterium-proton exchange in high overall yield (44% and 24%, respectively).     

Low-lying electronic states and Cl-loss photodissociation of the C2H3Cl+ ion studied using multiconfiguration second-order perturbation theory

We studied the 1(2)A' '(X2A' '), 1(2)A' (A2A'), 2(2)A' ' (B2A' '), and 2(2)A' (C2A') states of the C2H3Cl+ ion using the complete active space self-consistent field (CASSCF) and multiconfiguration second-order perturbation theory (CASPT2) methods. For the four ionic states, we calculated the equilibrium geometries, adiabatic (T0) and vertical (Tv) excitation energies, and relative energies (Tv') at the geometry of the molecule at the CASPT2 level and the Cl-loss dissociation potential energy curves (PECs) at the CASPT2//CASSCF level. The computed oscillator strength f value for the X2A' ' <-- A2A' transition is very small, which is in line with the experimental fact that the A state has a long lifetime. The CASPT2 geometry and T0 value for the A2A' state are in good agreement with experiment. The CASPT2 Tv' values for the A2A', B2A' ', and C2A' states are in good agreement with experiment. The Cl-loss PEC calculations predict that the X2A' ', A2A', and C2A' states correlate to C2H3+ (XA1) and the BA' ' state to C2H3+ (1A' ') (the B2A' ' and C2A' PECs cross at R(C-Cl) approximately 2.24 A). Our calculations indicate that at 357 nm the X2A' ' state can undergo a transition to B2A' ' followed by a predissociation of B2A' ' by the repulsive C2A' state (via the B/C crossing), leading to C2H3+ (X1A1), and therefore confirm the experimentally proposed pathway for the photodissociation of X2A' ' at 357 nm. Our CASPT2 D0 calculations support the experimental fact that the X state does not undergo dissociation in the visible spectral region and imply that a direct dissociation of the A state to C2H3+ (X1A1) is energetically feasible.     

Bimetallic effects in homopolymerization of styrene and copolymerization of ethylene and styrenic comonomers: scope, kinetics, and mechanism

This contribution describes the homopolymerization of styrene and the copolymerization of ethylene and styrenic comonomers mediated by the single-site bimetallic "constrained geometry catalysts" (CGCs), (mu-CH2CH2-3,3'){(eta(5)-indenyl)[1-Me2Si(tBuN)](TiMe2)}2 [EBICGC(TiMe2)2; Ti2], (mu-CH2CH2-3,3'){(eta(5)-indenyl)[1-Me2Si(tBuN)](ZrMe2)}2 [EBICGC(ZrMe2)2; Zr2], (mu-CH2-3,3'){(eta(5)-indenyl)[1-Me2Si(tBuN)](TiMe2)}2 [MBICGC(TiMe2)2; C1-Ti2], and (mu-CH2-3,3'){(eta(5)-indenyl)[1-Me2Si(tBuN)](ZrMe2)}2 [MBICGC(ZrMe2)2; C1-Zr2], in combination with the borate activator/cocatalyst Ph3C+ B(C6F5)4- (B1). Under identical styrene homopolymerization conditions, C1-Ti2 + B1 and Ti2 + B1 exhibit approximately 65 and approximately 35 times greater polymerization activities, respectively, than does monometallic [1-Me2Si(3-ethylindenyl)(tBuN)]TiMe2 (Ti1) + B1. C1-Zr2 + B1 and Zr2 + B1 exhibit approximately 8 and approximately 4 times greater polymerization activities, respectively, than does the monometallic control [1-Me2Si(3-ethylindenyl)(tBuN)]ZrMe2 (Zr1) + B1. NMR analyses show that the bimetallic catalysts suppress the regiochemical insertion selectivity exhibited by the monometallic analogues. In ethylene copolymerization, Ti2 + B1 enchains 15.4% more styrene (B), 28.9% more 4-methylstyrene (C), 45.4% more 4-fluorostyrene (D), 41.2% more 4-chlorostyrene (E), and 31.0% more 4-bromostyrene (F) than does Ti1 + B1. This observed bimetallic chemoselectivity effect follows the same general trend as the pi-electron density on the styrenic ipso carbon (D > E > F > C > B). Kinetic studies reveal that both Ti2 + B1 and Ti1 + B1-mediated ethylene-styrene copolymerizations follow second-order Markovian statistics and tend to be alternating. Moreover, calculated reactivity ratios indicate that Ti2 + B1 favors styrene insertion more than does Ti1 + B1. All the organozirconium complexes (C1-Zr2, Zr2, and Zr1) are found to be incompetent for ethylene-styrene copolymerization, yielding only mixtures of polyethylene and polystyrene. Model compound (mu-CH2CH2-3,3'){(eta(5)-indenyl)[1-Me2Si(tBuN)][Ti(CH2Ph)2]}2 {EBICGC[Ti(CH2Ph)2]2; Ti2(CH2Ph)4} was designed, synthesized, and structurally characterized. In situ activation studies with cocatalyst B(C6F5)3 suggest an eta(1)-coordination mode for the benzyl groups, thus supporting the proposed polymerization mechanism. For ethylene-styrene copolymerization, polar solvents are found to increase copolymerization activities and coproduce atactic polystyrene impurities in addition to ethylene-co-styrene, without diminishing the comonomer incorporation selectivity. Both homopolymerization and copolymerization results argue that substantial cooperative effects between catalytic sites are operative.     

Bidirectional synthesis of the central amino acid of chloptosin

[reaction: see text] An efficient total synthesis of (2S,2'S,3aR,3'aR,8aR,8'aR)-6,6'-dichloro-3a,3'a-dihydroxy-1,1',2,2',3,3a,3',3'a,8,8a,8',8'a-dodecahydro-5,5'-bipyrrolo[2,3-b]indole-2,2'-dicarboxylic acid, the central amino acid component of chloptosin (1), is described. Starting from m-chloronitrobenzene, this C(2)-symmetrical amino acid was synthesized by using a 14-step route, in which a Zinin benzidine rearrangement, intramolecular Heck reaction, and selenocyclization and oxidative deselenation served as key steps. The absolute stereochemistry of the target was confirmed by X-ray single-crystal studies on a key intermediate (17).     

Hydrogen abstraction from deoxyribose by a neighbouring uracil-5-yl radical

Hydrogen abstraction from the C1' and C2' positions of deoxyadenosine by a neighbouring uracil-5-yl radical in the 5'-AU*-3' DNA sequence is explored using DFT. This hydrogen abstraction is the first step in a sequence leading to single or double strand break in DNA. The uracil-5-yl radical can be the result of photolysis or low-energy electron (LEE) attachment. If the radical is produced by photolysis the neighbouring adenine will become a cation radical and if it is produced by LEE the adenine will remain neutral. The hydrogen abstraction reactions for both cases were investigated. It is concluded that it is possible for the uracil-5-yl to abstract hydrogen from C1' and C2'. When adenine is neutral there is a preference for the C1' site and when the adenine is a radical cation the C2' site is the preferred. If adenine is positively charged, the rate-limiting step when abstracting hydrogen from C1' is the formation of an intermediate crosslink between uracil and adenine. This crosslink might be avoided in dsDNA, making C1' the preferred site for abstraction.     

Observation of vibronically excited thioformaldehyde at 62,000-72,000cm(-1) by 1+1'+1' resonance enhanced multiphoton ionization spectroscopy

Vibronically excited thioformaldehyde (H(2)CS) has been studied by two-color 1+1'+1' resonance enhanced multiphoton ionization (REMPI) spectroscopy, in which the C (1)B(2)0(0)(0) state of H(2)CS was selected as an intermediate state for the resonant excitation to high-lying electronic states at 62,000-72,000cm(-1). In light of the distinctive selection rules for the 1+1'+1' REMPI and one-photon direct absorption transitions excited from the C (1)B(2) and X (1)A(1) states of H(2)CS, respectively, we have been able to identify 1 valence state (npi, pi*(2)), and 14 Rydberg states (n, 5s), (pi, 4s), (n, 3d(xz)), (n, 3d(yz)), (n, 5p(z)), (n, 5p(x)), (n, 5p(y)), n,4d(z)2), (n, 4d(xz)), (n, 4d(yz)), (n, 6s), (pi, 4p(y)), (n, 6p(z)), and (n, 6p(y)), in this study.     

Stereocontrolled syntheses of carbocyclic C-nucleosides and related compounds.

Carbocyclic 9-deazapurine nucleosides (1-4), a spiranic pyrimidone carbocyclic compound (5), and an unusual carbocyclic isonucleoside (6) were prepared as enantiomerically pure compounds via the key intermediates 10 and 21 from 1,4-gamma-ribonolactone. The key intermediate 10 was prepared by stereoselective reduction with Bu3SnH and then converted to carbocyclic C-ribonucleosides 1, 3, and 4. 2',3'-Didehydro-2',3'-dideoxycarbocyclic 9-deazainosine (2) was prepared from a 2',3'-dimesylate 17 by treatment with Li2Te followed by an acidic deprotection. The key bicyclic intermediate 21 was prepared from a diol 20 by an intramolecular cyclization using CHI3-Ph3P-imidazole and converted to the spiranic compound 5 and an olefinic nucleoside 6 by the construction of the heterocyclic moiety followed by deprotection.     

Microbial metabolism. Part 12. Isolation, characterization and bioactivity evaluation of eighteen microbial metabolites of 4'-hydroxyflavanone

Fermentation of 4'-hydroxyflavanone (1) with fungal cultures, Beauveria bassiana (ATCC 13144 and ATCC 7159) yielded 6,3',4'-trihydroxyflavanone (2), 3',4'-dihydroxyflavanone 6-O-β-D-4-methoxyglucopyranoside (3), 4'-hydroxyflavanone 3'-sulfate (4), 6,4'-dihydroxyflavanone 3'-sulfate (5) and 4'-hydroxyflavanone 6-O-β-D-4-methoxyglucopyranoside (7). B. bassiana (ATCC 13144) and B. bassiana (ATCC 7159) in addition, gave one more metabolite each, namely, flavanone 4'-O-β-D-4-methoxyglucopyranoside (6) and 6,4'-dihydroxyflavanone (8) respectively. Cunninghamella echinulata (ATCC 9244) transformed 1 to 6,4'-dihydroxyflavanone (8), flavanone-4'-O-β-D-glucopyranoside (9), 3'-hydroxyflavanone 4'-sulfate (10), 3',4'-dihydroxyflavanone (11) and 4'-hydroxyflavanone-3'-O-β-D-glucopyranoside (12). Mucor ramannianus (ATCC 9628) metabolized 1 to 2,4-trans-4'-hydroxyflavan-4-ol (13), 2,4-cis-4'-hydroxyflavan-4-ol (14), 2,4-trans-3',4'-dihydroxyflavan-4-ol (15), 2,4-cis-3',4'-dihydroxyflavan-4-ol (16), 2,4-trans-3'-hydroxy-4'-methoxyflavan-4-ol (17), flavanone 4'-O-α-D-6-deoxyallopyranoside (18) and 2,4-cis-4-hydroxyflavanone 4'-O-α-D-6-deoxyallopyranoside (19). Metabolites 13 and 14 were also produced by Ramichloridium anceps (ATCC 15672). The former was also produced by C. echinulata. Structures of the metabolic products were elucidated by means of spectroscopic data. None of the metabolites tested showed antibacterial, antifungal and antiprotozoal activities against selected organisms.     

Theoretical study on the hydrolysis mechanism of N,N-dimethyl-N'-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine: water-assisted mechanism and cluster-continuum model

The hydrolysis reaction of N,N-dimethyl-N'-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine (DMPFA), a model compound of the antivirus drug amidine-3TC (3TC = 2', 3'-dideoxy-3'-thiacytidine), is investigated by the hybrid density functional theory B3LYP/6-31+G (d,p) method. The hydrolysis reaction of the title compound is predicted to undergo via two pathways, each of which is a stepwise process. Path A is the addition of H2O to the C=N double bond in the amidine group to form a tetrahedral structure in its first step, and then the transfer of the H atom of hydroxyl leads to the corresponding products via four possible channels. Path B simultaneously involves the nucleophilic attack of H2O to the C atom of the C=N bond and the proton transfer to the N atom of amino group leading to the cleavage of the C-N single bond in the amidine group. The results indicate that path A is more favorable than path B in the gas phase. Moreover, to simulate the title reaction in aqueous solution, water-assisted mechanism and the cluster-continuum model, based on the SCRF/CPCM model, are taken into account in our work. The results indicate that it is rational for two water molecules served as a bridge to assist in the first step of path A and that cytosine rather than the cytosine-substituted formamide should be released from the tetrahedral intermediate via s six-membered cycle transition state (channel 2). Our calculations exhibit that the process toward the tetrahedral intermediate is the rate-determining step both in the gas phase and in aqueous solution.     

Taiwankadsurins A, B, and C, three new C19 homolignans from Kadsura philippinensis

[structures: see text] Three novel C19 homolignans, designated taiwankadsurins A (1), B (2), and C (3), were isolated from the aerial parts of Taiwanese medicinal plant Kadsura philippinensis. The structures of 1-3, which have a 3,4-{1'-[(Z)-2'-methoxy-2'-oxo-ethylidene]}-pentano(2,3-dihydro-benzo[b]furano)-3-(2'-methoxycarbonyl-2'-hydroxy-2',3'-epoxide) skeleton, were determined by spectroscopic analyses, especially 2D NMR techniques (HMBC and NOESY). Compound 2 exhibited mild cytotoxicity against human KB and Hela tumor cells.     

Acid-promoted reaction of the stilbene antioxidant resveratrol with nitrite ions: mild phenolic oxidation at the 4'-hydroxystiryl sector triggering nitration, dimerization, and aldehyde-forming routes

In 0.1 M phosphate buffer, pH 3.0, and at 37 degrees C, resveratrol ((E)-3,4',5-trihydroxystilbene, 1a), an antioxidant and cancer chemopreventive phytoalexin, reacted smoothly at 25 microM or 1 mM concentration with excess nitrite ions (NO2(-)) to give a complex pattern of products, including two novel regioisomeric alpha-nitro (3a) and 3'-nitro (4) derivatives along with some (E)-3,4',5-trihydroxy-2,3'-dinitrostilbene (5), four oxidative breakdown products, 4-hydroxybenzaldehyde, 4-hydroxy-3-nitrobenzaldehyde, 3,5-dihydroxyphenylnitromethane, and 3,5-dihydroxybenzaldehyde, two dimers, the resveratrol (E)-dehydrodimer 6 and restrytisol B (7), and the partially cleaved dimer 2. The same products were formed in the absence of oxygen. 1H,15N HMBC and LC/MS analysis of the crude mixture obtained by reaction of 1a with Na (15)NO2 suggested the presence of 3,4',5,beta-tetrahydroxy-alpha-nitro-alpha,beta-dihydrostilbene (8) as unstable intermediate which escaped isolation. Under similar conditions, the structurally related catecholic stilbene piceatannol ((E)-3,3',4,5'-tetrahydroxystilbene, 1b) gave, besides (E)-3,3',4,5'-tetrahydroxy-beta-nitrostilbene (3b), 3,4-dihydroxybenzaldehyde and small amounts of 3,5-dihydroxybenzaldehyde. Mechanistic experiments were consistent with the initial generation of the phenoxyl radical of 1a at 4'-OH, which may undergo free radical coupling with NO2 at the alpha- or 3'-position, to give eventually nitrated derivatives and/or oxidative double bond fission products, or self-coupling, to give dimers. The oxygen-independent, NO2(-)-mediated oxidative fission of the double bond under mild, physiologically relevant conditions is unprecedented in stilbene chemistry and is proposed to involve breakdown of hydroxynitro(so) intermediates of the type 8.     

Dynamic stereochemistry of erigeroside by measurement of 1H-1H and 13C-1H coupling constants

Erigeroside was extracted from Satureja khuzistanica Jamzad (Marzeh Khuzistani in Persian, family of lamiaceae), and (1)H, (13)C, (13)C{(1)H}, (1)H-(1)H COSY, HMQC and J-HMBC were obtained to identify this compound and determine a complete set of J-coupling constants ((1)J(C-H), (2)J(C-H), (3)J(C-H) and (3)J(H-H)) values within the exocyclic hydroxymethyl group (CH(2)OH) and anomeric center. In parallel, density functional theory (DFT) using B3LYP functional and split-valance 6-311++G** basis set has been used to optimized the structures and conformers of erigeroside. In all calculations solvent effects were considered using a polarized continuum (overlapping spheres) model (PCM). The dependencies of (1)J, (2)J and (3)J involving (1)H and (13)C on the C(5')-C(6') (omega), C(6')-O(6') (theta) and C(1')-O(1') (phi) torsion angles in erigeroside were computed using DFT method. Complete hyper surfaces for (1)J(C1',H1'), (2)J(C5',H6'R), (2)J(C5',H6'S), (2)J(C6',H5'), (3)J(C4',H6'R), (3)J(C4',H6'S) and (2)J(H6'R-H5'S) as well as (3)J(H5',H6'R) were obtained and used to derive Karplus equations to correlate these couplings to omega, theta and phi. These calculated J-couplings are in agreement with experimental values. These results confirm the reliability of DFT calculated coupling constants in aqueous solution.     

Ketene-ketenimine rearrangements in the gas phase and in polar media. 1,3-Migration intermediates and sequential transition states

[reaction: see text] Calculations of the activation barrier for the 1,3-shifts of substituents X in alpha-imidoylketenes 1 (HN=C(X)-CH=C=O), which interconverts them with alpha-oxoketenimines 3 (HN=C=CH-C(X)=O) via a four-membered cyclic transition state TS2 have been performed at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G* level. Substituents with accessible lone pairs have the lowest activation barriers for the 1,3-shift (halogens, OR, NR2). The corresponding activation barriers for the alpha-oxoketene-alpha-oxoketene rearrangement of 4 via TS5 are generally lower by 1-30 kJ/mol. A polar medium (acetonitrile, epsilon = 36.64) was simulated using the polarizable continuum (PCM) solvation model. The effect of the solvent field is a reduction of the activation barrier by an average of 12 kJ/mol. In the cases of 1,3-shifts of amino and dimethylamino groups, the stabilization of the transition state TS2 in a solvent field is so large that it becomes an intermediate, Int2, flanked by transition states (TS2' and TS2') that are due primarily to internal rotation of the amine functions, and secondarily to the 1,3-bonding interaction. In the case of the alpha-oxoketene-alpha-oxoketene rearrangement of 4, there is a corresponding intermediate Int5 for the 1,3-amine shift already in the gas phase.     

2'-hydroxypyridoxol, a biosynthetic precursor of vitamins B(6) and B(1) in yeast

In separate experiments cultures of the yeast Saccharomyces cerevisiae ATTC 7752 were grown in the presence of [5',5'-2H2]- or of [2',2',5',5'-2H4]-3-hydroxy-2,4,5-tri(hydroxymethyl)pyridine (i.e., 2'-hydroxypyridoxol). The 2H NMR spectra of the samples of pyridoxamine dihydrochloride and of thiamin chloride hydrochloride that were isolated from the two experiments showed the presence of deuterium at the corresponding sites. Entry of deuterium from the specifically 2H-labeled samples of 2'-hydroxypyridoxol into the predicted sites of pyridoxamine and of the pyrimidine unit of thiamin provides the first unequivocal evidence that, in yeast, 2'-hydroxypyridoxol is an intermediate on the route from a C5-sugar into vitamin B6, and adds to the evidence that pyridoxol serves as a precursor of the pyrimidine unit of thiamin, supplying the C5N unit, C-2',2,N-1,C-6,5,5' as an intact unit.     

Low-temperature photosensitized oxidation of a guanosine derivative and formation of an imidazole ring-opened product

An organic-soluble guanosine derivative, 2',3',5'-O-(tert-butyldimethylsilyl)guanosine (1), was prepared and its photosensitized oxidation was carried out in several solvents at various temperatures. Singlet oxygen is the reactive oxidizing agent responsible for this reaction. Neither an endoperoxide nor a dioxetane intermediate was detected by low-temperature NMR even at -78 degrees C. A product (A) with an oxidized imidazole ring was the only major product detected at room temperature; this compound could be isolated by low-temperature column chromatography and was characterized by (1)H and (13)C and mass spectroscopy. CO(2) was the other major product. A small amount of the corresponding 8-oxo-7,8-dihydroguanosine derivative B was detected during the initial stage of the photooxidation and was shown to be intermediate in the formation of two products of extensive degradation, C and D. Reaction of 1 with the singlet oxygen analogues 4-methyl-1,2,4-triazoline-3,5-dione (MTAD) and 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD) gave products consistent with a proposed mechanism involving the rearrangement of an initially formed endoperoxide to give A and B from reaction of 1 with singlet oxygen.     

Structures of novel epipolythiodioxopiperazines, emethallicins B, C, and D, potent inhibitors of histamine release, from Emericella heterothallica

Novel compounds designated emethallicins B (1), C (2), and D (3), along with emethallicin A (4), were isolated from the mycelium of the heterothallic fungus, Emericella heterothallica (mating type a). The structures of emethallicins B (1), C (2), and D (3) were determined on the basis of spectroscopic and chemical investigations. Emethallicins B (1) and C (2) are epitetrathiodioxopiperazines, which have the same basic carbon skeleton as apoaranotin (19) and acetylaranotin (17), respectively, whereas emethallicin D (3) is an epitrithiodioxopiperazine derivative, which has the same carbon skeleton as apoaranotin (19). It is very interesting that a large amount of the disulfide, emethallicin A (4), was isolated from the strain of mating type A and that the corresponding tetrasulfide, emethallicin B (1), and trisulfide, emethallicin D (3), were isolated from the other mating type strain, along with a small amount of the disulfide (4). Emethallicins B (1), C (2), and D (3) have potent inhibitory activity against compound 48/80-induced histamine release from mast cells, like emethallicin A (4).     

Overcrowding motifs in large PAHs. An ab initio study.

Planar and overcrowded LPAHs C(34)H(18) anthra[9,1,2-cde]benzo[rst]penaphene (1), benzo[rst]phenanthro[10,1,2-cde]pentaphene (2), tetrabenzo[a,cd,j,lm]perylene (3), tetrabenzo[a,cd,lm,o]perylene (4), and LPAHs C(38)H(18) anthra[2,1,9,8-klmno]naphtho[3,2,1,8,7-vwxyz]hexaphene (5), dianthra[2,1,9,8-stuva;2',1',9',8'-hijkl]pentacene (6), dibenzo[jk,uv]dinaphtho[2,1,8,7-defg;2',1',8',7'-opqr]perylene (7), diphenanthro[5,4,3-abcd;3',4',5'-lmno]perylene (8), potential products of peri-peri reductive couplings of benzanthrone and of naphthanthrone, respectively, were subjected to an ab initio study with emphasis on overcrowding motifs. The HF and DFT B3LYP methods were employed to calculate energies and geometries of the minima conformations of these LPAHs. The most stable LPAHs in these series were found to be planar C(2)(v)()-1 and C(2)(v)()-5, respectively. Among overcrowded LPAHs, twisted-folded C(2)-3 and C(2)-7 with two cove regions were found to be more stable than their respective isomers twisted-folded C(2)-4 and C(2)-8 with one fjord region each, in contrast to the semiempirical predictions. The energy differences between the most stable planar isomer and the overcrowded isomers were significantly smaller in the C(38)H(18) series, than in the C(34)H(18) series. Overcrowded twisted-folded C(2)-7 with two coves was found to be more stable than planar C(2)(h)()-6 by 2.0 kJ/mol (at B3LYP/6-311G), indicating enhanced role of aromatic stabilization and decreased destabilization due to overcrowding, with increasing the number of aromatic rings. Heats of formation of LPAHs 1-8 were derived from the ab initio total energies (at B3LYP/6-31G). A search of the conformational spaces of 3 and 4 revealed an anti-folded local minimum C(i)()-3 and a syn-folded transition state C(s)()-4, 23.7 and 120.3 kJ/mol higher in energy than the twisted-folded C(2)-3 and C(2)-4, respectively (at B3LYP/6-31G). The cove and fjord torsion angles in the C(38)H(18) series were found to be smaller than in the C(34)H(18) series. The nonbonding distances between carbon atoms at cove and fjord regions of the overcrowded LPAHs were found to be smaller than the sum of the van der Waals radii of two carbon atoms     

Characterization of the lnmKLM genes unveiling key intermediates for β-alkylation in leinamycin biosynthesis

Leinamycin (LNM, 1) biosynthesis is proposed to involve β-alkylation of the polyketide intermediate, catalyzed by LnmKLM. Inactivation of lnmK, lnmL, or lnmM afforded mutant strains that accumulated LNM K-1 (2), K-2 (3), K-3 (4), and isomers LNM K-1' (5), K-2' (6), and K-3' (7) whose polyketide origin was established by feeding experiments with sodium [1-(13)C]acetate. These findings confirm the indispensability of LnmKLM in 1 biosynthesis and suggest that β-alkylation proceeds on the growing polyketide intermediate while bound to the LNM polyketide synthase.     

Formation of a N2-dG:N2-dG carbinolamine DNA cross-link by the trans-4-hydroxynonenal-derived (6S,8R,11S) 1,N2-dG adduct

Michael addition of trans-4-hydroxynonenal (HNE) to deoxyguanosine yields diastereomeric 1,N(2)-dG adducts in DNA. When placed opposite dC in the 5'-CpG-3' sequence, the (6S,8R,11S) diastereomer forms a N(2)-dG:N(2)-dG interstrand cross-link [Wang, H.; Kozekov, I. D.; Harris, T. M.; Rizzo, C. J. J. Am. Chem. Soc.2003, 125, 5687-5700]. We refined its structure in 5'-d(G(1)C(2)T(3)A(4)G(5)C(6)X(7)A(8)G(9)T(10)C(11)C(12))-3'·5'-d(G(13)G(14)A(15)C(16)T(17)C(18)Y(19)C(20)T(21)A(22)G(23)C(24))-3' [X(7) is the dG adjacent to the C6 carbon of the cross-link or the α-carbon of the (6S,8R,11S) 1,N(2)-dG adduct, and Y(19) is the dG adjacent to the C8 carbon of the cross-link or the γ-carbon of the HNE-derived (6S,8R,11S) 1,N(2)-dG adduct; the cross-link is in the 5'-CpG-3' sequence]. Introduction of (13)C at the C8 carbon of the cross-link revealed one (13)C8→H8 correlation, indicating that the cross-link existed predominantly as a carbinolamine linkage. The H8 proton exhibited NOEs to Y(19) H1', C(20) H1', and C(20) H4', orienting it toward the complementary strand, consistent with the (6S,8R,11S) configuration. An NOE was also observed between the HNE H11 proton and Y(19) H1', orienting the former toward the complementary strand. Imine and pyrimidopurinone linkages were excluded by observation of the Y(19)N(2)H and X(7) N1H protons, respectively. A strong H8→H11 NOE and no (3)J((13)C→H) coupling for the (13)C8-O-C11-H11 eliminated the tetrahydrofuran species derived from the (6S,8R,11S) 1,N(2)-dG adduct. The (6S,8R,11S) carbinolamine linkage and the HNE side chain were located in the minor groove. The X(7)N(2) and Y(19)N(2) atoms were in the gauche conformation with respect to the linkage, maintaining Watson-Crick hydrogen bonds at the cross-linked base pairs. A solvated molecular dynamics simulation indicated that the anti conformation of the hydroxyl group with respect to C6 of the tether minimized steric interaction and predicted hydrogen bonds involving O8H with C(20)O(2) of the 5'-neighbor base pair G(5)·C(20) and O11H with C(18)O(2) of X(7)·C(18). These may, in part, explain the stability of this cross-link and the stereochemical preference for the (6S,8R,11S) configuration.     

Sequence selective recognition in the minor groove of dsDNA by pyrrole,imidazole-substituted bis-benzimidazole conjugates

A series of pyrrole, imidazole-substituted bis-benzimidazole conjugates, Py-Py-Im-gamma-biBenz, Py-Py-gamma-biBenz, Py-Im-gamma-biBenz, and Im-Py-gamma-biBenz (1-4), were prepared in an attempt to target dsDNA sequences possessing both A/T and G/C bps. The dsDNA interactions and sequence specificity of the conjugates have been characterized via spectrofluorometric titrations and thermal melting studies. All conjugates form 1:1 complexes with dsDNA at subnanomolar concentrations. The Im moiety selectively recognizes a G/C bp embedded in the A/T-rich binding site. This represents the first clear example of sequence selective recognition in a 1:1 motif.(1) The equilibrium association constant (K(1)) for complexation of a specific nine-bp dsDNA site, 5'-gcggTATGAAATTcgacg-3', by conjugate 1 is approximately 2.6 x 10(9) M(-1). Displacement of the G/C position or G/C-->A/T substitution within the nine-bp site decreases the K(1) by approximately 8-fold, whereas two continuous G/C bps decrease the K(1) by approximately 50-fold magnitude. The K(1) values for seven-bp dsDNA, 5'-gcggtaTGAAATTcgacg-3' and 5'-gcggtaCAAAATTcgacg-3', binding sites by conjugates Py-Im-gamma-biBenz (3) and Im-Py-gamma-biBenz (4) are approximately 2.3 x 10(9) and approximately 1.2 x 10(9) M(-1), respectively. However, the conjugates with no Im moiety, Py-Py-gamma-biBenz (2) and Py-Py-Py-gamma-biBenz (5 and 6), are specific for seven- to nine-bp A/T-rich sites and single A/T-->G/C bp substitution within the binding site decreases the K(1) values by 1-2 orders of magnitude.