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PubMed2002

Theoretical study of factors controlling rates of cyclization of radical intermediates from diallylamine and diallylammonium monomers in radical polymerizations.

The radical cyclization reactions of models for the growing radical chains formed from N,N-diallylamine (1), N-methyl-N,N-diallylamine (2), N,N-diallylammonium (3), N-methyl-N,N-diallylammonium (4) and N,N-dimethyl-N,N-diallylammonium (5) have been investigated computationally by DFT theory, using the B3LYP functional. Models formed by hydrogen atom addition to dienes 1-5 undergo five-membered ring cyclization reactions with activation energies predicted to be 7.2, 5.0, 8.6, 6.4, and 6.2 kcal/mol, respectively. Methyl substitution on nitrogen decreases the barrier to cyclization. One methyl has a larger effect on the cyclization rate than the second methyl. This rate enhancement is attributed to a decrease in gauche interactions in the transition state as compared to the initial structure and to different destabilizing effects when an H is replaced by a methyl group. These predicted rate effects are in agreement with the experimental data on polymerization efficiencies.

Alkylation↗

PubMed2006

Synthesis of 2,4-disubstituted piperidines via radical cyclization: unexpected enhancement in diastereoselectivity with tris(trimethylsilyl)silane.

A novel approach to 2,4-disubstituted piperidines is reported, involving the radical cyclization of 7-substituted-6-aza-8-bromooct-2-enoates. Cyclization with tributyltin hydride affords the trans piperidines with trans/cis diastereomeric ratios ranging typically from 3:1 to 6:1. Cyclization with tris(trimethylsilyl)silane affords the same products with diastereomeric ratios of up to 99:1 in certain cases. The enhancement in diastereoselectivity results from the selective rearrangement of the minor stereoisomer through a cascade process involving radical cyclization to the piperidine radical, 1,5-radical translocation, and attack of the translocated radical onto the sulfonamide with extrusion of SO2 in a Smiles-type rearrangement. Slower trapping of the piperidine radical by tris(trimethylsilyl)silane compared to tributyltin hydride accounts for the occurrence of the rearrangement cascade in the former case.

Cyclization↗

PubMed2006

Ring size and substituent effects in oxyanion-promoted cyclizations of enyne-allenes: observation of a Myers-Saito cycloaromatization at cryogenic temperature.

A series of acetoxy-substituted enyne-allenes, fused to cyclopentene and cyclohexene ring systems, were synthesized and treated with methyllithium to generate the corresponding enolates. It was found that whereas the cyclohexannulated examples underwent either C2-C7 (Myers-Saito) cycloaromatization or C2-C6 (Schmittel) cyclization depending on their terminal subsituents, the cyclopentannulated examples either failed to cyclize altogether or underwent C2-C7 cyclization. Both of these results lie in contrast to the behavior of their benzannulated analogues, which underwent exclusive C2-C6 cyclization independent of substituents. These findings are rationalized on the basis of both ring strain effects and the steric encumbrance of the terminal alkynyl and allenyl subsituents.

Alkadienes↗

PubMed2000

Selective and facile cyclization of N-chloroacetylated peptides from the C4 domain of HIV Gp120 in LiCl/DMF solvent systems.

Lithium salts have been reported to mediate the solubilization of peptides in organic solvents in 1989 (Seebach, D., Thaler, A. & Beck, A. K. Helv. Chim. Acta 1989; 72, 857-867). The use of Li salts in an organic solvent to influence cyclization of a reactive peptide that only polymerizes in an aqueous solvent, has not been reported. Here, the selective and facile cyclization of N-chloroacetylated, C-cysteine amide peptides from the C4 domain of HIV-1 gp120 in LiCl/DMF solvent systems is demonstrated. The addition of stoichiometric amounts of Tris base to 1 mg/mL peptide in LiCl/DMF solutions was sufficient to drive the cyclization to completion within 3 h at ambient temperatures. Cyclic peptides were the only detectable reaction products and these were confirmed using reversed-phase HPLC and mass spectrometric analyses of the final products. In aqueous solutions at pH 7.4, only polymers were obtained as judged by HPLC and SDS-PAGE. The method of using Li salts in an organic solvent to enhance the cyclization of unprotected amphipathic peptides may be useful in many situations beyond those described here.

Acetylation↗

PubMed2005

Enzymatic cyclizations of squalene analogs with threo- and erythro-diols at the 6,7- or 10,11-positions by recombinant squalene cyclase. Trapping of carbocation intermediates and mechanistic insights into the product and substrate specificities.

In order to trap the carbocation intermediates formed during the squalene cyclization cascade, squalene analogs with threo- and erythro-diols at the 6,7- and 10,11-positions were incubated with the recombinant squalene cyclase from Alicyclobacillus acidocaldarius, leading to the construction of the triterpenes with tetrahydropyran, octahydrochromene, decahydronaphthalene with a carbonyl group, dodecahydrobenzo[f]chromene, tetradecahydronaphtho[2,1-b]oxepine and malabaricane skeletons, almost of which are novel compounds. These products indicate that 6-membered monocyclic, 6/6-fused bicyclic and 6/6/5-fused tricyclic cations were involved in the cyclization reaction in addition to acyclic cation. All the trapped cations were the stable tertiary cation, but not the secondary one, indicating that the polycyclization reaction proceeds with a Markovnikov closure. The product profiles revealed that the cyclization reactions proceeded with the product and substrate specificities in addition to enantioselectivity. Mechanistic insight into the observed stereochemical specificities indicated that the pre-organized chair-conformation of squalene-diols is tightly constricted by the cyclase and a free motion or a conformational change is not allowed in the reaction cavity, thus, the substrate and product specificities are dominantly directed by the least motion of the nucleophilic hydroxyl group toward the intermediary carbocation; a small rotation of the hydroxyl group afforded the cyclization products in a good yield, but a large rotation of the hydroxyl group gave a marginal or no detectable amount of products.

Carbohydrate Conformation↗

PubMed2006

Mechanistic insights into triterpene synthesis from quantum mechanical calculations. Detection of systematic errors in B3LYP cyclization energies.

Most quantum mechanical studies of triterpene synthesis have been done on small models. We calculated mPW1PW91/6-311+G(2d,p)//B3LYP/6-31G* energies for many C30H51O+ intermediates to establish the first comprehensive energy profiles for the cationic cyclization of oxidosqualene to lanosterol, lupeol, and hopen-3beta-ol. Differences among these 3 profiles were attributed to ring strain, steric effects, and proton affinity. Modest activation energy barriers and the ample exothermicity of most annulations indicated that the cationic intermediates rarely need enzymatic stabilization. The course of reaction is guided by hyperconjugation of the carbocationic 2p orbital with parallel C-C and C-H bonds. Hyperconjugation for cations with a horizontal 2p orbital (in the plane of the ABCD ring system) leads to annulation and ring expansion. If the 2p orbital becomes vertical, hyperconjugation fosters 1,2-methyl and hydride shifts. Transition states leading to rings D and E were bridged cyclopropane/carbonium ions, which allow ring expansion/annulation to bypass formation of undesirable anti-Markovnikov cations. Similar bridged species are also involved in many cation rearrangements. Our calculations revealed systematic errors in DFT cyclization energies. A spectacular example was the B3LYP/6-311+G(2d,p)//B3LYP/6-31G* prediction of endothermicity for the strongly exothermic cyclization of squalene to hopene. DFT cyclization energies for the 6-311+G(2d,p) basis set ranged from reasonable accuracy (mPW1PW91, TPSSh with 25% HF exchange) to underestimation (B3LYP, HCTH, TPSS, O3LYP) or overestimation (MP2, MPW1K, PBE1PBE). Despite minor inaccuracies, B3LYP/6-31G* geometries usually gave credible mPW1PW91 single-point energies. Nevertheless, DFT energies should be used cautiously until broadly reliable methods are established.

Cations↗

PubMed2006

Comparison of endotoxin antagonism of linear and cyclized peptides derived from limulus anti-lipopolysaccharide factor.

BACKGROUND: Limulus anti-lipopolysaccharide (LPS) factor (LALF) is a 102-amino acid LPS-binding protein from the horseshoe crab, Limulus polyphemus. The peptide includes the LPS-binding domain of holoLALF, yet it lacks the loop structure stabilized by disulfide or other covalent bonds that is a common motif in the LPS-binding regions of holo- LALF and several other LPS-binding proteins. Although it neutralizes LPS and is bactericidal against Pseudomonas aeruginosa, the LALF 28-54 portion of LALF is not protective in a murine model of intraperitoneal sepsis compared with holoLALF. We examined the effects of cyclizing this linear peptide to determine if this action would recapitulate the stable loop-type structure and enhance its LPS-neutralization and bactericidal activity in vitro. METHODS: Cyclic LALF 28-54 was produced by oxidizing linear LALF 28-54. Each peptide, along with appropriate controls, was assayed for LPS neutralization using the chromogenic Limulus amebocyte lysate (LAL) assay and a bioassay to measure inhibition of LPS-stimulated production of tumor necrosis factor-alpha (TNF-alpha) by murine macrophages. Bactericidal activity against Pseudomonas aeruginosa was also assessed. Data were analyzed using a two-tailed Student t-test. RESULTS: Polymyxin B and holoLALF exhibited potent endotoxin antagonism in both assays, as well as bactericidal activity. Concordant with prior studies, the linear form of LALF 28-54 exhibited either similar or a slightly lesser degree of activity in all assays. However, cyclization was associated with significantly diminished endotoxin neutralization in both assays (p < 0.05) and decreased bactericidal activity (p < 0.05) compared with linear LALF 28-54. CONCLUSIONS: Whereas a synthetic linear peptide based on the endotoxin-binding region of holoLALF retained activity, cyclization was associated with a diminution in potency in vitro. We postulate that cyclization does not constrain the peptide in a manner that recreates the loop structure necessary for potent endotoxin antagonism.

Animals↗

PubMed2000

Total synthesis of prostaglandin F2alpha using nickel-catalyzed stereoselective cyclization of 1,3-diene and tethered aldehyde via transmetalation of nickelacycle with diisobutylaluminum acetylacetonate.

Total synthesis of prostaglandin F2alpha utilizing a nickel(0)-catalyzed cyclization of 1,3-diene and tethered aldehyde was achieved. The cyclization proceeded via a transmetalation of nickelacycle with diisobutylaluminum acetylacetonate (iBu2-ALAC). Thus, the reaction of 19, having a side chain corresponding to the alpha-chain in PGF2alpha with Ni(cod)2 (10 mol %), PPh3 (20 mol %), and 1,3-cyclohexadiene (25 mol %) in the presence of iBu2-ALAC (1.5 eq) proceeded stereoselectively to give the cyclized product 26 in 54% yield. During the cyclization of 19, the Z-olefin at C-5 in the side chain completely retained its geometry, and the four contiguous chiral carbon centers in PGF2alpha were stereoselectively constructed. Transformation of the key intermediate 19 into PGF2alpha was successfully achieved.

Aldehydes↗

PubMed2000

Application of Rh-catalyzed cyclization to the formation of a chiral quaternary carbon.

Rh-Catalyzed cyclization was applied to the formation of a chiral quaternary carbon. It has become clear that the Rh-complex can discriminate between isopropenyl and 2-isopentenyl (or isopentyl) substituents, and the cyclization afforded 3,3,4-trisubstituted cyclopentanones with a chiral quaternary carbon in a stereoselective manner. The cyclization of 4-pentenals 6a, b by an achiral neutral Rh(PPh3)3Cl afforded 3,3,4-cis-trisubstituted cyclopentanones (+/-)-7a,b in 86-96%, and the cyclization by a cationic Rh[(R)-BINAP]CIO4 afforded 3,3,4-trans-trisubstituted cyclopentanones (-)-8a, b of 82-86% ee in 88-98% yields. The mechanism of stereoselection by Rh-complexes is also discussed.

Catalysis↗

PubMed2003

Super acid-induced Pummerer-type cyclization reaction: improvement in the synthesis of chiral 1,3-dimethyl-1,2,3,4-tetrahydroisoquinolines.

Improved synthesis of four stereoisomeric chiral 1,3-dimethyl-1,2,3,4-tetrahydroisoquinolines (1a, b, ent-1a, b) was achieved via the super acid-induced cyclization of chiral N-[1-methyl-2-(phenylsulfinyl)ethyl]-N-(1-phenylethyl)formamides (4a, b, ent-4a, b) using the Pummerer-type cyclization reaction as a key step. The cyclization leading to the isoquinoline ring proceeded in a quantitative manner when trifluoromethane sulfonic acid (TFSA) was used as the super acid, although Friedel-Crafts-type alkylation of 4-phenylsulfanyl TIQ derivatives (5) with benzene used as the solvent accompanied cyclization to yield the 4-phenyl-TIQs (7). The byproduct (7) was exclusively formed when a large excess amount of TFSA was used.

Cyclization↗

PubMed2003

Oxidative cyclization of D-fructose thiosemicarbazones to 2-amino-5-(D-arabino-1,2,3,4-tetrahydroxybut-1-yl)-1,3,4-thiadiazoles through carbon-carbon bond cleavage of the sugar chain.

Condensation of D-fructose (1) with thiosemicarbazide or 4-phenylthiosemicarbazide gave the corresponding D-fructose thiosemicarbazones (3a and 3b). The latter compounds underwent oxidative cyclization with 10% ethanolic ferric chloride to give mixtures of 2-amino-5-(D-arabino-1,2,3,4-tetrahydroxybut-1-yl)-1,3,4-thiadiazole (6a) and 2-amino-5-hydroxymethyl-1,3,4-thiadiazole (5a) from 3a and the corresponding 2-phenylamino compounds 6b and 5b from 3b. These products were formed as a result of cyclization of the thiosemicarbazone entity accompanied by C-1-C-2 or C-2-C-3 bond cleavage of the sugar chain. Structures of the 1,3,4-thiadiazole acyclo C-nucleosides 6a and 5b were confirmed by comparison with the unequivocally prepared compounds obtained by the dehydrogenative cyclization of D-arabinose thiosemicarbazones 11a and 11b with ethanolic ferric chloride. Structures of the 5-hydroxymethyl-1,3,4-thiadiazoles 5a and 5b were also confirmed by comparison with 5a and 5b unequivocally prepared by periodate cleavage of the alditolyl chain of 6a and 6b followed by reduction of the resulting aldehydes 8a and 8b with sodium borohydride. Compounds 6a and 6b were further characterized as their acetates 7a and 7b and were found to exist in the extended planar zizag conformation 13. Condensative cyclization of the D-arabinose thiosemicarbazones 11a and 11b by boiling with acetic anhydride afforded the 1,3,4-thiadiazoline acyclo C-nucleoside acetates 9a and 9b which exist in the sickle (bent) conformation 14. De-N- and de-O-acetylation with concomitant aromatization of 9a and 9b with 10% ethanolic FeCl3 gave the 1,3,4-thiadiazole acyclo C-nucleosides 6a and 6b. The assigned structures were corroborated by 2D 1H-1H HOMCOR and 2D 1H-13C HETCOR NMR spectroscopy.

Acetylation↗

PubMed1991

Covalently cyclized agonist and antagonist analogues of bombesin and related peptides.

During a search for possible cyclization points in shortened, potent bombesin agonists and antagonists, it was found that the joining of amino acid residues in positions 6 and 14 by various means resulted in retention of significant binding affinity for rat pancreatic acini and murine Swiss 3T3 cells. In one series of analogues, Cys residues in these positions were used for bridging via a disulfide bond. (D)-C-Q-W-A-V-G-H-L-C-NH2 retained significant binding affinity for rat pancreatic acini cells and was a full amylase releasing agonist (EC50 187 nM). Potency was markedly increased by substituting D-Ala for Gly (EC50 67 nM compared to 10 nM for its linear counterpart) and was decreased by substituting L-Cys for D-Cys in this analogue (EC50 214 nM), thus strongly suggesting stabilization of peptide folding by the D residues. Elimination of the COOH-terminal amino acid produces competitive antagonists in the linear analogues; however, (D)-C-Q-W-A-V-G-H-C-NH2 was devoid of activity. Likewise, cyclization to position 13 with the 14 amino acids intact to give (D)-C-Q-W-A-V-G-H-C-L-NH2 resulted in an almost inactive peptide. On the other hand, as in the linear series, the reduced peptide bond analogue, (D)-C-Q-W-A-V-(D)-A-H-L-psi (CH2NH)-C-NH2, was a receptor antagonist (IC50 5.7 mM), albeit much weaker than the corresponding linear analogues, but with no residual agonist activity. Direct head-to-tail cyclization was also tried. Both cyclo[(D)-F-Q-W-A-V-G-H-L-L] (EC50 346 nM) and the shorter cyclo [Q-W-A-V-G-H-L-L] (EC50 1236 nM) were full agonists. Elimination of the COOH-terminal residue in cyclo[(D)-p-Cl-F-Q-W-A-V-(D)-A-H-L] produced an agonist (EC50 716 nM) rather than an antagonist. These results provide support for the proposal that both bombesin agonists and antagonists adopt a folded conformation at their receptor(s). Furthermore, the retention of appreciable potencies using several cyclization strategies and chain lengths suggests that further optimization of these structures both in terms of potency and ring size is possible. Since these peptides have increased conformational restriction, they should begin to serve as useful substrates for NMR and molecular modeling studies aimed at comparing the obviously subtle differences between agonist and antagonist structures.

Amino Acid Sequence↗

PubMed2006

Facile and versatile annulation of the imidazole ring: Single and sequential cyclization reactions of Fischer carbene complexes with 1,4-diazafulvenes.

We examined the reactivity of dimethylaminodiazafulvene 1 toward Fischer alkenylcarbene 2 and alkynylcarbene 3 complexes. Diazafulvene 1 reacts with alkenylcarbenes 2 through a formal [6+3] heterocyclization in a regio- and stereoselective manner to afford dihydroimidazo[1,2-a]pyridines 4. Acid-promoted dimethylamine elimination in compound 4 c gives rise to the aromatic imidazo pyridine 5. A likely mechanism for this reaction is a 1,2-nucleophilic addition/[1,2]-shift metal-promoted cyclization sequence. On the other hand, diazafulvene 1 and alkynyl carbenes 3 undergo a [6+2] cyclization to afford pyrrolo[1,2-a]imidazole carbene complex 6 that can be readily oxidized to the corresponding esters 7. When enynylcarbenes 3 e-i are treated with diazafulvene 1, consecutive and diastereoselective [6+2]/cyclopentannulation cyclization reactions take place affording new polycyclic complex systems 8, 9, and 12 that can be appropriately demetallated to the corresponding imidazole-based polyfused systems 10, 11, and 13 respectively. Finally, enynylcarbenes 3 d,f undergo consecutive [6+2]/[5+1] cyclization reactions with diazafulvene 1 and tBuNC, respectively, to yield tetracyclic adducts 14 and 15. All these processes result in high yields and provide a route to the preparation of imidazopyridines and pyrroloimidazoles as well as other polycyclic molecules that contain imidazole groups, which are interesting from a pharmacological and biological point of view.

Journal Article↗

PubMed2003

1,2-Silyl-migrative cyclization of vinylsilanes bearing an amino group.

In the presence of an acid catalyst, alpha-alkyl-substituted (Z)-vinylsilanes 1, bearing a tosylamino group, were smoothly cyclized to trans-2-alkyl-3-silylpiperidines 2 (1,2-silyl-migration products) and (2R*, 1'S*)-2-(1'-silylalkyl)pyrrolidines 3. The elaboration of the reaction conditions enabled the selective preparation of each cyclized product. The acid-catalyzed cyclization of (Z)-vinylsilane 5, whose methylene tether is shorter than that of 1 by one carbon, formed only the 1,2-silyl-migration product 6 with high trans-selectivity. These cyclizations were found to proceed in a stereospecific manner.

Journal Article↗

PubMed1987

Complementary base-pairing properties of cyclized and linear oligonucleotides.

Oligouridylates of varying chain lengths were synthesized by polynucleotide phosphorylase and cyclized by RNA ligase. Over chain lengths from 7 to 15, the bindings of the cyclized and linear oligomers to polyadenylate were measured on the basis of differential migration of bound and free oligomers on a gel exclusion column. Binding of the cyclized oligomers was found to be far weaker than that of their linear counterparts of equal length. Such a general reduction in base-pairing capacity due to the cyclized conformation, by limiting the strength of unintended base-pairing without obstructing the possible development of strong specific base-pairing, may represent an advantage important to the function and evolution of loop structures in tRNA and other RNA molecules.

Base Composition↗

PubMed2005

Regio- and stereoselective cyclizations of dianhydro sugar alcohols catalyzed by a chiral (salen)Co(III) complex.

The (salen)Co(III)OAc ((R,R)-1 and (S,S)-1) catalyzed cyclizations of the chiral dianhydro sugars, 1,2:5,6-dianhydro-3,4-di-O-methyl-D-glucitol (2), 1,2:5,6-dianhydro-3,4-di-O-methyl-D-mannitol (3), 1,2:5,6-dianhydro-3,4-di-O-methyl-L-iditol (4), and 1,2:4,5-dianhydro-3-O-methyl-L-arabinitol (5), is a facile method for the synthesis of anhydroalditol alcohols. Cyclization of 2 using (R,R)-1 and (S,S)-1 proceeded diastereoselectively to form 2,5-anhydro-3,4-di-O-methyl-D-mannitol (6) and 2,5-anhydro-3,4-di-O-methyl-L-iditol (7), respectively. The cyclization of 3 and 5 is a novel method for obtaining 1,6-anhydro-3,4-di-O-methyl-D-mannitol (11) and a stereoselective route to 1,5-anhydro-3-O-methyl-L-arabinitol (13). It is proposed that the reaction occurs via endo-selective cyclization of an epoxy alcohol produced by the endo-selective ring-opening of one of the two epoxide moieties in the starting material.

Carbohydrate Conformation↗

PubMed1999

Circular beta-lactamase: stability enhancement by cyclizing the backbone.

We have cyclized the polypeptide backbone of beta-lactamase with a short peptide loop as a novel method for protein stabilization, using intein-mediated protein ligation. Successful cyclization was proven by mass spectrometry and subsequent re-linearization by proteolytic cleavage, as well as by resistance against carboxypeptidase. Under the conditions of the experiment, no disulfide bond is present. The circular form of beta-lactamase was found to be significantly more stable against irreversible aggregation upon heating than the linear form. The circular form could be purified from the linear one either by this heat treatment or by a his-tag which became exopeptidase-resistant by cyclization. The increased stability of the circular form is probably due to the decreased conformational entropy in the unfolded state and in the intermediate states. While the introduction of additional disulfide bonds for protein stabilization follows the same rationale, the cyclization strategy may disturb the structure less and thus constitute a general method for stabilizing those proteins with N- and C-termini in close proximity.

Amino Acid Sequence↗

PubMed2001

Individually selecting multi-reference CI and its application to biradicalic cyclizations.

In the present review a new algorithm to perform individually selecting MR-CI calculations is discussed. The new algorithm exploits the advantages arising from the subdivision of the molecular orbitals (MOs) into an internal and an external part and avoids the recalculation of representation matrices by the use of a specially designed cache. With the new algorithms we are able to perform calculations including more than 10 million selected configurations state functions (CSFs) as a matter of routine. As an example for the possibilities of the new approach the regioselectivity of thermal biradical cyclizations (C2-C7 vs. C2-C6 cyclization) is investigated in the second part of the present work. After studying the accuracy of various quantum chemical methods (MR-CI, density functional theory, and coupled cluster approaches) using (Z)-1,2,4 Heptatriene-6-yne as a model system the influence of substituents (R = H, Ph, t-Bu, NH2) on the regioselectivity is investigated. Our results rationalize the switch between the two biradical cyclizations on the basis of mainly steric (t-Bu) or electronic (Ph) substituent effects. Moreover, the results for R = NH2 predict that the activation energy of the C2-C6 cyclization can be lowered even more. However, a change in the reaction mechanism is found.

Journal Article↗