Evidence for coupling between nitrile groups using DNA templates: a promising new method for monitoring structures with infrared spectroscopy

Infrared spectroscopy is a common method for monitoring biomolecular structures but suffers from spectral congestion. Non-natural vibrational probes provide a way to regain structural specificity because they provide a unique vibrational signature and can be incorporated into proteins or other biomolecules at specific locations. A popular probe is the nitrile group because its frequency is sensitive to the electrostatics of its environment. In this work, we show that pairs of nitrile groups can be used to directly probe distances and angles in dual labeled molecules. By labeling model DNA oligomers with pairs of nitrile tags, we demonstrate that the vibrational coupling between two nitrile groups is strong enough that Fourier transform infrared (FTIR) spectra can be used to probe relative nitrile distances >4.5 A. Our approach is similar in spirit to monitoring structures with fluorescence resonance energy transfer (FRET) using a pair of fluorescent labels or a pair of spin labels in electron spin resonance spectroscopy. The small sizes of nitrile groups make especially valuable probes of sterically confined regions like the inner cores of large biomolecules where other spectroscopic probes do not fit.     

Inverse electron-demand 1,3-dipolar cycloaddition of nitrile oxide with common nitriles leading to 3-functionalized 1,2,4-oxadiazoles

A carbamoyl-substituted nitrile oxide was generated upon treatment of easily available 2-methyl-4-nitro-3-isoxazolin-5(2H)-one with THF (not dried); the reaction proceeded efficiently even in the absence of any special reagents and reaction conditions. The nitrile oxide caused 1,3-dipolar cycloaddition with common aliphatic nitriles or electron-rich aromatic nitriles to afford 3-functionalized 1,2,4-oxadiazoles, which are expected to serve as precursors for the preparation of a variety of functional materials by the chemical transformation of the carbamoyl group. While conventional preparative methods for 1,2,4-oxadiazoles involve the cycloaddition of an electron-rich nitrile oxide with an electron-deficient nitrile or a nitrile activated by a Lewis acid, our method employs the complementary combination of an electron-rich nitrile and an electron-deficient nitrile oxide- the inverse electron-demand 1,3-cycloaddition. The DFT calculations using B3LYP 6-31G* supported the abovementioned inverse reactivity, and also suggested the presence of an accelerating effect by the carbamoyl group as a result of hydrogen bond formation with a dipolarophilic nitrile.     

An anomalous hydration/dehydration sequence for the mild generation of a nitrile oxide

A nitrile oxide containing a carbamoyl group is readily generated upon the treatment of 2-methyl-4-nitro-3-isoxazolin-5(2H)-one with water under mild reaction conditions, even in the absence of special reagents. The obtained nitrile oxide undergoes cycloaddition with dipolarophiles, alkynes and alkenes, to afford the corresponding isoxazol(in)es, which are useful intermediates in the synthesis of polyfunctionalized compounds. A plausible mechanism underlying the formation of the nitrile oxide is proposed, which involves an anomalous hydration/dehydration sequence. DFT calculations were also performed to support this mechanism.     

Polyamide synthesis from 6-aminocapronitrile, part 1: N-alkyl amide formation by amine amidation of a hydrolyzed nitrile

The synthesis of N-hexylpentanamide from a stoichiometric amount of pentanenitrile and hexylamine has been studied as a model reaction for the synthesis of nylon-6 from 6-aminocapronitrile. The reaction was carried out under mild hydrothermal conditions and in the presence of a homogeneous ruthenium catalyst. For the mild hydrothermal conditions the presence of hexylamine distinctively increases the nitrile hydrolysis compared to the nitrile hydrolysis in the absence of hexylamine. Amine-catalyzed nitrile hydrolysis mainly produces the N-substituted amide. A clear product development is observed, consisting of first the terminal amide formation and second the accumulation of N-hexylpentanamide. With a maximum conversion of only 80 % after 18 h, the nitrile hydrolysis rate at 230 degrees C is still much too low for nylon-6 synthesis. Ruthenium dihydride phosphine was therefore used as a homogeneous catalyst, which significantly increases the nitrile hydrolysis rate. At a temperature of 140 degrees C and with only 0.5 mol % [RuH(2)(PPh(3))(4)] a 60 % nitrile conversion is already reached within 2 h. Initially the terminal amide is the sole product, which is gradually converted into N-hexylpentanamide. The reaction has a high initial rate, however, for higher conversions a strong decrease in hydrolysis rate is observed. This is ascribed to product inhibition, which results from the equilibrium nature of the reaction.     

Bioconversion of acrylonitruke to acrylamide using a thermostable nitrile hydratase

Although providing an attractive route for production of crrylamide from acrylonitrile, utilization of nitrile hydratase en zymes has been limited by the requirement for low temperatu rebioconversion conditions. Thisrreportsummarizes a search for thermostable nitrile hydratases from aerobic moderate thermophiles screened for ability to grow on acrylonitrileatt concentrations to 1% at elevated temperatures. A new isolate Bacillus sp. BR449 constitutively expresses a thermostble nitrile hydratase with properties iccluding low substrate inhibition and broad temperature range with optimal activity at 55°C. With prolonged exposure, BR449 nitrile hydratase exhibited temperature-dependent inactivation by acrylonitrile, which is attributed to alkylation of nucleophilic sites on the enzymes/     

Synthesis of C-protected alpha-amino aldehydes of high enantiomeric excess from highly epimerizable N-protected alpha-amino aldehydes

A new procedure for the preparation of C-protected alpha-amino aldehydes of high enantiomeric excess is illustrated using five differently substituted alpha-(N-Fmoc)amino aldehydes as starting materials. Highly epimerization-prone substrates were converted to the corresponding morpholino nitrile-protected alpha-amino aldehydes with minimal racemization (products >/= 89% ee). Morpholino nitrile derivatives of phenylglycinal were crystallized and subjected to X-ray structural analysis, allowing for definitive determination of the stereochemistry of amino nitrile formation. A rationale for the stereoselectivity of amino nitrile formation is presented.     

Biotransformation of nitriles using the solvent-tolerant nitrile hydratase from Rhodopseudomonas palustris CGA009

A study has been carried out into the biocatalytic hydration of nitriles using the nitrile hydratase enzyme from Rhodopseudomonas palustris CGA009. It has been shown that this nitrile hydratase can hydrate aliphatic, aromatic and heterocyclic nitriles under very mild conditions, in mixtures of pH 7 buffer and a range of organic solvents, often with excellent chemoselectivity. The major determinant of hydration occurring is the degree of steric hindrance around the nitrile moiety and/or size of the substrates.     

A modular approach to polyketide building blocks: cycloadditions of nitrile oxides and homoallylic alcohols

A general approach to the diastereoselective synthesis of Delta(2)-isoxazolines via magnesium-mediated, hydroxyl-directed diastereoselective nitrile oxide cycloadditions of homoallylic alcohols and monoprotected homoallylic diols is disclosed. A broad spectrum of aliphatic and aromatic nitrile oxides and a variety of homoallylic alcohols participate in the cycloaddition, thus expanding the scope of polyketide building blocks that can be accessed using this strategy.     

Molecular sieve 4 Å generates nitrile oxides from hydroximoyl chlorides. Development of catalyzed enantioselective nitrile oxide cycloadditions to monosubstituted alkenes

The effective generation of nitrile oxide 1,3-dipoles from hydroximoyl chlorides can be achieved with powdered molecular sieves 3 Å and 4 Å as mild solid bases. Rate of nitrile oxide generation depends upon the choice of reaction solvents, among which alcohols are the best media. A catalytic process is achieved by use of a catalytic amount of amine in the presence of MS 4 Å leading to the amine-catalytic generation of nitrile oxides. This new synthetic method can be applied to the catalytic enantioselective nitrile oxide 1,3-dipolar cycloaddition reactions with monosubstituted alkenes.     

A high-yielding preparation of beta-ketonitriles

[reaction: see text] beta-Ketonitriles are important precursors for a wide variety of biologically active heterocycles. A facile procedure for the high-yielding acylation of nitrile anions with unactivated esters to provide beta-ketonitriles is reported. The procedure is successful with enolizable and nonenolizable esters as well as hindered nitrile anions.     

Role of conformational effects on the regioselectivity of macrocyclic INOC reactions: two new asymmetric total syntheses of (+)-brefeldin A

We have gained some insight into the role of conformational effects on the regioselectivity of the macrocyclic intramolecular nitrile oxide cycloaddition observed in our (+)-brefeldin A synthesis. During the course of this regiochemical study, we have developed two novel stereoselective and regioselective schemes for total synthesis of (+)-brefeldin A (i.e. intramolecular nitrile oxide cycloaddition-isomerization and intermolecular nitrile oxide cycloaddition-ring closing metathesis strategies).     

Magtrieve™ (CrO2) and MnO2 mediated oxidation of aldoximes: studying the reaction course

Magtrieve™ (CrO₂) and MnO₂ mediated oxidation of aldoximes to nitrile oxides were studied in details. In presence of external radical source, TEMPO, these reagents did not furnish nitrile oxides, instead favoured deoximation to aldehydes. A common trend of deoximation was established from electronically tuned aldoximes, which is: aliphatic>aromatic>aldoximes with strong electron-withdrawing group, though the extent of deoximation was less in case of CrO₂. Above effects were not observed with chloramine-T and diacetoxyiodobenzene, reagents known to produce nitrile oxides via hydroximoyl halide or equivalent ionic intermediates. A putative reaction mechanism is proposed for MO₂ (M=Cr, Mn) mediated oxidation of aldoximes through formation of a nitroso-oxime tautomeric pair. Formation of nitrile oxide is possibly occurred from the oxime tautomer via a σ-type iminoxy radical intermediate. The deoximation process, dominating in presence of external radical environment, is explained following decomposition of the nitroso tautomer.     

N-bromosuccinimide initiated one-pot synthesis of imidazoline

A novel cationic Br initiated one-pot imidazoline synthesis has been developed using olefin, nitrile, amine, and N-bromosuccinimide. The olefinic substrates and the nitrile partners can be flexibly varied to achieve a range of imidazoline derivatives.     

Synthesis of a new class of keto-linked bis heterocycles

A new class of keto-linked bis heterocycles have been prepared by 1,3-dipolar cycloaddition of tosyl methyl isocyanide, nitrile imines and nitrile oxides to unsymmetrical bischalcones.     

Catalyst- and solvent-free click synthesis of cyclodextrin-based polyrotaxanes exploiting a nitrile N-oxide

A catalyst- and solvent-free synthesis of cyclodextrin-based polyrotaxanes exploiting a stable nitrile N-oxide as an end-capping agent was achieved. The C-C bond-forming end-capping reaction of an allyl-terminated pseudopolyrotaxane with the nitrile N-oxide proceeded smoothly by solid-state grinding in a mortar to afford a polyrotaxane.     

2-quinoxalinylnitrenes and 4-quinazolinylnitrenes: rearrangement to cyclic and acyclic carbodiimides and ring-opening to nitrile ylides

This work was undertaken with the aim to obtain direct evidence for the interrelationships between hetarylnitrenes, their ring-expanded cyclic carbodiimide isomers, and ring-opened nitrile ylides. Tetrazolo[1,5-a]quinoxaline 11T and tetrazolo[5.1-c]quinazoline 13T undergo valence tautomerization to the corresponding azides 11A and 13A on mild flash vacuum thermolysis (FVT). Photolysis in Ar matrixes at ca. 15 K affords the triplet nitrenes 12 and 14, identified by ESR, UV, and IR spectroscopy. The nitrenes are converted photochemically to the seven-membered ring carbodiimide 15 followed by the open-chain carbodiimide 22. The 3-methoxy- and 3-chloro-2-quinoxalinylnitrenes 24 yield the ring-expanded carbodiimides 26 very cleanly on matrix photolysis, whereas FVT affords N-cyanobenzimidazoles 28. The ring-opened nitrile ylides 36 and 49 are identified as intermediates in the photolyses of 2-phenyl-4-quinazolinylnitrene 32 and 7-nitro-2-phenyl-4- quinazolinylnitrene 47. In these systems, a photochemically reversible interconversion of the seven-membered ring carbodiimides 35 and 48 and the nitrile ylides 36 and 49 is established. Recyclization of open-chain nitrile ylides is identified as an important mechanism of formation of ring contraction products (N-cyanobenzimidazoles).     

1,3-Dipolar Cycloaddition of Dipolar Reagents to Bifunctional Olefins with Chloramine-T --- Part-II

A one pot synthesis of pyrazoles and isoxazoles was achieved by 1,3-dipolar cycloaddition of nitrile imines and nitrile oxides to an activated olefins in the presence of chloramine-T.     

Water‐Assisted Nitrile Oxide Cycloadditions: Synthesis of Isoxazoles and Stereoselective Syntheses of Isoxazolines and 1,2,4‐Oxadiazoles

Conventional methods generate nitrile oxides from oxime halides in organic solvents under basic conditions. However, the present work revealed that water‐assisted generation of nitrile oxides proceeds under mild acidic conditions (pH 4–5). Cycloadditions of nitrile oxides with alkynes and alkenes easily occurred in water without using catalysts, thus yielding isoxazoles and isoxazolines, respectively, with excellent stereoselectivity toward five‐ and six‐membered cyclic alkenes. A double stereoselective cycloaddition of two units of a nitrile oxide with cyclohexene was also achieved, thus yielding 1,2,4‐oxadiazole derivatives having a unique hybrid isoxazoline‐oxadiazole skeleton. Enantiomerically pure isoxazolines were prepared from monoterpenes with a ring strain. In one case, the isoxazoline with a butterfly‐like structure was simply prepared, and it might be used as a ligand in asymmetric catalysis.     

Iron‐Catalyzed Dehydration of Aldoximes to Nitriles Requiring Neither Other Reagents Nor Nitrile Media

The dehydration of aldoximes is an environmentally benign reaction affording the desired nitrile and water as a by‐product. However, most of the reported catalytic dehydration reactions of aldoximes require a solvent containing nitrile to synthesize the corresponding nitrile compounds. Inspired by recent reports on the enzymatic synthesis under nitrile‐free conditions, we here describe that a simple iron salt catalyzes the dehydration of aldoximes requiring neither other reagents nor nitrile media. Our method can be applied to the one‐pot synthesis of nitiriles from aldehydes.     

Cobalt-catalyzed alkyne-nitrile cyclotrimerization to form pyridines in aqueous solution

A new, water-soluble cobalt(I) catalyst has been used in the aqueous, chemospecific, cyclotrimerization of one nitrile with two alkynes for the synthesis of highly functionalized pyridines. Several different functional groups are well incorporated in this transformation, including unprotected alcohols, ketones, and amines. Double isotopic crossover data, as well as nitrile dependence on the rate of product formation, suggest associative rate-determining coordination of the nitrile.