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PubMed2002

Twisted amides inferred from QSAR analysis of hydrophobicity and electronic effects on the affinity of fluoroaromatic inhibitors of carbonic anhydrase.

QSAR has been used to elucidate the origin of the hydrophobicity and binding affinity of a small library of fluoroaromatic inhibitors of F131V carbonic anhydrase II. Our analysis predicted the presence of a twisted amide conformation for several bound inhibitors, which we confirmed crystallographically. We also determined that the hydrophobicity of the inhibitors as a whole results from the fragment hydrophobicities of their fluorobenzyl rings, corrected for field effects and the presence of an intramolecular F.H contact in solution. The loss of this interaction on binding to the enzyme makes the affinity sensitive to the same terms, but with the opposite dependence on the F.H contact. In the case of the four inhibitors bound as twisted amides, this F.H contact must be retained to some extent in the bound state in order for their affinities to be consistent with our QSAR analysis of the entire set of 17 molecules.

Amides↗
PubMed2002

Sheet structure of an L,D-dipeptide aggregate: inclusion compounds of (S)-phenylglycyl-(R)-phenylglycine with amides.

A simple dipeptide, (S)-phenylglycyl-(R)-phenylglycine (S,R-1), formed inclusion compounds with a small amide such as formamide, acetamide, N,N-dimethylformamide (DMF), or N,N-dimethylacetamide. By single-crystal X-ray analysis, the inclusion compounds were shown to have a wavy layer structure. The molecules of S,R-1 are arranged in parallel via ionic pairing of the carboxyl and amino groups to construct the wavy layers. The guest molecules were accommodated in a channel cavity between the layers by means of hydrogen bonding with (+)NH(3) of S,R-1. The cavity is surrounded by the phenyl groups of S,R-1 that conformationally rotate so as to make the cavity size fit the guest amide.

Amides↗
PubMed2002

Photocycloaddition of four-carbon-tethered pyridones. Intramolecular hydrogen bonding and facilitated amide hydrolysis by a proximal secondary alcohol.

Four-carbon-tethered pyridones undergo photocycloaddition to give exclusively trans-[4 + 4] products. The presence of a tether alcohol engenders a solvent-dependent diastereoselectivity for the cycloaddition by intramolecular hydrogen bonding to the adjacent pyridone. Following cycloaddition, the alcohol can deliver a carbonyl group to the proximal, hindered amide nitrogen, leading to a very facile amide hydrolysis.

Alcohols↗
PubMed2002

Practical and convenient enzymatic synthesis of enantiopure alpha-amino acids and amides.

Catalyzed by the nitrile hydratase and the amidease in Rhodococcus sp. AJ270 cells under very mild conditions, a number of alpha-aryl- and alpha-alkyl-substituted DL-glycine nitriles 1 rapidly underwent a highly enantioselective hydrolysis to afford D-(-)-alpha-amino acid amides 2 and L-(+)-alpha-amino acids 3 in high yields with excellent enantiomeric excesses in most cases. The overall enantioselectivity of the biotransformations of nitriles originated from the combined effects of a high L-enantioselective amidase and a low enantioselective nitrile hydratase. The influence of the substrates on both reaction efficiency and enantioselectivity was also discussed in terms of steric and electronic effects. Coupled with chemical hydrolysis of D-(-)-alpha-phenylglycine amide, biotransformation of DL-phenylglycine nitrile was applied in practical scale to produce both D- and L-phenylglycines in high optical purity.

Amides↗
PubMed2003

Zinc carbenoid-mediated chain extension: preparation of alpha,beta-unsaturated-gamma-keto esters and amides.

An efficient one-pot preparation of alpha,beta-unsaturated-gamma-keto esters and amides has been developed. A zinc carbenoid-mediated chain extension of a beta-dicarbonyl substrate provides access to an intermediate zinc enolate, which is treated sequentially with a halogen and amine base. This method has been applied to a variety of ester and amide starting materials, as well as to amino acid-derived substrates and to a formal synthesis of (R,R)-(-)-pyrenophorin.

Amides↗
PubMed2002

Addition of organocerium reagents to morpholine amides: synthesis of important pheromone components of Achaea janata.

Readily preparable morpholine amides hitch in good yields with organocerium reagents to produce ketones. Even in the presence of substrates and reagents with high steric hindrance, the organometallic compounds prepared from dry cerium(III) chloride and organomagnesium or organolithium compounds at -78 degrees C add cleanly to morpholine amides. The low cost of starting materials makes this new scheme of synthesis very interesting for the preparation of biologically important pheromones.

Amides↗
PubMed2004

Straightforward synthesis of sphinganines via a serine-derived Weinreb amide.

Sphinganines can be synthesized in just three steps from easily prepared serine-derived Weinreb amide 4. Pre-deprotonation of the acidic (N-H and O-H) protons of 4 allows for its efficient conversion to amino ketones 5. Such ketones can be selectively reduced to either erythro- or threo-sphinganines. Partially protected sphinganines 11 are also readily accessible in five steps from 4. Thus, Weinreb amide 4 represents one of the most versatile templates described to date for sphinganine synthesis.

Amides↗
PubMed2003

Early amidation approach to 3-[(4-amido)pyrrol-2-yl]-2-indolinones.

A new synthesis of 3-[(4-amido)pyrrol-2-yl]-2-indolinones has been developed, where the amide side chain was installed prior to pyrrole formation. This strategy precludes the need to use any coupling reagents to install the amide side chain. This process includes a zinc-free alternative to the Knorr pyrrole synthesis.

Amides↗
PubMed2003

Michael addition of amines and thiols to dehydroalanine amides: a remarkable rate acceleration in water.

In water, the rate of Michael addition of amines and thiols to dehydroalanine amides was greatly accelerated, leading to shorter reaction times and higher yields. The scope of the new conditions was tested with a range of amines, thiols, and dehydroalanine amides. The ease and efficiency of this method provides an attractive route to the synthesis of natural and unnatural amino acid derivatives.

Alanine↗
PubMed2004

Novel chimeric scaffolds to extend the exploration of receptor space: hybrid beta-D-glucose-benzoheterodiazepine structures for broad screening. Effect of amide alkylation on the course of cyclization reactions.

New molecular platforms which are hybrids of two scaffolds-namely, beta-d-glucose and benzodiazepine, each able to bind several proteins-were designed, synthesized and functionalized to serve as probes for broad biological screening. Herein, we describe the syntheses and chemical properties of these novel chimeric scaffolds. Attempted cyclization of the functionalized analogues (-)-96 and (-)-97 afforded the corresponding dimers (-)-98 and (-)-99, respectively, under a variety of reaction conditions, even at concentrations of only 0.001 N. Consideration of factors affecting the conformation of amide bonds and their effects on cyclization reactions led us to alkylate the amide bond. As expected, the cyclization of the N-methyl derivative (-)-110 afforded exclusively the unimolecular cyclization product (+)-111. These compounds are only now undergoing broad screening and represent therefore at present a "prospecting library."

Alkylation↗
PubMed2005

Asymmetric synthesis of beta-amino carbonyl compounds with N-sulfinyl beta-amino Weinreb amides.

[reaction: see text] Diverse organometallic reagents readily add to enantiopure N-sulfinyl beta-amino Weinreb amides providing the corresponding, stable, N-sulfinyl beta-amino carbonyl compounds in good to excellent yields. This new methodology represents a general solution to the problem of beta-amino carbonyl syntheses, which are important chiral building blocks and constituents of natural products. N-Sulfinyl beta-amino Weinreb amides are prepared by reaction of the potassium enolate of N-methoxy N-methylacetamide with sulfinimines (N-sulfinyl imines) or lithium N,O-dimethylhydroxylamine with N-sulfinyl beta-amino esters.

Aldehydes↗
PubMed2004

Self-assembly of nanoscopic coordination cages using a flexible tripodal amide containing linker.

Flexible, nanoscopic 3D cages containing the amide functionality were prepared via coordination-driven self-assembly from palladium(II) based 90 degrees ditopic acceptor units and a tripod N,N',N''-tris(3-pyridyl)trimesic amide. Both cages were characterized by NMR ((31)P, (1)H) and electrospray ionization mass spectrometry. An MM2 force field simulation of one cage showed that the shape is likely pseudo trigonal bipyramidal with the diameter of the inner cavity of the cage about 1.9 nm.

Amides↗
PubMed2005

Efficient synthesis of chiral beta-seleno amides via ring-opening reaction of 2-oxazolines and their application in the palladium-catalyzed asymmetric allylic alkylation.

[structure: see text] A set of chiral beta-seleno amides have been efficiently synthesized via the ring-opening reaction of chiral 2-oxazolines by selenium nucleophiles. The present method is applicable to the synthesis of beta-seleno amides containing thioether, alcohol, and ether moieties in good yields. As an application, the synthesis of a selenocysteine derivative has been accomplished. Additionally, these new compounds were evaluated in the palladium-catalyzed asymmetric allylic alkylation, giving the alkylated products in up to 98% ee.

Alkylation↗
PubMed2005

Monomers for preparation of amide-linked RNA: asymmetric synthesis of all four nucleoside 5'-azido 3'-carboxylic acids.

[reaction: see text] Recent discovery of RNA interference as an efficient and naturally occurring mechanism of gene regulation has reinvigorated the interest in chemically modified RNA. For potential in-vivo applications small interfering RNAs require chemical modifications to fine-tune the thermal stability and increase the cellular delivery and potency and in vivo half-life of the RNA duplexes. From this perspective, amides as neutral and hydrophobic internucleoside linkages in RNA are highly interesting modifications for RNA interference. Amides are remarkably good mimics of the phosphodiester backbone of RNA and can be prepared using a relatively straightforward peptide coupling chemistry. However, the progress in the field has been hampered by the shortage of efficient methods to synthesize the monomeric building blocks for such couplings, the nucleoside amino acid equivalents. Herein, we report enantioselective synthesis of 5'-azido 3'-carboxylic acid derivatives of all four natural ribonucleosides. The key transformations in our synthesis are a double asymmetric ene reaction and a stereoselective iodolactonization that form the basic carbon skeleton of the modified ribose. Standard nucleoside synthesis is followed by a short and highly efficient protecting group manipulation to give the enantiomerically pure (>98%) title compounds in 9-10 steps and 15-19% overall yields starting from small achiral molecules. The present results are a significant improvement over our first-generation racemic synthesis and compare favorably with the previously reported synthesis from nucleoside and carbohydrate precursors.

Amides↗
PubMed2006

Intramolecular additions of various pi-nucleophiles to chemoselectively activated amides and application to the synthesis of (+/-)-tashiromine.

[reaction: see text] Vilsmeier-Haack type cyclizations proved to be particularly efficient for generating parts of the polycyclic cores of many alkaloids, although only monocyclizations have so far been reported. With the goal of rapidly and efficiently constructing polycyclic alkaloids, we decided to exploit the Vilsmeier-Haack reaction by utilizing iminium ions successively generated and trapped with tethered nucleophiles. To develop such a strategy, we had to set the first cyclization. This constitutes a great challenge in itself because amide activation conditions are usually not compatible with tethered nucleophiles, except for indoles and aromatic rings which have already been reported. This paper describes the comprehensive study of intramolecular addition of silyl enol ethers, allylsilanes, and enamines to chemoselectively activated formamides, aliphatic amides, and lactams. Good to excellent yields were obtained for the 5-exo, 6-exo, and 6-endo modes of cyclization. Moreover, we demonstrated that the species in solution after the cyclization are iminium ions. This is highly encouraging for the development of bis-cyclization strategies. An expeditious total synthesis of (+/-)-tashiromine is also reported.

Alkaloids↗
PubMed2006

Halo substituent effects on intramolecular cycloadditions involving furanyl amides.

Intramolecular Diels-Alder reactions involving a series of N-alkenyl-substituted furanyl amides were investigated. Stable functionalized oxanorbornenes were formed in high yield upon heating at 80-110 degrees C. The cycloaddition reactions include several bromo-substituted furanyl amides, and these systems were found to proceed at a much faster rate and in higher yield than without substitution. This effect was observed by incorporating a halogen in the 3- or 5-position of the furan ring and appears to be general. The origin of increased cycloaddition rates for halo-substituted furans has been investigated with quantum mechanical calculations. The success of these reactions is attributed to increases in reaction exothermicities; this both decreases activation enthalpies and increases barriers to retrocycloadditions. Halogen substitution on furan increases reactant energy and stabilizes the product, which is attributed to the preference of electronegative halogens to be attached to a more highly alkylated and therefore more electropositive framework.

Amides↗
PubMed2000

An activated O --> N acyl transfer auxiliary: efficient amide-backbone substitution of hindered "difficult" peptides.

Overcoming the phenomenon known as "difficult" synthetic sequences has been a major goal in solid-phase peptide synthesis for over 30 years. In this work the advantages of amide backbone-substitution in the solid-phase synthesis of "difficult" peptides are augmented by developing an activated N(alpha)()-acyl transfer auxiliary. Apart from disrupting troublesome intermolecular hydrogen-bonding networks, the primary function of the activated N(alpha)()-auxiliary was to facilitate clean and efficient acyl capture of large or beta-branched amino acids and improve acyl transfer yields to the secondary N(alpha)()-amine. We found o-hydroxyl-substituted nitrobenzyl (Hnb) groups were suitable N(alpha)()-auxiliaries for this purpose. The relative acyl transfer efficiency of the Hnb auxiliary was superior to the 2-hydroxy-4-methoxybenzyl (Hmb) auxiliary with protected amino acids of varying size. Significantly, this difference in efficiency was more pronounced between more sterically demanding amino acids. The Hnb auxiliary is readily incorporated at the N(alpha)()-amine during SPPS by reductive alkylation of its corresponding benzaldehyde derivative and conveniently removed by mild photolysis at 366 nm. The usefulness of the Hnb auxiliary for the improvement of coupling efficiencies in the chain-assembly of difficult peptides was demonstrated by the efficient Hnb-assisted Fmoc solid-phase synthesis of a known hindered difficult peptide sequence, STAT-91. This work suggests the Hnb auxiliary will significantly enhance our ability to synthesize difficult polypeptides and increases the applicability of amide-backbone substitution.

Acylation↗
PubMed2005

Dynamics of amide-I modes of the alanine dipeptide in D2O.

The equilibrium dynamics of the acetyl and amino amide-I groups of the alanine dipeptide were examined separately using (13)C isotopic selection and 2D IR. The population relaxation times of the amide transitions were measured to be in the range 500 fs by means of heterodyne transient grating methods. The vibrational frequency correlation functions consisted in all cases of a motionally narrowed part, a component near 800 fs, and a constant part representing a distribution of structures that is static on the few ps time scale. The intermediate time scale is attributed to fluctuations in the stretching and bending of hydrogen bonds between the carbonyl and water.

Alanine↗