A "nanonecklace" synthesized from monofunctionalized gold nanoparticles

Gold nanoparticles with a single carboxylic acid group on the surface were prepared from a solid phase place exchange reaction and then coupled to polylysine using an in situ activation agent, diisopropylcarbodiimide (DIPCDI). The covalent amide bond linkage between the nanoparticles and polylysine and the ring closure of the polylysine chain have led to the formation of a nanoparticle/polymer hybrid material with "nanonecklace" structures.     

Neighboring pyrrolidine amide participation in thioether oxidation. Methionine as a "hopping" site

Methionine residues have been shown to function as efficient "hopping" sites in long-range electron transfer in model polyprolyl peptides. We suggest that a key to this ability of methionine is stabilization of the transient sulfur radical cation by neighboring proline amide participation. That is, in a model system a neighboring pyrrolidine amide lowers the oxidation potential of the thioether by over 0.5 V by formation of a two-center three-electron SO bond.     

A versatile synthetic approach to peptidyl privileged structures using a "safety-catch" linker

Peptidyl privileged structures have been widely used by many groups to discover biologically active molecules. In this context, privileged substructures are used as "hydrophobic anchors", to which peptide functionality is appended to gain specificity. Utilization of this concept has led to the discovery of many different active compounds at a wide range of biological receptors. A synthetic approach to these compounds has been developed on a "safety-catch" linker that allows rapid preparation of large libraries of these molecules. Importantly, amide bond formation/cleavage through treatment with amines is the final step; it is a linker strategy that allows significant diversification to be easily incorporated, and it only requires the inclusion of an amide bond. In addition, chemistry has been developed that permits the urea moiety to be inserted at the N-terminus of the peptide, allowing the same set of amines (either privileged substructures or amino acid analogues) to be used at both the N- and C-termini of the molecule. To show the robustness of this approach, a small library of peptidyl privileged structures were synthesized, illustrating that large combinatorial libraries can be synthesized using these technologies.     

Azide-derivatized gold nanorods: functional materials for "click" chemistry

We describe herein the synthesis of functional gold nanorods suitable for carrying out "click" chemistry reactions. Gold nanorods modified with a copolymer containing sulfonate and maleic acid groups have been conjugated to a bifunctional azide molecule (amine-PEG-azide). The maleic acid molecules in the copolymer participate in carbodiimide-mediated amide bond formation with amine groups of the azide linker, whereas the sulfonate groups prevent nanorod aggregation in water. Spectroscopic and zeta-potential measurements have been used to confirm the successful surface modification of the gold nanorods. These azide-functionalized nanorods can carry out chemical reactions based on click chemistry. As a case study, we have demonstrated the "clicking" of azide-nanorods to an acetylene-functionalized enzyme, trypsin, by a copper-catalyzed 1,3-dipolar cycloaddition reaction. The enzyme is not only stable after bioconjugation but is also biologically active, as demonstrated by its digestion of the protein casein. For comparison, the biological activity of trypsin conjugated to gold nanorods by two other commonly used methods (carbodiimide-mediated covalent attachment via amide bond formation and simple electrostatic adsorption) has been studied. The enzyme conjugated by click chemistry demonstrates improved biological activity compared with other forms of bioconjugation. This general and simple approach is easy, specific with higher yields, environmentally benign, and applicable to a wide range of analytes and biomolecules.     

"Amide resonance" correlates with a breadth of C-N rotation barriers

Complete basis set calculations (CBS-QB3) were used to compute the CN rotation barriers for acetamide and eight related compounds, including acetamide enolate and O-protonated acetamide. Natural resonance theory analysis was employed to quantify the "amide resonance" contribution to ground-state electronic structures. A range of rotation barriers, spanning nearly 50 kcal/mol, correlates well to the ground-state resonance weights without the need to account for transition-state effects. Use of appropriate model compounds is crucial to gain an understanding of the structural and electronic changes taking place during rotation of the CN bond in acetamide. The disparate changes in bond length (DeltarCO < DeltarCN) are found to be consonant with the resonance model. Similarly, charge differences are consistent with donation from the nitrogen lone pair electrons into the carbonyl pi* orbital. Despite recent attacks on the resonance model, these findings demonstrate it to be a sophisticated and highly predictive tool in the chemist's arsenal.     

Synthesis and antibiofilm activity of a second-generation reverse-amide oroidin library: a structure-activity relationship study

A second-generation library of 2-aminoimidazole-based derivatives incorporating a "reversed amide" (RA) motif in comparison to the marine natural product oroidin were synthesized and subsequently assayed for antibiofilm activity against the medically relevant Gram-negative proteobacteria P. aeruginosa and A. baumannii. Most notably, an in-depth activity profile is reported for the most active subclass of derivatives that bear linear aliphatic chains off the amide bond. Additionally, further structural modifications of the core template, such as removal of the amide bond or substitution with a triazole isostere, resulted in the discovery of analogues with antibiofilm activities that varied with respect to their inhibition and dispersal properties of P. aeruginosa and A. baumannii biofilms.     

Ab initio computational study of 1-methyl-4-silatranone and attempts at its conventional synthesis

1-Methyl-4-silatranone could exhibit the structural aspects of a typical silatrane including a short N–Si bond distance reflecting a dative bond. But given the significant amide resonance in a [3.3.3] bridgehead bicyclic lactam, the lone pair could be shared with the carbonyl group leading to a very long N–Si bond, essentially a “non-silatrane.” Ab initio calculations (MP2/6-311 + G*) predict that ground state conformations of this molecule are best regarded as lactams rather than silatranes, the most stable having a calculated N–Si bond length of 2.902 Å and an N–CO bond length of 1.387 Å. The calculated transition state for inversion of the amide ring retains very little amide resonance (N–CO, 1.440 Å). Some of this loss is compensated through tightening of the N–Si bond (2.422 Å), leading to a net energy of activation of ca 8 kcal/mol. Attempts to synthesize 1-methyl-4-silatranone using conventional pathways successful for 1-methylsilatrane [condensations employing N,N-bis(2-hydroxyethyl)glycolamide in place of tris(2-hydroxyethyl)amine] were unsuccessful. This is due to the net loss in resonance energy of the amide reactant relative to that in the [3.3.3] system, the essential absence of the N–Si dative bond, and the rigidity introduced by the planar amide linkage in the starting material. A more likely pathway to successful synthesis should be formation of the amide linkage in the final step.     

Solvatochromism of heteroaromatic compounds: XXX. <Emphasis Type="Italic">N</Emphasis>-Methyltrifluoromethanesulfonamide as hydrogen-bond donor

In two-centered H-complexes with protophilic solvents, the monomer of N-methyltrifluoromethanesulfonamide I behaves as a strong H-bond donor, stronger than 4-fluorophenol and ranking second after 4-nitrophenol. In protophilic media, amide I exists as monomeric H-complexes with a two-centered H-bond and 1:2 H-complexes of the open-chair dimer with a bifurcated (three-centered) hydrogen bond. The formation of a strong bifurcated H-bond weaken the bridging N-H.‥O=S bond.     

Toward a general mechanism of electron capture dissociation

The effects of positive charge on the properties of ammonium and amide radicals were investigated by ab initio and density functional theory calculations with the goal of elucidating the energetics of electron capture dissociation (ECD) of multiply charged peptide ions. The electronic properties of the amide group in N-methylacetamide (NMA) are greatly affected by the presence of a remote charge in the form of a point charge, methylammonium, or guanidinium cations. The common effect of the remote charge is an increase of the electron affinity of the amide group, resulting in exothermic electron capture. The N-Calpha bond dissociation and transition state energies in charge-stabilized NMA anions are 20-50 kJ mol(-1) greater than in the hydrogen atom adduct. The zwitterions formed by electron capture have proton affinities that were calculated as 1030-1350 kJ mol(-1), and are sufficiently basic for the amide carbonyl to exothermically abstract a proton from the ammonium, guanidinium and imidazolium groups in protonated lysine, arginine, and histidine residues, respectively. A new mechanism is proposed for ECD of multiply charged peptide and protein cations in which the electron enters a charge-stabilized electronic state delocalized over the amide group, which is a superbase that abstracts a proton from a sterically proximate amino acid residue to form a labile aminoketyl radical that dissociates by N-Calpha bond cleavage. This mechanism explains the low selectivity of N-Calpha bond dissociations induced by electron capture, and is applicable to dissociations of peptide ions in which the charge carriers are metal ions or quaternary ammonium groups. The new amide superbase and the previously proposed mechanisms of ECD can be uniformly viewed as being triggered by intramolecular proton transfer in charge-reduced amide cation-radicals. In contrast, remote charge affects N-H bond dissociation in weakly bound ground electronic states of hypervalent ammonium radicals, as represented by methylammonium, CH3NH3*, but has a negligible effect on the N-H bond dissociation in the strongly bound excited electronic states. This refutes previous speculations that loss of "hot hydrogen" can occur from an excited state of an ammonium radical.     

Photochemistry of <Emphasis Type="Italic">N</Emphasis>-substituted salicylic acid amides

The products of photolysis of N-substituted salicylic acid amides, viz., 2-hydroxy-3-tert-butyl-5-ethylbenzoic acid N-(4-hydroxy-3,5-di-tert-butylphenyl)amide (1) and 2-hydroxybenzoic acid N-[3-(4-hydroxy-3,5-di-tert-butylphenyl)prop-1-yl]amide (2), in heptane were studied by optical spectroscopy and stationary and nanosecond laser photolysis (Nd: YAG laser, 355 nm). It was shown by the method of partial deuteration of amides 1 and 2 that they exist in both the unbound state and as complexes with intraand intermolecular hydrogen bond. Amides 1 and 2 are subjected to photolysis, which results in the formation of a triplet state and phenoxyl radicals RO? presumably due to the absorption of the second photon by the excited singlet state. The formation of radical products due to N–H bond ionization was not observed. The main channel of decay of the triplet state and radicals RO? is triplet–triplet annihilation and recombination (k _r ≈ 2.3?10⁸ L mol^–1 s^–1), respectively. The UV irradiation of compounds 1 and 2 leads to the excitation of the amide groups, and no formation of radical products due to N–H bond ionization was observed.     

Amide bond cleavage: acceleration due to a 1,3-diaxial interaction with a carboxylic acid

To independently assess the contribution of ground-state pseudoallylic strain to the enormous rates of amide bond cleavage in tertiary amide derivatives of Kemp's triacid, we have studied four amide derivatives of (1alpha-3alpha-5beta)-5-tert-butyl-1,3-cyclohexanedicarboxylic acid. Our results demonstrate that absent pseudoallylic strain, a 1,3-diaxial interaction of an amide with a carboxylic acid leads to only a 2400-fold increase in the rate of amide bond cleavage as compared with the rate of hydrolysis of an unactivated peptide bond.     

Total synthesis of (+)-galanthamine starting from d-glucose

The stereoselective total synthesis of (+)-galanthamine (+)-1 starting from d-glucose is described. The cyclohexene ring in (+)-1 was prepared in an optically active form from d-glucose using Ferrier’s carbocyclization reaction, and the critical quaternary carbon was stereoselectively generated via chirality transfer based on the Claisen rearrangement of a cyclohexenol. The dibenzofuran skeleton was effectively constructed by the bromonium ion-mediated intramolecular cyclization of a cyclohexene possessing a phenolic ether function. After the introduction of a carbon-carbon double bond, the Pictet-Spengler type cyclization, followed by the reduction of the amide function completed the chiral synthesis of (+)-1.     

Synthesis of organogelling, fluoride ion-responsive, cholesteryl-based benzoxazole containing intra- and intermolecular hydrogen-bonding sites

A cholesteryl-based 2-(2′-hydroxyphenyl)benzoxazole (HPB) derivative 3 linked with an amide bond was prepared through an efficient synthetic pathway. The HPB, amide, and cholesteryl groups play important roles in constructing the supramolecular gel structure. UV-vis and fluorescence spectroscopy also showed that HPB and amide groups, which provide intra- and intermolecular hydrogen bonding, respectively, also contribute the recognition of fluoride anions.     

Chemoselective Intramolecular Formal Insertion Reaction of Rh–Nitrenes into an Amide Bond Over C−H Insertion

The past few decades have witnessed extensive efforts to disclose the unique reactivity of metal–nitrenes, because they could be a powerful synthetic tool for introducing the amine functionality into unactivated chemical bonds. The reactivity of metal–nitrenes, however, is currently mainly confined to aziridination (an insertion into a C=C bond) and C−H amination (an insertion into a C−H bond). Nitrene insertion into an amide C−N bond, however, has not been reported so far. In this work we have developed a rhodium-catalyzed one-nitrogen insertion into amide C−N and sulfonamide S−N bonds. Experimental and theoretical analyses based on density functional theory indicate that the formal amide insertion proceeds via a rhodium-coordinated ammonium ylide formed between the nitrene and the amide nitrogen, followed by acyl group transfer concomitant with C−N bond cleavage. Mechanistic studies have allowed rationalization of the origin of the chemoselectivity observed between the C−H and amide insertion reactions. The methodology presented herein is the first example of an insertion of nitrene into amide bonds and provides facile access to unique diazacyclic systems with an N−N bond linkage.     

A novel salt bridge mechanism highlights the need for nonmobile proton conditions to promote disulfide bond cleavage in protonated peptides under low-energy collisional activation

The gas-phase fragmentation mechanisms of small models for peptides containing intermolecular disulfide links have been studied using a combination of tandem mass spectrometry experiments, isotopic labeling, structural labeling, accurate mass measurements of product ions, and theoretical calculations (at the MP2/6-311 + G(2d,p)//B3LYP/3-21G(d) level of theory). Cystine and its C-terminal derivatives were observed to fragment via a range of pathways, including loss of neutral molecules, amide bond cleavage, and S-S and C-S bond cleavages. Various mechanisms were considered to rationalize S-S and C-S bond cleavage processes, including charge directed neighboring group processes and nonmobile proton salt bridge mechanism. Three low-energy fragmentation pathways were identified from theoretical calculations on cystine N-methyl amide: (1) S-S bond cleavage dominated by a neighboring group process involving the C-terminal amide N to form either a protonated cysteine derivative or protonated sulfenyl amide product ion (44.3 kcal mol(-1)); (2) C-S bond cleavage via a salt bridge mechanism, involving abstraction of the alpha-hydrogen by the N-terminal amino group to form a protonated thiocysteine derivative (35.0 kcal mol(-1)); and (3) C-S bond cleavage via a Grob-like fragmentation process in which the nucleophilic N-terminal amino group forms a protonated dithiazolidine (57.9 kcal mol(-1)). Interestingly, C-S bond cleavage by neighboring group processes have high activation barriers (63.1 kcal mol(-1)) and are thus not expected to be accessible during low-energy CID experiments. In comparison to the energetics of simple amide bond cleavage, these S-S and C-S bond cleavage reactions are higher in energy, which helps rationalize why bond cleavage processes involving the disulfide bond are rarely observed for low-energy CID of peptides with mobile proton(s) containing intermolecular disulfide bonds. On the other hand, the absence of a mobile proton appears to "switch on" disulfide bond cleavage reactions, which can be rationalized by the salt bridge mechanism. This potentially has important ramifications in explaining the prevalence of disulfide bond cleavage in singly protonated peptides under MALDI conditions.     

Chemical transformations of tetracyclo[3.3.1.1<Superscript>3,7</Superscript>.0<Superscript>1,3</Superscript>]decane (1,3-dehydroadamantane): II. Reaction of 1,3-dehydroadamantane with <Emphasis Type="Italic">N,N</Emphasis>-dialkylcarboxamides

Alkylation of N,N-dialkylcarboxamides with 1,3-dehydroadamantane has been accomplished for the first time. The reaction involves the C–H bond in the α-position with respect to the carbonyl group and provides a convenient one-step preparation of substituted carboxylic acid amides containing an 1-adamantyl substituent and a pharmacophoric group in the amide moiety.     

Toward assessing the position-dependent contributions of backbone hydrogen bonding to beta-sheet folding thermodynamics employing amide-to-ester perturbations

An amide-to-ester backbone substitution in a protein is accomplished by replacing an alpha-amino acid residue with the corresponding alpha-hydroxy acid, preserving stereochemistry, and conformation of the backbone and the structure of the side chain. This substitution replaces the amide NH (a hydrogen bond donor) with an ester O (which is not a hydrogen bond donor) and the amide carbonyl (a strong hydrogen bond acceptor) with an ester carbonyl (a weaker hydrogen bond acceptor), thus perturbing folding energetics. Amide-to-ester perturbations were used to evaluate the thermodynamic contribution of each hydrogen bond in the PIN WW domain, a three-stranded beta-sheet protein. Our results reveal that removing a hydrogen bond donor destabilizes the native state more than weakening a hydrogen bond acceptor and that the degree of destabilization is strongly dependent on the location of the amide bond replaced. Hydrogen bonds near turns or at the ends of beta-strands are less influential than hydrogen bonds that are protected within a hydrophobic core. Beta-sheet destabilization caused by an amide-to-ester substitution cannot be directly related to hydrogen bond strength because of differences in the solvation and electrostatic interactions of amides and esters. We propose corrections for these differences to obtain approximate hydrogen bond strengths from destabilization energies. These corrections, however, do not alter the trends noted above, indicating that the destabilization energy of an amide-to-ester mutation is a good first-order approximation of the free energy of formation of a backbone amide hydrogen bond.     

Transformation of a [4+6] Salicylbisimine Cage to Chemically Robust Amide Cages

In recent years, interest in shape‐persistent organic cage compounds has steadily increased, not least because dynamic covalent bond formation enables such structures to be made in high to excellent yields. One often used type of dynamic bond formation is the generation of an imine bond from an aldehyde and an amine. Although the reversibility of the imine bond formation is advantageous for high yields, it is disadvantageous for the chemical stability of the compounds. Amide bonds are, in contrast to imine bonds much more robust. Shape‐persistent amide cages have so far been made by irreversible amide bond formations in multiple steps, very often accompanied by low yields. Here, we present an approach to shape‐persistent amide cages by exploiting a high‐yielding reversible cage formation in the first step, and a Pinnick oxidation as a key step to access the amide cages in just three steps. These chemically robust amide cages can be further transformed by bromination or nitration to allow post‐functionalization in high yields. The impact of the substituents on the gas sorption behavior was also investigated.     

The recognition and sensing of anions through "positive allosteric effects" using simple urea-amide receptors

The design, synthesis, and X-ray crystallographic analysis of three simple diaryl-urea based anion receptors possessing an amide moiety on one of the aryl groups, and an electron withdrawing CF(3) group on the other, is described. The three receptors differ only in the position of the amide functionality relative to the hydrogen bonding urea moiety (being para, meta, and ortho for 1, 2, and 3, respectively). This simple modification was shown to have a significant effect on the anion recognition ability, the strength of the recognition process, and the stoichiometry (host/guest) for these sensors. We demonstrate, by using both UV-vis absorption and (1)H NMR spectroscopy, that these factors are caused by the ability of the amide moiety to both modulate the anion binding selectivity and the sensitivity of the urea moiety. We also demonstrate that, in the case of 1 and 2, this anion recognition at the urea moiety leads to concomitant activation (through enhanced inductive effect) in the amide functionality toward anions, which leads to the formation of an overall 1:2 (sensor/anion) binding stoichiometry for these receptors. This "activation" we describe as being an example of a "positive allosteric activation" by the urea site, caused directly by the first anion binding interaction, which to the best of our knowledge, has not been previously demonstrated for anion recognition and sensing.