Broadband Multidimensional Spectroscopy Identifies the Amide II Vibrations in Silkworm Films

We used two-dimensional infrared spectroscopy to disentangle the broad infrared band in the amide II vibrational regions of Bombyx mori native silk films, identifying the single amide II modes and correlating them to specific secondary structure. Amide I and amide II modes have a strong vibrational coupling, which manifests as cross-peaks in 2D infrared spectra with frequencies determined by both the amide I and amide II frequencies of the same secondary structure. By cross referencing with well-known amide I assignments, we determined that the amide II (N-H) absorbs at around 1552 and at 1530 cm^–1 for helical and β-sheet structures, respectively. We also observed a peak at 1517 cm⁻¹ that could not be easily assigned to an amide II mode, and instead we tentatively assigned it to a Tyrosine sidechain. These results stand in contrast with previous findings from linear infrared spectroscopy, highlighting the ability of multidimensional spectroscopy for untangling convoluted spectra, and suggesting the need for caution when assigning silk amide II spectra.     

Vibrational relaxation pathways of amide I and amide II modes in N-methylacetamide

We studied the vibrational energy relaxation mechanisms of the amide I and amide II modes of N-methylacetamide (NMA) monomers dissolved in bromoform using polarization-resolved femtosecond two-color vibrational spectroscopy. The results show that the excited amide I vibration transfers its excitation energy to the amide II vibration with a time constant of 8.3 ± 1 ps. In addition to this energy exchange process, we observe that the excited amide I and amide II vibrations both relax to a final thermal state. For the amide I mode this latter process dominates the vibrational relaxation of this mode. We find that the vibrational relaxation of the amide I mode depends on frequency which can be well explained from the presence of two subbands with different vibrational lifetimes (~1.1 ps on the low frequency side and ~2.7 ps on the high frequency side) in the amide I absorption spectrum.     

Amide Synthesis by Nickel/Photoredox‐Catalyzed Direct Carbamoylation of (Hetero)Aryl Bromides

Herein, we report a one‐electron strategy for catalytic amide synthesis that enables the direct carbamoylation of (hetero)aryl bromides. This radical cross‐coupling approach, which is based on the combination of nickel and photoredox catalysis, proceeds at ambient temperature and uses readily available dihydropyridines as precursors of carbamoyl radicals. The method's mild reaction conditions make it tolerant of sensitive‐functional‐group‐containing substrates and allow the installation of an amide scaffold within biologically relevant heterocycles. In addition, we installed amide functionalities bearing electron‐poor and sterically hindered amine moieties, which would be difficult to prepare with classical dehydrative condensation methods.     

Unprecedented Sequence Control and Sequence-Driven Properties in a Series of AB-Alternating Copolymers Consisting Solely of Acrylamide Units

Herein, we report a method to synthesize a series of alternating copolymers that consist exclusively of acrylamide units. Crucial to realizing this polymer synthesis is the design of a divinyl monomer that contains acrylate and acrylamide moieties connected by two activated ester bonds. This design, which is based on the reactivity ratio of the embedded vinyl groups, allows a “selective” cyclopolymerization, wherein the intramolecular and intermolecular propagation are repeated alternately under dilute conditions. The addition of an amine to the resulting cyclopolymers afforded two different acryl amide units, i.e., an amine-substituted acryl amide and a 2-hydroxy-ethyl-substituted acryl amide in alternating sequence. Using this method, we could furnish ten types of alternating copolymers; some of these exhibit unique properties in solution and in the bulk, which are different from those of the corresponding random copolymers, and we attributed the differences to the alternating sequence.     

A case study of solid state inhibition lock opening of pyridine N-oxide in dicarboxylic acid recognition

An ethylene-linked mixed pyridine diamide receptor 1 is synthesised to study the binding with dicarboxylic acid in solid phase. In ¹H NMR, the amide proton adjacent to pyridine N-oxide shows almost negligible shift, which suggests the non-participation of the amide proton for acid binding in solution. However, in solid phase (X-ray, IR), we have found significant role of this amide proton in binding.     

Unveiling the Role of Hydrogen Bonds in Luminescent N-Annulated Perylene Liquid Crystals

We report the liquid-crystalline (LC) and luminescent properties of a series of N-annulated perylenes ( 1 – 4 ) in whose molecular structures amide and ester groups alternate. We found that the LC properties of these compounds not only depend on the number of hydrogen-bonding units, but also on the relative position of the amide linkers in the molecule. The absence of amide groups in compound 1 leads to no LC properties, whereas four amide groups induce the formation of a wide temperature range columnar hexagonal phase in compound 4 . Remarkably, compound 3 , with two amide groups in the inner part of the structure, stabilizes the columnar LC phases better than its structural isomer 2 , with the amide groups in the outer part of the molecule. Similarly, we found that only compounds 1 and 2 , which have no hydrogen bonding units in the inner part of the molecule, exhibit luminescence vapochromism upon exposure to organic solvent vapors.     

Unprecedented Sequence Control and Sequence‐Driven Properties in a Series of AB‐Alternating Copolymers Consisting Solely of Acrylamide Units

Herein, we report a method to synthesize a series of alternating copolymers that consist exclusively of acrylamide units. Crucial to realizing this polymer synthesis is the design of a divinyl monomer that contains acrylate and acrylamide moieties connected by two activated ester bonds. This design, which is based on the reactivity ratio of the embedded vinyl groups, allows a “selective” cyclopolymerization, wherein the intramolecular and intermolecular propagation are repeated alternately under dilute conditions. The addition of an amine to the resulting cyclopolymers afforded two different acryl amide units, i.e., an amine‐substituted acryl amide and a 2‐hydroxy‐ethyl‐substituted acryl amide in alternating sequence. Using this method, we could furnish ten types of alternating copolymers; some of these exhibit unique properties in solution and in the bulk, which are different from those of the corresponding random copolymers, and we attributed the differences to the alternating sequence.     

A "traceless" Staudinger ligation for the chemoselective synthesis of amide bonds

[reaction: see text] Here we report a novel modification of our previously reported "Staudinger ligation" that generates an amide bond from an azide and a specifically functionalized phosphine. This method for the selective formation of an amide bond, which does not require the orthogonal protection of distal functional groups, should find general utility in synthetic and biological chemistry.     

In situ Detection of Amide A Bands of Proteins in Water by Raman Ratio Spectrum

The amide A band of protein is sensitive to the hydrogen bands of amide groups of proteins. However, it is hard to distinguish the amide A band of aqueous protein in situ directly, since it overlaps with O-H stretching vibration of water. In this work, we presented a new analytical method of Raman ratio spectrum, which can extract the amide A band of proteins in water. To obtain the Raman ratio spectrum, the Raman spectrum of aqueous protein was divided by that of pure water. A mathematical simulation was employed to examine whether Raman ratio spectrum is effective. Two kinds of protein, lysozyme and α-chymotrypsin were employed. The amide A bands of them in water were extracted from Raman ratio spectra. Additionally, the process of thermal denaturation of lysozyme was detected from Raman ratio spectrum. These results demonstrated the Raman ratio spectra could be employed to study the amide A modes of proteins in water.     

Synthesis of the molecular hybrid inspired by Largazole and Psammaplin A

One important class of HDAC (histone deacetylation enzymes) inhibitors is the sulfur-containing marine natural products with structural diversity. Inspired by two structurally distinguishing examples, Largazole and Psammaplin A, which possess macrocyclic depsipeptide and simple linear amide scaffold respectively, we designed one novel molecular hybrid by replacing the alkene moiety in Largazole with a semirigid amide bond. This hybrid compound has been synthesized from l-malic acid in 10 steps with an overall yield of 7%. The preliminary biological assays suggest that the replacement of trans olefin moiety with amide bond will lead to an unbeneficial effect on the inhibition against HDACs.     

Thiostrepton maturation involving a deesterification-amidation way to process the C-terminally methylated peptide backbone

Thiopeptides are a class of clinically interesting and highly modified peptide antibiotics. Their biosyntheses share a common paradigm for characteristic core formation but differ in tailoring to afford individual members. Herein we report an unusual deesterification-amidation process in thiostrepton maturation to furnish the terminal amide moiety. TsrB, serving as a carboxylesterase, catalyzes the hydrolysis of the methyl ester intermediate to provide the carboxylate intermediate, which can be converted to the amide product by an amidotransferase, TsrC. These findings revealed a C-terminal methylation of the precursor peptide, which is cryptic in thiostrepton biosynthesis but potentially common in the formation of its homologous series of thiopeptides that vary in the C-terminal form as methyl ester, carboxylate, or amide.     

Does Urea Preferentially Interact with Amide Moieties or Nonpolar Sidechains? A Question Answered Through a Judicious Selection of Model Systems

The transfer model suggests that urea unfolds proteins mainly by increasing the solubility of the amide backbone, probably through urea-induced increase in hydrogen bonding. Other studies suggest that urea addition increases the magnitude of solvent-solute van der Waals interactions, which increases the solubility of nonpolar sidechains. More recent analyses hypothesize that urea has a similar effect in increasing the solubility of backbone and sidechain groups. In this work, we compare the effects of urea addition on the solvation of amides and alkyl groups. At first, we study the effects of urea addition upon solvent hydrogen bonding acidity and basicity through the perturbation in the fluorescence spectrum of probes 1-AN and 1-DMAN. Our results demonstrate that the solvent's hydrogen bonding properties are minimally affected by urea addition. Subsequently, we show that urea addition does not perturb the intra-molecular hydrogen bonding in salicylic acid significantly. Finally, we investigate how urea preferentially interacts with amide and alkyl groups moieties in water by comparing the effects of urea addition upon the solubility of acetaminophen and 4-tertbutylphenol. We show that urea affects amide and t-butyl solubility (lowers the transfer free energy of both amide (backbone) and alkyl (sidechain) groups) in a similar fashion. In other words, preferential interaction of urea with both moieties contributes to protein denaturation.     

Powerful amide synthesis from alcohols and amines under aerobic conditions catalyzed by gold or gold/iron, -nickel or -cobalt nanoparticles

Considering the importance of the development of powerful green catalysts and the omnipresence of amide bonds in natural and synthetic compounds, we report here on reactions between alcohols and amines for amide bond formation in which heterogeneous gold and gold/iron, -nickel, or -cobalt nanoparticles are used as catalysts and molecular oxygen is used as terminal oxidant. Two catalysts show excellent activity and selectivity, depending on the type of alcohols used. A wide variety of alcohols and amines, including aqueous ammonia and amino acids, can be used for the amide synthesis. Furthermore, the catalysts can be recovered and reused several times without loss of activity.     

Surface-enhanced Raman spectroscopic studies of coactivator-associated arginine methyltransferase 1

We report, for the first time, the surface-enhanced Raman spectra of an important enzyme, coactivator-associated arginine methyltransferase 1 (CARM1), involved in various biological activities such as tumor suppressor function and stem cell differentiation. We have employed surface-enhanced Raman scattering (SERS) to obtain insight into the structural details of CARM1 by adsorbing it to silver (Ag) nanoparticles. The enzyme retains its activity even after its adsorption onto Ag nanoparticles. We observe strong SERS modes arising from amide vibrations and aromatic ring amino acids. The SERS spectra revealed amide I bands at 1637 cm(-1) and 1666 cm(-1), which arise as a result of the alpha helix of the protein and the polypeptide backbone vibration of a random coil, respectively. In order to confirm the amide vibrations, we have performed SERS on deuterated CARM1, which exhibits a clear red shift in amide band positions. The SERS spectra may provide useful information, which could be harnessed to study the functional interactions of CARM1 with small molecule modulators.     

Rapid cleavage of unactivated, unstrained amide bonds at neutral pH

Building upon the discovery of Suggs and Pires that N-(2-hydroxyethyl)glycine amides undergo rapid amide cleavage under mild conditions [ Suggs, J. W. ; Pires, R. M. Tetrahedron Lett. 1997, 38, 2227-2230 ], we synthesized the derivatives (4aalpha,8beta,8aalpha)-1-ethylamido-8-hydroxydecahydroquinoline ( 4) and (4aalpha,8alpha,8abeta)-1-ethylamido-8-hydroxydecahydroquinoline ( 5). These two species are conformationally constrained, but steric compression is not introduced between the hydroxyl group and the amide functionality it attacks. At 20 degrees C and slightly basic pH, derivatives 4 and 5 undergo amide cleavage with half-lives of 21 min and 14 h, respectively, which correspond to rate increases of 251- and 6.3-fold relative to the acyclic analogue N-(2-hydroxyethyl)glycine amide ( 3).     

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.     

Label-free detection of protein-protein interactions at the GaAs/water interface through surface infrared spectroscopy: discrimination between specific and nonspecific interactions by using secondary structure analysis

Here, we propose a label-free detection of protein-protein interactions that enables simultaneous qualitative analysis of target proteins by using Fourier transform infrared (FTIR) absorption spectroscopy in multiple internal reflection geometry (MIR-FTIR). Using this method, the target proteins were detected based on the peak height of the amide I and amide II bands, while discrimination of specific and nonspecific signals is made based on the secondary structure of the analytes, which is determined through second-derivative analysis of the amide I band. As a model system, an antigen peptide was immobilized on the surface of GaAs, which was transparent to mid-infrared light, and the interaction with its antibody was examined in aqueous media. We demonstrated that the binding of the antibody to the antigen immobilized on a GaAs surface selectively gave rise to beta-sheet amide I vibrations (1639 and 1690 cm-1), while no structurally related signals were induced by nonspecifically adsorbed proteins. The peak height of the beta-peak (1639 cm-1) in the amide I band linearly increased with the antiserum concentration as well as that of the amide II band. The detection limit (S/N = 3) was a 1:36 000 dilution for the amide I signal. In addition, through the use of surface-sensitive MIR-FTIR, the present sensor selectively detected the antigen-antibody interactions at the surfaces without being affected by the presence of bulk species, enabling rapid and wash-free detection. Our method provides not only rapid label-free detection of protein-protein interactions but a more accurate discrimination between specific and nonspecific interactions through the use of the secondary structure of the target proteins as a measure for the specific signals.     

Contribution of intramolecular C=O...H-N hydrogen bonding to the solvent-induced reentrant phase separation of poly(N-isopropylacrylamide)

Changes in the local environment around amide groups of poly(N-isopropylacrylamide) (PNiPA) during a solvent-induced reentrant phase separation have been investigated by infrared spectroscopy combined with quantum chemical calculations. The addition of methanol or tetrahydrofuran as a cosolvent to an aqueous solution of PNiPA causes spectral changes in the amide I regions. By preparing a dimer model compound for PNiPA, we can establish the assignment of the amide I bands for the polymer in solutions. Hydrogen-deuterium exchange experiments of the amide protons of PNiPA and its dimer models have revealed that the amide groups of PNiPA form an intramolecular C=O...H-N hydrogen bond even in a good solvent. The result has suggested that the change in the amide I envelope of PNiPA observed during the solvent-induced phase transition reflects the modification of the intramolecular C=O...H-N hydrogen bond of PNiPA as well as the variation in solvation state of the amide groups. On the basis of the assignment, we have discussed contributions of the intramolecular C=O...H-N hydrogen bond to the phase behavior of PNiPA.     

Mechanical Activation Drastically Accelerates Amide Bond Hydrolysis,Matching Enzyme Activity

Amide bonds, which include peptide bonds connecting amino acids in proteins and polypeptides, give proteins and synthetic polyamides their enormous strength. Although proteins and polyamides sustain mechanical force in nature and technology, how forces affect amide and peptide bond stability is still unknown. Using single‐molecule force spectroscopy, we discover that forces of only a few hundred pN accelerate amide hydrolysis 10⁹‐fold, an acceleration hitherto only known from proteolytic enzymes. The drastic acceleration at low force precedes a moderate additional acceleration at nN forces. Quantum mechanochemical ab initio calculations explain these experimental results mechanistically and kinetically. Our findings reveal that, in contrast to previous belief, amide stability is strongly force dependent. These calculations provide a fundamental understanding of the role of mechanical activation in amide hydrolysis and point the way to potential applications from the recycling of macromolecular waste to the design of bioengineered proteolytic enzymes.     

液晶性芳香酰胺化合物的合成

合成了一系列炖粹以酰胺基为中心桥键的刚性芳香酰胺小分子化合物，并对其作了表征，发现其中有些化合物具有液晶性。酰胺键之间能形成很强的分子间氢键，使芳香酰胺小分子化合物的熔点很高，难于形成液成液晶态。研究发现，如果在这类化合物的中心苯环上引入合适的取代基以减弱分子间氢键，同时引入合适的末端基时，则可使芳香酰胺化合物生成液晶相的能力增强。