N,N'-linked oligoureas as foldamers: chain length requirements for helix formation in protic solvent investigated by circular dichroism, NMR spectroscopy, and molecular dynamics

N,N'-linked oligoureas with proteinogenic side chains are peptide backbone mimetics belonging to the gamma-peptide lineage. In pyridine, heptamer 4 adopts a stable helical fold reminiscent of the 2.6(14) helical structure proposed for gamma-peptide foldamers. In the present study, we have used a combination of CD and NMR spectroscopies to correlate far-UV chiroptical properties and conformational preferences of oligoureas as a function of chain length from tetramer to nonamer. Both the intensity of the CD spectra and NMR chemical shift differences between alphaCH2 diastereotopic protons experienced a marked increase for oligomers between four and seven residues. No major change in CD spectra occurred between seven and nine residues, thus suggesting that seven residues could be the minimum length required for stabilizing a dominant conformation. Unexpectedly, in-depth NMR conformational investigation of heptamer 4 in CD3OH revealed that the 2.5 helix probably coexists with partially (un)folded conformations and that Z-E urea isomerization occurs, to some degree, along the backbone. Removing unfavorable electrostatic interactions at the amino terminal end of 4 and adding one H-bond acceptor by acylation with alkyl isocyanate (4 --> 7) was found to reinforce the 2.5 helical population. The stability of the 2.5 helical fold in MeOH is further discussed in light of unrestrained molecular dynamics (MD) simulation. Taken together, these new data provide additional insight into the folding propensity of oligoureas in protic solvent and should be of practical value for the design of helical bioactive oligoureas.     

α‐Peptide–Oligourea Chimeras: Stabilization of Short α‐Helices by Non‐Peptide Helical Foldamers

Short α‐peptides with less than 10 residues generally display a low propensity to nucleate stable helical conformations. While various strategies to stabilize peptide helices have been previously reported, the ability of non‐peptide helical foldamers to stabilize α‐helices when fused to short α‐peptide segments has not been investigated. Towards this end, structural investigations into a series of chimeric oligomers obtained by joining aliphatic oligoureas to the C‐ or N‐termini of α‐peptides are described. All chimeras were found to be fully helical, with as few as 2 (or 3) urea units sufficient to propagate an α‐helical conformation in the fused peptide segment. The remarkable compatibility of α‐peptides with oligoureas described here, along with the simplicity of the approach, highlights the potential of interfacing natural and non‐peptide backbones as a means to further control the behavior of α‐peptides.     

Anion Recognition by Aliphatic Helical Oligoureas

Anion binding properties of neutral helical foldamers consisting of urea type units in their backbone have been investigated. ¹H NMR titration studies in various organic solvents including DMSO suggest that the interaction between aliphatic oligoureas and anions (CH₃COO^?, H₂PO₄^?, Cl^?) is site‐specific, as it largely involves the urea NHs located at the terminal end of the helix (positive pole of the helix), which do not participate to the helical intramolecular hydrogen‐bonding network. This mode of binding parallels that found in proteins in which anion‐binding sites are frequently found at the N‐terminus of an α‐helix. ¹H NMR studies suggest that the helix of oligoureas remains largely folded upon anion binding, even in the presence of a large excess of the anion. This study points to potentially useful applications of oligourea helices for the selective recognition of small guest molecules.     

Calculations on the electronic excited states of ureas and oligoureas

We report CASPT2 calculations on the electronic excited states of several ureas. For monoureas, we find an electric dipole forbidden n --> pi* transition between 180 and 210 nm, dependent on the geometry and substituents of the urea. We find two intense pinb --> pi* transitions between 150 and 210 nm, which account for the absorptions seen in the experimental spectra. The n' --> pi* and pib --> pi* transitions are at wavelengths below 125 nm, which is below the lower limit of the experimental spectra. Parameter sets modeling the charge densities of the electronic transitions have been derived and permit calculations on larger oligoureas, using the exciton matrix method. For glycouril, a urea dimer, both the CASPT2 method and the matrix method yield similar results. Calculations of the electronic circular dichroism spectrum of an oligourea containing eight urea groups indicate that the experimental spectrum cannot be reproduced without the inclusion of electronic excitations involving the side chains. These calculations are one of the first attempts to understand the relationship between the structure and excited states of this class of macromolecule.     

Sequencing of Oligourea Foldamers by Tandem Mass Spectrometry

This study is focused on sequence analysis of peptidomimetic helical oligoureas by means of tandem mass spectrometry, to build a basis for de novo sequencing for future high-throughput combinatorial library screening of oligourea foldamers. After the evaluation of MS/MS spectra obtained for model compounds with either MALDI or ESI sources, we found that the MALDI-TOF-TOF instrument gave more satisfactory results. MS/MS spectra of oligoureas generated by decay of singly charged precursor ions show major ion series corresponding to fragmentation across both CO-NH and N′H-CO urea bonds. Oligourea backbones fragment to produce a pattern of a, x, b, and y type fragment ions. De novo decoding of spectral information is facilitated by the occurrence of low mass reporter ions, representative of constitutive monomers, in an analogous manner to the use of immonium ions for peptide sequencing.      

Mimicking helical antibacterial peptides with nonpeptidic folding oligomers

Unnatural oligomeric scaffolds designed to adopt defined secondary structures (e.g., helices), while retaining the chemical diversity of amino acid side chains, are of practical value to elaborate functional mimetics of bioactive alpha-polypeptides. Enantiopure N,N'-linked oligoureas as short as seven residues long have been previously shown to fold into a stable helical structure, stabilized by 12- and 14-membered H-bonded rings. We now report that eight-residue oligoureas designed to mimic globally amphiphilic alpha-helical host-defense peptides are effective against both gram-negative and gram-positive bacteria (including methicillin-resistant Staphylococcus aureus [MRSA]) and exhibit selectivity for bacterial versus mammalian cells. Circular dichroism (CD) spectroscopy studies suggest enhanced helical propensity of oligoureas in the presence of phospholipid vesicles. The utility of this new class of nonpeptidic foldamers for biological applications is highlighted by high resistance to proteolytic degradation.     

Aromatic oligoureas: enforced folding and assisted cyclization

[STRUCTURE: SEE TEXT] Aromatic oligoureas are forced into well-defined conformation by incorporated intramolecular hydrogen bonds. Shape-persistent tetraureas macrocycles were obtained in a one-step [2+2] reaction in good yields.     

Helix persistence and breakdown in oligoureas of metaphenylenediamine: apparent diastereotopicity as a spectroscopic marker of helix length in solution

Oligomeric ureas derived from m-phenylenediamine with chain lengths of up to seven urea linkages were made by iterative synthetic pathways. Three families were synthesized: 4 and 20, bearing a terminal chiral sulfinyl group; 24, bearing a terminal rotationally restricted amide group, and 30 bearing a terminal achiral bromophenyl group. The distal end of the oligomers was capped with an N-benzyl group to act as a diastereotopic probe. With a terminal sulfinyl group, the 1H NMR signals arising from the CH2 group of the diastereotopic probe remained anisochronous even when separated from the stereogenic center by up to 24 bonds (in 20c). With a rotationally restricted amide, anisochronicity was no longer apparent beyond 17 bond lengths (in 24c). No anisochronicity was observable with a terminal bromophenyl group. We interpret these results as indicating that the oligoureas of short lengths adopt a defined helical secondary structure in solution, but that in longer oligomers the helicity breaks down and transmission of chirality in these systems is limited to about 24 bond lengths. We propose that "apparent diastereotopicity" (anisochronicity) provides a general empirical method for identifying secondary structure in solution.     

The meso Helix: Symmetry and Symmetry‐Breaking in Dynamic Oligourea Foldamers with Reversible Hydrogen‐Bond Polarity

Oligoureas (up to n=6) of meso cyclohexane‐1,2‐diamine were synthesized by chain extension with an enzymatically desymmetrized monomer 2 . Despite being achiral, the meso oligomers adopt chiral canonical 2.5‐helical conformations, the equally populated enantiomeric screw‐sense conformers of which are in slow exchange on the NMR timescale, with a barrier to screw‐sense inversion of about 70 kJ mol^?1. Screw‐sense inversion in these helical foldamers is coupled with cyclohexane ring‐flipping, and results in a reversal of the directionality of the hydrogen bonding in the helix. The termini of the meso oligomers are enantiotopic, and desymmetrized analogues of the oligoureas with differentially and enantioselectively protected termini display moderate screw‐sense preferences. A screw‐sense preference may furthermore be induced in the achiral, meso oligoureas by formation of a 1:1 hydrogen‐bonded complex with the carboxylate anion of Boc‐d ‐proline. The meso oligoureas are the first examples of hydrogen‐bonded foldamers with reversible hydrogen‐bond directionality.     

Mixed Oligoureas Based on Constrained Bicyclic and Acyclic β‐Amino Acids Derivatives: On the Significance of the Subunit Configuration for Folding

The combination of a non‐functionalized constrained bicyclo[2.2.2]octane motif along with urea linkages allowed the formation of a highly rigid 2.5_12/14 helical system both in solution and the solid state. In this work, we aimed at developing stable and functionalized systems as promising materials for biological applications in investigating the impact of this constrained motif and its configuration on homo and heterochiral mixed‐oligourea helix formation. Di‐, tetra‐, hexa‐, and octa‐oligoureas alternating the highly constrained bicyclic motif of (R) or (S) configuration with acyclic (S)‐β³‐amino acid derivatives were constructed. Circular dichroism (CD), NMR experiments, and the X‐ray crystal structure of the octamer unequivocally proved that the alternating heterochiral R/S sequences form a stable left‐handed 2.5‐helix in contrast to the mixed (S/S)‐oligoureas, which did not adopt any defined secondary structure. We observed that the (?)‐synclinal conformation around the C_α? C_β bond of the acyclic residues, although sterically less favorable than the (+)‐synclinal conformation, was imposed by the (R)‐bicyclic amino carbamoyl (BAC) residue. This highlighted the strong ability of the BAC residue to drive helical folding in heterochiral compounds. The role of the stereochemistry of the BAC unit was assessed and a model was proposed to explain the misfolding of the S/S sequences.     

Preparation, isolation, and characterization of Nalpha-Fmoc-peptide isocyanates: solution synthesis of oligo-alpha-peptidyl ureas

The N(alpha)-Fmoc-peptide isocyanates 3a-q, 4a-c, and 5a-c were prepared by the Curtius rearrangement of N(alpha)-Fmoc-peptide acid azides in toluene under thermal, microwave, and ultrasonic conditions. All the N(alpha)-Fmoc-oligo-peptide isocyanates made were isolated as stable crystalline solids with 71 to 94% yield and were fully characterized by 1H NMR, 13C NMR, and mass spectroscopy. Their utility for the synthesis of oligo-alpha-peptidyl ureas 7a-f and 8a-c by the divergent coupling approach was demonstrated. The coupling of N(alpha)-Fmoc-dipeptide isocyanates with amino acid ester or with N,O-bis(trimethylsilyl)amino acids resulted in N(alpha)-Fmoc-tripeptidyl urea ester and acids containing one each of peptide bond and urea bond. The divergent approach is extended to the synthesis of tetrapeptidyl ureas by the 2 + 2 strategy using bis-TMS-peptide acid as an amino component. To incorporate urea bonds in adjacent positions, N(alpha)-Fmoc-peptidyl urea isocyanates 9a-d were prepared and employed in the synthesis of three tetrapeptidyl ureas 10a-b and 11 containing one peptide bond and two urea bonds in series from the N-terminal end. The protocol was then employed for the synthesis of five urea analogues 13-15, 18, and 21 of [Leu5]enkephalin containing urea bonds at the 2, 3, 4 positions as well as at the 2, 4 and 2, 3, 4 positions. The analogue 2l was made by the convergent synthesis by the N --> C terminal chain extension. Finally, two urea analogues 22 and 23 of repeat units of bioelasto polymers, namely Val-Pro-Gly-Val-Gly-OH and Pro-Gly-Val-Gly-Val-OH, were synthesized incorporating the urea bond by the concomitant isocyanate generation and urea bond formation under thermal conditions.     

Electrocatalytic Urea Synthesis with 63.5 % Faradaic Efficiency and 100 % N-Selectivity via One-step C−N coupling

Electrocatalytic urea synthesis via coupling N₂ and CO₂ provides an effective route to mitigate energy crisis and close carbon footprint. However, the difficulty on breaking N≡N is the main reason that caused low efficiencies for both electrocatalytic NH₃ and urea synthesis, which is the bottleneck restricting their industrial applications. Herein, a new mechanism to overcome the inert of the nitrogen molecule was proposed by elongating N≡N instead of breaking N≡N to realize one-step C−N coupling in the process for urea production. We constructed a Zn−Mn diatomic catalyst with axial chloride coordination, Zn−Mn sites display high tolerance to CO poisoning and the Faradaic efficiency can even be increased to 63.5 %, which is the highest value that has ever been reported. More importantly, negligible N≡N bond breakage effectively avoids the generation of ammonia as intermediates, therefore, the N-selectivity in the co-electrocatalytic system reaches100 % for urea synthesis. The previous cognition that electrocatalysts for urea synthesis must possess ammonia synthesis activity has been broken. Isotope-labelled measurements and Operando synchrotron-radiation Fourier transform infrared spectroscopy validate that activation of N−N triple bond and nitrogen fixation activity arise from the one-step C−N coupling process of CO species with adsorbed N₂ molecules.     

基于尿素电合成反应的电催化剂研究进展

尿素是一种重要的化工原料并作为氮源广泛应用于化肥生产。工业合成尿素由氮气加氢合成氨气以及氨气和二氧化碳转化为尿素两步实现,存在高能耗和高污染等问题。通过电催化碳氮偶联,将二氧化碳和氮源（氮气、硝酸根、亚硝酸根、一氧化氮等）转化为尿素,可直接跳过合成氨反应并在温和的反应条件下同时实现人工固氮和固碳。因此,尿素电合成技术不仅避免了高能耗和高污染,还能够实现惰性气体分子的高效利用,对于加快实现“碳达峰碳中和”战略有着重要的意义。本文聚焦尿素电合成这一前沿研究热点,结合领域内最新研究进展,首先介绍了不同电催化剂的设计策略及其催化机制,随后总结了电催化碳氮偶联合成尿素的反应机理,并对尿素电合成的后续研究方向进行了展望。     

Catalytic performance of metal oxides for the synthesis of propylene carbonate from urea and 1,2-propanediol

The influences of acid–base properties of metal oxides on the catalytic performance for synthesis of propylene carbonate from urea and 1,2-propanediol was investigated, and the reaction was stepwise. The amphoteric ZnO showed the best activity, and the yield of propylene carbonate reached 98.9%. The urea decomposition over oxides was characterized by using FTIR. ZnO, CaO, MgO and La₂O₃ were favorable to promote urea decomposition to form the isocyanate species, and the formation of isocyanate species was the key to urea alcoholysis. The catalytic activity of urea decomposition was consistency to the catalytic performance for synthesis of propylene carbonate. Based on these, the probable reaction mechanism was proposed.     

SnCl<Subscript>2</Subscript>-catalyzed synthesis of carbamates from renewable origin alcohols

Effects of structure and reactivity of renewable origin alcohols in the conversion and selectivity of the SnCl₂-catalyzed reactions in the presence and absence of urea were assessed. Convenient simple and suitable method for the synthesis of carbamates from renewable origin alcohols and urea in one-step are provided. We have assessed the activity of SnCl₂ catalyst, a commercially affordable Lewis acid, in reactions of urea alcoholysis with different natural origin alcohols (geranyl, neryl, bornyl, cinnamyl, α-terpinyl and benzyl alcohols), aiming to synthesize carbamates, which are biologically active compounds, building blocks in organic synthesis and raw material to synthesize polyurethanes. The low cost of urea, the water tolerant catalyst and phosgene free reaction are positive aspects of this carbamates synthesis process. The different reaction pathways were assessed. A mechanism was proposed based on FT-IR experiments and experimental data.     

Synthesis and characterization of photolabile o-nitrobenzyl derivatives of urea

We present here the synthesis and characterization of four photolabile derivatives of urea in which alpha-substituted 2-nitrobenzyl groups are covalently attached to the urea nitrogen. These derivatives photolyze readily in aqueous solution to release free urea. The alpha-substituents of the 2-nitrobenzyl group strongly influence the rate of the photolysis reaction measured with transient absorption spectroscopy. Rates of photolysis at pH 7.5 and room temperature (approximately 22 degrees C) for N-(2-nitrobenzyl)urea, N-(alpha-methyl-2-nitrobenzyl)urea, N-(alpha-carboxymethyl-2-nitrobenzyl)urea, and N-(alpha-carboxy-2-nitrobenzyl)urea are, respectively, 1.7 x 10(4), 8.5 x 10(4), 4.0 x 10(4), and 1.1 x 10(5) s(-)(1). The quantum yields determined by measurement of free urea following irradiation by a single laser pulse at 308 nm were 0.81 for N-(2-nitrobenzyl)urea, 0.64 for N-(alpha-methyl-2-nitrobenzyl)urea, and 0.56 for N-(alpha-carboxy-2-nitrobenzyl)urea. The caged N-(alpha-carboxy-2-nitrobenzyl)urea is not a substrate of the enzyme urease, while the photolytically released urea is. Also, neither this caged urea nor its photolytic side products inhibit hydrolysis of free urea by urease. Thus, the alpha-carboxy-2-nitrobenzyl derivative of urea is suitable for mechanistic investigations of the enzyme urease.     

Solar Urea: Towards a Sustainable Fertilizer Industry

Urea, an agricultural fertilizer, nourishes humanity. The century-old Bosch–Meiser process provides the world's urea. It is multi-step, consumes enormous amounts of non-renewable energy, and has a large CO₂ footprint. Thus, developing an eco-friendly synthesis for urea is a priority. Herein we report a single-step Pd/LTA-3A catalyzed synthesis of urea from CO₂ and NH₃ under ambient conditions powered solely by solar energy. Pd nanoparticles serve the dual function of catalyzing the dissociation of NH₃ and providing the photothermal driving force for urea formation, while the absorption capacity of LTA-3A removes by-product H₂O to shift the equilibrium towards urea production. The solar urea conversion rate from NH₃ and CO₂ is 87 μmol g^?1 h^?1. This advance represents a first step towards the use of solar energy in urea production. It provides insights into green fertilizer production, and inspires the vision of sustainable, modular plants for distributed production of urea on farms.     

Solid state NMR studies of oligourea foldamers: interaction of 15N-labelled amphiphilic helices with oriented lipid membranes

Synthetic oligomers that are derived from natural polypeptide sequences, albeit with unnatural building blocks, have attracted considerable interest in mimicking bioactive peptides and proteins. Many of those compounds adopt stable folds in aqueous environments that resemble protein structural elements. Here we have chemically prepared aliphatic oligoureas and labeled them at selected positions with (15)N for structural investigations using solid-state NMR spectroscopy. In the first step, the main tensor elements and the molecular alignment of the (15)N chemical shift tensor were analyzed. This was possible by using a two-dimensional heteronuclear chemical shift/dipolar coupling correlation experiment on a model compound that represents the chemical, and thereby also the chemical shift characteristics, of the urea bond. In the next step (15)N labeled versions of an amphipathic oligourea, that exert potent antimicrobial activities and that adopt stable helical structures in aqueous environments, were prepared. These compounds were reconstituted into oriented phospholipid bilayers and the (15)N chemical shift and (1)H-(15)N dipolar couplings of two labeled sites were determined by solid-state NMR spectroscopy. The data are indicative of an alignment of this helix parallel to the membrane surface in excellent agreement with the amphipathic character of the foldamer and consistent with previous models explaining the antimicrobial activities of α-peptides.     

Synthesis and helical properties of aromatic multilayered oligoureas

Several aromatic multilayered oligoureas with different chain lengths and different numbers of chiral N-substituents were synthesized, and their helical conformation and induced handedness were examined by means of CD spectroscopy. Introduction of one chiral N-substituent is enough to induce handedness, and all the oligoureas examined exist predominantly as helical structures with all-S axial chirality. The hexaureas 6 and 7 had similar CD intensity to the tetraureas 4 and 5, and had larger CD intensity than diurea 8. The results indicate that the effect of a chiral N-substituent at the central benzene ring in inducing well-ordered handedness at the terminal positions of hexaureas 6 and 7 is relatively weak, even though these compounds mainly take the form of aromatic multilayered foldamers.