Direct Spectroscopic Evidence of Hyperconjugation Unveils the Conformational Landscape of Hydrazides

α-Hydrazino Acid Insertion Governs Peptide Organization in Solution by Local Structure Ordering

In this work, we have applied the concept of α-hydrazino acid insertion in a peptide sequence as a means of structurally organizing a potential protein-protein interactions (PPI) inhibitor. Hydrazino peptides characterized by the incorporation of an α-hydrazino acid at specific positions introduce an additional nitrogen atom into their backbone. This modification leads to a change in the electrostatic properties of the peptide and induces the restructuring of its hydrogen bonding network, resulting in conformational changes toward more stable structural motifs. Despite the successful use of synthetic hydrazino oligomers in binding to nucleic acids, the structural changes due to the incorporation of α-hydrazino acid into short natural peptides in solution are still poorly understood. Based on NMR data, we report structural models of p53-derived hydrazino peptides with elements of localized peptide structuring in the form of an α-, β-, or γ-turn as a result of hydrazino modification in the peptide backbone. The modifications could potentially lead to the preorganization of a helical secondary peptide structure in a solution that is favorable for binding to a biological receptor. Spectroscopically, we observed that the ensemble averaged rapidly interconverting conformations, including isomerization of the E-Z hydrazide bond. This further increases the adaptability by expanding the conformational space of hydrazine peptides as potential protein-protein interaction antagonists.

Synthesis and Primary Activity Assay of Novel Benitrobenrazide and Benserazide Derivatives

Schiff bases attract research interest due to their applications in chemical synthesis and medicinal chemistry. In recent years, benitrobenrazide and benserazide containing imine moiety have been synthesized and characterized as promising inhibitors of hexokinase 2 (HK2), an enzyme overexpressed in most cancer cells. Benserazide and benitrobenrazide possess a common structural fragment, a 2,3,4-trihydroxybenzaldehyde moiety connected through a hydrazone or hydrazine linker acylated on an N' nitrogen atom by serine or a 4-nitrobenzoic acid fragment. To avoid the presence of a toxicophoric nitro group in the benitrobenrazide molecule, we introduced common pharmacophores such as 4-fluorophenyl or 4-aminophenyl substituents. Modification of benserazide requires the introduction of other endogenous amino acids instead of serine. Herein, we report the synthesis of benitrobenrazide and benserazide analogues and preliminary results of inhibitory activity against HK2 evoked by these structural changes. The derivatives contain a fluorine atom or amino group instead of a nitro group in BNB and exhibit the most potent inhibitory effects against HK2 at a concentration of 1 µM, with HK2 inhibition rates of 60% and 54%, respectively.

Hydrazinolysis Products of Selected Sugar Lactones-Crystal Structure and Microbiological Activity

Commercially available lactones, as well as those synthesized by us, turned out to be good substrates for the synthesis of sugar hydrazides. The exception was L-ascorbic acid, whose hydrazinolysis led to the formation of a hydrazinium salt, not the hydrazide as expected. The structure of all compounds was confirmed by NMR and X-ray analyses. The lower durability of hydrazinium L-ascorbate was additionally confirmed by thermogravimetric tests. All products were tested for biological activity against Gram-negative bacteria strains Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 27853 and against Gram-positive Staphylococcus aureus ATCC 25923 and Staphylococcus aureus ATCC 29213. Their antifungal activity against Candida albicans SC5314, Candida glabrata DSM 11226 SM 11226, Candida krusei DSM 6128, and Candida parapsilosis DSM 5784 was also tested. The most interesting results of microbiological activity were obtained for D-gluconic acid hydrazide and hydrazinium L-ascorbate. The results of the latter encourage more extensive testing.

Synergistic effect of intra- and intermolecular hydrogen bond in 2-haloethanols probed by infrared

Fluorine is often considered the only halogen to effectively engage in hydrogen bonds, while the other halogens, particularly iodine, are not electronegative enough to participate as hydrogen bond acceptors in electrostatic interactions. 2-Fluoroethanol and 2-iodoethanol have been studied herein to test this assumption, since a highly stable gauche conformation can experience the intramolecular hydrogen bond. However, the infrared O  H stretching frequency indicates that the hydroxyl group in 2-fluoroethanol is not engaged in intramolecular hydrogen bond, while the corresponding vibration mode for 2-iodoethanol suggests that not only the O  H is engaged in such interaction, but also that intramolecular hydrogen bond may drive the conformational equilibrium in this molecule. Theoretical calculations support the covalent nature of this interaction, and provide evidence that intermolecular hydrogen bond with a water molecule, and probably with the polar solvents tested experimentally, occurs with the hydroxyl rather than with the iodine substituent, as conventionally, in order to keep the intramolecular hydrogen bond effective.

Electron delocalisation in conjugated sulfur heterocycles probed by resonant Auger spectroscopy

We propose a novel approach for an indirect probing of conjugation and hyperconjugation in core-excited molecules using resonant Auger spectroscopy. Our work demonstrates that the changes in the electronic structure of thiophene (C₄H₄S) and thiazole (C₃H₃NS), occurring in the process of resonant sulfur K-shell excitation and Auger decay, affect the stabilisation energy resulting from π-conjugation and hyperconjugation. The variations in the stabilisation energy manifest themselves in the resonant S KL_2,3L_2,3 Auger spectra of thiophene and thiazole. The comparison of the results obtained for the conjugated molecules and for thiolane (C₄H₈S), the saturated analogue of thiophene, has been performed. The experimental observations are interpreted using high-level quantum-mechanical calculations and the natural bond orbital analysis.

Different Schiff Bases-Structure, Importance and Classification

Schiff bases are a vast group of compounds characterized by the presence of a double bond linking carbon and nitrogen atoms, the versatility of which is generated in the many ways to combine a variety of alkyl or aryl substituents. Compounds of this type are both found in nature and synthesized in the laboratory. For years, Schiff bases have been greatly inspiring to many chemists and biochemists. In this article, we attempt to present a new take on this group of compounds, underlining of the importance of various types of Schiff bases. Among the different types of compounds that can be classified as Schiff bases, we chose hydrazides, dihydrazides, hydrazones and mixed derivatives such as hydrazide-hydrazones. For these compounds, we presented the elements of their structure that allow them to be classified as Schiff bases. While hydrazones are typical examples of Schiff bases, including hydrazides among them may be surprising for some. In their case, this is possible due to the amide-iminol tautomerism. The carbon-nitrogen double bond present in the iminol tautomer is a typical element found in Schiff bases. In addition to the characteristics of the structure of these selected derivatives, and sometimes their classification, we presented selected literature items which, in our opinion, represent their importance in various fields well.

nN → π*Ar interactions stabilize the E-ac isomers of arylhydrazides and facilitate their SNAr autocyclizations

We describe a novel mechanism of stabilization of the E-ac isomer of an arylhydrazide via n_N → π*_Ar interactions. We further show that when a leaving group (F) is present at the ortho-position of the carbonyl group of such an arylhydrazide, the n_N → π*_Ar interaction facilitates an S_NAr autocyclization reaction to produce indazolone, an important heterocycle with biological activity. Faster autocyclization of arylhydrazide is observed when an electron withdrawing group is present in the aryl ring, which is a characteristic of S_NAr reactions.

A theoretical and experimental case study of the hydrogen bonding predilection of S-methylcysteine

S-containing amino acids can lead to two types of local NH···S interactions which bridge backbone NH sites to the side chain to form either intra- or inter-residue H-bonds. The present work reports on the conformational preferences of S-methyl-L-cysteine, Cys(Me), using a variety of investigating tools, ranging from quantum chemistry simulations, gas-phase UV and IR laser spectroscopy, and solution state IR and NMR spectroscopies, on model compounds comprising one or two Cys(Me) residues. We demonstrate that in gas phase and in low polarity solution, the C- and N-capped model compound for one Cys(Me) residue adopts a preferred C5-C6γ conformation which combines an intra-residue N-H···O=C backbone interaction (C5) and an inter-residue N-H···S interaction implicating the side-chain sulfur atom (C6γ). In contrast, the dominant conformation of the C- and N-capped model compound featuring two consecutive Cys(Me) residues is a regular type I β-turn. This structure is incompatible with concomitant C6γ interactions, which are no longer in evidence. Instead, C5γ interactions occur, that are fully consistent with the turn geometry and additionally stabilize the structure. Comparison with the thietane amino acid Attc, which exhibits a rigid cyclic side chain, pinpoints the significance of side chain flexibility for the specific conformational behavior of Cys(Me).

An intraresidue H-bonding motif in selenocysteine and cysteine, revealed by gas phase laser spectroscopy and quantum chemistry calculations

Models of protein chains containing a seleno-cysteine (Sec) residue have been investigated by gas phase laser spectroscopy in order to document the effect of the H-bonding properties of the SeH group in the folding of the Sec side chain, by comparison with recent data on Ser- and Cys-containing sequences. Experimental data, complemented by quantum chemistry calculations and natural bonding orbital (NBO) analyses, are interpreted in terms of the formation of a so-called 5γ intra-residue motif, which bridges the acceptor chalcogen atom of the side chain to the NH bond of the same residue. This local structure, in which the O/S/Se atom is close to the plane of the N-terminal side amide, is constrained by local backbone-side chain hyperconjugation effects involving the S and Se atoms. Theoretical investigations of the Cys/Sec side chain show that (i) this 5γ motif is an intrinsic feature of these residues, (ii) the corresponding H-bond is strongly non-linear and intrinsically weak, (iii) but enhanced by γ- and β-turn secondary structures, which promote a more favorable 5γ H-bonding approach and distance. The resulting H-bonds are slightly stronger in selenocysteine than in cysteine, but nearly inexistent in serine, whose side chain in contrast behaves as a H-bonding donor. The modest spectral shifts of the Cys/Sec NH stretches measured experimentally reflect the moderate strength of the 5γ H-bonding, in agreement with the correlation obtained with a NBO-based H-bond strength indicator. The evolution along the Ser, Cys and Sec series emphasizes the compromise between the several factors that control the H-bonding in a hyperconjugation-constrained geometry, among them the chalcogen van der Waals and covalent radii. It also illustrates the 5γ H-bond enhancements with the Sec and Cys residues favoured by the constraints imposed by the γ- and β-turn structures of the peptide chain.

Intrinsic folding of the cysteine residue: competition between folded and extended forms mediated by the -SH group

A dual microwave and optical spectroscopic study of a capped cysteine amino acid isolated in a supersonic expansion, combined with quantum chemistry modelling, enabled us to characterize the conformational preferences of Cys embedded in a protein chain. IR/UV double resonance spectroscopy provided evidence for the coexistence of two conformers, assigned to folded and extended backbones (with classical C7 and C5 backbone H-bonding respectively), each of them additionally stabilized by specific main-chain/side-chain H-bonding, where the sulfur atom essentially plays the role of H-bond acceptor. The folded structure was confirmed by microwave spectroscopy, which demonstrated the validity of the DFT-D methods currently used in the field. These structural and spectroscopic results, complemented by a theoretical Natural Bond Orbital analysis, enabled us to document the capacity of the weakly polar -CH2-SH side chain of Cys to adapt itself to the intrinsic local preferences of the peptide backbone, i.e., a γ-turn or a β-sheet extended secondary structure. The corresponding local H-bonding bridges the side chain acceptor S atom to the backbone NH donor site of the same or the next residue along the chain, through a 5- or a 6-membered ring respectively.

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.

Rationalizing the diversity of amide-amide H-bonding in peptides using the natural bond orbital method

Natural bond orbital (NBO) analysis of electron delocalization in a series of capped isolated peptides is used to diagnose amide-amide H-bonding and backbone-induced hyperconjugative interactions, and to rationalize their spectral effects. The sum of the stabilization energies corresponding to the interactions between NBOs that are involved in the H-bonding is demonstrated as an insightful indicator for the H-bond strength. It is then used to decouple the effect of the H-bond distance from that, intrinsic, of the donor/acceptor relative orientation, i.e., the geometrical approach. The diversity of the approaches given by the series of peptides studied enables us to illustrate the crucial importance of the approach when the acceptor is a carbonyl group, and emphasizes that efficient approaches can be achieved despite not matching the usual picture of a proton donor directly facing a lone pair of the proton acceptor, i.e., that encountered in intermolecular H-bonds. The study also illustrates the role of backbone flexibility, partly controlled by backbone-amide hyperconjugative interactions, in influencing the equilibrium structures, in particular by frustrating or enhancing the HB for a given geometrical approach. Finally, the presently used NBO-based HB strength indicator enables a fair prediction of the frequency of the proton donor amide NH stretching mode, but this simple picture is blurred by ubiquitous hyperconjugative effects between the backbone and amide groups, whose magnitude can be comparable to that of the weakest H-bonds.

Aza-proline effectively mimics l-proline stereochemistry in triple helical collagen

Chenoweth and co-workers provide an atomic resolution crystal structure and computational analysis illustrating that aza-proline mimics l-proline stereochemistry in collagen.

The prevalence of l-amino acids in biomolecules has been shown to have teleological importance in biomolecular structure and self-assembly. Recently, biophysical studies have demonstrated that natural l-amino acids can be replaced with non-natural achiral aza-amino acids in folded protein structures such as triple helical collagen. However, the structural consequences of achiral aza-amino acid incorporation has not been elucidated in the context of any relevant folded biomolecule. Herein, we use X-ray crystallography to provide the first atomic resolution crystal structure of an achiral aza-amino acid residue embedded within a folded protein structure, definitively illustrating that achiral aza-proline has the capacity to effectively mimic the stereochemistry of natural amino acids within the context of triple helical collagen. We further corroborate this finding with density functional theory computational analysis showing that the natural l-amino acid stereochemistry for aza-proline is energetically favored when arranged in the aza-proline-hydroxyproline-glycine motif. In addition to providing fundamental insight into peptide and protein structure, the incorporation of achiral stereochemical mimics such as aza-amino acids could have far reaching impacts in areas ranging from synthetic materials to drug design.

A conformation-specific IR spectroscopic signature for weak CO⋯CO n→π* interaction in capped 4R-hydroxyproline

CO⋯CO n→π*-amide interaction in the monomeric building block of collagen is probed using conformation-specific IR spectroscopy.

Infrared Fingerprints of nN → σ*NH Hyperconjugation in Hydrazides

An earlier study demonstrated that hyperconjugation operates in hydrazides by analyzing the N-H stretching mode in gas phase infrared (IR) spectroscopy, and then observing two very distinct bands corresponding to isolated isomers experiencing or not the n_N → σ*_N-H electron delocalization. The present work reports a chemical method to obtain insight on the hyperconjugation in hydrazide derivatives from solution IR spectroscopy. The analogous amides did not show a ν_N-H red-shifted band, as the electron donor orbital in the above hyperconjugative interaction does not exist. In addition, the effect of electron withdrawing groups bonded to a nitrogen atom, namely the trifluoroacetyl and the methanesulfonyl groups, was analyzed on the conformational isomerism and on the ability to induce a stronger hyperconjugation in the resulting compounds.

Spectroscopic Evidences for Strong Hydrogen Bonds with Selenomethionine in Proteins

Careful protein structure analysis unravels many unknown and unappreciated noncovalent interactions that control protein structure; one such unrecognized interaction in protein is selenium centered hydrogen bonds (SeCHBs). We report, for the first time, SeCHBs involving the amide proton and selenium of selenomethionine (Mse), i.e., amide-N-H···Se H-bonds discerned in proteins. Using mass selective and conformer specific high resolution vibrational spectroscopy, gold standard quantum chemical calculations at CCSD(T), and in-depth protein structure analysis, we establish that amide-N-H···Se and amide-N-H···Te H-bonds are as strong as conventional amide-NH···O and amide-NH···O═C H-bonds despite smaller electronegativity of selenium and tellurium than oxygen. It is in fact, electronegativity, atomic charge, and polarizability of the H-bond acceptor atoms are at play in deciding the strength of H-bonds. The amide-N-H···Se and amide-N-H···Te H-bonds presented here are not only new additions to the ever expanding world of noncovalent interactions, but also are of central importance to design new force-fields for better biomolecular structure simulations.

Local NH–π interactions involving aromatic residues of proteins: influence of backbone conformation and ππ* excitation on the π H-bond strength, as revealed from studies of isolated model peptides

Gas phase conformer-selective IR spectroscopy combined and relevant quantum chemistry methods document the NH–π interactions in Phe residues.

Isolated neutral peptides

This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.

Critical Assessment of the Strength of Hydrogen Bonds between the Sulfur Atom of Methionine/Cysteine and Backbone Amides in Proteins

Gas-phase vibrational spectroscopy, coupled cluster (CCSD(T)), and dispersion corrected density functional (B97-D3) methods are employed to characterize surprisingly strong sulfur center H-bonded (SCHB) complexes between cis and trans amide NH and S atom of methionine and cysteine side chain. The amide N-H···S H-bonds are compared with the representative classical σ- and π-type H-bonded complexes such as N-H···O, N-H···O═C and N-H···π H-bonds. With the spectroscopic, theoretical, and structural evidence, amide N-H···S H-bonds are found to be as strong as the classical σ-type H-bonds, despite the smaller electronegativity of sulfur in comparison to oxygen. The strength of backbone-amide N-H···S H-bonds in cysteine and methionine containing peptides and proteins are also investigated and found to be of similar magnitudes as those observed in the intermolecular model complexes studied in this work. All such SCHBs also confirm that the electronegativities of the acceptors are not the sole criteria to predict the H-bond strength.