Phosphoryl group differentiating α‐amino acids from β‐ and γ‐amino acids in prebiotic peptide formation

In recent years β‐amino acids have increased their importance enormously in defining secondary structures of β‐peptides. Interest in β‐amino acids raises the question: Why and how did nature choose α‐amino acids for the central role in life? In this article we present experimental results of MS and ³¹P NMR methods on the chemical behavior of N‐phosphorylated α‐alanine, β‐alanine, and γ‐amino butyric acid in different solvents. N‐Phosphoryl α‐alanine can self‐assemble to N‐phosphopeptides either in water or in organic solvents, while no assembly was observed for β‐ or γ‐amino acids. An intramolecular carboxylic–phosphoric mixed anhydride (IMCPA) is the key structure responsible for their chemical behaviors. Relative energies and solvent effects of three isomers of IMCPA derived from α‐alanine (2a–c), with five‐membered ring, and five isomers of IMCPA derived from β‐alanine (4a–e), with six‐membered ring, were calculated with density functional theory at the B3LYP/6‐31G** level. The lower relative energy (3.2 kcal/mol in water) of 2b and lower energy barrier for its formation (16.7 kcal/mol in water) are responsible for the peptide formation from N‐phosphoryl α‐alanine. Both experimental and theoretical studies indicate that the structural difference among α‐, β‐, and γ‐amino acids can be recognized by formation of IMCPA after N‐phosphorylation. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 232–241, 2003     

Photolysis of α,β‐Epoxyketones: A Green Synthesis of β‐Hydroxyenones through Tandem H‐Abstraction,Ring Cleavage and Isomerisation

The photochemical behavior of various substituted epoxycarbonyl compounds consisting of more than one possible photo‐labile site (i.e. δ‐hydrogen, β‐hydrogen and epoxide ring) has been investigated. These compounds on photo‐irradiation produced the β‐hydroxyenones in an eco‐friendly green approach. Mechanistically, these photo‐transformations have been envisaged to occur via an intramolecular β‐hydrogen abstraction by the carbonyl group of benzoyl moiety to generate the 1,3‐biradical followed by epoxide ring opening that isomerizes into the photoproducts. The photolysis of the probed epoxy ketones didn’t furnish any photoproduct through δ‐hydrogen abstraction, whatsoever. This exclusive preference for β‐H abstraction over δ‐H abstraction by carbonyl group has been vindicated by the MM2 energy mini‐ mized program for the investigated photochemical substrates. The structures of these photoproducts were established from the analysis of their spectral parameters (IR, ¹H/¹³C NMR and Mass) and single crystal X‐ray crystallography data.     

Theoretical Study Of β2,3‐Peptide Models

Conformational features of α,β‐disubstituted β^2,3‐dipeptide models have been studied with quantum mechanics method. Geometries were optimized with the HF/6‐31G** method, and energies were evaluated with the B3LYP/6‐31G** method. Solvent effect was evaluated with the SCIPCM method. For (2S,3S)‐β^2,3‐dipeptide model 1 , a six‐membered‐ring hydrogen bonded structure is most stable. However, the conformation corresponding to the formation of the 14‐helix is only about 1.7 kcal/mol less stable in methanol solution, indicating that the 14‐helix is favored if a (2S,3S)‐β^2,3‐polypeptide contains more than 5 residues. On the other hand, the conformation corresponding to the formation of β‐sheet is most stable for (2R,3S)‐β^2,3‐dipeptide model 2 , suggesting that this type of β‐peptides is intrinsically favored for the formation of β‐sheet secondary structure.     

The effect of amino acid backbone length on molecular packing: crystalline tartrates of glycine, β‐alanine, γ‐aminobutyric acid (GABA) and dl‐α‐aminobutyric acid (AABA)

We report a novel 1:1 cocrystal of β‐alanine with dl ‐tartaric acid, C₃H₇NO₂·C₄H₆O₆, (II), and three new molecular salts of dl ‐tartaric acid with β‐alanine {3‐azaniumylpropanoic acid–3‐azaniumylpropanoate dl ‐tartaric acid–dl ‐tartrate, [H(C₃H₇NO₂)₂]⁺·[H(C₄H₅O₆)₂]⁻, (III)}, γ‐aminobutyric acid [3‐carboxypropanaminium dl ‐tartrate, C₄H₁₀NO₂⁺·C₄H₅O₆⁻, (IV)] and dl ‐α‐aminobutyric acid {dl ‐2‐azaniumylbutanoic acid–dl ‐2‐azaniumylbutanoate dl ‐tartaric acid–dl ‐tartrate, [H(C₄H₉NO₂)₂]⁺·[H(C₄H₅O₆)₂]⁻, (V)}. The crystal structures of binary crystals of dl ‐tartaric acid with glycine, (I), β‐alanine, (II) and (III), GABA, (IV), and dl ‐AABA, (V), have similar molecular packing and crystallographic motifs. The shortest amino acid (i.e. glycine) forms a cocrystal, (I), with dl ‐tartaric acid, whereas the larger amino acids form molecular salts, viz. (IV) and (V). β‐Alanine is the only amino acid capable of forming both a cocrystal [i.e. (II)] and a molecular salt [i.e. (III)] with dl ‐tartaric acid. The cocrystals of glycine and β‐alanine with dl ‐tartaric acid, i.e. (I) and (II), respectively, contain chains of amino acid zwitterions, similar to the structure of pure glycine. In the structures of the molecular salts of amino acids, the amino acid cations form isolated dimers [of β‐alanine in (III), GABA in (IV) and dl ‐AABA in (V)], which are linked by strong O—H…O hydrogen bonds. Moreover, the three crystal structures comprise different types of dimeric cations, i.e. (A…A)⁺ in (III) and (V), and A⁺…A⁺ in (IV). Molecular salts (IV) and (V) are the first examples of molecular salts of GABA and dl ‐AABA that contain dimers of amino acid cations. The geometry of each investigated amino acid (except dl ‐AABA) correlates with the melting point of its mixed crystal.     

Synthesis and High‐Resolution NMR Structure of a β3‐Octapeptide with and without a Tether Introduced by Olefin Metathesis

Bridging between (i)‐ and (i+3)‐positions in a β³‐peptide with a tether of appropriate length is expected to prevent the corresponding 3₁₄‐helix from unfolding (Fig. 1). The β³‐peptide H‐β³hVal‐β³hLys‐β³hSer(All)‐β³hPhe‐β³hGlu‐β³hSer(All)‐β³hTyr‐β³hIle‐OH ( 1 ; with allylated βhSer residues in 3‐ and 6‐position), and three tethered β‐peptides 2 – 4 (related to 1 through ring‐closing metathesis) have been synthesized (solid‐phase coupling, Fmoc strategy, on chlorotrityl resin; Scheme). A comparative CD analysis of the tethered β‐peptide 4 and its non‐tethered analogue 1 suggests that helical propensity is significantly enhanced (threefold CD intensity) by a (CH₂)₄ linker between the β³hSer side chains (Fig. 2). This conclusion is based on the premise that the intensity of the negative Cotton effect near 215 nm in the CD spectra of β³‐peptides represents a measure of ‘helical content’. An NMR analysis in CD₃OH of the two β³‐octapeptide derivatives without (i.e., 1 ) and with tether (i.e., 4 ; Tables 1–6, and Figs. 4 and 5) provided structures of a degree of precision (by including the complete set of side chain–side chain and side chain–backbone NOEs) which is unrivaled in β‐peptide NMR‐solution‐structure determination. Comparison of the two structures (Fig. 5) reveals small differences in side‐chain arrangements (separate bundles of the ten lowest‐energy structures of 1 and 4 , Fig. 5, A and B ) with little deviation between the two backbones (superposition of all structures of 1 and 4 , Fig. 5, C ). Thus, the incorporation of a CH₂? O? (CH₂)₄? O? CH₂ linker between the backbone of the β³‐amino acids in 3‐ and 6‐position (as in 4 ) does accurately constrain the peptide into a 3₁₄‐helix. The NMR analysis, however, does not suggest an increase in the population of a 3₁₄‐helical backbone conformation by this linkage. Possible reasons for the discrepancy between the conclusion from the CD spectra and from the NMR analysis are discussed.     

Tetrylenes chelated by bifunctional β‐diketiminate ligand: structure and possible applications

The synthesis and structure of heteroleptic tetrylenes containing bifunctional β‐diketiminate ligand are reported. Compounds were prepared via a protolytic reaction of free β‐diketimine {N‐[(2‐MeO)C₆H₅]}N═C(Me)CH═C(Me)N(H){N′‐[(2‐MeO)C₆H₅]} (L^COH) and {N‐[(2‐MeO)C₆H₅]}N?CHCH?CHN(H){N′‐[(2‐MeO)C₆H₅]} (L^HOH), respectively, with corresponding bis(amide) – M[N(SiMe₃)₂]₂ (M = Ge, Sn, Pb) – in equimolar ratio or via the salt elimination route from lithium precursors generated from L^HOH/L^COH species and slight excess of SnCl₂ or GeCl₂.dioxane complex. Only heteroleptic complexes were obtained by the mentioned methods. Products were characterized by multinuclear NMR spectroscopy techniques and structures of four of them have been determined by X‐ray diffraction methods. Complexes L^HOGeCl and L^COSnN(SiMe₃)₂ crystallize as monomers with the three‐coordinated metal centres by one chloro or amido ligand and one bidentate β‐diketiminato unit, in contrast to the structure of L^COSnCl, which reveals a dimeric character and compound L^COPbN(SiMe₃)₂, where the central atom of lead is five‐coordinated by methoxy groups of the ligand. Complex L^COSnN(SiMe₃)₂ was tested as a catalyst for polymerization of various epoxides_. Copyright © 2014 John Wiley & Sons, Ltd.     

The structure–activity relationship of some hexacoordinated dimethyltin(IV) complexes of fluorinated β‐diketone/β‐diketones and sterically congested heterocyclic β‐diketones

The study was focused on the structure–activity relationship of some newly synthesized hexacoordinated dimethyltin(IV) complexes of fluorinated β‐diketone/β‐diketones and sterically congested heterocyclic β‐diketones. These complexes were screened for their antibacterial activity against a Gram‐negative bacterium (Pseudomonas aeruginosa) and Gram‐positive bacteria (Streptomyces griseus, Staphylococcus aureus, Bacillus subtilis) and the results were compared with those of a standard antibacterial drug. Some of the complexes were also screened for their antifungal activity against various fungi (Aspergillus niger, A. flavus, Trichoderma viride, Fusarium oxysporum) and were found to be active. These new hexacoordinated complexes of dimethyltin(IV) were generated by reactions of dimethyltin(IV) dichloride and sodium salts of fluorinated β‐diketone/β‐diketones and sterically congested heterocyclic β‐diketones in 1:1:1 molar ratio in refluxing dry benzene. Plausible structures of these complexes were suggested with the aid of physicochemical and spectroscopic studies. ¹¹⁹Sn NMR spectral data revealed the presence of a hexacoordinated tin centre in these dimethyltin(IV) complexes. Copyright © 2015 John Wiley & Sons, Ltd.     

Supramolecular inclusion complexes of a star polymer containing cholesterol end‐capped poly(ε‐caprolactone) arms with β‐cyclodextrin

A novel hexa‐armed and star‐shaped polymer containing cholesterol end‐capped poly(ε‐caprolactone) arms emanating from a phosphazene core (N₃P₃‐(PCL‐Chol)₆) was synthesized by a combination of ring‐opening polymerization and “click” chemistry techniques. For this purpose, the terminal ? OH groups of the synthesized precursor (N₃P₃‐(PCL‐OH)₆) were converted into –Chol through a series of reaction. Both N₃P₃‐(PCL‐OH)₆ and N₃P₃‐(PCL‐Chol)₆ were then employed in the preparation of supramolecular inclusion complexes (ICs) with β‐cyclodextrin (β‐CD). The latter formed ICs with β‐CD in higher yield. The host–guest stoichiometry (ε‐CL:β‐CD, mol:mol) in the ICs of N₃P₃‐(PCL‐Chol)₆ was found to be 1.2. The formation of supramolecular ICs of N₃P₃‐(PCL‐Chol)₆ with β‐CD was confirmed by using Fourier transform infrared (FTIR) and ¹H nuclear magnetic resonance (NMR) spectroscopic methods, wide‐angle X‐ray diffraction (WAXD), and thermal analysis techniques. WAXD data showed that the obtained ICs with N₃P₃‐(PCL‐Chol)₆ had a channel‐type crystalline structure, indicating the suppression of the original crystallization of N₃P₃‐(PCL‐Chol)₆ in β‐CD cavities. Moreover, the thermal stabilities of ICs were found to be higher than those of the free star polymer and β‐CD. Furthermore, the surface properties of N₃P₃‐(PCL‐Chol)₆ and its ICs with β‐CD were investigated by static contact angle measurements. The obtained results proved that the wettability of N₃P₃‐(PCL‐Chol)₆ successfully increased with the formation of its ICs with β‐CD. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 3406–3420     

Synthesis,and Helix or Hairpin‐Turn Secondary Structures of ‘Mixed’ α/β‐Peptides Consisting of Residues with Proteinogenic Side Chains and of 2‐Amino‐2‐methylpropanoic Acid (Aib)

Twelve peptides, 1 – 12 , have been synthesized, which consist of alternating sequences of α‐ and β‐amino acid residues carrying either proteinogenic side chains or geminal dimethyl groups (Aib). Two peptides, 13 and 14 , containing 2‐methyl‐3‐aminobutanoic acid residues or a ‘random mix’ of α‐, β²‐, and β³‐amino acid moieties were also prepared. The new compounds were fully characterized by CD (Figs. 1 and 2), and ¹H‐ and ¹³C‐NMR spectroscopy, and high‐resolution mass spectrometry (HR‐MS). In two cases, 3 and 14 , we discovered novel types of turn structures with nine‐ and ten‐membered H‐bonded rings forming the actual turns. In two other cases, 8 and 11 , we found 14/15‐helices, which had been previously disclosed in mixed α/β‐peptides containing unusual β‐amino acids with non‐proteinogenic side chains. The helices are formed by peptides containing the amino acid moiety Aib in every other position, and their backbones are primarily not held together by H‐bonds, but by the intrinsic conformations of the containing amino acid building blocks. The structures offer new possibilities of mimicking peptide–protein and protein–protein interactions (PPI).     

Synthesis of ferrocene‐containing N‐aryloxo β‐ketoiminate lanthanide complexes and polymerization of ε‐caprolactone

The synthesis, characterization and ε‐caprolactone polymerization behavior of lanthanide amido complexes stabilized by ferrocene‐containing N‐aryloxo functionalized β‐ketoiminate ligand FcCOCH₂C(Me)N(2‐HO‐5‐Bu^t‐C₆H₃) (LH₂, Fc = ferrocenyl) are described. The lanthanide amido complexes [LLnN(SiMe₃)₂(THF)]₂ [Ln = Nd ( 1 ), Sm ( 2 ), Yb ( 3 ), Y ( 4 )] were synthesized in good yields by the amine elimination reactions of LH₂ with Ln[N(SiMe₃)₂]₃(µ‐Cl)Li(THF)₃ in a 1:1 molar ratio in THF. These complexes were characterized by IR spectroscopy and elemental analysis, and ¹H NMR spectroscopy was added for the analysis of complex 4 . The definitive molecular structures of complexes 1 and 3 were determined by X‐ray diffraction studies. Complexes 1 – 4 can initiate the ring‐opening polymerization of ε‐caprolactone with moderate activity. Copyright © 2011 John Wiley & Sons, Ltd.     

The Contrasting Recognition Behavior of β‐Cyclodextrin and Its Sulfobutylether Derivative towards 4′,6‐Diamidino‐2‐phenylindole

The noncovalent interactions between 4′, 6‐diamidino‐2‐phenylindole (DAPI) and sulfobutylether β‐cyclodextrin (SBE₇β‐CD) are evaluated by using photochemical measurements and compared with that of native β‐CD. Contrasting recognition behavior and intriguing modulations in the photochemical behavior of DAPI were observed. In particular, a large enhancement in the fluorescence emission and excited‐state lifetime were seen upon binding to SBE₇β‐CD, with the SBE₇β‐CD inclusion complex being approximately 1000 times stronger than that of β‐CD. The ensuing fluorescence “turn on” was demonstrated to be responsive to chemical stimuli, such as metal ions and adamantylanmine (AD). Upon addition of Ca²⁺/AD, nearly quantitative dissociation of the complex was established to regenerate the free dye and result in fluorescence “turn off”. The SO₃^? groups are believed to be critical for the strong and selective binding of the chromophore and the stimuli‐responsive tuning. This is as an important design criterion for the optimization of host–guest properties through supramolecular association, which is relevant for drug‐delivery applications.     

A novel silk‐based segmented block copolymer containing GlyAlaGlyAla β‐sheets templated by phenoxathiin

A novel segmented block copolymer, containing polyethylene glycol segment and GlyAlaGlyAla sequence derived from B. mori silk, has been prepared as a model for silk‐based materials using both solution and interfacial techniques. Inherent viscosity, size exclusion chromatography, and light‐scattering measurements gave molecular weight between M_w 34,000–39,000. Evidence for phase separation was provided by differential scanning calorimetry, which gave two T_g's at −57 °C and 111 °C, and transmission electron microscopy, which showed a morphology in which the peptide domain, estimated to be about 20–50 nm, was dispersed in the continuous polyether phase. Solid‐state FTIR spectroscopic results showed that the polymer contained both parallel and antiparallel β‐sheet stacks, and that the solution‐polymerized material has the higher β‐sheet content. This was further confirmed by ¹³C NMR, which gave about 80% total β‐sheet content for the solution‐polymerized product and about 40% for the polymer obtained by interfacial polymerization. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 352–366, 2000     

[Leu2]Gramicidin S preserves the structural properties of its parent peptide and forms helically aligned β‐sheets

For crystallographic analysis, Leu was substituted for Orn in Gramicidin S (LGS) to suppress interactions with hydrophilic solvent molecules, which increased the flexibility of the Orn side chains, leading to disorder within the crystals. The asymmetric unit (C₆₂H₉₄N₁₀O₁₀·1.296C₃H₈O·1.403H₂O) contains three LGS molecules (A, B and C) forming β‐turn and intramolecular β‐sheet structures. With the exception of one motif in molecule C, d ‐Phe‐Pro turn motifs (Phe is phenylalanine and Pro is proline) were classed as type II′ β‐turns. The peptide backbones twist slightly to the right along the long axis of the molecule. The puckering of Pro is in a Cγ‐endo or twisted Cγ‐endo–Cβ‐exo form. Flanking molecules are arranged such that the angles (A…B = 104°, B…C = 139° and C…A = 117°) form helical β‐sheets. Solvent molecules interact with the peptide backbones supporting the β‐sheets. The forms of the replacement Leu side chains are consistent with the e‐form of the Orn side chain in GS analogues. No hydrophilic region composed of solvent molecules, such as that observed in Gramicidin S hydrochloride (GS·HCl) crystals, was found. The perturbation of αH chemical shifts and coupling constants of CONH showed that the structural properties of GS·HCl and LGS are similar to each other in solution. CD spectra also supported the structural similarity. With the sequence cyclo(–Val–Leu–Leu–d ‐Phe–Pro–)₂ (Val is valine and Leu is leucine), LGS lacks the amphiphilicity and antimicrobial activity of parental Gramicidin S (GS). However, the structure of LGS reflects the structural characteristics of GS and no disordering inconvenient for structural analysis was found. Thus, LGS could be a novel scaffold useful for studying β‐turn and sheet structures.     

A pH Switch for β‐Sheet Protein Folding

Protein design advancements have led to biotechnological strategies based on more stable and more specific structures. Herein we present a 6‐residue sequence (HPATGK) that acts as a stable structure‐nucleating turn at physiological and higher pH but is notably unfavorable for chain direction reversal at low pH. When placed into the turn of a β‐sheet, this leads to a pH switch of folding. Using a standard 3‐stranded β‐sheet model, the WW domain, it was found that the pH switch sequence insertion caused minimal change at pH 8 but a ca. 50 °C drop in the melting temperature (T_m) was observed at pH 2.5: ΔΔG_F ≥11.3 kJ mol⁻¹. Using the strategies demonstrated in this article, the redesign of β‐sheets to contain a global, or local, pH‐dependent conformational switch should be possible.     

Structure and Isotope Effects of the β‐H Agostic (α‐Diimine)Nickel Cation as a Polymerization Intermediate

Single‐crystal X‐ray characterization of cationic (α‐diimine)Ni‐ethyl and isopropyl β‐agostic complexes, which are key intermediates in olefin polymerization and oligomerization, are presented. The sharp Ni‐C_α‐C_β angles (75.0(3)° and 74.57(18)°) and short C_α−C_β distances (1.468(7) and 1.487(5) Å) provide unambiguous evidence for a β‐agostic interaction. An inverse equilibrium isotope effect (EIE) for ligand coordination upon cleavage of the agostic bond highlights the weaker bond strength of Ni−H relative to the C−H bond. An Eyring plot for β‐hydride elimination–olefin rotation–reinsertion is constructed from variable‐temperature NMR spectra with ¹³C‐labeled agostic complexes. The enthalpy of activation (ΔH ^≠) for β‐H elimination is 13.2 kcal mol⁻¹. These results offer important mechanistic insight into two critical steps in polymerization: ligand association upon cleavage of the β‐agostic bonds and chain‐migration via β‐H elimination.     

Establishing effective simulation protocols for β‐ and α/β‐peptides. III. Molecular mechanical model for acyclic β‐amino acids

All‐atom molecular mechanics (MM) force field parameters are developed for the backbone of acyclic β‐amino acid using an improved version of the multiobjective evolutionary algorithm (MOEA). The MM model is benchmarked using β³‐homo‐Alanine (β³‐hAla) diamide in water with SCC‐DFTB/MM simulations as the reference. Satisfactory agreements are found between the MM and SCC‐DFTB/MM results regarding the distribution of key dihedral angles for the β³‐hAla diamide in water. The MM model is further applied to a β‐hepta‐peptide in methanol solution. The calculated NOE values and ³J coupling constants averaged over different trajectories are consistent with experimental data. By contrast, simulations using parameters directly transferred from the CHARMM22 force field for proteins lead to much worse agreement, which highlights the importance of careful parameterization for non‐natural peptides, for which the improved MOEA is particularly useful. Finally, as an initial application of the new force field parameters, the behaviors of a short random copolymer consisting of β amino acids in bulk solution and membrane/water interface are studied using a generalized Born implicit solvent model (GBSW). Results for four selected sequences show that segregation of hydrophobic and cationic groups occur easily at the membrane/solution interface for all sequences. The sequence that features alternating short blocks exhibits signs of lower stability at the interface compared to other sequences. These results confirm the hypothesis in recent experimental studies that β‐amino‐acid based random copolymers can develop a high degree of amphiphilicity without regular three‐dimensional structure. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Helical‐Ribbon Formation by a β‐Amino Acid Modified Amyloid β‐Peptide Fragment

An addition to the family : The introduction of β‐amino acid residues into a modified amyloid β peptide fragment resulted in well‐defined helical nanoribbons (see cryo‐TEM image) comprising β strands mainly oriented perpendicular to the ribbon axis. The nanoribbons order into a flow‐aligning nematic phase at higher concentration. The β‐strand nanoribbon structure is an addition to the known set of secondary structures adopted by β‐peptides.

     

Synthesis and Structures of β‐Diketoiminate Complexes of Magnesium

The reaction of the β‐diketoiminate lithium complex (dipp)NacNacLi · OEt₂ ((dipp)NacNac = 2‐((2,6‐diisopropylphenyl)amino)‐4‐((2,6‐diisopropylphenyl)imino)‐pent‐2‐enyl) with iPrMgCl and MgI₂ yield the corresponding (dipp)NacNacMgiPr · OEt₂ ( 1 ) and (dipp)NacNacMgI · OEt₂ ( 2 ). The reaction of 2 with NaBH₄ in diethylether gives (dipp)NacNacMg(μ‐H)₃BH · OEt₂ ( 3 ). The core element of compounds 1 – 3 is a six‐membered ring formed by N(1)–C(1)–C(2)–C(3)–N(2) and magnesium. The structures of 1 and 2 show the β‐diketoiminate backbone in a boat‐conformation with the tetrahedrally coordinated metal center at the prow and the opposing carbon atom at the stern. The magnesium atom in 3 is octahedrally coordinated and out of the β‐diketoiminate plane.     

Conformational structure of peptides containing dehydroalanine: Formation of β‐bend ribbon structure

α,β‐Unsaturated amino acids (dehydroamino acids) have been found in naturally occurring antibiotics of microbial origin and in some proteins. Due to the presence of the C_αC_β double bond, the dehydroamino acids influence the main‐chain and the side‐chain conformations. The lowest‐energy conformational state of the model tripeptides, Ac–X–ΔAla–NHMe, (X=Ala, Val, Leu, Abu, or Phe) corresponds to ϕ₁=−30°, ψ₁=120° and ϕ₂=ψ₂=30°. This structure is stabilized by the hydrogen bond between CO of the acetyl group and the NH of the amide group, resulting in the formation of a 10‐membered ring. In the model heptapeptide containing ΔAla at alternate position with Ala, Abu, and Leu, the lowest‐energy conformation corresponds to ϕ=−30° and ψ=120° for all the Ala, Abu, and Leu residues and ϕ=ψ=30° for all ΔAla residues. A graphical view of the molecule in this conformation reveals the formation of three hydrogen bonds involving the CO moiety of the ith residue and the NH moiety of the i+3th residue, resulting in a 10‐membered ring formation. In this structure, only alternate peptide bonds are involved in the intramolecular hydrogen‐bond formation unlike the helices and it has been named the β‐bend ribbon structure. The helical structures were predicted to be the most stable structures in the heptapeptide Ac–(Aib–ΔAla)₃–NHMe with ϕ=±30°, ψ=±60° for Aib residues and ϕ=ψ=±30° for ΔAla residues. The computational results reveal that the ΔAla residue does not induce an inverse γ‐turn in the preceding residue. It is the competitive interaction of small solvent molecules with the hydrogen‐bonding sites of the peptide which gives rise to the formation of an inverse γ‐turn (ϕ₁=−54°, ψ₁=82°; ϕ₂=44°, ψ₂=3°) in the preceding residue to ΔAla. The computational studies for the positional preference of ΔAla in the peptide containing one ΔAla and nine Ala residues reveals the formation of a 3₁₀ helical structure in all the cases with the terminal preferences for ΔAla, consistent with the position of ΔAla in the natural antibiotics. The extended structures is found to be the most stable for poly‐ΔAla. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 72: 15–23, 1999     

Tautomerism and isotopic multiplets in the 13C NMR spectra of partially deuterated 3‐arylpyrimido[4,5‐c]pyridazine‐5,7(6H,8H)‐diones and their sulfur analogs—evidence for elucidation of the structure backbone and tautomeric forms

The tautomerism of the synthesized 3‐arylpyrimido[4,5‐c]pyridazine‐5,7(6H,8H)‐diones ( 1a–d ) and 3‐aryl‐7‐thioxo‐7,8‐dihydro‐6H‐pyrimido[4,5‐c]pyridazine‐5‐ones ( 2a–d ) was studied in dimethyl sulfoxide (DMSO)‐d₆. ¹H NMR spectra of 1a–d showed a clustered water molecule in the structure backbone that is attached by strong intermolecular H bonding. The relation between the temperature and H bonding of the clustered water molecule with 1a was also studied as representative. The relation between the electronegativity (χ) of the substituent on phenyl ring and the chemical shifts of clustered water protons in 1a–d was also studied. All of 1a–d and also 2d compounds existed in lactam ( I ) form, whereas 2a–c compounds have two distinguished tautomers in DMSO‐d₆ [lactam ( I ) and lactim ( II ) forms]. The solvent‐substrate proton exchange was examined in compounds 1a–d and 2a–d by adding one drop of D₂O. All compounds (except 1d ) showed proton/deuterium exchange of the clustered water protons in DMSO by adding one drop of D₂O. Some compounds (but not all of them) that are easily soluble in DMSO‐d₆ containing D₂O showed isotopic splitting (β‐isotope effect) in their ¹³C NMR spectra. Among them, compound 1a was the best evidence to help the spectral assignments and structure determination of predominant tautomer by carbon‐13 splitting (β‐isotope effect). Copyright © 2010 John Wiley & Sons, Ltd.