Dawid Siodłak

Effects of side-chain orientation on the backbone conformation of the dehydrophenylalanine residue. Theoretical and X-ray study.

Two E isomers of α,β-dehydro-phenylalanine, Ac-(E)-ΔPhe-NHMe (1a) and Ac-(E)-ΔPhe-NMe(2) (2a), have been synthesized and their low temperature structures determined by single-crystal X-ray diffraction. A systematic theoretical analysis was performed on these molecules and their Z isomers (1b and 2b). The ϕ,ψ potential energy surfaces were calculated at the MP2/6-31+G(d,p) and B3LYP/6-31+G(d,p) levels in the gas phase and at the B3LYP/6-31+G(d,p) level in the chloroform and water solutions with the SCRF-PCM method. All minima were fully optimized by the MP2 and DFT methods, and their relative stabilities were analyzed in terms of π-conjugation, internal H-bonds, and dipole-dipole interactions between carbonyl groups. The results indicate that all the studied compounds can adopt the conformation H (ϕ, ψ ≈ ±40°, ∓120°) which is atypical for standard amino acids residues. A different arrangement of the side chain in the E and Z isomers causes them to have different conformational preferences. In the presence of a polar solvent both Z isomers of ΔPhe (1b and 2b) are found to adopt the 3(10)-helical conformation (left- and right-handed are equally likely). On the other hand, this conformation is not accessible or highly energetic for E isomers of ΔPhe (1a and 2a). Those isomers have an intrinsic inclination to have an extended conformation. The conformational space of the Z isomers is much more restricted than that of the E derivative both in the gas phase and in solution. In the gas phase the E isomers of ΔPhe have lower energies than the Z ones, but in the aqueous solution the energy order is reversed.

The conformational properties of dehydrobutyrine and dehydrovaline: theoretical and solid-state conformational studies.

Dehydrobutyrine is the most naturally occurring dehydroamino acid. It is also the simplest dehydroamino acid having the geometrical isomers E/Z. To investigate its conformational properties, a theoretical analysis was performed on N‐acetyl‐α,β‐dehydrobutyrine N′‐methylamides, Ac‐(E)‐ΔAbu‐NHMe and Ac‐(Z)‐ΔAbu‐NHMe, as well as the dehydrovaline derivative Ac‐ΔVal‐NHMe. The ϕ, ψ potential energy surfaces and the localised conformers were calculated at the B3LYP/6‐311 + + G(d,p) level of theory both in vacuo and with inclusion of the solvent (chloroform, water) effect (SCRF method). The X‐ray crystal structures of Ac‐(Z)‐ΔAbu‐NHMe and Ac‐ΔVal‐NHMe were determined at 85 and 100 K, respectively. The solid‐state conformational preferences for the studied residues have been analysed and compared with the other related structures. Despite the limitations imposed by the Cα = Cβ double bond on the topography of the side chains, the main chains of the studied dehydroamino acids are more flexible than in standard alanine. The studied dehydroamino acids differ in their conformational preferences, which depend on the polarity of the environment. This might be a reason why the nature quite precisely differentiates between ΔVal and each of the ΔAbu isomers, and why, particularly so with the latter, they are used as a conformational tool to influence the biological action of usually small, cyclic dehydropeptides. Copyright

The conformational properties of α,β-dehydroamino acids with a C-terminal ester group

α,β‐Dehydroamino acid esters occur in nature. To investigate their conformational properties, a systematic theoretical analysis was performed on the model molecules Ac‐ΔXaa‐OMe [ΔXaa = ΔAla, (E)‐ΔAbu, (Z)‐ΔAbu, ΔVal] at the B3LYP/6‐311+ + G(d,p) level in the gas phase as well as in chloroform and water solutions with the self‐consistent reaction field‐polarisable continuum model method. The Fourier transform IR spectra in CCl4 and CHCl3 have been analysed as well as the analogous solid state conformations drawn from The Cambridge Structural Database. The ΔAla residue has a considerable tendency to adopt planar conformations C5 (ϕ, ψ ≈ − 180°, 180°) and β2 (ϕ, ψ ≈ − 180°, 0°), regardless of the environment. The ΔVal residue prefers the conformation β2 (ϕ, ψ ≈ − 120°, 0°) in a low polar environment, but the conformations α (ϕ, ψ ≈ − 55°, 35°) and β (ϕ, ψ ≈ − 55°, 145°) when the polarity increases. The ΔAbu residues reveal intermediate properties, but their conformational dispositions depend on configuration of the side chain of residue: (E)‐ΔAbu is similar to ΔAla, whereas (Z)‐ΔAbu to ΔVal. Results indicate that the low‐energy conformation β2 is the characteristic feature of dehydroamino acid esters. The studied molecules constitute conformational patterns for dehydroamino acid esters with various side chain substituents in either or both Z and E positions. Copyright

Conformational properties of the residues connected by ester and methylated amide bonds: theoretical and solid state conformational studies

Peptides produced by bacteria and fungi often contain an ester bond in the main chain. Some of them have both an ester and methylated amide bond at the same residue. A broad spectrum of biological activities makes these depsipeptides potential drug precursors. To investigate the conformational properties of such modified residues, a systematic theoretical analysis was performed on N‐acetyl‐L‐alanine N′‐methylamide (Ac‐Ala‐NHMe) and the analogues with the ester bond on the C‐terminus (Ac‐Ala‐OMe), N‐terminus (Ac‐[psi](COO)‐Ala‐NHMe) as well as the analogues methylated on the N‐terminus (Ac‐(Me)Ala‐OMe) and C‐terminus (Ac‐[psi](COO)‐Ala‐NMe2). The ϕ, ψ potential energy surfaces and the conformers localised were calculated at the B3LYP/6‐311++G(d,p) level of theory both in vacuo and with inclusion of the solvent (chloroform, water) effect (SCRF method). The solid state conformations of the studied residues drawn from The Cambridge Structural Database have been also analysed. The residues with a C‐terminal ester bond prefer the conformations β, C5, and αR, whereas those with N‐terminal ester bond prefer the conformations β, αR, and the unique conformation α′ (ϕ, ψ = −146°, −12°). The residues with N‐terminal methylated amide and a C‐terminal ester bond prefer the conformations β, β2, and interestingly, the conformation αL. The residues with a C‐terminal methylated amide and an N‐terminal ester bond adopt primarily the conformation β. The description of the selective structural modifications, such as those above, is a step towards understanding the structure‐activity relationship of the depsipeptides, limited by the structural complexity of these compounds. Copyright

The effect of β‐methylation on the conformation of α, β‐dehydrophenylalanine: a DFT study

Dehydroamino acids are non‐coded amino acids that offer unique conformational properties. Dehydrophenylalanine (ΔPhe) is most commonly used to modify bioactive peptides to constrain the topography of the phenyl ring in the side chain, which commonly serves as a pharmacophore. The Ramachandran maps (in the gas phase and in CHCl3 mimicking environments) of ΔPhe analogues with methyl groups at the β position of the side chain as well as at the C‐terminal amide were calculated using the B3LYP/6‐31 + G** method. Unexpectedly, β‐methylation alone results in an increase of conformational freedom of the affected ΔPhe residue. However, further modification by introducing an additional methyl group at C‐terminal methyl amide results in a steric crowding that fixes the torsion angle ψ of all conformers to the value 123°, regardless of the Z or E position of the phenyl ring. The number of conformers is reduced and the accessible conformational space of the residues is very limited. In particular, (Z)‐Δ(βMe)Phe with the tertiary C‐terminal amide can be classified as the amino acid derivative that has a single conformational state as it seems to adopt only the β conformation. Copyright

Conformational Properties of Oxazole-Amino Acids: Effect of the Intramolecular N−H···N Hydrogen Bond

Oxazole ring occurs in numerous natural peptides, but conformational properties of the amino acid residue containing the oxazole ring in place of the C-terminal amide bond are poorly recognized. A series of model compounds constituted by the oxazole-amino acids occurring in nature, that is, oxazole-alanine (L-Ala-Ozl), oxazole-dehydroalanine (ΔAla-Ozl), and oxazole-dehydrobutyrine ((Z)-ΔAbu-Ozl), was investigated using theoretical calculations supported by FTIR and NMR spectra and single-crystal X-ray diffraction. It was found that the main feature of the studied oxazole-amino acids is the stable conformation β2 with the torsion angles φ and ψ of -150°, -10° for L-Ala-Ozl, -180°, 0° for ΔAla-Ozl, and -120°, 0° for (Z)-ΔAbu-Ozl, respectively. The conformation β2 is stabilized by the intramolecular N-H···N hydrogen bond and predominates in the low polar environment. In the case of the oxazole-dehydroamino acids, the π-electron conjugation that is spread on the oxazole ring and C(α)═C(β) double bond is an additional stabilizing interaction. The tendency to adopt the conformation β2 clearly decreases with increasing the polarity of environment, but still the oxazole-dehydroamino acids are considered to be more rigid and resistant to conformational changes.

The cis-trans isomerization of N-methyl-α,β-dehydroamino acids†‡

Dehydroamino acids with the methylated N‐terminal peptide group occur in natural small cyclic peptides. The structural analysis was used to investigate the cis‐trans isomerization of the N‐terminal tertiary amide group of diamides: Ac‐(Z)‐Δ(Me)Abu‐NHMe (1), Ac‐(Z)‐Δ(Me)Phe‐NHMe (2), Ac‐(E)‐Δ(Me)Phe‐NHMe (3), Ac‐Δ(Me)Ala‐NHMe (4), and Ac‐(Me)Ala‐NHMe (5). The compounds were analyzed in the solid state by an X‐ray crystallography (1–3), and in the solution by FTIR (MeCN and CHCl3) and NMR (DMSO‐d6 and CDCl3) methods (1–5). In the solid state, the studied compounds adopt the cis configuration of N‐terminal amide. In solution, this configuration also prevails for the dehydroamino acids 1–4, in contrast to the saturated analog 5. The results indicate that N‐methyldehydroamino acids present a promising tool to induce the cis configuration of the amide bond.

The impact of model peptides on structural and dynamic properties of egg yolk lecithin liposomes - experimental and DFT studies

Electron spin resonance (ESR), 1H‐NMR, voltage and resistance experiments were performed to explore structural and dynamic changes of Egg Yolk Lecithin (EYL) bilayer upon addition of model peptides. Two of them are phenylalanine (Phe) derivatives, Ac‐Phe‐NHMe (1) and Ac‐Phe‐NMe2 (2), and the third one, Ac‐(Z)‐ΔPhe‐NMe2 (3), is a derivative of (Z)‐α,β‐dehydrophenylalanine. The ESR results revealed that all compounds reduced the fluidity of liposomes membrane, and the highest activity was observed for compound 2 with N‐methylated C‐terminal amide bond (Ac‐Phe‐NMe2). This compound, being the most hydrophobic, penetrates easily through biological membranes. This was also observed in voltage and resistance studies. 1H‐NMR studies provided a sound evidence on H‐bond interactions between the studied diamides and lecithin polar head. The most significant changes in H‐atom chemical shifts and spin‐lattice relaxation times T1 were observed for compound 1. Our experimental studies were supported by theoretical calculations. Complexes EYLAc‐Phe‐NMe2 and EYLAc‐(Z)‐ΔPhe‐NMe2, stabilized by NH⋅⋅⋅O or/and CH⋅⋅⋅O H‐bonds were created and optimized at M06‐2X/6‐31G(d) level of theory in vacuo and in H2O environment. According to our molecular‐modeling studies, the most probable lecithin site of H‐bond interaction with studied diamides is the negatively charged O‐atom in phosphate group which acts as H‐atom acceptor. Moreover, the highest binding energy to hydrocarbon chains were observed in the case of Ac‐Phe‐NMe2 (2).

Experimental and theoretical NMR studies of interaction between phenylalanine derivative and egg yolk lecithin

The interaction of phenylalanine diamide (Ac‐Phe‐NHMe) with egg yolk lecithin (EYL) in chloroform was studied by 1H and 13C NMR. Six complexes EYL–Ac‐Phe‐NHMe, stabilized by N–H···O or/and C–H···O hydrogen bonds, were optimized at M06‐2X/6‐31G(d,p) level. The assignment of EYL and Ac‐Phe‐NHMe NMR signals was supported using GIAO (gauge including atomic orbital) NMR calculations at VSXC and B3LYP level of theory combined with STO‐3Gmag basis set. Results of our study indicate that the interaction of peptides with lecithin occurs mainly in the polar ‘head’ of the lecithin. Additionally, the most probable lecithin site of H‐bond interaction with Ac‐Phe‐NHMe is the negatively charged oxygen in phosphate group that acts as proton acceptor. Copyright

The conformation cis of N-acetyl-N-methyl-α, β -dehydroalanine N'-methylamide and saturated analogues

A series of three homologous amino acids derivatives: N-acetyl-N-methyl-α,β–dehydroalanine N′-methylamide (1), N-acetyl-N-methyl-L-alanine N′-methylamide (2), and N-acetyl-N-methyl-DL-alanine N′-methylamide have been synthesised. The racemic species undergoes spontaneous separation into L and D-enantiomers. From these two chiral forms, the structure of L-enantiomer (3) was analysed. The molecules of 1 – 3 adopt the cis arrangement of the N-terminal amide bond. The molecular conformations are similar for 1 (φ, ψ = 94.6(1)°, −1.7(1)°) and 3 (φ, ψ = 111.5(1)°, −23.8(1)°), and also 2 (φ, ψ = −114.8(2)°, 29.5(2)°), if inversion through the chiral C2 carbon is considered. They are stabilised by intramolecular N—H…N hydrogen bond. In the case of 1, the π—electron conjugation resulting from the planar arrangement of the C2—C21 double bond and C-terminal amide group is another stabilising force of this conformation. Thus, the N-methyldehydroalanine residue should promotes trans-cis isomerisation to a greater extend than the saturated analogue. The compounds 1 – 3 reveal similar associative pattern and form centrosymmetric dimers linked by the intermolecular N—H…O hydrogen bonds.