Crystal structure and molecular conformation of N-boc-L-pro-dehydro-leu-OCH₃

Abstract

The peptide N-Boc-L-Pro-dehydro-Leu-OCH₃ was synthesized by coupling dehydroleucine methyl ester with Boc-Pro-OH. It was crystallized from its solution in a methanol-water mixture at 4°C and the crystals belong to the orthorhombic space group P2₁2₁2₁ with a = 10.239(1) Å, b = 19.276(4) Å, c = 20.319(3) Å, V = 4010(1) ų, and Z = 8. The structure was solved by direct methods using MULTAN 80. The structure was refined to an R value of 0.095 for 1871 observed reflections. There are two crystallographically independent molecules in the unit cell. The molecular dimensions of the two molecules are very similar. The backbone conformation angles of these molecules are as follows: θ¹ = −176(1)°, ω₀ = −2(2)°, Φ₁ = −72(1)°, ψ₁ = 141(1)°, ω₁ =169(1)°, Φ₂ = −98(1)°, ψ₂ = −179(1)°, θ_T = 179(1)°, θ¹₁ = 174(1)°, ω₁₀ = −3cm⁻¹, Φ₁₁ = −64(1)°, ψ ₁₁ = 148(1)°, ω₁₁ = 167(1)°, Φ₁₂ = −67(1)°, ψ₁₂ = 175(1)°, and θ_1T = 172(1)°, respectively. Other torsion angles such as θ²₁ = 86(1)°, χ₂ = −5(2)°, = 131(1)°, and χ₁₂ = −16(2)° are interesting to define the backbone conformation together with the dehydro-Leu side chain as a conformation similar to that of the β-bend type II. The central amide bond of Pro-dehydro-Leu segment is deviated from the planarity. The Boc group adopts a trans-cis conformation. The side-chain torsion angles χ¹, χ², χ³, χ⁴, and χ⁰ for Pro-residue in the two molecules are 11(2)°, −11(2)°, 6(2)°, 2(1)°, −9(1)° and −18(1)°, 31(1)°, −31(1)°, 21(1)°, and −1(1)° respectively. The side chain of the Pro residue of molecule A is in the flattened C γ-endo conformation while the pyrrolidine ring in miolecule B adopts the well-known C^γ-exo conformation. The side-chain torsion angles χ , χ ^2,1, and χ ^2,2 in the leucyl residues of molecules A and B are −5(2)°, −111(2)°, 126(2)° and −16(2)°, −110(2)°, and 133(2)°, respectively. The molecular packing is stabilized by intermolecular hydrogen bonds and van der Waals interactions.