Experimental studies of peptide bonds: Identification of the C7eq conformation of the alanine dipeptide analog N-acetyl-alanine N′-methylamide from torsion-rotation interactions

Abstract

Rotational spectra of the biomimetic molecule, alanine dipeptide and the double N15(N215) isotopomer have been observed using a pulsed-molecular-beam Fourier transform microwave spectrometer. The spectra reveal tunneling splittings from the torsional mode structure of two of its three methyl rotors. The torsional states assigned include one AA-state and two AE-states (i.e., AE and EA) for each isotopomer. The AA-states are well-fit to A-reduction asymmetricrotor Hamiltonians. The “infinite-barrier-limit” rotational constants of the N214 isotopomer are A=1710.97(8) MHz, B=991.89(9) MHz, and C=716.12(6) MHz. The AE-states are analyzed independently using “high-barrier” torsion-rotation Hamiltonians, yielding observedminus-calculated standard deviations of <400 kHz. The fits improve substantially (>100-fold for the N215 isotopomer) when analyzed in a ρ-axis frame where ρb=ρc=0. The best-fit torsion-rotation parameters provide accurate V3 barriers and C3 rotor axis angles for both methyl groups. The observed angles are shown to uniquely correlate with those calculated for the acetyl and amide methyl groups in the C7eq conformational form. The V3 barriers of the amide and acetyl methyl groups are 84.0(3) cm−1 and 98.4(2) cm−1 for the N214 and 84.1(1) cm−1 and 98.65(8) cm−1 for the N215 isotopomers, respectively. These results are in good agreement with prior geometry optimizations and with current V3 barrier calculations which predict the C7eq conformation as the lowest energy form in the gas phase. Under certain conditions, the spectrum is dominated by transitions from a thermal decomposition product formed by dehydration of alanine dipeptide. This molecule is tentatively identified as 3,5-dihydro-2,3,5-trimethyl-(9CI) 4H imidazole-4-one (CAS registry #32023-93-1).

Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package

“…Recent experimental results suggest that the backbone preferences in proteins are already present in blocked aminoacids. 55,56 A number of experimental 55,[57][58][59][60] and theoretical, [61][62][63][64][65][66][67][68][69][70][71][72][73][74][75][76][77][78] studies indicate that the potential energy surface for AD in vacuum and in solution are considerably different: While in the gas-phase the global minimum is believed to be a C7 eq structure (ϕ− 83°, ψ~73°), 70 interaction with water favors the polyproline-II (P II , (ϕ~−75°, ψ~150°) conformation. 60 AD has also been used previously to investigate the performance of the SCC-DFTB method as compared to different classical force fields.…”

Fourier transform microwave spectroscopy of Ac-Ser-NH2: the role of side chain interactions in peptide folding

“…5 Therefore, it is particularly well suited for studying dipeptides containing amino acids as relevant as glycine, alanine or proline, elusive to IR/UV double resonance experiments. Lavrich et al 6 investigated the alanine dipeptide N-acetyl-alanine N 0 -methylamide (Ac-Ala-NHMe) and observed only a C eq 7 conformation using heating methods to bring molecules into the gas phase. Very recently, the combination of FTMW spectroscopic techniques with laser ablation methods [7][8][9][10] has been successfully applied in the investigation of the conformational preferences of isolated protected dipeptides such as N-acetyl-glycinamide (Ac-Gly-NH 2 ), 11 N-acetyl-alaninamide (Ac-Ala-NH 2 ) 12 and N-acetyl-prolinamide (Ac-Pro-NH 2 ).…”

Methyl torsional state analysis of the jet-cooled microwave spectrum of N-acetylglycine

“…A second set of favorable configurations includes a hydrogen bond linking the carbonyl or amide groups of the peptide bond to the hydroxyl group, acting as either proton donor or acceptor. This seven membered ring is similar to the lowest energy form reported for N-acetylalanine-N 0 -methyl amide (Alanine Dipeptide) [25]. Two additional constraints further simplify the possible geometries of Nacetylglycine.…”

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