The microwave spectrum of a two-top peptide mimetic: The N-acetyl alanine methyl ester molecule

Abstract

The rotational spectrum of N-acetyl alanine methyl ester, a derivative of the biomimetic, N-acetyl alanine N'-methyl amide or alanine dipeptide, has been measured using a mini Fourier transform spectrometer between 9 and 25 GHz as part of a project undertaken to determine the conformational structures of various peptide mimetics from the torsion-rotation parameters of low-barrier methyl tops. Torsion-rotation splittings from two of the three methyl tops capping the acetyl end of the -NH-C(=O)- and the methoxy end of -C(=O)-O- groups account for most of the observed lines. In addition to the AA state, two E states have been assigned and include an AE state having a torsional barrier of 396.45(7) cm(-1) (methoxy rotor) and an EA state having a barrier of 64.96(4) cm(-1) (acetyl rotor). The observed torsional barriers and rotational constants of alanine dipeptide and its methyl ester are compared with predictions from Möller-Plesset second-order perturbation theory (MP2) and density functional theory (DFT) in an effort to explore systematic errors at the two levels of theory. After accounting for zero-point energy differences, the torsional barriers at the MP2/cc-pVTZ level are in excellent agreement with experiment for the acetyl and methoxy groups while DFT predictions range from 8% to 80% too high or low. DFT is found to consistently overestimate the overall molecular size while MP2 methods give structures that are undersized. Structural discrepancies of similar magnitude are evident in previous DFT results of crystalline peptides.

The microwave spectrum of the trans conformer of ethyl acetate

“…The method based on the work of Kirtman [13], Lees and Baker [14] and Herbst et al [15] takes its name from the choice of the axis system, the rho-axis system, which is related to the principal axis system by a rotation chosen to eliminate the À2FP c q x J x and À2FP c q y J y coupling terms in the kinetic energy operator where F is the internal rotation constant, P c is the internal angular momentum, J x and J y are the usual x and y components of the global rotation angular momentum and q is a vector that expresses the coupling between the angular momentum of the internal rotation P c and the global rotation J. Unlike XIAM, BELGI-C s which was used successfully to describe the spectra for internal rotors with very low internal rotation barriers (V 3 ffi 25 cm À1 ) such as acetamide [16], and also for peptide mimetics such as the ethylacetamidoacetate molecule [17] and the N-acetyl alanine methyl ester [18] allows for fitting many higher order terms not only in the total angular momentum J, but also in the angular momentum of the internal rotor P c and in cross-terms between them. BELGI-C s uses a two-step diagonalisation procedure in which the first step is the diagonalisation of the torsional Hamiltonian consisting of the one dimensional potential function V(c) together with a torsionrotation kinetic operator diagonal in K, the rotational quantum number.…”

Equilibrium structure in the presence of internal rotation: A case study of cis-methyl formate

“…The reduced barrier is actually rather large and q is small (0.08), thus not much torsional information is transferred to the rotational transitions. The same type of situation occurred with our study of the ester of the dialanine [46], for the case of the methyl group which has the ''high" barrier: D ab was not so well determined, so the cosine angles between the PAS and the symmetry axis of the methyl group have also a few degrees discrepancy and the rotational constants have large standard deviations.…”

The ground and first excited torsional states of methyl carbamate

“…[15]), methanol (e.g. [16]), acetic acid [17], acetamide [18] or even for peptide mimetics such as ethylacetamidoacetate [19] and N-acetyl alanine methyl ester [20].…”