The infrared and ultraviolet spectra of single conformations of methyl-capped dipeptides: N-acetyl tryptophan amide and N-acetyl tryptophan methyl amide

Abstract

A combination of methods, including laser-induced fluorescence excitation, fluorescence-dip infrared ͑FDIR͒ spectroscopy, and UV-UV hole-burning spectroscopy, have been used to study the infrared and ultraviolet spectra of single conformations of two methyl-capped dipeptides: N-acetyl tryptophan amide ͑NATA͒ and N-acetyl tryptophan methyl amide ͑NATMA͒. Density functional theory calculations predict that all low-energy conformers of NATA and NATMA belong to one of two conformational families: C5, with its extended dipeptide backbone, or C7 eq , in which the dipeptide backbone forms a seven-membered ring joined by a H bond between the-amide NH and the-amide carbonyl groups. In NATA ͑NATMA͒, the LIF spectrum has contributions from two ͑three͒ conformers. FDIR spectroscopy has been used to record infrared spectra of the individual conformers over the 2800-3600 cm Ϫ1 region, free from interference from one another. The NH stretch region provides unequivocal evidence that one of the conformers of NATA is C5, while the other is C7 eq. Similarly, in NATMA, there are two C5 conformers, and one C7 eq structure. Several pieces of evidence are used to assign spectra to particular C5 and C7 eq conformers. NATA͑A͒ and NATMA͑B͒ are both assigned as C5͑AP͒ structures, NATA͑B͒ and NATMA͑C͒ are assigned as C7 eq ͑⌽P͒, and NATMA͑A͒ is assigned as C5͑A⌽͒. In both molecules, the C5 structures have sharp vibronic spectra, while the C7 eq conformers are characterized by a dense, highly congested spectrum involving long progressions that extend several hundred wave numbers to the red of the C5 S 1-S 0 origins. N-acetyl tryptophan ethyl ester ͑NATE͒, which can only form C5 conformers, shows only sharp transitions in its LIF spectrum due to four C5 conformers, with no evidence for the broad absorption due to C7 eq. This provides direct experimental evidence for the importance of the peptide backbone conformation in controlling the spectroscopic and photophysical properties of tryptophan.

Secondary structures of short peptide chains in the gas phase: Double resonance spectroscopy of protected dipeptides

“…For instance, the study of protected amino-acids permits to address the issue of local preferences. A ␥-fold with the formation of a H-bond in a seven-atom ring ͑named C 7 , see Chart 1͒ has been found experimentally for protected alanine ͑Ala͒, 37 tryptophan ͑Trp͒, 31,32 and phenylalanine ͑Phe͒ 34 -36 and has been confirmed by high level ab initio calculations. 2,4,6,8,10,38 -40 In the case of the aromatic residues Trp and Phe, extended ␤-strandlike structures ͑referred to as ␤ L ) energetically compete with ␥-folds and are also observed experimentally.…”

“…2,4,6,8,10,38 -40 In the case of the aromatic residues Trp and Phe, extended ␤-strandlike structures ͑referred to as ␤ L ) energetically compete with ␥-folds and are also observed experimentally. 31,32,35,36 Their stability results from the existence of a weak C 5 interaction between neighboring NH and CO moieties, resulting in an extended backbone, which also allows the formation of a stabilizing NH¯in-teraction between the aromatic ring and the trans NH of the C-terminal amide group. 35,41 Chart 1.…”

“…After the pioneering work of Levy and co-workers on the amino acid tryptophan and its derivatives, 20 several experimental groups focused their efforts on other amino acids and peptides molecules, either having the N-and C-termini unmodified 24 -30 or chemically protected. [31][32][33][34][35][36] In particular, N-acetylated and C-amidated termini ͑chart 1͒ allow to study a͒ Author to whom correspondence should be addressed. Electronic mail: mmons@cea.fr the intrinsic folding properties of the peptide backbone as they introduce peptide bonds in the system.…”

First-principles anharmonic quantum calculations for peptide spectroscopy: VSCF calculations and comparison with experiments

“…The first two systems are the two lowest energy conformers of methyl-capped dipeptides: N-acetyl tryptophan amide (NATA) represented by two different structural motifs, say C5 and C7. 8 The C5 structure (NATA-C5) consists of extended peptide backbone and the C7 structure (NATA-C7) contains a hydrogen bond of c-amide NH to f-amide carbonyl group forming a seven member ring. The third structure is a dipeptide of Ac-Val-Phe-OMe (AVPO), protected at both the terminal positions by an acetyl and methyl group.…”

Derivation of the generalized Langevin equation in nonstationary environments

“…Sometimes one also excites the bath mode vibrations to obtain different reaction product. [22][23][24] How we can acquire a low-dimensional description for such nonstationary systems has been a contemporary intriguing subjects to be resolved. For the last decade there have been several attempts at establishing the nonstationary representation termed as the irreversible generalized Langevin equation (iGLE).…”