IR−UV Ion-Dip Spectroscopy of N-Benzylformamide Clusters:  Stepwise Hydration of a Model Peptide

Abstract

Fluorescence excitation, resonant two-photon ionization (R2PI) and IR-UV ion dip spectroscopy have been used to study conformers of N-benzylformamide (NBFA) and associated clusters including hydrates with up to n ) 3 water molecules. The most stable conformer has a trans arrangement of the HNCO atoms. It is distinguished from the cis conformer by a higher frequency for the NH stretch (3478 cm -1 , compared to 3443 cm -1 ) and lower frequency for the amide I overtone (3435 cm -1 , compared to 3465 cm -1 ). The cis conformer forms cyclic H-bonded structures with one or two water molecules, binding via strong H-bonds to the neighboring CdO and NH groups. With the addition of a third water molecule, the cyclic water trimer binds to both these groups in preference to a linear chain of three waters. For trans-NBFA, a single water binds to the carbonyl group and is further stabilized by dispersive CH‚‚‚O water interactions. Two water molecules bind to the NH group instead and form a bridge to the π-system of the aromatic ring. A heterodimer species is also observed, composed of cis-and trans-NBFA. It is stabilized by NH trans ‚‚‚OdC cis and NH cis ‚‚‚π trans H-bonds, which give rise to shifts in the NH stretch frequency of -102 and -28 cm -1 , respectively. Flexibility of the amide side chain plays a key role in promoting additional CH‚‚‚O water interactions in these clusters. When compared to the unsolvated conformers, some of the clusters exhibit considerable distortion in the dihedral angle τ 1 (C 2 C 1 C R N) and in τ 2 (C 1 C R NC), equivalent to the Ramachandran angle φ in proteins. Solvation also affects the photophysics of NBFA, as the clusters show normal fluorescence behavior while the S 1 states of the isolated molecules are affected by a competing, nonfluorescent decay process.

Structure of hydrated clusters of tetrahydroisoquinoline [THIQ–(H2O)n=1,3] investigated by jet spectroscopy

“…This assignment may be compared with that of cis-NBF-water 1:1 cluster. 28 The OH and NH modes in spectrum 4͑b͒ are 77 and 52 cm Ϫ1 and, in spectrum 4͑e͒, 33 and 66 cm Ϫ1 , more redshifted compared to similar modes in the cis-NBF-water 1:1 cluster. This indicates that the hydrogen bond strength in THIQ cluster is greater than that in the NBF cluster.…”

“…It has been observed in the case of NBF clusters that the water molecule forms a hydrogen bond that bridges the lone pair of nitrogen and the electrons of benzene. 28 However, such a structure is clearly unfavorable in the THIQ cluster, presumably because the distance between the two possible hydrogenbonding sites, the N atom and the phenyl ring, is large. Figures 5͑a͒ and 5͑d͒ show three types of calculated N-bonded low-energy structures of 1:1 clusters of the two conformers.…”

“…26,27 The only exception perhaps is N-benzylformamide ͑NBF͒, where, as in THIQ, two conformers of the bare molecule have been observed. 28 The cis conformer of NBF forms 1:1, 1:2, and 1:3 hydrated clusters, all having cyclic H-bonded structures bridging the CvO and NH 2 groups. In the 1:1 cluster of the trans conformer, however, water is bound only to the carbonyl group; for the 1:2 cluster, one end of the water chain is bound to the NH group and the other forms a loose bond to the electrons of the benzene ring.…”

Isolated Neutral Peptides

“…At the turn of the century, this rationale has led gas phase spectroscopists to devote experimental effort towards simple systems of biological relevance [12,13]. Small building blocks of proteins were first targeted: conformational distributions of these flexible systems, as well as the interactions that shape molecules, in particular their H-bonding networks, have been the focus of these pioneering studies [14][15][16][17][18][19][20]. In this spirit, the classical gas-phase methods of the physicist, inherited from atomic or small molecule spectroscopy, namely optical absorption, either in the microwave, IR/Raman or UV spectral range, have been mobilised to tackle these issues.…”

Gas phase conformation in the ibuprofen analogues isobutylbenzene and 2-phenylpropionic acid

“…Furthermore, the relative intensity of peak 'B' is not affected by variation of the expansion conditions (e.g. entrainment in helium instead of argon, or changing the delay time between the pulsed valve opening and the laser firing to control the degree of cooling observed in the spectrum [20]). This also rules out hot-band transitions or transitions pertaining to photo-dissociated clusters.…”