Ir spectra and conformational behavior of <i>N</i>‐acetyl‐(glycine, <scp>L</scp>‐alanine, <scp>L</scp>‐leucine)‐<i>N</i>′‐methylamides in chloroform

Jose, C. I.; Belhekar, A.A.; Agashe, M. S.

doi:10.1002/bip.360260808

Cited by 18 publications

(3 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Ab Initio Calculations. Fully optimized DFT calculations of the molecules I and II at the B3LYP/6-31G** level revealed that they each have two low-energy conformers within the second quadrant of the Ramachandran plot, C5 and C7 eq , consistent with experimental studies of N -acetyl- N ‘-methylamides of l -alanine and glycine in nonpolar solvents by NMR and IR spectroscopy and previous theoretical considerations. ,,− , Figure illustrates the minimum-energy conformational transition within molecules I and II upon the increase of the H-bond distance d 1 . The two energy minima of the single β-strand units correspond to two H-bonded conformations.…”

Section: Resultssupporting

confidence: 78%

Theoretical Studies on the Origin of β-sheet Twisting

2000

View full text Add to dashboard Cite

Right-handed twisting is a fundamental structural feature of β-pleated sheets in globular proteins which is critical for their geometry and function. The origin of this twisting is poorly understood and has represented a challenge for theoretical chemistry for almost 30 years. Density functional theory using the B3LYP exchange-correlation functional and the split-valence 6-31G** basis set has been utilized to investigate the structure and conformational transitions of single and double-stranded antiparallel β-sheet models to determine the driving force for the right-handed twisting. Right-handed twisting is found to be an intrinsic property of a peptide main chain because of the difference in rotational potentials around N(sp2)−Cα(sp3) and C(sp2)−Cα(sp3) bonds. The difference arises from a tendency of the single Cα(sp3)−C(sp2) bonds to eclipse the lone pair of atoms N(sp2), which results in decreasing absolute values of dihedral angles φ but not ψ. This tendency is suppressed by hydrogen bonding between adjacent CO and NH groups within single β-strands, and released only when these bonds are disrupted by the interstrand CO···HN hydrogen bonding. The results obtained constitute the following paradigm of the origin of β-sheet twist: although right-handed twisting of β-sheets in globular proteins is an inherent property of the peptide backbone within single β-strands, it is unleashed by the interstrand hydrogen bonding in multistranded β-sheets. The observed pleating, right-handed twisting, skewed mutual orientation of β-strands, and intrinsic conformational variability of double-stranded antiparallel β-sheet motifs in globular proteins are explained from the first principles.

show abstract

Section: Resultssupporting

confidence: 78%

Theoretical Studies on the Origin of β-sheet Twisting

2000

View full text Add to dashboard Cite

show abstract

“…The formerly investigated IR spectra recorded in CHCl 3 solution were also consistent with a single conformer. 68,69 The amide I region of the VCD spectra observed in DCM and DMSO solutions are also found to be consistent with the conformational assignment above. In contrast to this, in the amide II region the discrepancy between the calculations and the observed spectra could most probably be interpreted by the effect of the coordination on the rotatory strengths.…”

Section: Discussionsupporting

confidence: 81%

A matrix isolation study on Ac-Gly–NHMe and Ac-l-Ala–NHMe, the simplest chiral and achiral building blocks of peptides and proteins

Pohl

Perczel

Vass

et al. 2007

Phys. Chem. Chem. Phys.

View full text Add to dashboard Cite

The infrared absorption (IR) spectra of acetyl-N-methyl-glycine and acetyl-N-methyl-alanine have been recorded in dichloromethane and dimethyl sulfoxide-d(6) solution, as well as in Ar and Kr matrices. The spectra were assigned with the help of quantum chemical calculations. Based on the assignments of the matrix-isolation IR spectra, in line with theoretical predictions, two different hydrogen bonded conformers were identified, furthermore a third conformer is likely to be present, which cannot be unambiguously identified. In dichloromethane two conformers could be observed, while in dimethyl sulfoxide a single conformer could be identified. Vibrational circular dichroism (VCD) spectra of acetyl-N-methyl-l-alanine have also been recorded in solutions and matrices. These matrix-isolation VCD spectra not only support the assignments of the matrix-isolation IR spectra, but also demonstrate that these spectra can be interpreted much easier with the help of quantum chemical calculations than the VCD spectra recorded in solutions. It is also shown that the rotatory strength of some vibrational transitions changes rapidly as a function of the backbone torsional coordinates; hence the appearance of some regions in the VCD spectra is extremely dependent on any perturbations, e.g. weak intermolecular interactions.

show abstract

“…After the curve-fitting procedure (see Fig. 2) their positions are at =3448,3431 and 3413 cm-' (for Ac-Phe-NHMe 3447, 3421 and 3410 cm-') with the average A V , ,~ 20, 25 and 35 cm-', respectively. This proves that there are two N-H groups free and that some part of the N'-H' groups is involved with the C5 structure as proposed by numerous IR studies in CCI4 and CHC1, solutions (38,42,43). Only two v,(N-H) bands occur for unsaturated analogs, however, at ~3 4 5 3 and 3412 cm-' (for Ac-(a-APhe-NHMe at 3451 and 3401 cm-I) with the average AvIR 25 and 34 cm-'.…”

Section: Conformation Of Ac-axaa-nhmesupporting

confidence: 64%

Conformational investigation of α, β‐dehydropeptides. VIII.*N‐Acetyl‐α, β‐dehydroamino acid N'‐methylamides: conformation and electron density perturbation from infrared and theoretical studies

Broda

Rzeszotarska

Smelka

et al. 1997

The Journal of Peptide Research

View full text Add to dashboard Cite

The Fourier transform infrared spectra are analyzed in the regions of vs(N‐H), amide I, amide II and vs(Cα=Cβ) bands for a series of Ac‐ΔXaa‐NHMe, where ΔXaa =ΔAla, (Z)‐ΔAbu, (Z)‐ΔLeu, (Z)‐ΔPhe and AVal, to determine the predominant solution conformation of these α, β‐dehydropeptide‐related molecules and the electron distribution perturbation in their amide bonds. The measurements were performed in dichloromethane (DCM). To confirm and rationalize the assignments, the spectra of the respective series of saturated Ac‐Xaa‐NHMe, recorded in DCM, and the spectra of these two series of unsaturated and saturated compounds, recorded in acetonitrile, were examined. To help interpret the spectroscopic results, the equilibrium geometrical parameters for some selected amides were used. These were optimized with ab initio methods in the 6‐31G** basis set. Each of the dehydroamides studied adopted a C5 structure, which in Ac‐ΔAla‐NHMe is fully extended and accompanied by the strong C5 hydrogen bond. Interaction with the Cα=Cβ bond lessened the amidic resonance within each of the flanking amide groups. The N‐terminal C=O bond was noticeably shorter, both amide bonds were longer than the corresponding bonds in the saturated entities and the N‐terminal amide system was distorted. Ac‐ΔAla‐NHMe constituted an exception. Its C‐terminal amide bond was shorter than the standard one and both amide systems were prototypically planar.

show abstract

Ir spectra and conformational behavior of N‐acetyl‐(glycine, L‐alanine, L‐leucine)‐N′‐methylamides in chloroform

Cited by 18 publications

References 24 publications

Theoretical Studies on the Origin of β-sheet Twisting

Theoretical Studies on the Origin of β-sheet Twisting

A matrix isolation study on Ac-Gly–NHMe and Ac-l-Ala–NHMe, the simplest chiral and achiral building blocks of peptides and proteins

Conformational investigation of α, β‐dehydropeptides. VIII.*N‐Acetyl‐α, β‐dehydroamino acid N'‐methylamides: conformation and electron density perturbation from infrared and theoretical studies

Contact Info

Product

Resources

About