Influence of the Nonplanarity of the Amide Moiety on Computed Chemical Shifts in Peptide Analogs. Is the Amide Nitrogen Pyramidal?

Sulzbach, Horst M.; Schleyer, Paul von Ragué; Schaefer, Henry F.

doi:10.1021/ja00114a028

Cited by 36 publications

(28 citation statements)

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“…30 The experimental values and the GIAO-SCF and DFT theoretical shieldings are listed in Table 1. Our results support the conclusion of a previous study by Sulzbach et al 25 on the effects of the electron correlation on the amide 15 N chemical shift. Moreover, it appears that inclusion of electron correlation enables quite good absolute shielding predictions to be made, even for planar fragments.…”

Section: N Chemical Shifts In Proteinssupporting

confidence: 93%

Ab Initio Studies of Amide-¹⁵N Chemical Shifts in Dipeptides: Applications to Protein NMR Spectroscopy

Oldfield

1996

J. Phys. Chem.

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The results of calculations aimed at providing a better understanding of how protein structural parameters affect 15 N nuclear magnetic resonance (NMR) chemical shifts, using ab initio quantum chemical methods, are reported. The results support previous empirical observations that the two backbone dihedral angles closest to the peptide group (ψ i-1 and φ i ) have the largest effects on 15 N chemical shifts, contributing a range of about 20 ppm. The adjacent torsion angles φ i-1 and ψ i have a smaller contribution, up to 8 ppm, but also need to be considered when predicting protein chemical shifts. Different side chain conformations produce chemical shift variations of up to ∼4 ppm. Hydrogen bonding to peptide carbonyl groups can also contribute to 15 N shielding, as can longer range electrostatic field effects, but these effects are smaller than those due to torsions. Calculations of 15 N chemical shifts of nonhelical alanine residues in a Staphylococcal nuclease, dihydrofolate reductase from Lactobacillus casei, and ferrocytochrome c 551 from Pseudomonas aeruginosa show a good correlation between experimental observation and ab initio prediction, but the shielding of helical residues is overestimated by ∼8 ppm, due most likely to electric field effects from the helix dipole. 15 N NMR chemical shifts are very sensitive probes of protein conformation and have potential for structure validation, although at present they are less useful than are 13 C shifts for prediction and refinement, because of their more complex dependence on multiple torsional, as well as electrostatic field, effects.

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Section: N Chemical Shifts In Proteinssupporting

confidence: 93%

Ab Initio Studies of Amide-¹⁵N Chemical Shifts in Dipeptides: Applications to Protein NMR Spectroscopy

Oldfield

1996

J. Phys. Chem.

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“…3 The bonds-to-nitrogen out-of-plane deformation can be quite large and for translike amides it approximately correlates with the x parameter by v N % 22Dx, where Dx 5 x 2 180. 6,17,18 The pyramid on carbonyl carbon is smaller and the observed distortions rarely exceed 58. 19,20 A correlation was observed of the sense of nonplanar deformation with the handedness of proteins main chain twist.…”

Section: Introductionmentioning

confidence: 99%

Spectroscopic properties of the nonplanar amide group: A computational study

2007

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Experimental studies suggest that amide bond may significantly deviate from planar arrangement even in linear peptides and proteins. In order to find out the extent to which such deviation may influence principal amide spectroscopic properties, we conducted a computational study of nonplanar N-methylacetamide (NMA) conformers. Vibrational absorption, Raman, and electronic spectra including optical activity were simulated with ab initio and density functional theory (DFT) methods. According to the results, small nonplanarity deviations may be detectable by nonpolarized spectroscopic techniques, albeit as subtle spectral changes. The optical activity methods, such as the vibrational circular dichroism (VCD), Raman optical activity (ROA), and electronic circular dichroism (CD, ECD), provide enhanced information about the amide nonplanarity, because planar amide is not optically active (chiral). For VCD, however, the inherently chiral contribution in most peptides and proteins most probably provides very weak signal in comparison with other contributions, such as the dipolar coupling. For the electronic CD, the nonplanarity contribution is relatively big and causes a strong CD couplet in the n-pi* absorption region accompanied by a red frequency shift. The pi-pi* CD region is relatively unaffected. The ROA spectroscopy appears most promising for the nonplanarity detection and the inherent chiral signal may dominate entire spectral parts. The amide I and III vibrational ROA bands are most challenging experimentally because of their relatively weak coupling to other peptide vibrations.

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“…The 1 H, 13 C, and 15 N NMR chemical shifts of nitrogen heterocyclic compounds have been the subject of a number of experimental and theoretical studies. − There have also been a number of NMR studies of chemical shifts in aminobenzenes , and aminopyrimidines. − An important aspect of magnetic shielding in amine-substituted aromatic compounds, which appears not to have been addressed in previous NMR studies, is the dependence of NMR chemical shifts on amine group orientations. Experimental and theoretical studies of amine substituted aromatic compounds show that the amine group hydrogens are out of the plane by an amount which depends on a balance between π-electron delocalization across the C−N bond and the tendency of the amine group to form strongly directed sp 3 -hybridized orbitals. − There are relatively few structural studies among these compounds because of spectral complexity arising from multiple, large-amplitude vibrations associated with low NH 2 torsion and inversion barriers.…”

Section: Introductionmentioning

confidence: 99%

Density Functional Theory/GIAO Studies of the ¹³C, ¹⁵N, and ¹H NMR Chemical Shifts in Aminopyrimidines and Aminobenzenes: Relationships to Electron Densities and Amine Group Orientations

1997

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The dependence of the 13C, 15N, and 1H isotropic NMR chemical shifts on amine substitution of aromatic ring systems are examined both experimentally and by DFT/GIAO (density functional theory/gauge including atomic orbitals) methods. There are large, monotonic decreases in the chemical shifts at odd-numbered (ortho and para) pyrimidine ring positions which do not occur at the even-numbered (ipso and meta) atoms as amine groups progressively replace hydrogens at the latter positions. This behavior parallels the computed 2p z electron densities which for the pyrimidine series increase monotonically at N1, N3, and C5 but exhibit small changes at the C2, C4, and C6 positions. Identical trends are noted for the aminobenzenes. The ring atom chemical shifts and 2p z electron densities at ortho and para (but not meta) positions are quite sensitive to the orientations of the amine groups which are pyramidalized as the result of balance between delocalization with the ring and the use of strongly directed sp3 orbitals at the nitrogen. The calculated results show that the barriers to amine group torsional and inversion motions are low, but averaging the chemical shifts over these appears to be relatively unimportant. Differences between the DFT and Hartree−Fock-based chemical shifts show that electron correlation effects monotonically increase with the number of NH2 substituents.

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Influence of the Nonplanarity of the Amide Moiety on Computed Chemical Shifts in Peptide Analogs. Is the Amide Nitrogen Pyramidal?

Cited by 36 publications

References 0 publications

Ab Initio Studies of Amide-¹⁵N Chemical Shifts in Dipeptides: Applications to Protein NMR Spectroscopy

Ab Initio Studies of Amide-¹⁵N Chemical Shifts in Dipeptides: Applications to Protein NMR Spectroscopy

Spectroscopic properties of the nonplanar amide group: A computational study

Density Functional Theory/GIAO Studies of the ¹³C, ¹⁵N, and ¹H NMR Chemical Shifts in Aminopyrimidines and Aminobenzenes: Relationships to Electron Densities and Amine Group Orientations

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Influence of the Nonplanarity of the Amide Moiety on Computed Chemical Shifts in Peptide Analogs. Is the Amide Nitrogen Pyramidal?

Cited by 36 publications

References 0 publications

Ab Initio Studies of Amide-15N Chemical Shifts in Dipeptides: Applications to Protein NMR Spectroscopy

Ab Initio Studies of Amide-15N Chemical Shifts in Dipeptides: Applications to Protein NMR Spectroscopy

Spectroscopic properties of the nonplanar amide group: A computational study

Density Functional Theory/GIAO Studies of the 13C, 15N, and 1H NMR Chemical Shifts in Aminopyrimidines and Aminobenzenes: Relationships to Electron Densities and Amine Group Orientations

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Ab Initio Studies of Amide-¹⁵N Chemical Shifts in Dipeptides: Applications to Protein NMR Spectroscopy

Ab Initio Studies of Amide-¹⁵N Chemical Shifts in Dipeptides: Applications to Protein NMR Spectroscopy

Density Functional Theory/GIAO Studies of the ¹³C, ¹⁵N, and ¹H NMR Chemical Shifts in Aminopyrimidines and Aminobenzenes: Relationships to Electron Densities and Amine Group Orientations