Experimental and theoretical NMR and IR studies of the side‐chain orientation effects on the backbone conformation of dehydrophenylalanine residue

Buczek, Aneta; Ptak, Tomasz; Kupka, Teobald; Broda, Małgorzata A.

doi:10.1002/mrc.2753

Cited by 17 publications

(18 citation statements)

References 33 publications

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“…However, our B3LYP/pcS-2//B3LYP/6-31G * calculated carbon shielding of 40.6296 ppm yielded a value underestimated by roughly 20 ppm! Thus, similar to our recent work, [56] for comparison with available experimental data we presented our theoretical chemical shifts of ith nucleus relative to a reference molecule, using carbon and proton chemical shift (in ppm) of benzene in solution:…”

Section: Methodsmentioning

confidence: 87%

DFT calculation of structures and NMR chemical shifts of simple models of small diameter zigzag single wall carbon nanotubes (SWCNTs)

Kupka¹,

Stachów²,

Nieradka³

et al. 2011

Magnetic Reson in Chemistry

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Linearly conjugated benzene rings (acenes), belt-shape molecules (cyclic acenes) and model single wall carbon nanotubes (SWCNTs) were fully optimized at the unrestricted level of density functional theory (UB3LYP/6-31G*). The models of SWCNTs were selected to get some insight into the potential changes of NMR chemical shift upon systematic increase of the molecular size. The theoretical NMR chemical shifts were calculated at the B3LYP/pcS-2 level of theory using benzene as reference. In addition, the change of radial breathing mode (RBM), empirically correlated with SWCNT diameter, was directly related with the radius of cyclic acenes. Both geometrical and NMR parameters were extrapolated to infinity upon increase in the studied systems size using a simple two-parameter mathematical formula. Very good agreement between calculated and available experimental CC bond lengths of acenes was observed (RMS of 0.0173 Å). The saturation of changes in CC bond lengths and (1)H and (13)C NMR parameters for linear and cyclic acenes, starting from 7-8 conjugated benzene rings, was observed. The (13)C NMR parameters of individual carbon atoms from the middle of ultra-thin (4,0) SWCNT formed from 10 conjugated cyclic acenes differ by about 130 ppm from the corresponding open end carbon nuclei.

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Section: Methodsmentioning

confidence: 87%

DFT calculation of structures and NMR chemical shifts of simple models of small diameter zigzag single wall carbon nanotubes (SWCNTs)

Kupka¹,

Stachów²,

Nieradka³

et al. 2011

Magnetic Reson in Chemistry

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“…To validate the performance of our estimation scheme of carbonyl anharmonic frequency, the E and Z isomers of Ac-ΔPhe-NMe 2 [34] were selected. Full geometry optimization of the tested diamides was performed with the B3LYP/6-311++G(p,d) method and both harmonic and anharmonic frequencies were calculated.…”

Section: Methodsmentioning

confidence: 99%

“…Next, the accurate band positions were determined by curve-fitting procedure with a mixed Gauss-Lorentz profile. More details concerning the experimental part were described in our earlier work [34].…”

Section: Ftir Measurementsmentioning

confidence: 99%

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Estimating the carbonyl anharmonic vibrational frequency from affordable harmonic frequency calculations

et al. 2011

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A linear correlation between harmonic and anharmonic frequencies of water calculated at B3LYP level of theory was observed with a number of basis sets. Similar relationships were found in both the gas phase and solution for several small molecules. The best correlation was found for C = O stretch mode in formaldehyde, formamide and N-methylacetamide. The average difference between B3LYP harmonic and anharmonic ν(C = O) frequencies calculated with several basis sets in these molecules was 30 cm(-1). The ad hoc correction of -30 cm(-1), added to harmonic frequencies of two different carbonyl groups present in a structure of a larger molecule was tested as a fast way of predicting anharmonic frequencies without elaborated calculations. The proposed approach was tested successfully on a larger molecule of E and Z isomers of N-acetyl-α,β-dehydrophenylalanine N',N'-dimethylamide [Ac-(E/Z)-ΔPhe-NMe(2)] and the estimated anharmonic ν(C = O) frequencies were close to directly calculated results.

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“…In case of large and flexible molecules,s uch as lecithin, it is difficult to find aglobal minimum structure.Thus,for optimization of the lecithinÀdiamidecomplexes, we selected the lecithin structure characterized by the lowest-energy screening several possible structures. Following our earlier studies [17] [19]f or Ac-Phe-NMe 2 (2)a nd Ac-(Z)-DPhe-NMe 2 (3)w et ook the appropriate low-energy conformers.…”

Section: Experimental Partmentioning

confidence: 99%

The Impact of Model Peptides on Structural and Dynamic Properties of Egg Yolk Lecithin Liposomes – Experimental and DFT Studies

Wałęsa

Man

Engel

et al. 2015

Chemistry & Biodiversity

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Electron spin resonance (ESR), (1) H-NMR, voltage and resistance experiments were performed to explore structural and dynamic changes of Egg Yolk Lecithin (EYL) bilayer upon addition of model peptides. Two of them are phenylalanine (Phe) derivatives, Ac-Phe-NHMe (1) and Ac-Phe-NMe2 (2), and the third one, Ac-(Z)-ΔPhe-NMe2 (3), is a derivative of (Z)-α,β-dehydrophenylalanine. The ESR results revealed that all compounds reduced the fluidity of liposome's membrane, and the highest activity was observed for compound 2 with N-methylated C-terminal amide bond (Ac-Phe-NMe2 ). This compound, being the most hydrophobic, penetrates easily through biological membranes. This was also observed in voltage and resistance studies. (1) H-NMR studies provided a sound evidence on H-bond interactions between the studied diamides and lecithin polar head. The most significant changes in H-atom chemical shifts and spin-lattice relaxation times T1 were observed for compound 1. Our experimental studies were supported by theoretical calculations. Complexes EYLAc-Phe-NMe2 and EYLAc-(Z)-ΔPhe-NMe2 , stabilized by NH⋅⋅⋅O or/and CH⋅⋅⋅O H-bonds were created and optimized at M06-2X/6-31G(d) level of theory in vacuo and in H2 O environment. According to our molecular-modeling studies, the most probable lecithin site of H-bond interaction with studied diamides is the negatively charged O-atom in phosphate group which acts as H-atom acceptor. Moreover, the highest binding energy to hydrocarbon chains were observed in the case of Ac-Phe-NMe2 (2).

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Experimental and theoretical NMR and IR studies of the side‐chain orientation effects on the backbone conformation of dehydrophenylalanine residue

Cited by 17 publications

References 33 publications

DFT calculation of structures and NMR chemical shifts of simple models of small diameter zigzag single wall carbon nanotubes (SWCNTs)

DFT calculation of structures and NMR chemical shifts of simple models of small diameter zigzag single wall carbon nanotubes (SWCNTs)

Estimating the carbonyl anharmonic vibrational frequency from affordable harmonic frequency calculations

The Impact of Model Peptides on Structural and Dynamic Properties of Egg Yolk Lecithin Liposomes – Experimental and DFT Studies

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