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Chain-length and mode-delocalization dependent amide-I anharmonicity in peptide oligomers
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10.1063/1.4725181
/content/aip/journal/jcp/136/21/10.1063/1.4725181
http://aip.metastore.ingenta.com/content/aip/journal/jcp/136/21/10.1063/1.4725181

Figures

Image of FIG. 1.
FIG. 1.

Molecular structures and the displacement vectors of two typical amide-I normal modes with either the largest (L) or the smallest (S) diagonal anharmonicity for ATTP, APP D_ADP molecules obtained using the B3LYP functional. The amide units were marked by ellipses.

Image of FIG. 2.
FIG. 2.

The relationship between the averaged diagonal anharmonicity ((a) and (b)), averaged off-diagonal anharmonicity ((c) and (d)), the sum of the averaged diagonal and off-diagonal anharmonicity ((e) and (f)) vs. the number of the amide unit (chain length) for the α-helical (left) and β-sheet (right) conformations at three different theory levels: B3LYP (□), HF(◯), and B3PW91 (Δ). The dashed lines in panels (e) and (f) indicate the mean values. The values for the double-stranded dipeptide were also given in right column (■).

Image of FIG. 3.
FIG. 3.

The correlation of the vibrational frequencies and diagonal anharmonicities among different calculate levels. (a) vs. ; (b) vs. ; (c) vs. ; (d) vs. ; (e) vs. ; (f) vs. .

Image of FIG. 4.
FIG. 4.

Potential energy distribution (PED) of the two typical amide-I modes with either the largest (L) or the smallest (S) diagonal anharmonicity in the α-helical and β-sheet conformations vs. the number of the amide units (chain length), obtained using the B3LYP functional.

Image of FIG. 5.
FIG. 5.

The correlation between Δ i and PEDmax for all the amide-I modes in the ADP, ATP, ATTP, APP, AHXP, AHPP oligermers at each of the three different levels of theories, as well as the overall evaluation. The results of D_ADP in anti-parallel β-sheet conformation are obtained at the B3LYP level (solid squares).

Image of FIG. 6.
FIG. 6.

Wave functions for the two typical amide-I modes with either the largest (L) or the smallest (S) diagonal anharmonicity for the all the structures in α-helical and single-stranded β-sheet conformations obtained using the B3LYP theory.

Image of FIG. 7.
FIG. 7.

The vibrational excitonic model of the amide-I mode of peptide oligomers. The diagram shows the one-excitonic sates (|i⟩, | j⟩) and the two-excitonic states (|ii⟩, |ij⟩, | jj⟩) formed from the coupled site-states |k⟩ and |l⟩.

Image of FIG. 8.
FIG. 8.

The relationship between the averaged diagonal anharmonicity ((a) and (b)), and averaged off-diagonal anharmonicity ((c) and (d)), vs. the number of the amide unit (chain length) for the α-helical (left) and single-stranded anti-parallel β-sheet (right) conformations, evaluated by using the exciton model. The results for the double-stranded dipeptide were also given in right column (■).

Image of FIG. 9.
FIG. 9.

The relationship between P i and PEDmax for the amide-I modes obtained at the B3LYP level.

Image of FIG. 10.
FIG. 10.

Isotopic effect on delocalization of the amide-I mode in ATTP examined using the B3LYP functional. Left: PED. Middle: wave functions. Right: structures of unlabeled and labeled species. From top to bottom: unlabeled, 13C=O and 13C=18O labeling on the second amide unit, respectively.

Image of FIG. 11.
FIG. 11.

Isotopic effect on diagonal anharmonicity (a) and mode delocalization (b) of one amide-I mode in ATP, ATTP, APP, AHXP, and AHPP examined using the B3LYP functional. The results of unlabeled, 13C=O or 13C=18O labeled on the second (ATTP and AHPP) or the third (ATP), or the fourth (APP and AHXP) amide unit in each case are given for comparison.

Tables

Generic image for table
Table I.

Diagonal anharmonicities (in cm−1) of the amide-I modes for all the structures in α-helical and anti-parallel β-sheet conformations at three different levels of theories. The results of D_ADP are listed in the parentheses.

Generic image for table
Table II.

Anharmonic frequencies (in cm−1) of the amide-I modes for all the structures in α-helical and anti-parallel β-sheet conformations at three different levels of theories. The results of D_ADP are listed in the parentheses.

Generic image for table
Table III.

Anharmonic frequencies and anharmonicities (in cm−1) and the PEDmax (in parenthesis) of the two amide-I modes of the deuterated alanine dipeptide in α-helix conformation in gas and solution phases.

Generic image for table
Table IV.

Isotopic effect on anharmonic frequency and anharmonicity (both in cm−1) of the amide-I modes in ATTP in the α-helical conformation obtained using the B3LYP functional.

Generic image for table
Table V.

Isotopic effect on the off-diagonal anharmonicity (Δ, in cm−1) of the amide-I modes in ATTP in the α-helical conformation obtained using the B3LYP functional.

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/content/aip/journal/jcp/136/21/10.1063/1.4725181
2012-06-07
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Chain-length and mode-delocalization dependent amide-I anharmonicity in peptide oligomers
http://aip.metastore.ingenta.com/content/aip/journal/jcp/136/21/10.1063/1.4725181
10.1063/1.4725181
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