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Instantaneous normal mode analysis of the vibrational relaxation of the amide I mode of alanine dipeptide in water
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10.1063/1.4805086
/content/aip/journal/jcp/138/20/10.1063/1.4805086
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/20/10.1063/1.4805086

Figures

Image of FIG. 1.
FIG. 1.

The alanine dipeptide molecule.

Image of FIG. 2.
FIG. 2.

Overlap matrix between ENMs and INMs obtained as defined in Eq. (5) using the EAMC method with a frequency window of Δω = 400 cm width and the ENMs corresponding to the C5 conformer as templates.

Image of FIG. 3.
FIG. 3.

Time evolution of the normalized vibrational energy of the (a) acetyl and (b) amino-end amide I modes of the C-AlaD- molecule in liquid DO, with respect to their equilibrium values, at 300 K (black lines), including in addition the corresponding fits to Eq. (9) (red dashed lines) and to the experimental data (blue lines), and time evolution of the normalized accumulated energy that flows from the (c) acetyl and (d) amino-end amide I modes into the remaining INMs of the C-AlaD- molecule through IVR processes (black lines) and into the solvent (blue lines), along with their fits (red dashed lines) to Eqs. (10) and (11) , respectively. Error bars are the standard deviations of the energy curves corresponding to the 400 trajectories statistics.

Image of FIG. 4.
FIG. 4.

Time evolution of the normalized vibrational energy of the C-AlaD- molecule in liquid DO after initial excitation of the (a) acetyl and (b) amino-end amide I modes (blue lines) and the corresponding fits to Eq. (13) (yellow line).

Image of FIG. 5.
FIG. 5.

Vibrational energy (in cm) transferred from the INMs of the C-AlaD- molecule into the DO solvent after initial excitation of the (a) acetyl and (b) amino-end amide I modes, as calculated using the SMF method. INMs are labeled as in Table V . Dashed lines indicate the average energy transfer per mode.

Image of FIG. 6.
FIG. 6.

Conformational populations (in %) as a function of time (averaged over 0.25 ps intervals) of the AlaD- molecule in liquid DO obtained from nonequilibrium MD simulations when the acetyl-end amide I was initially excited (blue lines) and the corresponding equilibrium values (dashed red lines).

Tables

Generic image for table
Table I.

Dihedral angles (ϕ/ψ) for the AlaD- molecule at different conformations.

Generic image for table
Table II.

Definition of the alpha and beta conformational regions for the CHARMM22 force field.

Generic image for table
Table III.

Atomic displacement contributions of the C and O atoms of the amino and acetyl-end carbonyl groups (in %) to the amide I ENMs for different conformations of the isolated AlaD- molecule, obtained using the AMBER94, OPLS-AA/L, and CHARMM22 force fields.

Generic image for table
Table IV.

Frequencies (in cm) of the amide I modes of the isolated AlaD- molecule.

Generic image for table
Table V.

Time averaged vibrational frequencies and standard deviations (in cm) of the INMs of the AlaD- and C-AlaD- molecules in liquid DO obtained using the EAMC method with a frequency window of Δω = 400 cm width. The ENMs used as templates are those of the C5 conformers.

Generic image for table
Table VI.

Vibrational relaxation times (in ps) and amplitudes of the acetyl and amino-end amide I modes of the C-AlaD- molecule in liquid DO.

Generic image for table
Table VII.

Parameter values obtained from the fits to Eq. (12) of the vibrational INM energy curves of the C-AlaD- molecule in liquid DO after initial excitation of the acetyl and amino-end amide I modes. The relaxation and excitation times are in ps and the values of the and parameters in cm.

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/content/aip/journal/jcp/138/20/10.1063/1.4805086
2013-05-24
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Instantaneous normal mode analysis of the vibrational relaxation of the amide I mode of alanine dipeptide in water
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/20/10.1063/1.4805086
10.1063/1.4805086
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