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2D IR spectra of cyanide in water investigated by molecular dynamics simulations
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10.1063/1.4815969
/content/aip/journal/jcp/139/5/10.1063/1.4815969
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/5/10.1063/1.4815969

Figures

Image of FIG. 1.
FIG. 1.

The simulation system used in the present work. The C and N atoms of the cyanide ion are displayed as van der Waals spheres. The atoms of the water molecules whose oxygen atoms are within 4 Å (1st solvation shell) from the center of the cyanide ion are shown as red spheres and those between 4 and 6 Å (2nd solvation shell) as green spheres. Other water molecules are depicted as lines.

Image of FIG. 2.
FIG. 2.

Electrostatic potential obtained from the SCF density of the DFT calculation (blue), MTP parameters (red), and 3-point charge model parameters (green). The geometric center of CN is at the origin and the atoms are placed at zero radial coordinate. The C atom is along the negative axis and the N atom is along the positive axis.

Image of FIG. 3.
FIG. 3.

1D IR spectra for various models computed with cumulant approximation (label CA, upper panel) or without cumulant approximation (label NCA, lower panel). Rotational contribution of CN has been incorporated in the spectra for CA and NCA. M0 is shown in black, M2 in green, M4 in red, and M6 in magenta. FWHMs (in cm) are 8.5 (M0), 9.0 (M1), 12.8 (M2), 8.6 (M4), 7.4 (M5), and 6.8 (M6) for CA and 9.2 (M0), 9.4 (M1), 13.3 (M2), 9.2 (M4), 7.4 (M5), and 7.1 (M6) for NCA. The experimental FWHM is shown as a gray bar at height 0.5 and the gray solid line represents the experimental spectrum with water background removed.

Image of FIG. 4.
FIG. 4.

The FFCFs from 0 to 1.5 ps obtained from the simulations of CN in DO with M0 (black), M2 (green), M4 (red), and M5 (blue). All frequencies were computed with water molecules within 5 Å from CN. The inset shows FFCFs in the range of 0–5 ps on a logarithmic scale.

Image of FIG. 5.
FIG. 5.

Fitting of Eq. (9) or (10) to the FFCFs obtained from the trajectories of CN in DO with models 0 (upper panel) and 4 (lower panel). Logarithmic scale is used for the vertical axis. Raw FFCFs are shown in solid lines, fitting with Eq. (9) in dashed lines, and fitting with Eq. (10) in dotted lines. In the inset of the lower panel, FFCFs obtained from the frequency calculation of CN with water molecules within 3 Å (violet), 5 Å (red), and ∞ (green) from CN are compared.

Image of FIG. 6.
FIG. 6.

The 2D IR spectra of CN in DO using model M0 computed using the cumulant approximation with numerically integrated () (1st row) and avoiding the cumulant approximation (2nd row). Waiting times are 100 fs (1st column), 1 ps (2nd column), and 10 ps (3rd column).

Image of FIG. 7.
FIG. 7.

Comparison of tilt angles as a function of mixing time . Left panel shows α( ) determined using the cumulant approximation with the line shape functions () obtained from FFCFs by numerical integration (solid lines). The inset compares the tilt angles from the numerical (solid circle) and the analytical line shape functions obtained from fitting of Eq. (9) to the FFCF (open circle) for M0. Black curve is from M0, cyan from M1, green from M2, red from M4, and blue from M5. Right panel shows α( ) determined by avoiding the cumulant approximation and the inset compares the tilt angles computed with (solid circle) and without (open circle) using the cumulant approximation for M0. The color scheme for M0, M2, M4, and M5 is the same as the left panel and M6 is shown in magenta. For comparison, tilt angles from experiment are shown in gray in both panels.

Image of FIG. 8.
FIG. 8.

(a) The distribution of water molecules around CN computed from the simulations with M0. The geometric center of CN is at the origin, and the probability of finding water oxygen atoms at certain axial and radial distances from CN is displayed in red contour. The maximum around ≈ 3 Å is labeled as “R3” and the maximum around ≈ 4 Å as “R4.” The probability of hydrogen atoms is displayed in green. The van der Waals radii of carbon and nitrogen atoms are shown in black semicircles. (b) The distance of the first radial from the origin as a function of the angle with respect to the axial coordinate, computed from the distribution of water molecules around CN. The result from M0 is shown in black and that from M4 in red.

Image of FIG. 9.
FIG. 9.

The occupation fluctuation correlation function () of δ() as a function of time. The solid lines are from M0 and the dotted lines from M4 for oxygen (green) and deuterium (blue) atoms with cutoff radius of 4 Å. The inset shows the occupation correlation function () of δ() as a function of time for M4.

Image of FIG. 10.
FIG. 10.

(a) Analysis of the jump angle between cyanide and the neighboring water at the carbon-end of CN. θ is the angle between the rotating O*H* bond and the bisector plane of the CO*O angle, where O is the new H-bond acceptor. (b) The change of direction of CN measured by for 50 ps.

Tables

Generic image for table
Table I.

Parameters of CN for (1) the multipole model and (2) the 3-point charge model. The reference data of CN were obtained from B3LYP/aug-cc-pVQZ around the equilibrium bond length. Each multipole component is denoted by , where represents angular momentum labels (00, 10, 11c, 11s, 20, 21c, 21s, 22c, and 22s). The molecular axis is oriented along the -axis, and only nonzero components are shown. For the 3-point charge model, charges on the C and N atoms are fitted to a function of the form = + + + , where is the bond distance of CN. The parameters of the fits are given in the last 4 columns.

Generic image for table
Table II.

Parameters for water potential reported in the work of Kumagai and used in this work. Atomic units are used for , β, , , , and . θ is given in degrees.

Generic image for table
Table III.

Water and cyanide models used in this study. The combination of them are called models 0 through 6. represents bonded interactions and electrostatic interactions. is electric charges, μ dipole moments, and Θ quadrupole moments. = is used for CN in the case of M5, whereas = 1.075 is used for all other models. “SHAKE” refers to simulations in which SHAKE is applied to all water molecules, as is typically done in biomolecular simulations. All models were run for 20 ns.

Generic image for table
Table IV.

Parameters obtained from fitting the FFCF. Equation (10) was fitted to FFCF data in the range of 0–20 ps for Fit 1 and Eq. (9) was used for Fit 2. For the calculation of CN frequencies for FFCFs, water molecules within 5 Å from CN have been included.

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/content/aip/journal/jcp/139/5/10.1063/1.4815969
2013-08-02
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: 2D IR spectra of cyanide in water investigated by molecular dynamics simulations
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/5/10.1063/1.4815969
10.1063/1.4815969
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