An algorithm allowing simulating vibrational spectra from classical time-dependent trajectories was applied for infrared absorption, vibrational circular dichroism, Raman, and Raman optical activity of model harmonic systems. The implementation of the theory within the TINKER molecular dynamics (MD) program package was tested with ab initio harmonic force fields in order to determine the feasibility for more extended MD simulations. The results suggest that sufficiently accurate frequencies can be simulated with integration time steps shorter than about 0.5fs. For a given integration time step, lower vibrational frequencies (02000cm1) could be reproduced with a higher accuracy than higher-frequency vibrational modes (e.g., O–H and C–H stretching). In principle, the algorithm also provides correct intensities for ideal systems. In applied simulations, however, the intensity profiles are affected by an unrealistic energy distribution between normal modes and a slow energy relaxation. Additionally, the energy fluctuations may cause weakening of the intensities on average. For ab initio force fields, these obstacles could be overcome by an arbitrary normal mode energy correction. For general MD simulations, averaging of many shorter MD trajectories started with randomly distributed atomic velocities provided the best spectral shapes. α-pinene, D-gluconic acid, formaldehyde dimer, and the acetylprolineamide molecule were used in the tests.

1.
R. G.
Gordon
,
J. Chem. Phys.
42
,
3658
(
1965
).
2.
R. G.
Gordon
,
J. Chem. Phys.
43
,
1307
(
1965
).
3.
D. W.
Noid
,
M. L.
Koszykowski
, and
R. A.
Marcus
,
J. Chem. Phys.
67
,
404
(
1977
).
4.
S.
Abbate
,
G.
Longhi
,
K.
Kwon
, and
A.
Moscowitz
,
J. Chem. Phys.
108
,
50
(
1998
).
5.
H.
Kim
and
P. J.
Rossky
,
J. Chem. Phys.
125
,
074107
(
2006
);
[PubMed]
C. S.
Kinnaman
,
M. E.
Cremeens
,
F. E.
Romesberg
, and
S. A.
Corcelli
,
J. Am. Chem. Soc.
128
,
13334
(
2006
).
[PubMed]
6.
The Encyclopedia of Computational Chemistry
, edited by
P. R.
Schleyer
,
N. L.
Allinger
,
T.
Clark
,
J.
Gasteiger
,
P. A.
Kollman
,
H. F.
Schaefer III
, and
P. R.
Schreiner
(
Wiley
,
Chichester
,
1998
).
7.
S.
Hahn
,
H.
Lee
, and
M.
Cho
,
J. Chem. Phys.
121
,
1849
(
2004
).
8.
P. K.
Mankoo
and
T.
Keyes
,
J. Chem. Phys.
124
,
204503
(
2006
).
9.
K. K.
Lee
,
S.
Hahn
,
K. I.
Oh
,
J. S.
Choi
,
C.
Joo
,
H.
Lee
,
H.
Han
, and
M.
Cho
,
J. Phys. Chem. B
110
,
18834
(
2006
).
10.
H.
Torii
,
J. Phys. Chem. A
110
,
9469
(
2006
);
[PubMed]
S.
Gnanakaran
and
R. M.
Hochstrasser
,
J. Am. Chem. Soc.
123
,
12886
(
2001
);
[PubMed]
J. J.
Loparo
,
S. T.
Roberts
, and
A.
Tokmakoff
,
J. Chem. Phys.
125
,
194521
(
2006
);
[PubMed]
A. T.
Krummel
and
M. T.
Zanni
,
J. Phys. Chem. B
110
,
24720
(
2006
).
[PubMed]
11.
Y.
Liang
,
C. R.
Miranda
, and
S.
Scandolo
,
J. Chem. Phys.
125
,
194524
(
2006
);
[PubMed]
S.
Yang
and
M.
Cho
,
J. Phys. Chem. B
111
,
605
(
2007
);
[PubMed]
R. D.
Gorbunov
,
P. H.
Nguyen
,
M.
Kobus
, and
G.
Stock
,
J. Chem. Phys.
126
,
054509
(
2007
).
[PubMed]
12.
Y.
Yamauchi
and
H.
Nakai
,
J. Chem. Phys.
121
,
11098
(
2004
);
[PubMed]
A.
Putrino
and
M.
Parrinello
,
Phys. Rev. Lett.
88
,
176401
(
2002
);
[PubMed]
J.
Seibt
and
V.
Engel
,
J. Chem. Phys.
126
,
074110
(
2007
).
[PubMed]
13.
L. D.
Barron
,
L.
Hecht
, and
A. D.
Bell
, in
Circular Dichroism and the Conformational Analysis of Biomolecules
, edited by
G. D.
Fasman
(
Plenum
,
New York
,
1996
),
653
pp.;
T. A.
Keiderling
, in
Spectroscopic Methods for Determining Protein Structure in Solution
, edited by
H.
Havel
(
VCH
,
New York
,
1995
),
163
pp.
14.
P. W.
Atkins
and
R. S.
Friedman
,
Molecular Quantum Mechanics
, 3rd ed. (
Oxford University Press
,
New York
,
1997
).
15.
D.
Papoušek
and
M. R.
Aliev
,
Molecular Vibrational/Rotational Spectra
(
Academia
,
Prague
,
1982
).
16.
L. D.
Barron
,
Molecular Light Scattering and Optical Activity
(
Cambridge University Press
,
Cambridge
,
2004
).
17.
P. J.
Stephens
,
J. Phys. Chem.
89
,
748
(
1985
).
18.
E.
Charney
,
The Molecular Basis of Optical Activity
(
Wiley-Interscience
,
New York
,
1979
).
19.
G.
Holzwarth
and
I.
Chabay
,
J. Chem. Phys.
57
,
1632
(
1972
).
20.
P.
Bouř
and
T. A.
Keiderling
,
J. Am. Chem. Soc.
114
,
9100
(
1992
).
21.
P. L.
Polavarapu
,
Vibrational Spectra: Principles and Applications with Emphasis on Optical Activity
(
Elsevier
,
Amsterdam
,
1998
).
22.
D. P.
Craig
and
T.
Thirunamachandran
,
Molecular Quantum Electrodynamics
(
Dover
,
New York
,
1998
).
23.
J.
Florian
,
V.
Baumruk
,
M.
Strajbl
,
L.
Bednárová
, and
J.
Štěpánek
,
J. Phys. Chem.
100
,
1559
(
1996
).
24.
M. J.
Frisch
,
G. W.
Trucks
,
H. B.
Schlegel
 et al, GAUSSIAN 0.3, Revision C.02, Gaussian, Inc., Wallingford, CT,
2004
.
25.
J. W.
Ponder
, TINKER, Software Tools for Molecular Design,
Washington University School of Medicine
, Saint Louis,
2000
.
26.
J. A.
Schellman
,
J. Chem. Phys.
58
,
2882
(
1973
).
27.
W. D.
Cornell
,
P.
Cieplak
,
C. I.
Bayly
,
I. R.
Gould
,
K. M.
Merz
,
D. M.
Ferguson
,
D. C.
Spellmeyer
,
T.
Fox
,
J. W.
Caldwell
, and
P. A.
Kollman
,
J. Am. Chem. Soc.
117
,
5179
(
1995
).
28.
M.
Martines
,
M. P.
Gaigeot
,
D.
Borgis
, and
R.
Vuilleumier
,
J. Chem. Phys.
125
,
144106
(
2006
).
29.
D.
Janezic
,
M.
Praprotnik
, and
F.
Merzel
,
J. Chem. Phys.
122
,
174101
(
2005
).
30.
L.
Verlet
,
Phys. Rev.
159
,
201
(
1967
).
31.
D.
Beeman
,
J. Comput. Phys.
20
,
130
(
1976
).
32.
H. J. C.
Berendsen
,
J. P. M.
Postma
,
W. F.
van Gunsteren
,
A.
Dinola
, and
J. R.
Haak
,
J. Chem. Phys.
81
,
3684
(
1984
).
33.
A.
Annamalai
,
T. A.
Keiderling
, and
J. S.
Chickos
,
J. Am. Chem. Soc.
106
,
6254
(
1984
).
34.
J.
Wang
,
P.
Cieplak
, and
P. A.
Kollman
,
J. Comput. Phys.
21
,
1049
(
2000
).
35.
W. L.
Jorgensen
,
J.
Chandrasekhar
, and
J. D.
Madura
,
J. Chem. Phys.
79
,
926
(
1983
).
36.
R. A. G. D.
Silva
,
J.
Kubelka
,
P.
Bouř
,
S. M.
Decatur
, and
T. A.
Keiderling
,
Proc. Natl. Acad. Sci. U.S.A.
97
,
8318
(
2000
);
[PubMed]
P.
Bouř
,
J.
Kubelka
, and
T. A.
Keiderling
,
Biopolymers
65
,
45
(
2002
);
[PubMed]
P.
Bouř
,
D.
Michalík
, and
J.
Kapitán
,
J. Chem. Phys.
122
,
144501
(
2005
).
[PubMed]
37.
A.
Klamt
, in
The Encyclopedia of Computational Chemistry
, edited by
P. R.
Schleyer
,
N. L.
Allinger
,
T.
Clark
,
J.
Gasteiger
,
P. A.
Kollman
,
H. F.
Schaefer III
, and
P. R.
Schreiner
(
Wiley
,
Chichester
,
1998
), Vol.
1
, p.
604
.
You do not currently have access to this content.