@article{ISI:000242974300117,
 abstract = {Recent time domain experiments have explored solvation dynamics of a
probe located inside a DNA duplex, in an effort to gain information,
e.g., on the dynamics of water molecules in the DNA major and minor
grooves and their environment. Multiple time constants in the range of a
few picoseconds to several nanoseconds were obtained. We have carried
out 15 ns long atomistic molecular dynamics simulations to study the
solvation dynamics of bases of a 38 base-pair long DNA duplex in an
aqueous solution containing counterions. We have computed the
energy-energy time correlation function (TCF) of the four individual
bases (A, T, G, and C) to characterize the solvation dynamics. All the
TCFs display highly nonexponential decay with time. When the
trajectories are analyzed with 100 fs time resolution, the TCF of each
base shows initial ultrafast decay (with tau(1) approximate to 60-80 fs)
followed by two intermediate components (tau(2) approximate to 1 ps,
tau(3) approximate to 20-30 ps), in near complete agreement with a
recent time domain experiment on DNA solvation. Interestingly, the
solvation dynamics of each of the four different nucleotide bases
exhibit rather similar time scales. To explore the existence of slow
relaxation at longer times reported recently in a series of experiments,
we also analyzed the solvation TCFs calculated with longer time
trajectories and with a larger time resolution of 1 ps. In this case, an
additional slow component with a time constant of the order of 250 ps is
observed. Through an analysis of partial solvation TCFs, we find that
the slow decay originates mainly from the interaction of the nucleotides
with the dipolar water molecules and the counterions. An interesting
negative cross-correlation between water and counterions is observed,
which makes an important contribution to relaxation at intermediate to
longer times.},
 author = {Pal, Subrata and Maiti, Prabal K. and Bagchi, Biman and Hynes, James T.},
 doi = {10.1021/jp065690t},
 issn = {1520-6106},
 journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
 month = {DEC 28},
 number = {51},
 orcid-numbers = {Maiti, Prabal/0000-0002-9956-1136
BAGCHI, BIMAN/0000-0002-7146-5994},
 pages = {26396-26402},
 researcherid-numbers = {Maiti, Prabal/B-6335-2009
},
 times-cited = {73},
 title = {Multiple time scales in solvation dynamics of DNA in aqueous solution:
The role of water, counterions, and cross-correlations},
 unique-id = {ISI:000242974300117},
 volume = {110},
 year = {2006}
}