Source data for the publication "Tracking excited state decay mechanisms of pyrimidine nucleosides in real time", Nature Communications, 2021

The archives contain the raw data used to generate the transient absorption spectra for uridine (Figure 1) and 5-methyluridine (Figure 2) presented in the main paper, as well as the trajectory plots and auxiliary spectra presented in the Supplementary Information of the paper "Tracking excited state decay mechanisms of pyrimidine nucleosides in real time" authored by R. Borrego-Varillas et al. published in Nature Communications, 2021. Specifically:

URD: folder with raw data from the uridine trajectories (56 trajectories) performed at the SS-CASPT2/SA-2-CASSCF(10,8) and SS-CASPT2/SA-2-CASSCF(10,10) level of theory

5mURD: folder with raw data from the 5-methyluridine trajectories (57 trajectories) performed at the SS-CASPT2/SA-2-CASSCF(10,8) and SS-CASPT2/SA-2-CASSCF(10,10) level of theory

The raw data of each trajectory is inside a folder named geom_XXX where XXX stands for a 3-digit label of the trajectory. The trajectories have been selected out of a pool of 500 trajectories according to the S0-S1 vertical gap so that only trajectories whose energy gap falls under the envelope of the pulse are selected

URD: 003 005 006 011 015 023 039 040 054 056 060 083 098 104 112 114 116 121 122 147 152 158 161 171 173 175 177 186 189 200 204 211 219 223 225 232 234 235 236 246 251 252 257 259 265 268 271 272 279 286 287 289 305 313 318 336

5mURD: 010 044 045 048 052 057 065 074 085 094 097 099 100 105 110 112 113 121 131 137 138 140 144 145 159 164 170 179 182 183 184 186 189 199 203 205 209 214 219 220 221 239 243 250 251 273 284 290 295 301 302 320 325 327 328 333 334

In each geom_XXX folder there are following files:

S1-SY.dat: ASCII files () in which the individual columns correspond to 

col1: time [fs]    

col2: transition energy of state SY with respect to S1 [cm-1] where S0 is the ground state

col3-5: X, Y and Z components of the transition dipole moment between S1 and SY [a.u.]

col6: magnitude of the transition dipole moment between S1 and SY [a.u.]  

col7: angle between transition dipole moment at time t and t=0 [deg]

Note that in URD S1-S0.dat contains in most cases about 500 data points (0-500 fs), in 5mURD S1-S0.dat contains 1000 data points (0-1000 fs) except for a few cases in which the trajectories were interrupted earlier. This data has been used to simulate the stimulated emission before the hopping event and the hot ground state photoinduced absorption after hopping. S1-SY.dat () contain only data points until the hopping event which have been used to simulate the excited state photoinduced absorption.

The spectra reported in the main article (Figs 1 & 2) as well as in the SI can be reproduced following eq. 13-18 in the Supplementary Information.

HighMediumLayer_traj.xyz.zip: archived Cartesian coordinates of the High Layer (nucleobase) and Medium Layer (sugar and waters within 5 Å distance from nucleobase) along the dynamics

Note that due to the different number of waters in each trajectory the size of the Medium layer (and thus the size of the system) may vary from trajectory to trajectory.

Note that due to the different duration of each trajectory the number of geometries may vary from trajectory to trajectory.

LowLayer.xyz: Cartesian coordinates of the Low Layer (waters > 5 Å from the nucleobase); the coordinates of these waters are kept fixed along the trajectory.

The coordinates of High, Medium and Low layers can be used to reproduce the QMMM calculations (energies, gradients and transition dipole moments along each trajectory) with the official COBRAMM release (https://gitlab.com/cobrammgroup/cobramm.git) following the parameters provided in Supplementary Note 2 of the Supplementary Information.