manu_with_reference

paper_UAR.tex

@@ -154,7 +154,7 @@ All the energy minima for (H$_2$O)$_{n=3-7}$UH$^+$, have already been obtained i
 
 \textbf{Dynamics Collision Simulations} 
 
-QM/MM method was used to describe the collision process of uracil protonated water cluster (QM) and Argon atom (MM) in the developed deMonNano code.\cite{Warshel1976} In the dynamics collision calculation, a Fermi distribution (Fermi temperature 2000 K) was applied to determine the molecular orbital occupations. It can avoid the oscillation problems during the search for a self-consistent solution, often appearing when DFTB energy for dissociated or close to dissociation system was calculated, which allows to recover the continuity in energy and gradients in the case of level crossing. \cite{Kukk2015} In the dynamics collision simulation, at the time of 200 fs, the Argon atom was given a velocity (0.0589 Å·fs$^{-1}$) corresponding to the 7.2 eV center of mass collision energy used in the experiment. \cite{Braud2019}. A series of dynamics collision simulation models were generated according to the distance between collision position and the center of size of the cluster. 600 dynamics collision simulations were performed every 0.5 Å from the center of size of each obtained lowest-energy cluster (H$_2$O)$_{n=3-7, 12}$UH$^+$ at molecular dynamics (MD) bath temperature 25 K. In case missing any collision, we set the biggest distance between collision position and the center of size of the cluster to be (R + 1) Å rather than the cluster radius R. So totally 600(2R + 3)  simulations were calculated. Owing to cluster was set to rotate regularly during the generation of the models, the Ar atom can collide at almost all the possible positions of the cluster. The total simulation time was divided into 600(2R + 3)  segments of 15 ps duration for each (H$_2$O)$_{n=3-7, 12}$UH$^+$. After the dynamics collision computation ends of every segment, the geometry of the system was analyzed to detect the possible fragments. A dissociation was defined to arise when the smallest distance between the atoms of two fragments is larger than a given critical distance 5.0 Å.
+QM/MM method was used to describe the collision process of uracil protonated water cluster (QM) and Argon atom (MM) in the developed deMonNano code.\cite{Warshel1976} In the dynamics collision calculation, a Fermi distribution (Fermi temperature 2000 K) was applied to determine the molecular orbital occupations. It can avoid the oscillation problems during the search for a self-consistent solution, often appearing when DFTB energy for dissociated or close to dissociation system was calculated, which allows to recover the continuity in energy and gradients in the case of level crossing. \cite{Kukk2015} In the dynamics collision simulation, at the time of 200 fs, the Argon atom was given a velocity (0.0589 Å·fs$^{-1}$) corresponding to the 7.2 eV center of mass collision energy used in the experiment. \cite{Braud2019}. A series of dynamics collision simulation models were generated according to the distance between collision position and the center of size of the cluster. 600 dynamics collision simulations were performed every 0.5 Å from the center of size of each obtained lowest-energy cluster (H$_2$O)$_{n=3-7, 12}$UH$^+$ at molecular dynamics (MD) bath temperature 25 K. In case missing any collision, we set the biggest distance between collision position and the center of size of the cluster to be (R + 1) Å rather than the cluster radius R. So totally 600(2R + 3) simulations were calculated. Owing to cluster was set to rotate regularly during the generation of the models, the Ar atom can collide at almost all the possible positions of the cluster. The total simulation time was divided into 600(2R + 3)  segments of 15 ps duration for each (H$_2$O)$_{n=3-7, 12}$UH$^+$. After the dynamics collision computation ends of every segment, the geometry of the system was analyzed to detect the possible fragments. A dissociation was defined to arise when the smallest distance between the atoms of two fragments is larger than a given critical distance 5.0 Å.
 
 \blue{i-PI?}
 
@@ -162,7 +162,7 @@ QM/MM method was used to describe the collision process of uracil protonated wat
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Results and Discussion} \label{resul_disc}
-\textbf{The Distributions of the Initial Collision Models} In order to simulate the collision process of the obtained lowest-energy configuration of (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters with Ar, a reasonable construction of the collision models are needed. In our dynamics collision simulations, totally 2R+3 series were performed for every (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster. And 600 models were conducted in every series. For visualization, the distribution maps of the initial positions of Ar atom with respect to each (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster configuration were made. Here we take the collision of Ar to (H$_2$O)$_4$UH$^+$ cluster as an example, Figure \ref{fig:sphere} displays the collision models of the relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration of the first series that the collision positions are at the center of size of the cluster. As shown in Figure \ref{fig:sphere}, the sphere in picture a is composed of 200 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series. The sphere in picture b is composed of 400 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series and the sphere in picture c is composed of 600 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series. From pictures a, b, and c in Figure \ref{fig:sphere}, it indicates the more simulations are performed, the more colliding opportunities at all the possible positions of (H$_2$O)$_4$UH$^+$ cluster Ar will have. As shown in picture d of Figure \ref{fig:sphere}, the outer layer of the sphere is the 200 relative Ar positions in the first series and the inner layer is the 200 relative Ar positions to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the last series (the distance between collision positions and the center of size of the cluster is (R(H$_2$O)$_4$UH$^+$) Å. The collision models of Ar and  (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters are displayed in Figure SX in the SI. In experiment, the collision positions are randomly, which means that Ar can reach any position of the clusters. All the collision model pictures of Ar and (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters shows our constructions for the collision simulation models are reliable and close to the collision situation in the experiment. With these reasonable models, the explicit collision simulations were conducted. To confirm the statistical convergence is reached, we compare the proportions of neutral uracil molecules loss and the total fragmentation cross sections of (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters with those in experiment. As shown in Table S1 in SI, the data of 200 simulations, 400 simulations, and 600 simulations in every series for all (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters were almost the same, which indicates 600(2R + 3) simulations are enough.
+\textbf{The Distributions of the Initial Collision Models} In order to simulate the collision process of the obtained lowest-energy configuration of (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters with Ar, a reasonable construction of the collision models are needed. In our dynamics collision simulations, totally 2R+3 series were performed for every (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster. And 600 models were conducted in every series. For visualization, the distribution maps of the initial positions of Ar atom with respect to each (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster configuration were made. Here we take the collision of Ar to (H$_2$O)$_4$UH$^+$ cluster as an example, Figure \ref{fig:sphere} displays the collision models of the relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration of the first series that the collision positions are at the center of size of the cluster. As shown in Figure \ref{fig:sphere}, the sphere in picture a is composed of 200 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series. The sphere in picture b is composed of 400 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series and the sphere in picture c is composed of 600 relative positions of Ar to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the first series. From pictures a, b, and c in Figure \ref{fig:sphere}, it indicates the more simulations are performed, the more colliding opportunities at all the possible positions of (H$_2$O)$_4$UH$^+$ cluster Ar will have. As shown in picture d of Figure \ref{fig:sphere}, the outer layer of the sphere is the 200 relative Ar positions in the first series and the inner layer is the 200 relative Ar positions to the initial (H$_2$O)$_4$UH$^+$ cluster configuration in the last series (the distance between collision positions and the center of size of the cluster is R$_{(H_2O)_4UH^+}$ Å. The collision models of Ar and (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters are displayed in Figure SX in the SI. In experiment, the collision positions are randomly, which means that Ar can reach any position of the clusters. All the collision model pictures of Ar and (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters shows our constructions for the collision simulation models are reliable and close to the collision situation in the experiment. With these reasonable models, the explicit collision simulations were conducted. To confirm the statistical convergence is reached, we compare the proportions of neutral uracil molecules loss and the total fragmentation cross sections of (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters with those in experiment. As shown in Table S1 in SI, the data of 200 simulations, 400 simulations, and 600 simulations in every series for all (H$_2$O)$_{n=3, 5-7, 12}$UH$^+$ clusters were almost the same, which indicates 600(2R + 3) simulations are enough.
 
   \begin{figure}
   \includegraphics[width=0.4\linewidth]{/home/linjie/Documents/uracil/collision/Paper_U/figure/sphere}
@@ -184,7 +184,7 @@ In this part, the proportion of neutral uracil molecule loss of each lowest-ener
     \label{fig:neutralUloss} 
  \end{figure}
 
-The neutral uracil molecule loss proportion, 0.0\%, of n = 3 in Figure \ref{fig:neutralUloss} is from the second lowest-energy isomer of (H$_2$O)$_3$UH$^+$ cluster shown in \ref{fig:3ato5d} (3b) that localization of the excess proton is on the uracil (U-H form). For the first lowest-energy isomer of (H$_2$O)$_3$UH$^+$ cluster (U-H form) shown in Figure \ref{fig:3ato5d} (3a), the proportion is 4.4\% (see Table \ref{tab:table1}), which is also very close to the one in experiment. The relative energy of 3a and 3b calculated at MP2/Def2TZVP level is only 0.3 kcal/mol. In experiment, the neutral uracil loss proportion of (H$_2$O)$_3$UH$^+$ cluster is about 1.0\%, which implies both the first and second lowest-energy isomers of (H$_2$O)$_3$UH$^+$ cluster are dominant. From the process of our dynamics collision simulations for (H$_2$O)$_3$UH$^+$ cluster with Ar, the dissociation occurred directly and the excess proton still stays on uracil. 
+The neutral uracil molecule loss proportion, 0.0\%, of n = 3 in Figure \ref{fig:neutralUloss} is from the second lowest-energy isomer of (H$_2$O)$_3$UH$^+$ cluster shown in \ref{fig:3ato5d} (3b) that localization of the excess proton is on the uracil (U-H form). For the first lowest-energy isomer of (H$_2$O)$_3$UH$^+$ cluster (U-H form) shown in Figure \ref{fig:3ato5d} (3a), the proportion is 4.4\% (see Table \ref{tab:table1}), which is also very close to the one in experiment. The relative energy of 3a and 3b calculated at MP2/Def2TZVP level is only 0.3 kcal$\cdot$mol$^{-1}$. In experiment, the neutral uracil loss proportion of (H$_2$O)$_3$UH$^+$ cluster is about 1.0\%, which implies both the first and second lowest-energy isomers of (H$_2$O)$_3$UH$^+$ cluster are dominant. From the process of our dynamics collision simulations for (H$_2$O)$_3$UH$^+$ cluster with Ar, the dissociation occurred directly and the excess proton still stays on uracil. 
    
 \begin{table}
   \begin{center}
@@ -205,7 +205,7 @@ The neutral uracil molecule loss proportion, 0.0\%, of n = 3 in Figure \ref{fig:
       6a & 36.6 & 41.2 & W-H\\
       6b & 30.0 & 42.9 & W-H\\
       6c & 31.2 & 43.7 & W-H\\
-      6d & xx.x & xx.x & W-H\\
+      6d & 28.5 & 41.5 & W-H\\
       6e & 30.1 & 47.8 & W-H-U\\
       6f & 14.2 & 52.3 & W-H-U\\
       7a & 27.7 & 51.0 & W-H\\
@@ -219,32 +219,32 @@ The neutral uracil molecule loss proportion, 0.0\%, of n = 3 in Figure \ref{fig:
 \begin{figure}
   \includegraphics[width=0.8\linewidth]{/home/linjie/Documents/uracil/collision/Paper_U/figure/3ato5d}
   \centering
-    \caption{Some lowest-energy configurations of clusters (H$_2$O)$_{n=3-5}$UH$^+$(H$_2$O)$_{12}$UH$^+$ (the distances are given in Å and relative binding energies are in kcal.mol$^{-1}$).}
+    \caption{Some lowest-energy configurations of clusters (H$_2$O)$_{n=3-5}$UH$^+$ (the distances are given in Å and relative binding energies are in kcal$\cdot$mol$^{-1}$.}
     \label{fig:3ato5d} 
  \end{figure}
 
-The neutral uracil molecule loss proportion, 2.2\%, of n = 4 in Figure \ref{fig:neutralUloss} is from the second lowest-energy isomer of (H$_2$O)$_4$UH$^+$ cluster (U-H form) shown in Figure \ref{fig:3ato5d} (4b). The proportion is 22.3\% (see Table \ref{tab:table1}) for the first lowest-energy isomer (see 4a in Figure \ref{fig:3ato5d}) of (H$_2$O)$_4$UH$^+$ cluster (U-H form) that the excess proton is close to the water cluster but is still bounded to uracil, which is too high compared with the corresponding proportion 1.8\% in experiment. The relative energy of 4a and 4b calculated at MP2/Def2TZVP level is only 0.9 kcal/mol. For ((H$_2$O)$_4$UH$^+$ cluster, our dynamics collision simulations shows the collision leads a direct dissociation. This indicates the collision of the second lowest-energy isomer of (H$_2$O)$_4$UH$^+$ cluster is dominant and the excess proton in (H$_2$O)$_4$UH$^+$ cluster is sensitive but is still bounded to uracil. 
+The neutral uracil molecule loss proportion, 2.2\%, of n = 4 in Figure \ref{fig:neutralUloss} is from the second lowest-energy isomer of (H$_2$O)$_4$UH$^+$ cluster (U-H form) shown in Figure \ref{fig:3ato5d} (4b). The proportion is 22.3\% (see Table \ref{tab:table1}) for the first lowest-energy isomer (see 4a in Figure \ref{fig:3ato5d}) of (H$_2$O)$_4$UH$^+$ cluster (U-H form) that the excess proton is close to the water cluster but is still bounded to uracil, which is too high compared with the corresponding proportion 1.8\% in experiment. The relative energy of 4a and 4b calculated at MP2/Def2TZVP level is only 0.9 kcal$\cdot$mol$^{-1}$. For ((H$_2$O)$_4$UH$^+$ cluster, our dynamics collision simulations shows the collision leads a direct dissociation. This indicates the collision of the second lowest-energy isomer of (H$_2$O)$_4$UH$^+$ cluster is dominant and the excess proton in (H$_2$O)$_4$UH$^+$ cluster is sensitive but is still bounded to uracil. 
 
-As displayed in Figure \ref{fig:neutralUloss}, the neutral uracil molecule loss proportion is 0.1\% for (H$_2$O)$_5$UH$^+$ cluster, which is from the fourth lowest-energy isomer (U-H form) shown in Figure \ref{fig:3ato5d} (5d). For the first lowest-energy configuration of (H$_2$O)$_5$UH$^+$ cluster that the localization of the excess proton is far from uracil and lies on the water cluster (W-H form) shown in Figure \ref{fig:3ato5d} (5a), the proportion is 34.9\% (see Table \ref{tab:table1}). For the second and third lowest-energy configurations of (H$_2$O)$_5$UH$^+$ cluster (U-H form) that the excess proton is close to water cluster but is still bounded to uracil shown in Figure \ref{fig:3ato5d} (5b, 5c), the proportion are 25.4\% and 23.5\% (see Table \ref{tab:table1}), separately. For clusters 5a, 5b, 5c, and 5d, our dynamics collision simulations show they have a direct dissociation after collision, thes explains why 5a has a higher proportion than other isomers. The relative energy of 5a and 5d calculated at MP2/Def2TZVP level is 2.4 kcal/mol, which is within the limit of error. From the neutral uracil molecule loss proportion of configurations 5a, 5b, 5c, and 5d the proportion of 5d, 0.1\%, is the closest to the one, 3.8\%, in experiment, it indicates the configuration that the excess proton lies on the uracil is dominant.
+As displayed in Figure \ref{fig:neutralUloss}, the neutral uracil molecule loss proportion is 0.1\% for (H$_2$O)$_5$UH$^+$ cluster, which is from the fourth lowest-energy isomer (U-H form) shown in Figure \ref{fig:3ato5d} (5d). For the first lowest-energy configuration of (H$_2$O)$_5$UH$^+$ cluster that the localization of the excess proton is far from uracil and lies on the water cluster (W-H form) shown in Figure \ref{fig:3ato5d} (5a), the proportion is 34.9\% (see Table \ref{tab:table1}). For the second and third lowest-energy configurations of (H$_2$O)$_5$UH$^+$ cluster (U-H form) that the excess proton is close to water cluster but is still bounded to uracil shown in Figure \ref{fig:3ato5d} (5b, 5c), the proportion are 25.4\% and 23.5\% (see Table \ref{tab:table1}), separately. For clusters 5a, 5b, 5c, and 5d, our dynamics collision simulations show they have a direct dissociation after collision, thes explains why 5a has a higher proportion than other isomers. The relative energy of 5a and 5d calculated at MP2/Def2TZVP level is 2.4 kcal$\cdot$mol$^{-1}$, which is within the limit of error. From the neutral uracil molecule loss proportion of configurations 5a, 5b, 5c, and 5d the proportion of 5d, 0.1\%, is the closest to the one, 3.8\%, in experiment, it indicates the configuration that the excess proton lies on the uracil is dominant.
 
-For (H$_2$O)$_6$UH$^+$ cluster, the neutral uracil molecule loss proportion is 14.2\% in Figure \ref{fig:neutralUloss}, which is from the sixth lowest-energy isomer (see 6f in Figure \ref{fig:6ato7b}) that the excess proton is bounded to water cluster but close to one oxygen atom of uracil (W-H-U form). For the first, second, third, fourth, and fifth lowest-energy configurations of (H$_2$O)$_6$UH$^+$ cluster (W-H form) (see 6a, 6b, 6c, 6d, and 6e in Figure \ref{fig:6ato7b}) and was separated by one water molecule from uracil, the proportion is 36.6\%, 30.0\%, 31.2\%, xx.x\%, and 30.1\% (see Table \ref{tab:table1}), respectively. The distances between OX and HX in 6a, 6c, 6d are 1.774 Å, 1.745 Å, 1.804 Å, and the distances between OY and HY in 6b and 6e are 1.660 Å and 1.614 Å, respectively. It implies that the neutral uracil loss proportion increases with the distance between uracil and the excess proton in (H$_2$O)$_6$UH$^+$ cluster, which is in line with the observation from dynamics collision simulations that  (H$_2$O)(H$_2$O)$_6$UH$^+$ cluster has a direct dissociation after collision. The relative energy of 6a and 6f calculated at MP2/Def2TZVP level is 2.7 kcal/mol. From the neutral uracil molecule loss proportion of configurations 6a, 6b, 6c, 6d, 6e, and 6f, the proportion of 6f, 14.2\% is the closest to the one, 14.3\%, in experiment, it indicates the configuration that the excess proton is close to water clusters but is still bounded to uracil is dominant.
+For (H$_2$O)$_6$UH$^+$ cluster, the neutral uracil molecule loss proportion is 14.2\% in Figure \ref{fig:neutralUloss}, which is from the sixth lowest-energy isomer (see 6f in Figure \ref{fig:6ato7b}) that the excess proton is bounded to water cluster but close to one oxygen atom of uracil (W-H-U form). For the first, second, third, fourth, and fifth lowest-energy configurations of (H$_2$O)$_6$UH$^+$ cluster (W-H form) (see 6a, 6b, 6c, 6d, and 6e in Figure \ref{fig:6ato7b}) and was separated by one water molecule from uracil, the proportion is 36.6\%, 30.0\%, 31.2\%, 28.5\%, and 30.1\% (see Table \ref{tab:table1}), respectively. The distances between OX and HX in 6a, 6c, 6d are 1.774 Å, 1.745 Å, 1.804 Å, and the distances between OY and HY in 6b and 6e are 1.660 Å and 1.614 Å, respectively. It implies that the neutral uracil loss proportion increases with the distance between uracil and the excess proton in (H$_2$O)$_6$UH$^+$ cluster, which is in line with the observation from dynamics collision simulations that (H$_2$O)$_6$UH$^+$ cluster has a direct dissociation after collision. The relative energy of 6a and 6f calculated at MP2/Def2TZVP level is 2.7 kcal$\cdot$mol$^{-1}$. From the neutral uracil molecule loss proportion of configurations 6a, 6b, 6c, 6d, 6e, and 6f, the proportion of 6f, 14.2\% is the closest to the one, 14.3\%, in experiment, it indicates the configuration that the excess proton is close to water clusters but is still bounded to uracil is dominant.
 
 \begin{figure}
   \includegraphics[width=0.8\linewidth]{/home/linjie/Documents/uracil/collision/Paper_U/figure/6ato7b}
-    \caption{Some lowest-energy configurations of clusters (H$_2$O)$_{n=6-7}$UH$^+$(H$_2$O)$_{12}$UH$^+$ (the distances are given in Å and relative binding energies are in kcal.mol$^{-1}$).}
+    \caption{Some lowest-energy configurations of clusters (H$_2$O)$_{n=6-7}$UH$^+$  (the distances are given in Å and relative binding energies are in kcal$\cdot$mol$^{-1}$.}
     \label{fig:6ato7b} 
  \end{figure}  
  
  \begin{figure}
   \includegraphics[width=0.5\linewidth]{/home/linjie/Documents/uracil/collision/Paper_U/figure/12ad.png}
   \centering
-    \caption{Some lowest-energy configurations of clusters (H$_2$O)$_{12}$UH$^+$ (the distances are given in Å and relative binding energies are in kcal.mol$^{-1}$).}
+    \caption{Some lowest-energy configurations of clusters (H$_2$O)$_{12}$UH$^+$ (the distances are given in Å and relative binding energies are in kcal$\cdot$mol$^{-1}$ ).}
     \label{fig:12ad} 
  \end{figure}
  
-Figure \ref{fig:neutralUloss} displays the neutral uracil molecule loss proportion 17.4\% of n=7, which is from the second lowest-energy isomer of (H$_2$O)$_7$UH$^+$ cluster (see 7b in Figure \ref{fig:6ato7b}) (W-H-U form).  As displayed in Figure \ref{fig:6ato7b}, the proportion of the first lowest-energy isomer 7a (W-H form) of (H$_2$O)$_7$UH$^+$ cluster is 27.7\% shown in Table \ref{tab:table1}. The proportion of 7b, 17.4\% is close to the experiment result 15.8\%. From the dynamics collision simulations process for (H$_2$O)$_7$UH$^+$ cluster, the direct dissociation is dominant. It implies the neutral uracil loss proportion is determined by the initial configuration of the cluster. The relative energy of 7a and 7b calculated at MP2/Def2TZVP level is only 0.3 kcal/mol. This indicates the exist of isomer 7b that the excess proton is between the water cluster and uracil plays a dominant role after collision.
+Figure \ref{fig:neutralUloss} displays the neutral uracil molecule loss proportion 17.4\% of n=7, which is from the second lowest-energy isomer of (H$_2$O)$_7$UH$^+$ cluster (see 7b in Figure \ref{fig:6ato7b}) (W-H-U form).  As displayed in Figure \ref{fig:6ato7b}, the proportion of the first lowest-energy isomer 7a (W-H form) of (H$_2$O)$_7$UH$^+$ cluster is 27.7\% shown in Table \ref{tab:table1}. The proportion of 7b, 17.4\% is close to the experiment result 15.8\%. From the dynamics collision simulations process for (H$_2$O)$_7$UH$^+$ cluster, the direct dissociation is dominant. It implies the neutral uracil loss proportion is determined by the initial configuration of the cluster. The relative energy of 7a and 7b calculated at MP2/Def2TZVP level is only 0.3 kcal$\cdot$mol$^{-1}$. This indicates the exist of isomer 7b that the excess proton is between the water cluster and uracil plays a dominant role after collision.
 
-From the determination conducted by Zamith’s \textit{et al.}, the neutral uracil loss proportion starts to decrease from n=9, this absorbed us to perform the dynamics collision simulation of big cluster (H$_2$O)$_{12}$UH$^+$ as an example to explore why it has this change.\cite{Braud2019} For cluster (H$_2$O)$_{12}$UH$^+$, Figure \ref{fig:neutralUloss} displays the neutral uracil molecule loss proportion, 14.0\%, which is from the XX lowest-energy isomer (W-H-U form) (see 12x in Figure \ref{fig:12ad}). For the first lowest-energy isomer 12a that the excess proton is completely on the water cluster (W-H form), the proportion is 17.8\%. According to the dynamics collision simulations process of (H$_2$O)$_{12}$UH$^+$ cluster, both the direct dissociation and with structural rearrangements before dissociation are dominant after collision. This can be illustrated through the data of neutral uracil molecule loss proportion. Through the comparison for the proportion of 5a (34.9\%), 6a (36.6\%), 7a (27.7\%), and 12a (17.8\%), whose excess proton is on the water cluster and far from uracil, it’s clear that with the increase of the number of water molecules in mixed clusters the evaporation of neutral uracil decreases. Especially for big cluster (H$_2$O)$_{12}$UH$^+$, the neutral uracil loss has a significant reduction, this implies it has a structure rearrangement before dissociation. For 6f and 12x, the excess proton is bounded to water cluster but close to an oxygen atom of uracil, the loss of neutral uracil of 12x is lower than it of 6f,  which also indicates the structure rearrangements occur in 12x. The proportion of 12x, 14.0\%, is closer to the one, 12.2\%, in experiment than 17.8\% of 12a. The relative energy of 12a and 12x calculated at MP2/Def2TZVP level is XX kcal/mol, it shows that the collision of 12x with Ar plays a dominant role.
+From the determination conducted by Zamith’s \textit{et al.}, the neutral uracil loss proportion starts to decrease from n=9, this absorbed us to perform the dynamics collision simulation of big cluster (H$_2$O)$_{12}$UH$^+$ as an example to explore why it has this change.\cite{Braud2019} For cluster (H$_2$O)$_{12}$UH$^+$, Figure \ref{fig:neutralUloss} displays the neutral uracil molecule loss proportion, 14.0\%, which is from the XX lowest-energy isomer (W-H-U form) (see 12x in Figure \ref{fig:12ad}). For the first lowest-energy isomer 12a that the excess proton is completely on the water cluster (W-H form), the proportion is 17.8\%. According to the dynamics collision simulations process of (H$_2$O)$_{12}$UH$^+$ cluster, both the direct dissociation and with structural rearrangements before dissociation are dominant after collision. This can be illustrated through the data of neutral uracil molecule loss proportion. Through the comparison for the proportion of 5a (34.9\%), 6a (36.6\%), 7a (27.7\%), and 12a (17.8\%), whose excess proton is on the water cluster and far from uracil, it’s clear that with the increase of the number of water molecules in mixed clusters the evaporation of neutral uracil decreases. Especially for big cluster (H$_2$O)$_{12}$UH$^+$, the neutral uracil loss has a significant reduction, this implies it has a structure rearrangement before dissociation. For 6f and 12x, the excess proton is bounded to water cluster but close to an oxygen atom of uracil, the loss of neutral uracil of 12x is lower than it of 6f,  which also indicates the structure rearrangements occur in 12x. The proportion of 12x, 14.0\%, is closer to the one, 12.2\%, in experiment than 17.8\% of 12a. The relative energy of 12a and 12x calculated at MP2/Def2TZVP level is XX kcal$\cdot$mol$^{-1}$, it shows that the collision of 12x with Ar plays a dominant role.
 
 From Table \ref{tab:table1}, we can see for clusters (H$_2$O)$_{n=3-4}$UH$^+$ with U-H form, the proportions of neutral uracil loss are about 0.0\%. For different isomers of clusters (H$_2$O)$_{n=5-7}$UH$^+$ with the W-H form, they have a relative high proportion. For clusters (H$_2$O)$_{n=4-7}$UH$^+$ with W-H-U form, they have a relative low proportion and the proportion decreases with distance between the excess proton and the adjacent oxygen atom of uracil. For cluster (H$_2$O)$_{12}$UH$^+$, when the excess proton has the W-H form localization, it also has a higher proportion of neutral uracil loss than the one when the excess proton is the W-H-U form. In general, for any cluster of (H$_2$O)$_{n=3-7, 12}$UH$^+$, the neutral uracil loss proportion has a direct relationship with the localization form of the excess proton: proportion (W-H form) $>$ proportion (W-H-U form) $>$ proportion (U-H form). In other words, it is obvious that the neutral uracil loss proportions of clusters (H$_2$O)$_{n=3-7, 12}$UH$^+$ are significantly affected by the initial configuration of the clusters. However, for cluster (H$_2$O)$_{12}$UH$^+$, even the excess proton is the W-H form, it didn’t have a too high proportion owing to the structural rearrangements that the excess proton goes back to uracil after collision of cluster (H$_2$O)$_{12}$UH$^+$ and Ar. It’s worth noticing that why cluster (H$_2$O)$_{12}$UH$^+$ has structural rearrangements prior to dissociation. We propose for cluster (H$_2$O)$_{12}$UH$^+$, there are more hydrogen bonds than the small clusters, which needs more energy to lose water molecules, so the proton has time to go back to uracil before dissociation.
 
@@ -266,7 +266,7 @@ If it needs to make a further detailed description of the total fragmentation cr
 \textbf{Mass Spectrum of Fragments with Excess Proton}
 Formula of calculating the fragment ratio:
 
-To explore the collision products, the branching ratios of different fragments with the excess proton were extracted from the dynamics collision simulations and compared with the mass spectrum obtained by colliding cluster (H$_2$O)$_7$UH$^+$ with Ne at 7.2 eV center of mass collision energy in experiment.\cite{Braud2019} Table \ref{tab:massspectrum} displays the specific fragment ratio in the total fragments from the collision of the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ with Ar. Fragments (H$_2$O)$_{3-5}$H$^+$ were not found in our calculation, which agrees with the very low intensity of fragments (H$_2$O)$_{3-5}$H$^+$ in experiment. This implies when (H$_2$O)$_{3-5}$ leave, they don’t have enough proton affinity to take away the excess proton. The intensity of fragments (H$_2$O)$_{6-7}$H$^+$ are higher than fragments (H$_2$O)$_{3-5}$H$^+$ in experiment results and we also  determined the fragments (H$_2$O)$_{6-7}$H$^+$ in our calculation, which indicate the proton affinity of (H$_2$O)$_{6-7}$ is higher than (H$_2$O)$_{3-5}$ that in line with the previous study. \cite{Magnera1991}
+To explore the collision products, the branching ratios of different fragments with the excess proton were extracted from the dynamics collision simulations and compared with the mass spectrum obtained by colliding cluster (H$_2$O)$_7$UH$^+$ with Ne at 7.2 eV center of mass collision energy in experiment.\cite{Braud2019} Table \ref{tab:massspectrum} displays the specific fragment ratio in the total fragments from the collision of the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ with Ar. Fragments (H$_2$O)$_{n=3-5}$H$^+$ were not found in our calculation, which agrees with the very low intensity of fragments (H$_2$O)$_{n=3-5}$H$^+$ in experiment. This implies when (H$_2$O)$_{n=3-5}$ leave, they don’t have enough proton affinity to take away the excess proton. The intensity of fragments (H$_2$O)$_{n=6-7}$H$^+$ are higher than fragments (H$_2$O)$_{n=3-5}$H$^+$ in experiment results and we also  determined the fragments (H$_2$O)$_{n=6-7}$H$^+$ in our calculation, which indicate the proton affinity of (H$_2$O)$_{n=6-7}$ is higher than (H$_2$O)$_{n=3-5}$ that in line with the previous study. \cite{Magnera1991}
 
 As shown in Table \ref{tab:massspectrum}, we didn’t get UH$^+$ but it was detected in experiment with time of flight 60 $\mu$s. For each dynamics collision simulation of cluster (H$_2$O)$_7$H$^+$ was performed with simulation time 15 ps, we cannot assert that the UH$^+$ will not appear in longer simulation. Modeling the complete duration of the experiment (up to $\mu$s) is out of reach with MD/SCC-DFTB simulations. Additionally, we calculated the energy of (H$_2$O)$_6$H$^+$, which is from (H$_2$O)$_7$H$^+$ cluster with the dissociation of one water after collision with Ar at SCC-DFTB level (see Table \ref{tab:fragenergy}). We also calculated the lowest energies of (H$_2$O)$_5$H$^+$ and water (see Table \ref{tab:fragenergy}). From the data in Table \ref{tab:fragenergy}, the relative energy $\Delta$E between energy of (H$_2$O)$_6$H$^+$ and lowest energy of (H$_2$O)$_5$H$^+$ plus H$_2$O can reach 1.007 eV, so it is possible for the fragment (H$_2$O)$_6$H$^+$ to lose more water molecules. From this, we suggest if the dynamics collision simulation is long enough, finally UH$^+$ can be obtained. 
 
@@ -299,14 +299,13 @@ As displayed in Table \ref{tab:fragenergy}, ratios of fragments (H$_2$O)$_{n=1-4
 
 \begin{table}
   \begin{center}
-    \caption{Energies of different (H$_2$O)$_6$UH$^+$ fragments selected from the dissociation of the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ at SCC-DFTB level, and the lowest energies (H$_2$O)$_5$UH$^+$ and (H$_2$O) at SCC-DFTB level. And the relative energies $\Delta$E between energy of (H$_2$O)$_6$UH$^+$ and energy of (H$_2$O)$_5$UH$^+$ plus (H$_2$O). All energies here are given in eV.}      
+    \caption{Energies of different (H$_2$O)$_6$UH$^+$ fragments selected from the dissociation of the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ at SCC-DFTB level, and the lowest energies (H$_2$O)$_5$UH$^+$ and (H$_2$O) at SCC-DFTB level. The relative energy $\Delta$E = E$_{(H_2O)_6UH^+}$ -(E$_{(H_2O)_5UH^+}$ + E$_{H_2O}$) . All energies here are given in eV.}      
     \label{tab:fragenergy}
     \begin{tabular}{c|c|c|c} 
-      \textbf{E((H$_2$O)$_6$UH$^+$)} & \textbf{E(H$_2$O)$_5$UH$^+$)} & \textbf{E(H$_2$O)} & \textbf{$\Delta$E}\\ 
+      \textbf{E$_{(H_2O)_6UH^+}$} & \textbf{E$_{(H_2O)_5UH^+}$} & \textbf{E$_{H_2O}$} & \textbf{$\Delta$E}\\ 
       \hline
       -44.361 &  -40.312 & -4.06 & 0.190 \\
       -44.331 &  -40.312 & -4.06 & 1.007 \\
-      -44.331 &  -40.312 & -4.06 & 1.007 \\
       -44.334 &  -40.312 & -4.06 & 0.925 \\
     \end{tabular}
   \end{center}
@@ -322,9 +321,9 @@ As displayed in Table \ref{tab:fragenergy}, ratios of fragments (H$_2$O)$_{n=1-4
 \textbf{Time-Dependent Proportion of Each Fragment}
 In addition, we got the time-dependent proportion of each fragment which confirm that up to 7 water molecules a direct dissociation mechanism occurs. For (H$_2$O)$_{12}$UH$^+$, the cluster undergoes structural rearrangements prior to dissociation, which is proof of a statistical dissociation mechanism.
 
-In addition, the time-dependent proportion of each fragment was extracted from 600(2R + 3) dynamics collision simulations. Here we take the time-dependent proportion of each fragment from second lowest-energy parent cluster (H$_2$O)$_7$UH$^+$ as an example. For the sake of seeing clearly, only the main fragment proportions plotted as a function of simulation time are showed in Figure 7. The proportions of the main fragment of clusters (H$_2$O)$_{3-6, 12}$UH$^+$ are shown in SI Figure SX. From Figure \ref{fig:proporEachFrag}, it clear that the parent cluster (H$_2$O)$_7$UH$^+$ exists from the beginning and different fragments starts to appear after collision. It can be seen when the collision is finished, the fragment proportions almost doesn’t change any more. It is worth noticing the fragment (H$_2$O)$_6$UH$^+$ increase first and then it decreases, which indicates there are water molecules dissociated form it. 
+In addition, the time-dependent proportion of each fragment was extracted from 600(2R + 3) dynamics collision simulations. Here we take the time-dependent proportion of each fragment from second lowest-energy parent cluster (H$_2$O)$_7$UH$^+$ as an example. For the sake of seeing clearly, only the main fragment proportions plotted as a function of simulation time are showed in Figure 7. The proportions of the main fragment of clusters (H$_2$O)$_{n=3-6, 12}$UH$^+$ are shown in SI Figure SX. From Figure \ref{fig:proporEachFrag}, it clear that the parent cluster (H$_2$O)$_7$UH$^+$ exists from the beginning and different fragments starts to appear after collision. It can be seen when the collision is finished, the fragment proportions almost doesn’t change any more. It is worth noticing the fragment (H$_2$O)$_6$UH$^+$ increase first and then it decreases, which indicates there are water molecules dissociated form it. 
 
-From the time-dependent proportion of each fragment from clusters (H$_2$O)$_{3-6, 12}$UH$^+$, it confirms that up to 7 water molecules a direct dissociation mechanism occurs. For cluster (H$_2$O)$_{12}$UH$^+$, it undergoes structural rearrangements prior to dissociation, which is proof of a statistical dissociation mechanism.
+From the time-dependent proportion of each fragment from clusters (H$_2$O)$_{n=3-6, 12}$UH$^+$, it confirms that up to 7 water molecules a direct dissociation mechanism occurs. For cluster (H$_2$O)$_{12}$UH$^+$, it undergoes structural rearrangements prior to dissociation, which is proof of a statistical dissociation mechanism.