12-1

paper_UAR.tex

@@ -125,7 +125,7 @@
 %% if an abstract is not used by the target journal.
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 \begin{abstract}
-A series of dynamics collision simulations between lowest-energy uracil protonated water clusters (H$_2$O)$_{n=3-7, 12}$UH$^+$ and Argon atom were performed with the self-consistent-charge density-functional based tight-binding {\bf remove acronyles in abvstract if not necessary ) : (SCC-DFTB)}  method to make a deep exploration of the collision process. From the dynamics collision simulations, the trend of different types of fragments and location of the excess proton were observed. {\bf MR  : remove the following sentence, details : Our initial geometries provided a reasonably uniform distribution of Argon projectiles around each uracil protonated water clusters leading Argon atom can collide at all the possible positions of each cluster. } The theoretical simulation data show that the proportion of neutral uracil molecule loss and total fragmentation cross sections are consistent with those in experiment. Additionally, we observed that up to 7 water molecules the clusters had a direct dissociation mechanism after collision \blue{whereas for 12 water molecules …...} Furthermore, the calculation results indicate the excess proton location is highly dependent on the initial isomer as stated in a previous study. {\bf put a reference in full text}  \blue{By conducting path-integral MD simulation, we finally observed that nuclear quantum effect XXX.} \blue{We are the first to perform this kind of simulation,} our dynamics collision simulations for predicting the type and amount of fragments and fragmentation cross sections of collision system provide a useful tool. 
+A series of dynamics collision simulations between lowest-energy uracil protonated water clusters (H$_2$O)$_{n=3-7, 12}$UH$^+$ and Argon atom were performed with the self-consistent-charge density-functional based tight-binding {\bf remove acronyles in abvstract if not necessary ) : (SCC-DFTB)}  method to make a deep exploration of the collision process. From the dynamics collision simulations, the trend of different types of fragments and location of the excess proton were observed. {\bf MR  : remove the following sentence, details : Our initial geometries provided a reasonably uniform distribution of Argon projectiles around each uracil protonated water clusters leading Argon atom can collide at all the possible positions of each cluster. } The theoretical simulation data show that the proportion of neutral uracil molecule loss and total fragmentation cross sections are consistent with those in experiment. Additionally, we observed that up to 7 water molecules the clusters had a direct dissociation mechanism after collision \blue{whereas for 12 water molecules …...} Furthermore, the calculation results indicate the excess proton location is highly dependent on the initial isomer as stated in a previous study {\bf put a reference in full text}  \blue{By conducting path-integral MD simulation, we finally observed that nuclear quantum effect XXX.} \blue{We are the first to perform this kind of simulation,} our dynamics collision simulations for predicting the type and amount of fragments and fragmentation cross sections of collision system provide a useful tool. 
 \end{abstract}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -353,11 +353,11 @@ As displayed in Figure \ref{fig:mass_spec}, the intensity of fragments (H$_2$O)$
     \label{fig:proporEachFrag-12-6} 
  \end{figure}
 
- \begin{figure}
-  \includegraphics[width=0.8\linewidth]{figure/proporEachFrag-12-5-s1.eps}
+\begin{figure}
+  \includegraphics[width=0.8\linewidth]{figure/proporEachFrag-12-1-s1.eps}
   \centering
-    \caption{The proportions of the main fragment from the dissociation of the fifth lowest-energy parent cluster (H$_2$O)$_{12}$UH$^+$.}
-    \label{fig:proporEachFrag-12-5-s1} 
+    \caption{The proportions of the main fragment from the dissociation of the first lowest-energy parent cluster (H$_2$O)$_{12}$UH$^+$.}
+    \label{fig:proporEachFrag-12-1-s1} 
  \end{figure}
 
 \begin{figure}
@@ -367,11 +367,19 @@ As displayed in Figure \ref{fig:mass_spec}, the intensity of fragments (H$_2$O)$
     \label{fig:proporEachFrag-12-2-s1} 
  \end{figure}
 
+ \begin{figure}
+  \includegraphics[width=0.8\linewidth]{figure/proporEachFrag-12-5-s1.eps}
+  \centering
+    \caption{The proportions of the main fragment from the dissociation of the fifth lowest-energy parent cluster (H$_2$O)$_{12}$UH$^+$.}
+    \label{fig:proporEachFrag-12-5-s1} 
+ \end{figure}
+
+
   
 \textbf{Time-Dependent Proportion of Each Fragment} 
 {\bf MR : this is a pure theory part, this deals with short times convergency, to me it should reinforce the result part analysing the theoretical results before any reference to the experiment is done.}
 
-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 the dissociation second lowest-energy parent cluster (H$_2$O)$_7$UH$^+$ and the sixth lowest-energy parent cluster (H$_2$O)$_{12}$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)$_{n=3-6}$UH$^+$ are shown in SI Figure SX. From Figure \ref{fig:proporEachFrag_7_2}, it is 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 from it. For fragment proportios of cluster (H$_2$O)$_{12}$UH$^+$, from Figure \ref{fig:proporEachFrag_12_6}, it shows fragments 
+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 the dissociation second lowest-energy parent cluster (H$_2$O)$_7$UH$^+$ and the sixth lowest-energy parent cluster (H$_2$O)$_{12}$UH$^+$ as an example. For the sake of seeing clearly, only the main fragment proportions plotted as a function of simulation time are displayed. The proportions of the main fragment of clusters (H$_2$O)$_{n=3-6}$UH$^+$ are shown in SI Figure SX. From Figure \ref{fig:proporEachFrag-7-2}, it is 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 from it. For fragment proportios of cluster (H$_2$O)$_{12}$UH$^+$, from Figure \ref{fig:proporEachFrag-12-6}, it shows fragments 
 (H$_2$O)$_{11}$UH$^+$ and (H$_2$O)$_{10}$UH$^+$ increase at the beginning and then decrease, and finally they tend to be steady. The second and the third or more times dissociation after collision and all the main fragment proportion do not tend to a constant so fast imply that there are more chances to rearrange prior to complete dissociation.
 
 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.