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biblio.bib
@ -63,6 +63,18 @@
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publisher={Royal Society of Chemistry}
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}
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@ -75,12 +87,187 @@
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|
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Title = {{Atomic hydrogen interactions with gas-phase coronene cations:
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hydrogenation versus fragmentation}},
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@ -126,34 +126,35 @@ A series of dynamics collision simulations between lowest-energy uracil protonat
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%% Start the main part of the manuscript here.
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\section{Introduction}
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\section{Introduction }
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The nucleobases in DNA and RNA play a very important role in the encoding and expression of genetic information in living systems while water represents the natural medium of many reactions in living organisms. Therefore, it is a significant point to study the interaction between nucleobase molecules and aqueous environment.
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The radiation effect on RNA and DNA molecules is still a medical challenge in modern times. The radiation can cause damages on these molecules. Radiation damages are proficiently applied in radiotherapy for cancer treatment. The major drawback in radiotherapy is the unselective damage in both healthy and tumor cells, which has a big side effect. This makes it particularly important to explore the radiation fragments. RNA nucleobase, uracil C$_4$H$_4$N$_2$O$_2$ (U), has attracted scientist’s attention a lot. Protonated uracil UH$^+$ can be generated by radiation damages. Through the study of hydration effects on cytosine, uracil, and thymine pyrimidines by including one and two water molecules explicitly, Schaefer III et al. found that a water molecule is more likely to interact with a charged species than with a neutral one.\cite{Rasmussen2010} However, the study about protonated necleobases in aqueous environment is not so much.
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The radiation effect on RNA and DNA molecules is still a medical challenge in modern times. The radiation can cause damages on these molecules. Radiation damages are proficiently applied in radiotherapy for cancer treatment. The major drawback in radiotherapy is the unselective damage in both healthy and tumor cells, which has a big side effect. This makes it particularly important to explore the radiation fragments. RNA nucleobase, uracil C$_4$H$_4$N$_2$O$_2$ (U), has attracted scientist’s attention a lot. Protonated uracil UH$^+$ can be generated by radiation damages. Through the study of hydration effects on cytosine, uracil, and thymine pyrimidines by including one and two water molecules explicitly, Schaefer III \textit{et al.} found that a water molecule is more likely to interact with a charged species than with a neutral one.\cite{Rasmussen2010} However, the study about protonated necleobases in aqueous environment is not so much.
|
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JC MUCH BLABLA
|
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JC Add a sentence to say hydration of molecules can help to do something in real life
|
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|
||||
Studying hydration of molecules and biomolecules is of paramount important to get insights into their behavior in aqueous medium, in particular their structure, stability and dynamics. To do so, gas phase investigations of molecules play an important role in understanding the intrinsic properties of molecules, which is free from the effects of solvents or other factors. It allows to study the evolution of this behavior as the function of the hydration degree of the molecule and also probe the influence of the protonated state.
|
||||
Collision experiments in the gas phase is a useful tool that can be applied to provide structural information about molecular species.\cite{Coates2018} For instance, considering U molecule, which has attracted scientist’s attention a lot due to its important role in the encoding and expression of genetic information in living systems, various collision experiments have been conducted. Fragmentation of halogen substituted uracil molecules in the gas phase through collisions experiments have been performed.\cite{Imhoff2007,Abdoul2000,Champeaux2010,Delaunay2014} The theoretical calculations about the charge-transfer processes induced by collision have been also reported.[Doi: 10.1103/PhysRevA.79.012710, DOI: 10.1039/c5cp01475a] Nevertheless, the gas phase study needs to be extended towards more realistic biomolecular systems, to reveal how the intrinsic molecular properties are affected by the surrounding medium when the biomolecules are in a natural environment.[DOI: 10.1002/cphc.201000823, DOI: 10.1088/1742-6596/373/1/012005, DOI: 10.1039/c6cp01940d, DOI: 10.1039/c7cp02233f] (JC, make this part smaller)
|
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Collision experiments in the gas phase is a useful tool that can be applied to provide structural information about molecular species.\cite{Coates2018} For instance, considering U molecule, which has attracted scientist’s attention a lot due to its important role in the encoding and expression of genetic information in living systems, various collision experiments have been conducted. Fragmentation of halogen substituted uracil molecules in the gas phase through collisions experiments have been performed.\cite{Imhoff2007,Abdoul2000,Champeaux2010,Delaunay2014} The theoretical calculations about the charge-transfer processes induced by collision have been also reported.\cite{Bacchus2009, Kossoski2015} Nevertheless, the gas phase study needs to be extended towards more realistic biomolecular systems, to reveal how the intrinsic molecular properties are affected by the surrounding medium when the biomolecules are in a natural environment.\cite{Maclot2011, Domaracka2012, Markush2016, Castrovilli2017}
|
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(JC, make this part smaller)
|
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|
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It is reported that many collision experiments have been made via threshold collision-induced dissociation (TCID) for the hermodynamic information, electron ionization and fragmentation, binding energies and other properties of biomolecules.\cite{Hayes1990, Coates2017, Neustetter2017, Coates2018} Fragmentation of isolated protonated uracil has been studied through collision-induced dissociation (CID) with tandem mass sepctrometry, \cite{Nelson1994, Molina2015, Molina2016, Sadr2014} however, there are few studies concerning the surrounding aqueous environment effect on such collision process in experiment. Some theory studies have been performed about this but those studies have been limited to small water clusters. \cite{Bakker2008} Recently, Zamith’s group in collaboration with our group reported the CID experiment on uracil protonated water clusters (H$_2$O)$_{n=1-15}$UH$^+$ and theoretical study to determine the lowest-energy structures. \cite{Braud2019} In Zamith’s experiment, the collisions only lead to intermolecular bond breaking rather than intramolecular bond breaking in the (H$_2$O)$_{n=1-15}$UH$^+$ clusters. The collisions were performed with with(H$_2$O)$_{n=1-15}$UH$^+$ clusters and M= H$_2$O, D$_2$O, Ne, and Ar. They found no matter which M was used, the results were the same. They only showed the results with Ne. The branching ratios of different charged fragments were determined through mass spectra of the collision products. Fragmentation cross section of (H$_2$O)$_{n=1-15}$UH$^+$ clusters were obtained at a collision energy 7.2 eV as a function of the total number molecules in the clusters. The proportion of neutral uracil molecules loss were detected as a function of the number n of water molecules in the (H$_2$O)$_{n=1-15}$UH$^+$ clusters at 7.2 eV of mass collision energy. From the proportion results of neutral uracil molecules loss, it shows where the excess proton lies after collision. An obvious growth of neutral uracil molecules loss was observed from n = 5-6. Those experiment were complemented by theoretical calculations that aim at finding the lowest-energy (H$_2$O)$_{n=1-7}$UH$^+$ clusters. From the structures of lowest-energy isomers, it clearly shows that (i) for small clusters (when n = 1-2), the excess proton is on the uracil; (ii) for n = 3-4, the excess proton is still on the uracil but it has a tendency to be displaced towards adjacent water molecules; (iii) when n is larger than 4, the excess proton is completely transferred to the water clusters. These results are in full agreement with the CID measurements.
|
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|
||||
It is reported that many collision experiments have been made via threshold collision-induced dissociation (TCID) for the hermodynamic information, electron ionization and fragmentation, binding energies and other properties of biomolecules.[doi: 10.1016/0076-6879(90)93418-K DOI: 10.1021/acs.jpca.7b00635, DOI: 10.1007/s13361-017-1634-y, DOI: 10.1039/c7cp05828d] Fragmentation of isolated protonated uracil has been studied through collision-induced dissociation (CID) with tandem mass sepctrometry,[doi: 10.1016/1044-0305(94)85049-6,
|
||||
doi:10.1002/jms.3704, doi: 10.1039/C6CP01657J, doi:10.1016/j.cplett.2014.05.026] however, there are few studies concerning the surrounding aqueous environment effect on such collision process in experiment. Some theory studies have been performed about this but those studies have been limited to small water clusters.[Doi: 10.1021/jp806396t] Recently, Zamith’s group in collaboration with our group reported the CID experiment on uracil protonated water clusters (H$_2$O)$_{n=1-15}$UH$^+$ and theoretical study to determine the lowest-energy structures.[doi: 10.1063/1.5044481] In Zamith’s experiment, the collisions only lead to intermolecular bond breaking rather than intramolecular bond breaking in the (H$_2$O)$_{n=1-15}$UH$^+$ clusters. The collisions were performed with H$_2$O, D$_2$O, Ne, and Ar, respectively. The branching ratios of different charged fragments were determined through mass spectra of the collision products. Fragmentation cross section of (H$_2$O)$_{n=1-15}$UH$^+$ clusters were obtained at a collision energy 7.2 eV as a function of the total number molecules in the clusters. The proportion of neutral uracil molecules loss were detected as a function of the number n of water molecules in the (H$_2$O)$_{n=1-15}$UH$^+$ clusters at 7.2 eV of mass collision energy. From the proportion results of neutral uracil molecules loss, it shows where the excess proton lies after collision. An obvious growth of neutral uracil molecules loss was observed from n=5-6. Those experiment were complemented by theoretical calculations that aim at finding the lowest-energy (H$_2$O)$_{n=1-7}$UH$^+$ clusters. From the structures of lowest-energy isomers, it clearly shows that (i) for small clusters (when n = 1-2), the excess proton is on the uracil; (ii) for n = 3-4, the excess proton is still on the uracil but it has a tendency to be displaced towards adjacent water molecules; (iii) when n is larger than 4, the excess proton is completely transferred to the water clusters. These results are in full agreement with the CID measurements.
|
||||
However, although the location of the excess proton in lowest-energy isomers is clear, there are still some issues that need to be settled: (i) What’s the main path of the fragmentation mechanisms? (ii) What are the fragments after the collision? (iii) How does the proportion of the fragments change according to the time? (iv) If the proportion of neutral uracil molecules loss only determined by the lowest-energy isomers? With interests in these questions, it pursues us to do an explicit dynamics exploration for these uracil protonated water clusters.
|
||||
|
||||
Some studies have already been done about the dynamics collision simulation.[Doi: 10.1063/1.1594717,DOI: 10.1021/acs.jpca.7b09217, Doi: 10.1098/rsta.2016.0195, DOI: 10.1039/c8cp03024c] In the present work, we made the dynamics simulation to investigate the collision of (H2O)$_{n=3-7, 12}$UH$^+$ clusters and Ar. Based on the dynamics collision simulations, we analyzed the fragmentation cross section of mixed (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters according to the total number molecules in the clusters. The branching ratios of different charged fragments were explored of the collision products. The proportion of neutral uracil molecules loss in the mixed (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters were also investigated. From all the above investigations, the two fragmentation mechanisms after collision, the mixed cluster has an immediately direct dissociation and the mixed cluster has a longer life before completed dissociation, who has the leading position are clear.
|
||||
Some studies have already been done about the dynamics collision simulation.\cite{Tomsic2013, Korchagina2017, Simon2017, Rapacioli2018} In the present work, we made the dynamics simulation to investigate the collision of (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters and Ar. Based on the dynamics collision simulations, we analyzed the fragmentation cross section of mixed (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters according to the total number molecules in the clusters. The branching ratios of different charged fragments were explored of the collision products. The proportion of neutral uracil molecules loss in the mixed (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters were also investigated. From all the above investigations, the two fragmentation mechanisms after collision, the mixed cluster has an immediately direct dissociation and the mixed cluster has a longer life before completed dissociation, which one is dominant is clear.
|
||||
\blue{All simulations are performed in the microcanonical ensemble within the Born–Oppenheimer??}
|
||||
|
||||
|
||||
\section{Computational Methods} \label{Comput_meth}
|
||||
\textbf{Exploration of the PES}
|
||||
|
||||
DFTB is approximated from DFT scheme whose efficiency relies on the use of parameterized integrals with a much lower computational cost. The DFTB approach has been particularly well studied and it has already proven its efficiency to describe chemical processes, such as the reactivity[]. In this work, we used the second-order version of DFTB, Self Consistent Charge [biblio] DFTB, with the mio-set for the Slater-Koster tables of integrals and repulsive interactions. To improve the intermolecular interaction, the class IV/charge model 3 (CM3) charges instead of the original Mulliken charges as well as the empirical terms were used to describe dispersion interactions. For the parameterization of CM3 charges, the bond parameter D$_{OH}$ = 0.129 proposed by Simon and co-workers was applied, \blue{DNH = 0.120 tested by ourselves, (part of this work has been published[])} while all other bond parameter values were set to be 0.000, which corresponds to a Mulliken evaluation of the charges. All the SCC-DFTB calculations in the present work were carried out with the deMonNano code.
|
||||
DFTB is approximated from DFT scheme whose efficiency relies on the use of parameterized integrals with a much lower computational cost. \cite{Elstner2014} The DFTB approach has been particularly well studied and it has already proven its efficiency to describe chemical processes. \cite{Kruger2005} In this work, we used the second-order version of DFTB, Self Consistent Charge DFTB, with the mio-set for the Slater-Koster tables of integrals. \cite{Elstner1998} To improve the intermolecular interaction, the class IV/charge model 3 (CM3) charges instead of the original Mulliken charges as well as the empirical terms were used to describe dispersion interactions. \cite{Rapacioli2009} For the parameterization of CM3 charges, the bond parameter D$_{OH}$ = 0.129 proposed by Simon and co-workers was applied, \blue{DNH = 0.120 tested by ourselves, (part of this work has been published[])} while all other bond parameter values were set to be 0.000, which corresponds to a Mulliken evaluation of the charges.\cite{Simon2012, Simon2013} All the SCC-DFTB calculations in the present work were carried out with the deMonNano code. \cite{demonnanoCode}
|
||||
|
||||
All the energy minima for (H2O)n=3-7, have already been obtained in a previous study.[] In this present work, we calculated the lowest-energy isomers of (H$_2$O)$_{12}$UH$^+$ cluster. To obtain them, the same two-step theoretical method with the one used for the calculation of lowest energy isomers of clusters (H$_2$O)$_{n=1-7}$UH$^+$ was applied. Firstly, the potential energy surface (PES) of (H$_2$O)$_{12}$UH$^+$ was roughly explored using the parallel temperature molecular dynamics (PTMD) simulations in combination with SCC-DFTB description of the energies and gradients. In the PTMD algorithm, 40 replicas with temperatures going linearly from 50 to 350 K were carried out. All the trajectories were 4 ns long, and the integration time step was 0.5 fs. A Nosé-Hoover chain of five thermostats with frequencies of 800 cm$^{-1}$ was used to achieve an exploration in the canonical emsemble.To avoid any spurious influence of the initial geometry on the PES exploration, three distinct PTMD simulations were carried out. In the three series, a distinct initial proton location was set: on the uracil in two cases and on the water molecules in another one. In the former cases, the u178 and u138 isomers of UH$^+$ were used as initial geometries, (see Ref.[Doi: 10.1021/jp504153p] for the isomer numbering and representation of UH$^+$ isomers) corresponding to the keto-enol and di-keto forms, respectively. 600 geometries per temperature were linearly selected along each PTMD simulation for subsequent geometry optimization leading to 72000 structures optimized at SCC-DFTB level. These structures were sorted in ascending energy order. Secondly, 23 isomers were selected from the 72000 optimized structures at SCC-DFTB level and were optimized at a high accurate MP2/Def2TZVP level, which is a tight criteria for geometry convergence and an ultrafine grid for the numerical integration. From the MP2/Def2TZVP calculation, the lowest energy isomers of cluster (H$_2$O)$_{12}$UH$^+$ were obtained. All MP2 calculations were carried out with the Gaussian 09 package.
|
||||
All the energy minima for (H$_2$O)$_{n=3-7}$UH$^+$, have already been obtained in the previous study.\cite{Braud2019} In this present work, we calculated the lowest-energy isomers of (H$_2$O)$_{12}$UH$^+$ cluster. To obtain them, the same two-step theoretical method with the one used for the calculation of lowest energy isomers of clusters (H$_2$O)$_{n=1-7}$UH$^+$ was applied.\cite{Braud2019} Firstly, the potential energy surface (PES) of (H$_2$O)$_{12}$UH$^+$ was roughly explored using the parallel temperature molecular dynamics (PTMD) simulations in combination with SCC-DFTB description of the energies and gradients.\cite{Sugita1999, Earl2005} In the PTMD algorithm, 40 replicas with temperatures going linearly from 50 to 350 K were carried out. All the trajectories were 4 ns long, and the integration time step was 0.5 fs. A Nosé-Hoover chain of five thermostats with frequencies of 800 cm$^{-1}$ was used to obtain an exploration in the canonical emsemble. \cite{Nose1984, Hoover1985} To avoid any spurious influence of the initial geometry on the PES exploration, three distinct PTMD simulations were carried out. In the three series, a distinct initial proton location was set: on the uracil in two cases and on the water cluster in another one. In the former cases, the u178 and u138 UH$^+$ isomers were used as initial geometries which was named by Pedersen \cite{Pedersen2014}. 600 geometries per temperature were linearly selected along each PTMD simulation for subsequent geometry optimization leading to 72000 structures optimized at SCC-DFTB level. These structures were sorted in ascending energy order. Secondly, 29 isomers were selected from the 72000 optimized structures at SCC-DFTB level and were optimized at a high accurate MP2/Def2TZVP level, which is a tight criteria for geometry convergence and an ultrafine grid for the numerical integration. \cite{Weigend2005, Weigend2006} From the MP2/Def2TZVP calculation, the lowest energy isomers of cluster (H$_2$O)$_{12}$UH$^+$ were obtained. All MP2 calculations were carried out with the Gaussian 09 package.\cite{GaussianCode}
|
||||
|
||||
\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. 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 taking place when computing DFTB energy for dissociated or close to dissociation systems, and allows to recover the continuity in energy and gradients in the case of level crossing. [doi: 10.1103/PhysRevA.91.043417] 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.[previous paper]. 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?}
|
||||
|
||||
@ -174,7 +175,7 @@ QM/MM method was used to describe the collision process of uracil protonated wat
|
||||
|
||||
Formula of calculating the proportion of neutral uracil loss:
|
||||
|
||||
In this part, the proportion of neutral uracil molecule loss of each lowest-energy (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster by colliding with Ar atom will be discussed. No neutral uracil loss for (H$_2$O)$_{n=1-4}$UH$^+$, the evaporation of uracil starts at n=5, and becomes significant at n=6 were observed in experiment.[doi: 10.1063/1.5044481] In our calculations, the proportions of neutral uracil molecule loss extracted from 600(2R + 3) dynamics collision simulations for (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters were plotted in Figure \ref{fig:neutralUloss} as a function of number of water molecules n. As displayed in Figure \ref{fig:neutralUloss}, the overall trend of the proportion of neutral uracil molecule loss in theory is consistent with the one in experiment except the case n=5.[doi: 10.1063/1.5044481] The evaporation of neutral uracil molecule means the excess proton stayed in the water clusters. When n = 3-4, and 6-7 the neutral uracil loss increases with n. It indicates with the increase of the number of water molecules in the cluster, the excess proton is more likely to lie in the water cluster after collision.
|
||||
In this part, the proportion of neutral uracil molecule loss of each lowest-energy (H$_2$O)$_{n=3-7, 12}$UH$^+$ cluster by colliding with Ar atom will be discussed. No neutral uracil loss for (H$_2$O)$_{n=1-4}$UH$^+$, the evaporation of uracil starts at n=5, and becomes significant at n=6 were observed in experiment.\cite{Braud2019} In our calculations, the proportions of neutral uracil molecule loss extracted from 600(2R + 3) dynamics collision simulations for (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters were plotted in Figure \ref{fig:neutralUloss} as a function of number of water molecules n. As displayed in Figure \ref{fig:neutralUloss}, the overall trend of the proportion of neutral uracil molecule loss in theory is consistent with the one in experiment except the case n=5. The evaporation of neutral uracil molecule means the excess proton stayed in the water clusters. When n = 3-4, and 6-7 the neutral uracil loss increases with n. It indicates with the increase of the number of water molecules in the cluster, the excess proton is more likely to lie in the water cluster after collision.
|
||||
|
||||
\begin{figure}
|
||||
\includegraphics[width=0.5\linewidth]{/home/linjie/Documents/uracil/collision/Paper_U/figure/neutralUloss}
|
||||
@ -206,7 +207,7 @@ The neutral uracil molecule loss proportion, 0.0\%, of n = 3 in Figure \ref{fig:
|
||||
6c & 31.2 & 43.7 & W-H\\
|
||||
6d & xx.x & xx.x & W-H\\
|
||||
6e & 30.1 & 47.8 & W-H-U\\
|
||||
6f & 13.6 & 52.3 & W-H-U\\
|
||||
6f & 14.2 & 52.3 & W-H-U\\
|
||||
7a & 27.7 & 51.0 & W-H\\
|
||||
7b & 17.4 & 49.5 & W-H-U\\
|
||||
12a & 17.8 & 49.0 & W-H\\
|
||||
@ -235,23 +236,23 @@ For (H$_2$O)$_6$UH$^+$ cluster, the neutral uracil molecule loss proportion is 1
|
||||
\end{figure}
|
||||
|
||||
\begin{figure}
|
||||
\includegraphics[width=0.5\linewidth]{/home/linjie/Documents/uracil/collision/Paper_U/figure/12ax.png}
|
||||
\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$^{-1}$).}
|
||||
\label{fig:12ax}
|
||||
\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.
|
||||
|
||||
From the determination conducted by Zamith’s et al., the neutral uracil loss proportion starts to decrease from n=9,[doi: 10.1063/1.5044481] 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. For cluster (H$_2$O)$_{12}$UH$^+$, Figure \ref{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:12ax}). 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/mol, 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.
|
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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.
|
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|
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\textbf{Total Fragmentation Cross Section} Formula of calculating the cross section:
|
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|
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In the light of the results of 600(2R + 3) dynamics collision simulations for each lowest-energy (H$_2$O)$_{n=3-7}$UH$^+$ cluster, the total fragmentation cross sections of the (H$_2$O)$_{n=3-7}$UH$^+$ clusters were determined and compared with those in experiment. As shown in Table \ref{tab:table1}, for different isomers of lowest-energy (H$_2$O)$_{n=3-7, 12}$UH$^+$ clusters, the total fragmentation cross sections are very close. So in this part, we only discuss the total fragmentation cross section of the lowest-energy (H$_2$O)$_{n=3-7}$UH$^+$ cluster who has the closest neutral uracil loss proportion compared with the one in experiment.
|
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|
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The total fragmentation cross sections of mixed (H$_2$O)$_{n=3-7}$UH$^+$ clusters from our simulation results of collision with Ar and Zamith’s experiment results of collision with Ne are plotted in Figure \ref{fig:crosssection} as a function of the number of water molecules n at 7.2 eV center of mass collision energy. (In Zamith’s experiment, collisions of cluster (H$_2$O)$_{n=1-15}$UH$^+$ with M (H$_2$O, D$_2$O, Ne, and Ar) were performed. They found no matter which M was used, the results were the same. They only showed the results with Ne.) As displayed in Figure \ref{fig:crosssection}, the curves in theory and in experiment have the same overall trend that the total fragmentation cross sections of mixed (H$_2$O)$_{n=3-7}$UH$^+$ clusters increase according to the number of water molecules. This indicates when the size of the clusters increase, the Ar and the cluster has a higher opportunity to collide. For (H$_2$O)$_7$UH$^+$ cluster, the value in theory is slightly lower than the one of (H2O)6UH+ cluster but the difference is only 1.3 Å$^2$, which is within the limit of error. Additionally, the absolute value of total fragmentation cross sections of (H$_2$O)$_{n=3-7}$UH$^+$ clusters in theory and experiment are close to each other. The biggest and smallest differences of the total fragmentation cross section for (H$_2$O)$_{n=3-7}$UH$^+$ clusters are 7.0 and 1.5 Å$^2$, separately between our calculation results and those in the experiment. Those results imply our simulations results are good enough.
|
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The total fragmentation cross sections of mixed (H$_2$O)$_{n=3-7}$UH$^+$ clusters from our simulation results of collision with Ar and the corresponding experiment results are plotted in Figure \ref{fig:crosssection} as a function of the number of water molecules n at 7.2 eV center of mass collision energy. As displayed in Figure \ref{fig:crosssection}, the curves in theory and in experiment have the same overall trend that the total fragmentation cross sections of mixed (H$_2$O)$_{n=3-7}$UH$^+$ clusters increase according to the number of water molecules. This indicates when the size of the clusters increase, the Ar and the cluster has a higher opportunity to collide. For (H$_2$O)$_7$UH$^+$ cluster, the value in theory is slightly lower than the one of (H$_2$O)$_6$UH$^+$ cluster but the difference is only 1.3 Å$^2$, which is within the limit of error. Additionally, the absolute value of total fragmentation cross sections of (H$_2$O)$_{n=3-7}$UH$^+$ clusters in theory and experiment are close to each other. The biggest and smallest differences of the total fragmentation cross section for (H$_2$O)$_{n=3-7}$UH$^+$ clusters are 7.0 and 1.5 Å$^2$, separately between our calculation results and those in the experiment. Those results imply our simulations results are good enough.
|
||||
|
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If it needs to make a further detailed description of the total fragmentation cross sections?
|
||||
|
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@ -265,9 +266,9 @@ 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.[doi: 10.1063/1.5044481] 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. [Title: The first twenty-eight gas-phase proton hydration energies]
|
||||
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}
|
||||
|
||||
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 energies 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.
|
||||
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.
|
||||
|
||||
As displayed in Table \ref{tab:fragenergy}, ratios of fragments (H$_2$O)$_{n=1-4}$UH$^+$ increase with the number of n which is in line with the results in experiment. It indicates the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ has more chances to lose three water molecules than to lose six water molecules. Ratio of fragment (H$_2$O)$_5$UH$^+$ is close to it of fragment (H$_2$O)$_4$UH$^+$ in theory which agree with the one in experiment. The ratio of fragment (H$_2$O)$_6$UH$^+$ increases a lot in the calculated results but it is not so high in experiment, which indicates in our simulations, the dissociation of the second lowest-energy cluster (H$_2$O)$_7$UH$^+$ losing one water molecule is dominant. The parent cluster (H$_2$O)$_7$UH$^+$ has the highest ratio among all fragments, which is fully consistent with it in experiment. From the analyses of the mass spectrum in theory and experiment, it implies our simulations can quantitatively describe the fragment ratios.
|
||||
|
||||
@ -298,10 +299,10 @@ 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 E$_{rela}$ 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. 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.}
|
||||
\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{E$_{rela}$}\\
|
||||
\textbf{E((H$_2$O)$_6$UH$^+$)} & \textbf{E(H$_2$O)$_5$UH$^+$)} & \textbf{E(H$_2$O)} & \textbf{$\Delta$E}\\
|
||||
\hline
|
||||
-44.361 & -40.312 & -4.06 & 0.190 \\
|
||||
-44.331 & -40.312 & -4.06 & 1.007 \\
|
||||
|
||||
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Reference in New Issue
Block a user