Ultrafast Coulomb explosion imaging of molecules and molecular clusters

Taking an image of their structure and a movie of their dynamics of small quantum systems have always been a dream of physicists and chemists. Laser-induced Coulomb explosion imaging(CEI) provides a great opportunity to make this dream a reality for small molecules or their aggregation — clusters. The method is unique for identifying the atomic locations with angstrom spatial resolution and capturing the structural evolution with a femtosecond time scale, in particular for imaging transient state products. This review summarizes the determination of three-dimensional equilibrium geometry of molecules and molecular cluster system through the reconstruction from the fragments momenta, and also shows that the dissociation dynamics on the complex potential energy surface can be tracked in real-time with the ultrafast CEI(UCEI).Furthermore, the detailed measurement and analysis procedures of the CEI, theoretical methods, exemplary results, and future perspectives of the technique are described.

Simulating the Dynamics of Bimetallic Clusters Deposited onto a Surface Using Molecular Dynamics

This paper examines the interface development between a single crystalline Ag matrix and core-shell AgnCom nanoclusters that have been deposited with energies varying between 0.25 eV and 1.5 eV per atom using computer modeling techniques. Clusters undergo deformation as a result of the slowing down;they may also become epitaxial with the substrate and maintain their core-shell structure. A detailed analysis of the effects of the cluster-surface interaction is conducted over a realistic size and energy range, and a model is created to show how clusters accumulate. It is discovered that both the silver shells and the cobalt cluster cores exhibit limited epitaxy with the substrate, and that the contact produced is only a few atomic layers thick. The effect is higher for Ag shells than for Co cores, and it is not very energy dependent.

K-means Find Density Peaks in Molecular Conformation Clustering

Performing cluster analysis on molecular conformation is an important way to find the representative conformation in the molecular dynamics trajectories.Usually,it is a critical step for interpreting complex conformational changes or interaction mechanisms.As one of the density-based clustering algorithms,find density peaks(FDP)is an accurate and reasonable candidate for the molecular conformation clustering.However,facing the rapidly increasing simulation length due to the increase in computing power,the low computing efficiency of FDP limits its application potential.Here we propose a marginal extension to FDP named K-means find density peaks(KFDP)to solve the mass source consuming problem.In KFDP,the points are initially clustered by a high efficiency clustering algorithm,such as K-means.Cluster centers are defined as typical points with a weight which represents the cluster size.Then,the weighted typical points are clustered again by FDP,and then are refined as core,boundary,and redefined halo points.In this way,KFDP has comparable accuracy as FDP but its computational complexity is reduced from O(n^(2))to O(n).We apply and test our KFDP method to the trajectory data of multiple small proteins in terms of torsion angle,secondary structure or contact map.The comparing results with K-means and density-based spatial clustering of applications with noise show the validation of the proposed KFDP.

Molecular Dynamics Studies of Solid-Liquid Phase Transitions Ⅱ——Homogeneous Nucleation of (KI)_(108) Clusters

在一系列分子动力学计算中，（ＫＩ）１０８离子簇冷却时自发地由液相变为立方面心相．在３５０Ｋ和４００Ｋ的成核速率大于１０３６核／ｍ３·ｓ．由成核速率得到的固－液界面自由能约为５０ｍＪ／ｍ２．

Kinetics Investigation of Sintering of Nanometer Size Metal Clusters:A Molecular Dynamics Study

The sintering process of nanometer size gold clusters is investigated by using molecular dynamics simulation in the frame of embedded atomistic method. Several molecular dynamics simulation techniques are used to observe and describe the evolution of the sintering process. The energy distribution for single cluster is examined and the snapshots of sintering process of two clusters are recorded. The evolution of sintering is also described by plotting the mass center changes with time for each cluster. The variations of kinetic and potential energy during the process of sintering are monitored and measured to analyze the dominant mechanisms of sintering from the energy point of view.

Molecular dynamics simulation of an argon cluster filled inside carbon nanotubes

The effects of the diameters of single-walled carbon nanotubes （SWCNTs） （7.83A to 27.40A） and temperature （20 K-45 K） on the equilibrium structure of an argon cluster are systematically studied by molecular dynamics simulation with consideration of the SWCNTs to be fixed. Since the diameters of SWCNTs with different chiralities increase when temperature is fixed at 20 K, the equilibrium structures of the argon cluster transform from monoatomic chains to helical and then to multishell coaxial cylinders. Chirality has almost no noticeable influence on these cylindrosymmetric structures. The effects of temperature and a non-equilibrium sudden heating process on the structures of argon clusters in SWCNTs are also studied by molecular dynamics simulation.

Quasi-aromaticity in Cluster Chemistry Ⅱ. Localized Molecular Orbital Studies on Co_6 (CO)_(14)^(4-) and Ni_2Co_4 (CO)_(14)^(2-) Cluster Anions

The energy-localized CNDO/2 molecular orbitals have been calculated for the cluster anions of [Co_6 (CO)_(14)]￣(4-) and [Ni_2Co_4 (CO)_(14)]￣(2-)in order to get a deeper insight into the nature of their skeletal bonding. The bonding characteristics of these hexanuclear carbonyl cobaltates are described from a localization bonding viewpoint. There are two typical M-CO bondings, one of which is formed by electron donation from the terminal and capping carbonyl ligands into the vacant hybrid orbitals on the metal atoms , leading to formation ofσ(C_t→Co) and σ(C_b→{Co_3})bonds. The other typical M-CO bonding is back donation of the lone d-electron pairs on the metal atoms into the carbonyl ligands, forming π(Co→C_t) bonds, σ(Co→{C_(b2)}) bonds and π(Co→{C_(b4)} ) bonds. It is found that there are no direct metalmetal bondings in the skeletons of these two cluster anions.The delocalization situation of the skeletal bonding electrons is briefly discussed.

Coalescence between Cu_(57) and Cu_(58) clusters at a room temperature:molecular dynamics simulations

Three coalescence processes of Cu57-Cu57, Cu57-Cu58, and Cu5s Cu58 clusters at 300 K are investigated by employing molecular dynamics simulations. According to the evolutions of mean square displacement and local atom packing, the coalescence process can be separated into three stages including an approaching stage, a coalescing stage, and a coalesced stage. The simulations show that the coalescence processes and the formed products are sensitive to the respective initial structures of, and the relative configuration between, the two coalescing icosahedron-based clusters.

Molecular dynamics simulation of thermodynamical properties of copper clusters

The melting and freezing processes of CUN （N =180, 256, 360, 408, 500, 628 and 736） nanoclnsters are simulated by using micro-canonical molecular dynamics simulation technique, The potential energies and the heat capacities as a function of temperature are obtained. The results reveal that the melting and freezing points increase almost linearly with the atom number in the cluster increasing. All copper nanoclusters have negative heat capacity around the melting and freezing points, and hysteresis effect in the melting/freezing transition is derived in CUN nanoclusters for the first time.

Quasi-aromaticity in Cluster Chemistry Ⅲ. Localized Molecular Orbital Study on Electron-rich Cobalt-sulfur Cluster Compounds[Co_6(μ_3-X)_8L_6]￣(n+)(X=S,Se;L=PPh_3,PEt_3,CO;n=0,1)

The localized molecular orbitals and energy levels for [Co_6 (μ_3-S)_8 (PH_3)_6]￣(n+)(n=0, 1) as model molecules of the electron-rich [Co_6 (μ_3-S)_8 (PPh_3)_6]￣(n+) (n=0,1) cluster compounds have been calculated by using Edmiston-Ruedenberg energy localization scheme under the spin-unrestricted CNDO/2 approximation. It is shown that the cluster skeletons of these two isostructural molecules consist of the edge-localized two-centered two-electron (Co-S) bonds plus a pair of the skeleton electrons delocalized on the whole cluster core,leading an extra stability of the cluster core.The one-electron oxidation for the neutral molecule gives rise to a one-electron σ (Co-Co) bond.which further resonates among the three diagonal lines of the {Co_6} octahedron. The comparison between [Co_6 (μ_3-S)_8(PPh_3)_6] and [Co_6(μ_3-CO)_8(CO)_6]￣(4-) indicates that the latter possesses face-localized bridging-bonds which are further delocalized on the whole surface of the cluster octahedron by the back-donation bonds from the lone electron pairs on the Co atoms to the capping carbonyl CO ligands. The structural features of the series of the [Co6(μ_3-X)_8L_6]￣(n+)(X =S, Se; L=PPh_3,PEt_3, CO;n=0, 1) cluster compounds are briefly rationalized on the basis of the localization description as well.

MOLECULAR AND CRYSTAL STRUCTURES OF TETRANUCLEAR MOLYBDENUM CLUSTER[Mo_4(μ_3-O)_2O_4Cl_2(o-CH_3C_6H_4COO)~6]■

The new cluster[Mo_4(μ_3-O)_2O_4Cl_2(o-CH_3C_6H_4COO)_6]has been prepared by the reaction of molybdenum pentachloride and o-methylbenzoic acid.The crystal and molecular structures were determined by the X-ray diffraction method.It crystallizes in the orthorhombic space group Pnna with cell parameters:Mr=1361.6,a=13.792(4), b=17.957(3),c=20.974(9) ,V=5194(2) ~3,Z=4,Dc=1.74/cm^3,F(OOO)=2704,μ(MoK ) =11.0/cm,R=0.074.

Molecular and Crystal Structure of Hexacobalt Carbonyl Cluster Containg Twin Co_3S(CO)_7 Fragments Linked by a Novel Phosphido-Thiolato Ligand as Backbone

Reaction of dimers of (R) thionophosphine sulfide (R = P - C6H4OMe,SMe ) with Co, (CO), yields the novel hexacobalt cluster [Co'(μ3, -S)2, (CO) 14 (μ4 -μ4- and the trinuclear clusterPSCH,)J 2' In 1, tw0 Co3S(C0)7 units linked by a novel phosphido-thio1ato bifunc-tiona1 bridging p'-SPR ligand as backbone.

Molecular Dynamics and Preparation of HO-PAMAM-2.5G Protected Lanthanum Cluster

HO-PAMAM-2. 5 G-protected lanthanum cluster was studied by Virtual Molecule （VM） software. Molecular dynamics （MD） simulation of the nanocomposite system was performed from the viewpoints of molecular structure and energy＇s fluctuation in NVT system. The motivation of this work was to understand the stability and mechanism of the nanocomposite in different proportion. simulation results reveal that The molecular dynamics when the quantity of La in per HO-PAMAM-2.5G amounted to 0 - 60, the radius of gyration of HO-PAMAM-2.5/La nanocomposite is obviously decreased.

MOLECULAR DYNAMICS SIMULATIONS OF FILLED AND EMPTY CAGE-LIKE WATER CLUSTERS IN LIQUID WATER AND THEIR SIGNIFICANCE TO GAS HYDRATE FORMATION MECHANISMS

Molecular dynamics simulations are performed to observe the evolutions of 512 and 51262 cage-like water clusters filled with or without a methane molecule immersed in bulk liquid water at 250 K and 230 K. The lifetimes of these clusters are calculated according to their Lindemann index δ (t) using the criteria of δ≥0.07. For both the filled and empty clusters, we find the dynamics of bulk water determines the lifetimes of cage-like water clusters, and that the lifetime of 512 62 cage-like cluster is the same as that of 512 cage-like cluster. Although the methane molecule indeed makes the filled cage-like cluster more stable than the empty one, the empty cage-like cluster still has chance to be long-lived compared with the filled clusters. These observations support the labile cluster hypothesis on the formation mechanisms of gas hydrates.

Molecular Design and Electronic Structure of Polynuclear Rare Earth Complexes and Clusters

Studies on the electronic structure,molecular design,syntheses of some novel series of tetranuclear rare earth complexes in our laboratory have been reviewed.Spin-unrestricted localized INDO method was used to calculate the electronic structure and the chemical bonding in the typical rare earth cluster Sc[Sc_6Cl_(12)Co]was discussed.

Quasi-aromaticity in Cluster Chemistry Ⅱ. Localized Molecular Orbital Studies on Co6 （CO）14 ￣（4-） and Ni2Co4 （CO）14 ￣（2-） Cluster Anions

The energy-localized CNDO/2 molecular orbitals have been calculated for the cluster anions of [Co6 （CO）14]￣（4-） and [Ni2Co4 （CO）14]￣（2-）in order to get a deeper insight into the nature of their skeletal bonding. The bonding characteristics of these hexanuclear carbonyl cobaltates are described from a localization bonding viewpoint. There are two typical M-CO bondings, one of which is formed by electron donation from the terminal and capping carbonyl ligands into the vacant hybrid orbitals on the metal atoms , leading to formation ofσ（Ct→Co） and σ（Cb→{Co3}）bonds. The other typical M-CO bonding is back donation of the lone d-electron pairs on the metal atoms into the carbonyl ligands, forming π（Co→Ct） bonds, σ(Co→{Cb2}) bonds and π(Co→{Cb4} ) bonds. It is found that there are no direct metalmetal bondings in the skeletons of these two cluster anions.The delocalization situation of the skeletal bonding electrons is briefly discussed.

Unimolecular Dissociation of H⁺<sub style="margin-left:-6px;">2n+1</sub>Hydrogen Clusters: Measured Cross Sections and Theoretically Calculated Rate Constants

In this paper, we studied the process of dissociation unimolecular of the evaporation of H+2n+1 hydrogen clusters according to size, using the Rice-Ramsperger-Kassel-Marcus (RRKM) theory. The rate constants k(E) were determined with the use of statistical theory of unimolecular reactions using various approximations. In our work, we used the products frequencies instead of transitions frequencies in the calculation of unimolecular dissociation rates obtained by three models RRKM. The agreement between the experimental cross section ratio and calculated rate ratio with direct count approximation seems to be reasonable.

Energetic Protons Emitted from Coulomb Explosion Dynamics of Large-Sized Hydrogen Clusters Driven by an Ultrashort Intense Laser Pulse

Protons with very high kinetic energy of about lOkeV and the saturation effect of proton energy for laser intensity have been observed in the interaction of an ultrashort intense laser pulse with large-sized hydrogen dusters. Including the cluster-size distribution as well as the laser-intensity distribution on the focus spot, the theoretical calculations based on a simplified Coulomb explosion model have been compared with our experimental measurements, which are in good agreement with each other.

Reactions of Laser Ablation-magnesium Plasma with Methanol Clusters

The laser ablation-molecular beam（LA-MB） method is useful for studying the reactions of metal ions with molecular clusters. Reactions of magnesium plasma with methanol clusters were studied by using this method. A specially designed reaction cell was used as a fast flow reactor operated under thermal conditions, and the reaction products were measured with a time-of-flight（TOF） mass spectrometer. Surprisingly, several series of cluster ions with complex sizes and intensity distributions were obtained when the laser ablating was applied to different parts of the molecular beam. In the front part of the molecular beam, strong Mg^＋ （CH3OH）n（ n = 0-5） and weak H^＋ （CH3OH）n（ n = 0-5 ） cluster ions were observed with relatively small cluster sizes ; in the middle part of the molecular beam, the main cluster ions were H^＋ （ CH3OH）n （ n = 6-17 ） and H^＋（ H2O） 2 （ CH3OH）n（ n = 6-17 ） with a relatively large cluster size and a weak intensity; in the back part of the molecular beam, two new series of cluster ions, MgO^＋ （ H2O） （ CH3 OH）n（ n = 6-10 ） and MgOCH3^＋ （ CH3OH）n（ n = 6-10）, were obtained and accompanied by weak H^＋（CH3OH）n（n = 4-7） and H^＋（ H2O）2 （CH3OH）n（ n = 3-6）. The formation mechanisms and speed characteristics of the cluster ions are discussed in this article.

Nuclear fusion from Coulomb explosions of deuterated methane clusters subjected to ultraintense femtosecond laser pulses

This paper reports that Coulomb explosions taken place in the experiment of heteronuclear deuterated methane clusters （（CD4）n） in a gas jet subjected to intense femtoseeond laser pulses （170 mJ, 70 fs） have led to table-top laser driven DD nuclear fusion. The clusters produced in supersonic expansion had an average size of about 5 nm in radius and the laser intensity used was 3 × 10^17 W/cm^2.The measured maximum and average energies of deuterons produced in the laser-cluster interaction were 60 and 13.5 keV, respectively. Prom DD collisions of energetic deuterons, a yield of 2.5（±0.4） × 10^4 fusion neutrons of 2.45 MeV per shot was realized, giving rise to a neutron production efficiency of about 1.5 × 10^5 per joule of incident laser pulse energy. Theoretical calculations were performed and a fairly good agreement of the calculated neutron yield with that obtained from the present experiment was found.