Dynamics and structural changes of small water clusters on ionization

Despite utmost importance in understanding water ionization process, reliable theoretical results of structural changes and molecular dynamics (MD) of water clusters on ionization have hardly been reported yet. Here, we investigate the water cations [(H₂O)_{n = 2–6}⁺] with density functional theory (DFT), Möller–Plesset second‐order perturbation theory (MP2), and coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The complete basis set limits of interaction energies at the CCSD(T) level are reported, and the geometrical structures, electronic properties, and infrared spectra are investigated. The characteristics of structures and spectra of the water cluster cations reflect the formation of the hydronium cation moiety (H₃O⁺) and the hydroxyl radical. Although most density functionals fail to predict reasonable energetics of the water cations, some functionals are found to be reliable, in reasonable agreement with high‐level ab initio results. To understand the ionization process of water clusters, DFT‐ and MP2‐based Born‐Oppenheimer MD (BOMD) simulations are performed on ionization. On ionization, the water clusters tend to have an Eigen‐like form with the hydronium cation instead of a Zundel‐like form, based on reliable BOMD simulations. For the vertically ionized water hexamer, the relatively stable (H₂O)₅⁺ (5sL4A) cluster tends to form with a detached water molecule (H₂O). © 2013 Wiley Periodicals, Inc.     

Influence of hydrostatic pressure on water absorption of polyoxymethylene: experiment and molecular dynamics simulation

This work experimentally investigated the influence of hydrostatic pressure on the water absorption of polyoxymethylene, followed by analyzing its micro‐mechanism via molecular dynamics simulation. Tests results show that the polyoxymethylene water absorption decreases with the increase in hydrostatic pressure when the latter is within 0–3.0 MPa; it subsequently increases with the increase in hydrostatic pressure in the range of 3.0–5.0 MPa. Simulation of water molecules diffusion on polyoxymethylene surface shows that water molecules diffuse into polyoxymethylene surface during an equilibration run, and water molecule displacement value of maximum relative concentration gives almost the same characteristics: firstly decreases and then increases with the increase of hydrostatic pressure. Simulation of water molecule diffusion inside polyoxymethylene suggests the following: (i) water molecules vibrate from the interior to the edge of polyoxymethylene cell during the equilibration run, and (ii) water diffusion coefficient in polyoxymethylene gives trend of firstly decreasing and then increasing with the increase of hydrostatic pressure. Copyright © 2016 John Wiley & Sons, Ltd.     

CENCALC: A computational tool for conformational entropy calculations from molecular simulations

We present the CENCALC software that has been designed to estimate the conformational entropy of single molecules from extended Molecular Dynamics (MD) simulations in the gas‐phase or in solution. CENCALC uses both trajectory coordinates and topology information in order to characterize the conformational states of the molecule of interest by discretizing the time evolution of internal rotations. The implemented entropy methods are based on the mutual information expansion, which is built upon the converged probability density functions of the individual torsion angles, pairs of torsions, triads, and so on. Particularly, the correlation‐corrected multibody local approximation selects an optimum cutoff in order to retrieve the maximum amount of genuine correlation from a given MD trajectory. We illustrate these capabilities by carrying out conformational entropy calculations for a decapeptide molecule either in its unbound form or in complex with a metalloprotease enzyme. CENCALC is distributed under the GNU public license at http://sourceforge.net/projects/cencalc/ .     

Melting behaviors of icosahedral metal clusters studied by Monte Carlo simulations

We present an atom‐resolved analysis method that traces physical quantities such as the root‐mean‐square bond length fluctuation and coordination number for individual atoms as functions of temperature or time. This method is applied to explain the temperature‐dependent behaviors of three types of Ni_N (N=12,13,14) clusters. The detailed studies for the three types of clusters reveal characteristics as follows: (a) as the temperature increases, all three types of clusters undergo two‐stage melting, irrespective of the existence of vacancy or adatom on the icosahedral surfaces, (b) the melting of icosahedral clusters with vacancy starts with vacancy hopping, which has not been observed for any type of small clusters (N<34), (c) the melting of the icosahedral clusters with adatom (N=14) is initiated by adatom hopping, followed by the site exchange between the adatom and surface atoms. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 380–387, 2000     

Grcarma: A fully automated task‐oriented interface for the analysis of molecular dynamics trajectories

We report the availability of grcarma, a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories of biological macromolecules. It is a cross‐platform, Perl/Tk‐based front‐end to the program carma and is designed to facilitate the needs of the novice as well as those of the expert user, while at the same time maintaining a user‐friendly and intuitive design. Particular emphasis was given to the automation of several tedious tasks, such as extraction of clusters of structures based on dihedral and Cartesian principal component analysis, secondary structure analysis, calculation and display of root‐mean‐square deviation (RMSD) matrices, calculation of entropy, calculation and analysis of variance–covariance matrices, calculation of the fraction of native contacts, etc. The program is free‐open source software available immediately for download. © 2013 Wiley Periodicals, Inc.     

Implicit and explicit solvent models for modeling a bifunctional arene ruthenium hydrogen‐storage catalyst: A classical and ab initio molecular simulation study

Classical and ab initio, density functional theory‐ and semiempirical‐based molecular simulation, including molecular dynamics, have been carried out to compare and contrast the effect of explicit and implicit solvation representation of tetrahydrofuran (THF) solvent on the structural, energetic, and dynamical properties of a novel bifunctional arene ruthenium catalyst embedded therein. Particular scrutiny was afforded to hydrogen‐bonding and energetic interactions with the THF liquid. It was found that the presence of explicit THF solvent molecules is required to capture an accurate picture of the catalyst's structural properties, particularly in view of the importance of hydrogen bonding with the surrounding THF molecules. This has implications for accurate modeling of the reactivity of the catalyst. © 2014 Wiley Periodicals, Inc.     

Structures and electronic properties of the small rubidium‐doped silicon RbSin (n = 1–12) clusters

The geometries, relative stabilities, and electronic properties of small rubidium‐doped silicon clusters RbSi_n (n = 1–12) have been systematically investigated using the density functional theory at the B3LYP/GENECP level. The optimized structures show that lowest‐energy isomers of RbSi_n are similar with the ground state isomers of pure Si_n clusters and prefer the three‐dimensional for n = 3–12. The relative stabilities of RbSi_n clusters have been analyzed on the averaged binding energy, fragmentation energy, second‐order energy difference, and highest occupied molecular orbital‐lowest unoccupied molecular orbital energy gap. The calculated results indicate that the doping of Rb atom enhances the chemical activity of Si_n frame and the magic number is RbSi₂. The Mulliken population analysis reveals that the charges in the corresponding RbSi_n clusters transfer from the Rb atom to Si atoms. The partial density of states and chemical hardness are also discussed. © 2014 Wiley Periodicals, Inc.     

Temperature and frequency dependencies of the complex dielectric constant of poly(ethylene oxide) under hydrostatic pressure

Electrical impedance measurements have been made in the frequency range 5 Hz to 10 MHz in pure poly(ethylene oxide) having a molecular weight of 600,000 from 12 K nearly up to the melting point of the crystalline phase (about 330 K). A pronounced relaxation peak in the dielectric loss and a corresponding step in the dielectric constant have been observed at about 240 K, which can be readily related to the glass-rubber transition in the amorphous region of the polymer. As the temperature approaches the melting point there are large increases in the real ϵ′ and imaginary e′ parts of the dielectric constant. The frequency dependence of ϵ′ is characterized by a primary relaxation process, whose frequency increases with increasing temperature as a consequence of decrease of the average structural relaxation time. There is strong evidence that this low-frequency dispersion arises mainly from the diffusive transport of ionic charge carriers rather than a purely orientation relaxation process. In addition, the effects of hydrostatic pressures (0–0.25 GPa) on the frequency dependencies of the real ϵ′ and imaginary ϵ′ parts of the dielectric constant have been measured in the temperature range from 254 to 329 K. An advantage of applying pressure is that it shifts the α_𝒶 relaxation peak into an experimentally accessible frequency window of the equipment; the lowering of frequency results from a decrease in the relaxation volume and a consequent reduction in the mobility of the molecular units. Results are discussed in terms of theoretical models of the effect of pressure on the glass transition, providing information on the cooperative dynamics. © 1996 John Wiley & Sons, Inc.     

Effect of high hydrostatic pressure on prebiotic peptide synthesis

Here we reported the high hydrostatic pressure, as a key factor of deep-sea environment conditions, promoted the peptide formation and should be considered as one of the significant factors in studying the origin of life.     

Study of small chlorine‐doped potassium clusters by thermal ionization mass spectrometry

The theoretical calculations have predicted that nonmetal‐doped potassium clusters can be used in the synthesis of a new class of charge‐transfer salts which can be considered as potential building blocks for the assembly of novel nanostructured material. In this work, K_nCl (n = 2–6) and K_nCl_n?1 (n = 3 and 4) clusters were produced by vaporization of a solid potassium chloride salt in a thermal ionization mass spectrometry. The ionization energies (IEs) were measured, and found to be 3.64 ± 0.20 eV for K₂Cl, 3.67 ± 0.20 eV for K₃Cl, 3.62 ± 0.20 eV for K₄Cl, 3.57 ± 0.20 eV for K₅Cl, 3.69 ± 0.20 eV for K₆Cl, 3.71 ± 0.20 eV for K₃Cl₂ and 3.72 ± 0.20 eV for K₄Cl₃. The K_nCl⁺ (n = 3–6) clusters were detected for the first time in a cluster beam generated by the thermal ionization source of modified design. Also, this work is the first to report experimentally obtained values of IEs for K_nCl⁺ (n = 3–6) and K_nCl_n?1⁺ (n = 3 and 4) clusters. The ionization energies for K_nCl⁺ and K_nCl_n?1⁺ clusters are much lower than the 4.34 eV of the potassium atom; hence, these clusters should be classified as ‘superalkali’ species. Copyright © 2012 John Wiley & Sons, Ltd.     

Molecular dynamics implementation in MSINDO: study of silicon clusters

Born-Oppenheimer molecular dynamics is implemented in the semiempirical self-consistent field molecular orbital method MSINDO. The method is employed for the investigation of the structure and dynamics of silicon clusters of various sizes. The reliability of the present parameterization for silicon compounds is demonstrated by a comparison of the results of simulated annealing and of density functional calculations of Si(n) clusters (n = 5-7). The melting behavior of the Si(7) cluster is investigated and the MSINDO results are compared to previous high-level calculations. The efficiency of the present approach for the treatment of large systems is demonstrated by an extensive simulated annealing study of the Si(45) and Si(60) clusters. New Si(45) and Si(60) structures are found and evaluated. The relative stability of various energy minimum structures is compared with density functional calculations and available literature data.     

A new perspective of shape recognition to discover the phase transition of finite‐size clusters

An ultrafast shape‐recognition technique was used to analyze the phase transition of finite‐size clusters, which, according to our research, has not yet been accomplished. The shape of clusters is the unique property that distinguishes clusters from bulk systems and is comprehensive and natural for structural analysis. In this study, an isothermal molecular dynamics simulation was performed to generate a structural database for shape recognition of Ag? Cu metallic clusters using empirical many‐body potential. The probability contour of the shape similarity exhibits the characteristics of both the specific heat and Lindemann index (bond‐length fluctuation) of clusters. Moreover, our implementation of the substructure to the probability of shapes provides a detailed observation of the atom/shell‐resolved analysis, and the behaviors of the clusters were reconstructed based on the statistical information. The method is efficient, flexible, and applicable in any type of finite‐size system, including polymers and nanostructures. © 2014 Wiley Periodicals, Inc.     

A study of surface diffusion of ternary (Cu-Ag-Zr) adatoms clusters for applications in thin film formation

This study presents the diffusion of heterogeneous ternary (Cu-Ag-Zr) adatoms clusters on Ag(111) using molecular dynamics techniques which could be important for the surface phenomena's and helpful for the ternary cluster's growth and formation of ternary alloy-based thin films. The mechanism of nanoscale surface diffusion is investigated for 1Cu-1Ag-1Zr, 2Cu-2Ag-2Zr, 3Cu-3Ag-3Zr, and 4Cu-4Ag-4Zr clusters at temperatures 300, 500, and 700 K. The diffusion mechanism displays that the diffusion of trimer cluster exhibits hopping, sliding, and shearing at 300 K, whereas for hexamer, nonamer, and decamer, the diffusion rate is low; however, breathing, anchoring, and concentrated motion dominates. At 500 K, trimer and hexamer show the process of atomic exchange; however, the atomic exchange is not observed in the case of nonamer and decamer diffusion. The atomic exchange mechanism of Cu and Zr adatoms dominates at 700 K for all size clusters, except Ag adatoms, where Zr adatoms show a relatively more tendency. Separation and rejoining of the one and two adatoms (likely Zr adatom) are also witnessed at high temperature. The pop-up of Ag adatoms also occurs in very short intervals over the remaining adatoms of clusters. Interestingly, during trimer diffusion, the adsorption of the Zr- or Cu-adatom among the trimer cluster into the substitutional site is found. At 700 K, vacancy generation, filling of vacancies, and migration of vacancy, in the neighborhood of the adatoms cluster, also observed. Moreover, the rate of diffusion decreases with the size increase of the clusters and increases with the increase in temperature.     

Ultrafast dynamics in noble metal clusters: The role of internal vibrational redistribution

We present a theoretical study of the ultrafast dynamics in noble metal clusters interacting with molecular oxygen which is of fundamental importance for the understanding and design of cluster-based heterogenous nanocatalysts. We demonstrate that intrinsic dynamical properties can significantly promote the reactivity of small noble metal clusters towards O₂. This concept is illustrated by performing collision simulations between and clusters and O₂ in the framework of the ab initio molecular dynamics (MD) using density functional theory (DFT). We show that different nature and efficiency of the internal vibrational energy redistribution (IVR) during the collisions with O₂ are responsible for considerably different sticking probabilities of O₂ to silver and gold clusters, respectively. In the case of , resonant IVR between the cluster and the O₂ subunit activates the O–O bond and promotes the subsequent oxidation reaction. In contrast, in the case of fast dissipative IVR on the time scale of 1 ps leads to a higher sticking probability for O₂ but the O–O bond is very rapidly deactivated and cannot participate in further oxidation processes. These findings allow us to introduce the nature of IVR as a criterion for promoting the reactivity of noble metal clusters. Such different behaviour of silver and gold clusters colliding with O₂ originates from difference in relativistic effects which are considerably more pronounced in the case of gold clusters causing more directional rigid bonding in contrast to silver clusters with more s-metallic floppy character. Moreover, we demonstrate that breaking of O–O bond can be induced in by a selective excitation of the O–O bond with an ultrashort pulse in the infrared spectral range. This opens the perspective to control the action of nanocatalysts by employing shaped laser pulses and thus bridges the fields of femtochemistry and cluster nanocatalysis.     

Unusual case of catalysis by palladium clusters

An unusual for Pd catalysts dehydration of α-alkyl and α, α′-dialkylbenzyl alcohols PhCR′R″OH (R′ = H, Me, Et, Bu; R″ = H, Me) occurs in the presence of the palladium(I) cluster [Pd₄(CO)₄(OAc)₄] (1) in an inert atmosphere to form ethers PhCR′R″-O-CR′ R″ and water. The catalyst is an intermediate of cluster 1 reduction to Pd black, while neither the starting cluster 1, nor Pd black, which is the decomposition product, are active in the catalysis of this reaction.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 788–791, March, 2005.     

The performance of density functional and wavefunction‐based methods for 2D and 3D structures of Au10

The transition from 2D to 3D structures in small gold clusters occurs around 10 atoms. Density functional theory predicts a planar structure for in contrast to recent second‐order Møller–Plesset perturbation theory calculations, which predict a 3D arrangement. The validity of the use of single‐reference second‐order Møller–Plesset theory for near metallic systems remains, however, questionable. On the other hand, it is less than clear how well density functional approximations perform for such clusters. We, therefore, decided to carry out quantum chemical calculations for using a variety of different density functionals as well as wavefunction‐based methods including coupled cluster theory to compare the different energetically low lying 2D and 3D cluster isomers. The results are perhaps not encouraging showing that most computational methods do not predict correctly the energetic sequence of isomers compared to coupled cluster theory. As perturbative triple corrections in the coupled cluster treatment change the order in cluster stability, the onset of 2D to 3D transition in these gold clusters remains elusive. As expected, second‐order Møller–Plesset theory is not suitable for correctly describing such systems.     

Parallel variable selection of molecular dynamics clusters as a tool for calculation of spectroscopic properties

Clusters of a solute and a few solvent molecules obtained from molecular dynamics (MD) are a powerful tool to study solvation effects by advanced quantum chemical (QC) methods. For spectroscopic properties strongly dependent on the solvation, however, a large number of clusters are needed for a good convergence. In this work, a parallel variable selection (PVS) method is proposed that in some cases efficiently reduces the number of clusters needed for the averaging. The mass, charge, or atomic density MD distributions are used as a secondary variable to preselect the most probable cluster geometries used for averaging of solute spectral properties. When applied to nuclear magnetic resonance chemical shift of a model alcohol, the method allowed one to significantly reduce the total computational time, by a factor of 10. Even larger savings were achieved for the modeling of Raman and Raman optical activity spectra of (S)‐lactamide molecule dissolved in water. The results thus suggest that the PVS method can be generally used for simulations of spectroscopic properties of solvated molecules and makes multiscale MD/QC computations more affordable. © 2012 Wiley Periodicals, Inc.     

Thermal decomposition of nickel(II) complexes under quasi-equilibrium conditions

The stoichiometry of thermal decomposition and the relationship between the thermal parameters (quasi-equilibrium decomposition temperaturesT _D and decomposition entalpies H _D) of NiL₄(NCS)₂ complexes (L=imidazole derivatives) were studied. It was found that changes in the experimental conditions strongly influence the decomposition stoichiometry. TheT _D and H _D can be ordered in the following sequence (according toL): imidazole<2-Me imidazole<2-Et imidazole相似文献   

Insights into the dynamics of evaporation and proton migration in protonated water clusters from Large‐scale Born–Oppenheimer direct dynamics

Large‐scale on‐the‐fly Born–Oppenheimer molecular dynamics simulations using recent advances in linear scaling electronic structure theory and trajectory integration techniques have been performed for protonated water clusters around the magic number (H₂O)_nH⁺, for n = 20 and 21. Besides demonstrating the feasibility and efficiency of the computational approach, the calculations reveal interesting dynamical details. Elimination of water molecules is found to be fast for both cluster sizes but rather insensitive to the initial geometry. The water molecules released acquire velocities compatible with thermal energies. The proton solvation shell changes between the well‐known Eigen and Zundel motifs and is characterized by specific low‐frequency vibrational modes, which have been quantified. The proton transfer mechanism largely resembles that of bulk water but one interesting variation was observed. © 2012 Wiley Periodicals, Inc.