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Unveiling the structure and dynamics of Ac³⁺ Ion in Aqueous Solution: Insight From Relativistic Hybrid Forces Molecular Mechanics Molecular dynamics Simulations

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INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2024年第16期124卷 e27464-e27464页

作者： Abimanyu, Muhammad Aditya Prasetyo, Niko Pradipta, Mokhammad Fajar Univ Gadjah Mada Fac Math & Nat Sci Dept Chem Yogyakarta Indonesia

This work describes a molecular dynamics simulation study (MP2-DKH2/MM) that explores the structural and dynamical properties of hydrated Ac3+ ions in an aqueous solution. Simulation results indicate that the ion formed three hydration shells. The hydrated Ac3+ had a first hydration shell comprising 8-9 water molecules. It showed similar probabilities for both coordination numbers, showing a flexible first hydration shell with eight registered successful ligand exchanges during the simulation. The water molecules' mean residence times (MRT) in the first, second, and third hydration shells were 131.8, 6.46, and 2.67 ps, respectively. The complexes of octahydrate ([Ac(H2O)(8)](3+)) and nonahydrate ([Ac(H2O)(9)](3+)) were observed in the first hydration shell. The square antiprism (SA) geometry was adopted for octahydrate, while the gyroelongated square antiprism (GySA) geometry was adopted for nonahydrate. The simulations provided valuable insights into the ion-oxygen stretching frequencies. Specifically, the average stretching frequency for Ac3+ was found to be 404 cm(-1), which is in good agreement with the calculated value from the CCSD(T) calculation of 398.78 cm(-1). These findings indicate that including DKH2 relativistic approximation increases the accuracy of the simulation results and can contribute to understanding these actinide ions' behavior in aqueous environments, shedding light on hydrated systems' structural arrangements and dynamics.

关键词： Ac3+ DKH2 molecular dynamics QM/MM structure and dynamics

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Revisiting the structure and dynamics of hydrated Cd²⁺ in aqueous solutions: Insights from the RI-SCS-MP2/MM molecular dynamics simulation

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INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2023年第1期124卷 e27236-e27236页

作者： Prasetyo, Niko Kusuma, Alberto Krishna Ksatria Winning Iqbal, La Ode Muhammad Univ Gadjah Mada Fac Math & Nat Sci Dept Chem Yogyakarta Indonesia Univ Gadjah Mada Fac Math & Nat Sci Dept Chem Yogyakarta 55281 Indonesia

The spin component scale MP2/molecular mechanics molecular dynamics simulation investigated the hydration shell formation and hydrated Cd2+ dynamics in the water environment. At the first hydration shell, six water molecules with 2.27 & Aring;for the average distance between water and Cd2+. Dynamical properties were analyzed by computing the water molecule's mean residence time (MRT) in its first and second hydration shells. The MRT of each shell was determined to be 31.8 and 1.92 ps, suggesting the strong influence of Cd2+ in the first hydration shell. The second shell was labile, with an average number of water molecules being 18. Despite the strong interaction between Cd2+ and water molecules in the first shell, the influence of ions in the second hydration shell remained weak.

关键词： hydrated Cd2+ MP2 QM/MM MD simulation structure and dynamics

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structure and dynamics in Liquid Iron at High Pressure and Temperature. A First Principles Study

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JOURNAL OF GEOPHYSICAL RESEARCH-SOLID EARTH 2023年第2期128卷 e2022JB025119-e2022JB025119页

作者： Gonzalez, Luis E. Gonzalez, David J. Univ Valladolid Dept Fis Teor Valladolid Spain

We have studied the evolution of structural and dynamic properties of liquid Fe as a function of pressure for 11 thermodynamic states close to the melting line. The pressure range considered goes from ambient pressure to 323 GPa, and the study has been carried out by using the ab-initio molecular dynamics technique. The agreement between the calculated static structure and the available experimental data is very good, including details like an asymmetric second peak, which remains over most of the whole pressure range and suggests a significant local icosahedral short-range order in the liquid. The dynamical structure is studied through the characteristics of the propagating density fluctuations and the associated longitudinal and transverse particle currents. The transverse dispersion relations expose two branches of modes for all pressures, whose range of appearance is analyzed and put in connection with the double-peak structure of the Fourier spectra of velocity autocorrelation functions. We have also investigated the existence of fingerprints of transverse acoustic excitation modes in the dynamic structure factor for the high pressure states similar to those observed in the inelastic X-ray scattering intensity data of liquid Fe at ambient pressure. The calculated electronic density of states shows that with increasing pressure there is a widening of the conduction band along with a decreasing significance of spin polarization. Finally, we also report results for transport coefficients like self-diffusion, shear viscosity and adiabatic sound velocity, which are compared with the available experimental data.

关键词： liquid iron structure and dynamics transport properties first principles simulations

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structure and dynamics behavior during the glass transition of the polyisoprene in the presence of pressure: A molecular dynamics simulation

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POLYMER 2022年 238卷 124433-124433页

作者： Sun, Wei Wu, Haoyu Luo, Yanlong Li, Bin Mao, Lixin Zhao, Xiuying Zhang, Liqun Gao, Yangyang Beijing Univ Chem Technol State Key Lab Organ Inorgan Composites Beijing 10029 Peoples R China Beijing Univ Chem Technol Key Lab Beijing City Preparat & Proc Novel Polyme Beijing 10029 Peoples R China Nanjing Forestry Univ Coll Sci Nanjing 210037 Peoples R China Sun Yat Sen Univ Sch Chem Engn & Technol Zhuhai 519082 Peoples R China

The static and dynamics behavior of the cis-1,4-polyisoprene during the glass transition is closely related to its macroscopic property, which will be significantly affected by the external pressure. Therefore, here an all-atom molecular dynamics simulation is performed to systemically investigate the effect of the pressure (P = 1-2000 atm) on the glass transition temperature (T-g) for cis-1,4-polyisoprene, which is dependent on the static and dynamic properties. For the static property, the polymer density and the energy are considered. It is found that the polymer density, the non-bond energy and the torsional energy play an important role during the glass transition process. Meanwhile, the T-g obtained from the non-bond energy and the torsional energy is larger than that from the polymer density. For the dynamic property, the translational mobility, the bond reorientation mobility, the torsional dynamics and the dynamic heterogeneity on the chain backbone are analyzed. The mobility on the chain backbone decreases with increasing the pressure, which gradually increases the T-g. In addition, the T-g obtained from the dynamic heterogeneity is largest compared to those from the bond reorientation mobility, the torsional dynamics or the atom translational mobility. Especially, according to the mean-square fluctuations of the backbone atoms, the immobile atoms are distinguished. Then, the percolation probability of the immobile domain is analyzed, which is further characterized by the size of the largest immobile domain and the number of the immobile domains. By observing the snapshot of the mean-square fluctuations of atoms, the percolation transition of the immobile domains is clearly observed, which can help to understand the glass transition process under the different pressures.

关键词： structure and dynamics The glass transition Polyisoprene

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Comparing the MP2, DKH2-MP2 and SCAN Hybrid Forces Molecular dynamics Simulation on the structure and dynamics of Hydrated Ion Ba²⁺ in Aqueous Solution

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CHEMISTRYSELECT 2024年第31期9卷

作者： Prasetyo, Niko Anjani, Seruni Gita Kusuma, Alberto Krishna Ksatria Winning Iqbal, La Ode Muhamad Univ Gadjah Mada Fac Math & Nat Sci Dept Chem Yogyakarta 55281 Indonesia

The study investigated the structural and dynamical properties of hydrated ion Barium (Ba2+) in aqueous solution using quantum mechanical/molecular mechanical molecular dynamics simulations (QM/MM MD simulation). The primary objective was to assess the performance of the SCAN functional in describing the structure and dynamics of formed Ba(2+ )hydration shells in aqueous solution. The SCAN/MM MD simulation demonstrated the closest agreement with previously reported experimental data regarding the structural and dynamical properties of hydrated ion Ba2+. Specifically, the Ba2+ and surrounding water molecules distance was determined to be 2.79 & Aring;, with equal distribution of coordination numbers of 8 and 9 in the first hydration shell. Moreover, the stretching frequency of 232.21 cm(-1) closely matched the CCSD(T) results. The obtained results from SCAN/MM MD has a better agreement than results from MP2/MM and DKH2 MP2/MM molecular dynamics simulation. These findings underscore the potential of SCAN/MM MD simulation as a promising method for investigating the structural and dynamical properties of hydrated ions.

关键词： SCAN/MM MD Ba2+ structure and dynamics Molecular dynamics simulation

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Influence of flow on the structure and dynamics of clusters in complex plasma systems

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CONTRIBUTIONS TO PLASMA PHYSICS 2020年第4期60卷 e201900190-e201900190页

作者： Liu, Y. Zhu, X. Wang, Y. Chen, Z. Huang, F. China Agr Univ Coll Sci Beijing 100083 Peoples R China Beijing Univ Chem Technol Dept Phys Beijing Peoples R China China Agr Univ Coll Informat & Elect Engn Beijing Peoples R China

The influence of flow with different strengths, positions, and widths on the structure and dynamics of clusters is studied by two-dimensional (2D) Langevin molecular dynamics simulations. The particles are confined by a quadratic confining potential. The horizontal position of the system centre, average inter-particle distance, and coupling parameter are calculated to characterize the effect of changing the strength, position, and width of the flow on the cluster structure. The trajectories, the velocity autocorrelation function, and the mean square displacement are obtained to further uncover the dynamic properties of the 2D dusty plasma system.

关键词： dusty plasma flow simulation structure and dynamics

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Study of the structure and dynamics at various parts of the antibacterial drug molecule cefpodoxime proxetil

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SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021年 115卷 101752-101752页

作者： Dey, Krishna Kishor Ghosh, Manasi Dr Harisingh Gour Cent Univ Dept Phys Sagar 470003 Madhya Pradesh India Banaras Hindu Univ Phys Sect MMV Varanasi 221005 Uttar Pradesh India

The structure and dynamics of cefpodoxime proxetil are elucidated by measuring chemical shift anisotropy (CSA) tensor, spin-lattice relaxation time, and local correlation time a twenty-one crystallographically different C-13 nuclei sites. The principal components of CSA tensor of cefpodoxime proxetil are extracted by the two-dimensional phase adjusted sinning sideband (2DPASS) cross-polarization magic angle spinning (CP-MAS) solid-state NMR experiment, and the spin-lattice relaxation time is measured by the method outlined by Torchia(T1CP). The local correlation time is calculated by bearing in mind that the spin-lattice relaxation mechanism of C-13 nuclei is mainly governed by the CSA interaction and the heteronuclear dipole-dipole interaction. The aminothiazole ring, beta-lactam ring, and dihydrothiazine ring provide stability to the drug molecule and increase the affinity of the drug to penicillin-binding proteins (PBPs) receptors. The principal components of CSA parameters, spin-lattice relaxation time, and local correlation time vary substantially for carbon nuclei residing on these three rings. These signify that not only the electronic environment, but the molecular conformation, and the local dynamics are also altered within the ring. The substitution of the acyl side chain, oxime group, and the aminothiazole ring at the C7 position of the beta-lactam ring enhances the antibacterial activity and the binding affinity of the drug. A huge variation of the spin-lattice relaxation time and local correlation time is observed in those regions. The change in the electron charge distribution and nuclear spin dynamics at different parts of the drug molecule is clear by CSA and spin-lattice relaxation measurements, which will enrich the field "NMR crystallography".

关键词： Solid state NMR CSA tensor Spin-lattice relaxation time Molecular correlation time structure and dynamics

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Molecular-level insights into structure and dynamics in ionic liquids and polymer gel electrolytes

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JOURNAL OF MOLECULAR LIQUIDS 2021年 329卷 115454-115454页

作者： Garaga, Mounesha N. Jayakody, Nishani Fraenza, Carla C. Itin, Boris Greenbaum, Steven CUNY Dept Phys & Astron Hunter Coll New York NY 10065 USA New York Struct Biol Ctr New York NY 10027 USA

Designing new electrolytes requires a better understanding of the correlation between their transport properties and their molecular structure. In this work, we present a detailed study of ionic liquids and polymer gel electrolytes probing their structure and dynamics by nuclear magnetic resonance (NMR) spectroscopy. In particular, ammonium- and phosphonium-based ionic liquids (ILs) are combined with different LiTFSI concentrations, and then with different ratios of poly(methylmethacrylate) polymer. The temperature dependence of self-diffusion coefficients of mobile species, DLi+, DTFSI- and DP4441+ or DN4441+, measured by pulsed field gradient (PFG) NMR spectroscopy obeys the Arrhenius equation. Diffusivity of [P4441][TFSI] ILs is found to be greater than those of the [N4441][TFSI] ILs in both liquid and gel electrolytes. Solid state NMR experiments including C-13 and F-19 MAS, C-13{F-19},C-13{H-1} CPMAS probe the local structure and molecular-level interactions between ions and polymer in gel electrolytes, particularly for samples with higher PMMA content (>= 25 wt%). Finally, the fast field cycling relaxometry has been used to unveil the rotational and translational dynamics of P4441(+) or N4441(+) and TFSI- by measuring H-1 and (FR1)-F-19 relaxation rate profiles at different temperatures. A comprehensive NMR analysis including relaxation studies at low magnetic field provides decisive new insights regarding the formation of ionic clusters and the interaction of ions with the polymer chain in the case of the gel electrolytes. (C) 2021 Elsevier B.V. All rights reserved.

关键词： Ionic liquids Polymer gel electrolytes PFG NMR structure and dynamics Solid state NMR Fast field cycling relaxometry

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Preface to the special issue on structure and dynamics of the Longmenshan fault zone

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JOURNAL OF ASIAN EARTH SCIENCES 2020年 200卷 104474-104474页

作者： Xu, Xiwei Lei, Jianshe China Earthquake Adm Key Lab Crustal Dynam Inst Crustal Dynam Beijing 100085 Peoples R China

• structure and dynamics of LMSFZ are investigated by various approaches. • Mechanisms of Wenchuan, Lushan and Jiuzhaigou earthquakes are further revealed. • The results are of significance to understand the evolution... 详细信息

关键词： Longmenshan fault zone Wenchuan earthquake structure and dynamics

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Static structure, collective dynamics and transport coefficients in the liquid Li-Pb alloy. An ab initio molecular dynamics study

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JOURNAL OF MOLECULAR LIQUIDS 2021年 344卷 117775-117775页

作者： Alemany, M. M. G. Souto-Casares, Jaime Gonzalez, Luis E. Gonzalez, David J. Univ Santiago de Compostela Fac Fis Dept Fis Particulas Area Fis Mat Condensada E-15706 Santiago De Compostela Spain Univ Valladolid Fac Ciencias Dept Fis Teor Atom & Opt E-47011 Valladolid Spain

Several static and dynamic properties of the liquid Li-Pb alloy at diverse compositions, have been calculated by means of ab initio molecular dynamics simulation study. This alloy has attracted much attention because of the finding of fast sound at the U0.80Pb0.20 composition and also the technological interest of the the eutectic composition, Li0.17Pb0.83, as a component of the blanket in fusion reactors. Results are reported for total static structure factors, which are compared with the available experimental data. An additional analysis of the structure allows the quantification of the heterocoordinating tendencies in this alloy, which at the Li0.80Pb0.20 composition are largest and lead to a Pb-centered polyhedral structure, where, however, Li4Pb units are not present. Regarding the collective dynamics, the calculated partial dynamic structure factors exhibit side peaks indicative of propagating density fluctuations, including density fluctuation modes with phase velocity greater than the hydrodynamic sound velocity. Also, the longitudinal and transverse dispersion relations have been calculated and its different branches analysed. We find all the high frequency branches to behave as optic-like modes, contrary to other interpretations in terms of an acoustic-like fast sound mode. Some transport coefficients such as self- and inter-diffusion coefficients, shear viscosities and adiabatic sound velocities, have also been calculated. Finally, the obtained results for the electronic density of states clearly indicate the metallic character of the liquid LixPb1-x alloy. (C) 2021 The Authors. Published by Elsevier B.V.

关键词： Liquid Li-Pb alloy structure and dynamics Ab initio simulations

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