Crystal Water Dynamics of Guanosine Dihydrate:  Analysis of Atomic Displacement Parameters, Time Profile of Hydrogen-Bonding Probability, and Translocation of Water by MD Simulation

2005 ◽  
Vol 109 (3) ◽  
pp. 1304-1312 ◽  
Author(s):  
Shigetaka Yoneda ◽  
Yoko Sugawara ◽  
Hisako Urabe
Keyword(s):  
Hydrogen Bonding ◽  
Md Simulation ◽  
Atomic Displacement ◽  
Time Profile ◽  
Water Dynamics ◽  
Crystal Water ◽  
Atomic Displacement Parameters

scholarly journals Molecular Dynamics Investigation of Phenolic Oxidative Coupling Protein Hyp-1 Derived from Hypericum perforatum

Crystals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 43
Author(s):  
Joanna Smietanska ◽  
Tomasz Kozik ◽  
Radoslaw Strzalka ◽  
Ireneusz Buganski ◽  
Janusz Wolny
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Hypericum Perforatum ◽  
Structural Model ◽  
Md Simulations ◽  
Atomic Displacement ◽  
Experimental Models ◽  
Coupling Protein ◽  
Atomic Displacement Parameters ◽  
Chain Conformations

Molecular dynamics (MD) simulations provide a physics-based approach to understanding protein structure and dynamics. Here, we used this intriguing tool to validate the experimental structural model of Hyp-1, a pathogenesis-related class 10 (PR-10) protein from the medicinal herb Hypericum perforatum, with potential application in various pharmaceutical therapies. A nanosecond MD simulation using the all-atom optimized potentials for liquid simulations (OPLS–AA) force field was performed to reveal that experimental atomic displacement parameters (ADPs) underestimate their values calculated from the simulation. The average structure factors obtained from the simulation confirmed to some extent the relatively high compliance of experimental and simulated Hyp-1 models. We found, however, many outliers between the experimental and simulated side-chain conformations within the Hyp-1 model, which prompted us to propose more reasonable energetically preferred rotameric forms. Therefore, we confirmed that MD simulation may be applicable for the verification of refined, experimental models and the explanation of their structural intricacies.

scholarly journals Crystal Structure of Moganite and Its Anisotropic Atomic Displacement Parameters Determined by Synchrotron X-ray Diffraction and X-ray/Neutron Pair Distribution Function Analyses

Minerals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 272
Author(s):  
Seungyeol Lee ◽  
Huifang Xu ◽  
Hongwu Xu ◽  
Joerg Neuefeind
Keyword(s):  
Crystal Structure ◽  
Distribution Function ◽  
Single Crystal ◽  
Pair Distribution Function ◽  
Atomic Displacement ◽  
Single Crystal Xrd ◽  
X Ray Diffraction ◽  
X Ray ◽  
Neutron Pair ◽  
Atomic Displacement Parameters

The crystal structure of moganite from the Mogán formation on Gran Canaria has been re-investigated using high-resolution synchrotron X-ray diffraction (XRD) and X-ray/neutron pair distribution function (PDF) analyses. Our study for the first time reports the anisotropic atomic displacement parameters (ADPs) of a natural moganite. Rietveld analysis of synchrotron XRD data determined the crystal structure of moganite with the space group I2/a. The refined unit-cell parameters are a = 8.7363(8), b = 4.8688(5), c = 10.7203(9) Å, and β = 90.212(4)°. The ADPs of Si and O in moganite were obtained from X-ray and neutron PDF analyses. The shapes and orientations of the anisotropic ellipsoids determined from X-ray and neutron measurements are similar. The anisotropic ellipsoids for O extend along planes perpendicular to the Si-Si axis of corner-sharing SiO4 tetrahedra, suggesting precession-like movement. Neutron PDF result confirms the occurrence of OH over some of the tetrahedral sites. We postulate that moganite nanomineral is stable with respect to quartz in hypersaline water. The ADPs of moganite show a similar trend as those of quartz determined by single-crystal XRD. In short, the combined methods can provide high-quality structural parameters of moganite nanomineral, including its ADPs and extra OH position at the surface. This approach can be used as an alternative means for solving the structures of crystals that are not large enough for single-crystal XRD measurements, such as fine-grained and nanocrystalline minerals formed in various geological environments.

scholarly journals Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters

2021 ◽  
Vol 8 (4) ◽  
pp. 044701
Author(s):  
Zhen Su ◽  
Medhanjali Dasgupta ◽  
Frédéric Poitevin ◽  
Irimpan I. Mathews ◽  
Henry van den Bedem ◽  
...  
Keyword(s):  
Diffuse Scattering ◽  
Atomic Displacement ◽  
Potential Utility ◽  
X Ray ◽  
Protein X ◽  
Atomic Displacement Parameters

Incommensurate modulation of calcium barium niobate (CBN28 and Ce:CBN28)

2012 ◽  
Vol 68 (2) ◽  
pp. 101-106 ◽  
Author(s):  
Heribert A. Graetsch ◽  
Chandra Shekhar Pandey ◽  
Jürgen Schreuer ◽  
Manfred Burianek ◽  
Manfred Mühlberg
Keyword(s):  
Crystal Structures ◽  
Tungsten Bronze ◽  
Atomic Displacement ◽  
Type Structure ◽  
Formula Unit ◽  
Tetragonal Tungsten Bronze ◽  
First Order ◽  
Oxygen Coordination ◽  
Incommensurate Modulation ◽  
Atomic Displacement Parameters

The incommensurately modulated crystal structures of Ca0.28Ba0.72Nb2O6 (CBN28) and Ce0.02Ca0.25Ba0.72Nb2O6 (Ce:CBN28) were refined in the supercentred setting X4bm(AA0,−AA0) of the 3 + 2-dimensional superspace group P4bm(aa½,−aa½). Both compounds are isostructural with a tetragonal tungsten bronze-type structure. The modulation of CBN28 consists of a wavy distribution of Ba and Ca atoms as well as vacancies on the incompletely occupied Me2 site with 15-fold oxygen coordination. The occupational modulation is coupled with a modulation of the atomic displacement parameters and a very weak modulation of the positional parameters of Me2. The surrounding O atoms show strong displacive modulations with amplitudes up to ca 0.2 Å owing to the cooperative tilting of the rigid NbO6 octahedra. The Me1 site with 12-fold coordination and Nb atoms are hardly affected by the modulations. Only first-order satellites were observed and the modulations are described by first-order harmonics. In Ce:CBN28 cerium appears to be located on both the Me2 and Me1 sites. Wavevectors and structural modulations are only weakly modified upon substitutional incorporation of 0.02 cerium per formula unit of calcium.

scholarly journals Structural analysis and multipole modelling of quercetin monohydrate – a quantitative and comparative study

2010 ◽  
Vol 67 (1) ◽  
pp. 63-78 ◽  
Author(s):  
Sławomir Domagała ◽  
Parthapratim Munshi ◽  
Maqsood Ahmed ◽  
Benoît Guillot ◽  
Christian Jelsch
Keyword(s):  
Comparative Study ◽  
Charge Density ◽  
Topological Analysis ◽  
Atomic Displacement ◽  
X Ray Diffraction ◽  
Experimental Database ◽  
Figures Of Merit ◽  
Atom Model ◽  
Atomic Displacement Parameters ◽  
Model Approach

The multipolar atom model, constructed by transferring the charge-density parameters from an experimental or theoretical database, is considered to be an easy replacement of the widely used independent atom model. The present study on a new crystal structure of quercetin monohydrate [2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-4H-chromen-4-one monohydrate], a plant flavonoid, determined by X-ray diffraction, demonstrates that the transferred multipolar atom model approach greatly improves several factors: the accuracy of atomic positions and the magnitudes of atomic displacement parameters, the residual electron densities and the crystallographic figures of merit. The charge-density features, topological analysis and electrostatic interaction energies obtained from the multipole models based on experimental database transfer and periodic quantum mechanical calculations are found to compare well. This quantitative and comparative study shows that in the absence of high-resolution diffraction data, the database transfer approach can be applied to the multipolar electron density features very accurately.

Investigation of Interatomic Potential on Chip Formation Mechanism in Nanometric Cutting Using MD Simulation

2011 ◽  
Vol 312-315 ◽  
pp. 983-988
Author(s):  
Seyed Vahid Hosseini ◽  
Mehrdad Vahdati ◽  
Ali Shokuhfar
Keyword(s):  
Single Crystal ◽  
Formation Mechanism ◽  
Chip Formation ◽  
Morse Potential ◽  
Md Simulation ◽  
Atomic Displacement ◽  
Cutting Process ◽  
Machining Process ◽  
Chip Formation Mechanism ◽  
Eam Potential

Nowadays, the nano-machining process is used to produce high quality finished surfaces with precise form accuracy. To understand and analyze the chip formation mechanism of nano-machining process on an atomistic scale, since the experimentation is not an easy task, numerical simulation such as molecular dynamic (MD) simulation is a very useful method. In this paper, MD simulation of the nano-metric cutting of single-crystal copper was performed with a single crystal diamond tool. The model was solved with both pair wise Morse potential function and embedded atom method (EAM) potential to simulate the inter-atomic force between the work-piece and a rigid tool. The chip formation mechanism, dislocation generation, tool forces and generated temperature were investigated. Results show that the Morse potential cannot perform an appropriate defect formation and plastic deformation in nano-metric cutting of metals. Also, tool forces in Morse potential are more than the forces in EAM potential. Furthermore, the fluctuations of resultant forces in Morse potential are greater than that of EAM. In addition, using many-body interaction potentials like EAM can lead to substantial changes in surface energies, elastic-plastic properties and atomic displacement, compared with the pair-wise potentials like Morse. Finally, the atomic displacement investigation shows that in EAM potential study, only the atoms in a local region near the cutting process are displaced, but in Morse potential a large portion of atoms has affected during cutting process. Subsequently, the chip temperature in EAM potential is more than that of Morse potential.

scholarly journals Non-metamict betafite from Le Carcarelle (Vico volcanic complex, Italy): occurrence and crystal structure

2004 ◽  
Vol 68 (6) ◽  
pp. 939-950 ◽  
Author(s):  
F. Cámara ◽  
C. T. Williams ◽  
G. Della Ventura ◽  
R. Oberti ◽  
E. Caprilli
Keyword(s):  
Structure Refinement ◽  
Atomic Displacement ◽  
Campi Flegrei ◽  
Volcanic Complex ◽  
Crystal Chemical Formula ◽  
Static Disorder ◽  
Pyrochlore Group ◽  
Atomic Displacement Parameters ◽  
Miarolitic Cavities ◽  
Ti Content

AbstractNon-metamict betafite, a pyrochlore-group mineral with general formula A2−mB2XO6Y(O,OH,F)1−n·pH2O and 2 Ti > Nb+Ta and U > 20% at the A site, has been found at Le Carcarelle, (Latium, Italy). It occurs within miarolitic cavities of a foid-bearing syenitic ejectum enclosed within the pyroclastic formation known as “ignimbrite C”, which belongs to the main effusive phase of the Vico volcanic complex. The host rock is composed of K-feldspar, biotite, augitic clinopyroxene, magnetite and minor sodalite. Electron microprobe analyses gave the following crystal-chemical formula: (Ca1.24Na0.17U0.49REE0.03)Σ=1.93 (Ti1.05Nb0.76Zr0.14Fe0.04Ta0.01)Σ=2.00O6(O,OH). Compared with other occurrences reported in the mineralogical literature, betafite from Le Carcarelle is extremely enriched in U and depleted in Th. Due to its young age of formation (∼150 k.y.), this betafite sample is highly crystalline, thus allowing structure refinement of unheated material. Betafite from Le Carcarelle is cubic Fd3̅m, with a = 10.2637(13) Å, and V = 1081.21(35) Å3, and has a smaller A site (consistent with the higher U content), and a larger and more distorted B site (consistent with the higher Ti content) than calciobetafite from Campi Flegrei, Italy (Mazzi and Munno, 1983). Analysis of the atomic displacement parameters provides evidence for static disorder at the X site.

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