scholarly journals Molecular Dynamics Modellization and Simulation of Water Diffusion through Plant Cutin

1999 ◽  
Vol 54 (11) ◽  
pp. 896-902 ◽  
Author(s):  
Antonio Matas ◽  
Antonio Heredia
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Structural Information ◽  
Md Simulations ◽  
Water Molecules ◽  
Plant Cuticle ◽  
X Ray Diffraction ◽  
Cross Link ◽  
X Ray ◽  
Good Agreement

Abstract A theoretical molecular modelling study has been conducted for cutin, the biopolyester that forms the main structural component of the plant cuticle. Molecular dynamics (MD) simulations, extended over several ten picoseconds, suggests that cutin is a moderately flexible netting with motional constraints mainly located at the cross-link sites of functional ester groups. This study also gives structural information essentially in accordance with previously reported experimental data, obtained from X -ray diffraction and nuclear magnetic resonance experiments. MD calculations were also performed to simulate the diffusion of water mole­cules through the cutin biopolymer. The theoretical analysis gives evidence that water perme­ation proceedes by a “hopping mechanism”. Coefficients for the diffusion of the water molecules in cutin were obtained from their mean-square displacements yielding values in good agreement with experimental data.

A Comparative X-Ray Diffraction Study of Aqueous MnSO4 and Crystals of MnSO4·5H2O

1982 ◽  
Vol 37 (6) ◽  
pp. 581-586 ◽  
Author(s):  
R. Caminiti ◽  
G. Marongiu ◽  
G. Paschina
Keyword(s):  
Crystal Structure ◽  
Experimental Data ◽  
Single Crystal ◽  
Diffraction Study ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Scattering ◽  
Good Agreement ◽  
Single Crystal Analysis

Abstract X-ray single crystal analysis of MnSO4·5H2O shows that the manganese atoms are octahedrally coordinated by oxygen atoms, four of which belong to water molecules and two to sulphate groups. A model derived from the crystal structure was fitted to the X-ray scattering intensities from aqueous MnSO4. Good agreement with experimental data is achieved using a model in which Mn(H2O)6-z(OSO3)z+2-2z interacts with about ten water molecules and each sulphate ion with about seven water molecules.

X-Ray Diffraction Study of a Concentrated Al(NO3 )3 Solution

1980 ◽  
Vol 35 (12) ◽  
pp. 1368-1372 ◽  
Author(s):  
R. Caminiti ◽  
T. Radnai
Keyword(s):  
Experimental Data ◽  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Nearest Neighbors ◽  
Water Molecules ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Weak Hydrogen Bonds ◽  
Good Agreement

Abstract The scattering of X-rays from a concentrated Al (NO3)3 aqueous solution has been measured and analyzed at 25 °C. Good agreement with experimental data is achieved through a model in which Al3+(H2O)6 interacts with twelve water molecules through short and linear H-bonds. The water molecules which are the nearest neighbors to the Al3+ ions have trigonal orientation and each 0 atom in the nitrate ion gives rise to about 2 weak hydrogen bonds with water molecules.

XRD Studies of Cement Embedding Matrices Containing Complexing Reagents From Decontamination Practices

2013 ◽  
Author(s):  
L. Ionascu ◽  
M. Nicu ◽  
C. Turcanu ◽  
F. Dragolici ◽  
Ghe. Rotarescu
Keyword(s):  
Experimental Data ◽  
Structural Investigation ◽  
Structural Information ◽  
Complexing Agents ◽  
X Ray Diffraction ◽  
X Ray ◽  
Safety Requirements ◽  
The Matrix ◽  
Radiological Safety ◽  
Xrd Studies

The study of embedding matrix of radioactive waste is an important issue concerning the need to assure the radiological safety requirements for final disposal. The conditioning of the radioactive wastes by cementation process involves also a structural investigation by X-ray diffraction (XRD) of the samples prepared with cement and complexing agents at different concentration. This paper gives useful information about the influence of complexing agents related to damages produced in concrete microstructures. The experimental data obtained on samples kept in real repository environment for a period up to 15 years, offer structural information regarding the interaction between the different decontamination agents with the major components of the matrix.

scholarly journals Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

2019 ◽  
Author(s):  
David C. Wych ◽  
James S. Fraser ◽  
David L. Mobley ◽  
Michael E. Wall
Keyword(s):  
Molecular Dynamics ◽  
Rigid Body ◽  
Diffraction Data ◽  
Md Simulations ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atom Pairs ◽  
Collective Motions ◽  
Rigid Body Motions ◽  
Insight Into

AbstractTo gain insight into crystalline protein dynamics, we performed molecular-dynamics (MD) simulations of a periodic 2×2×2 supercell of staphylococcal nuclease. We used the resulting MD trajectories to simulate X-ray diffraction and to study collective motions. The agreement of simulated X-ray diffraction with the data is comparable to previous MD simulation studies. We studied collective motions by analyzing statistically the covariance of alpha-carbon position displacements. The covariance decreases exponentially with the distance between atoms, which is consistent with a liquid-like motions (LLM) model, in which the protein behaves like a soft material. To gain finer insight into the collective motions, we examined the covariance behavior within a protein molecule (intra-protein) and between different protein molecules (inter-protein). The inter-protein atom pairs, which dominate the overall statistics, exhibit LLM behavior; however, the intra-protein pairs exhibit behavior that is consistent with a superposition of LLM and rigid-body motions (RBM). Our results indicate that LLM behavior of global dynamics is present in MD simulations of a protein crystal. They also show that RBM behavior is detectable in the simulations but that it is subsumed by the LLM behavior. Finally the results provide clues about how correlated motions of atom pairs both within and across proteins might manifest in diffraction data. Overall our findings increase our understanding of the connection between molecular motions and diffraction data, and therefore advance efforts to extract information about functionally important motions from crystallography experiments.

Hydration Phenomena in a Concentrated Aqueous Solution of Ce(NO3)3. X-ray Diffraction and Raman Spectroscopy

1983 ◽  
Vol 38 (5) ◽  
pp. 533-539 ◽  
Author(s):  
R. Caminiti ◽  
P. Cucca ◽  
A. D′Andrea
Keyword(s):  
Experimental Data ◽  
Aqueous Solution ◽  
Raman Spectroscopy ◽  
Correlation Function ◽  
Hydration Shell ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Experimental Correlation ◽  
Good Agreement

The scattering of X-rays from a concentrated Ce(NO3)3 aqueous solution has been measured and analyzed. The experimental correlation function appears to be mainly characterized by the hydration of the cation: peaks at about 2.55 and 4.65 Å. Good agreement with experimental data is achieved through a model in which the Ce(III) ions have a first and a second hydration shell and also the nitrate group is considered hydrated. Complex formation between cation and anion is confirmed by using Raman spectroscopy.

Identification of a deleterious phase in photocatalyst based on Cd1 − xZnxS/Zn(OH)2by simulated XRD patterns

2017 ◽  
Vol 73 (3) ◽  
pp. 360-368 ◽  
Author(s):  
Svetlana Cherepanova ◽  
Dina Markovskaya ◽  
Ekaterina Kozlova
Keyword(s):  
Experimental Data ◽  
Thermogravimetric Analysis ◽  
Variable Temperature ◽  
Interlayer Distance ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Xrd Pattern ◽  
X Ray ◽  
Diffraction Peaks ◽  
Xrd Patterns

The X-ray diffraction (XRD) pattern of a deleterious phase in the photocatalyst based on Cd1 − xZnxS/Zn(OH)2contains two relatively intense asymmetric peaks withd-spacings of 2.72 and 1.56 Å. Very small diffraction peaks with interplanar distances of (d) ≃ 8.01, 5.40, 4.09, 3.15, 2.49 and 1.35 Å are characteristic of this phase but not always observed. To identify this phase, the XRD patterns for sheet-like hydroxide β-Zn(OH)2and sheet-like hydrozincite Zn5(CO3)2(OH)6as well as for turbostratic hydrozincite were simulated. It is shown that the XRD pattern calculated on the basis of the last model gives the best correspondence with experimental data. Distances between layers in the turbostratically disordered hydrozincite fluctuate aroundd≃ 8.01 Å. This average layer-to-layer distance is significantly higher than the interlayer distance 6.77 Å in the ordered Zn5(CO3)2(OH)6probably due to a deficiency of CO32−anions, excess OH−and the presence of water molecules in the interlayers. It is shown by variable-temperature XRD and thermogravimetric analysis (TGA) that the nanocrystalline turbostratic nonstoichiometric hydrozincite-like phase is quite thermostable. It decomposes into ZnO in air above 473 K.

scholarly journals Spontaneous self-assembly and structure of perfluoroalkylalkane surfactant hemimicelles by molecular dynamics simulations

2019 ◽  
Vol 116 (30) ◽  
pp. 14868-14873 ◽  
Author(s):  
Gonçalo M. C. Silva ◽  
Pedro Morgado ◽  
Pedro Lourenço ◽  
Michel Goldmann ◽  
Eduardo J. M. Filipe
Keyword(s):  
Molecular Dynamics ◽  
Self Assembly ◽  
Md Simulation ◽  
Grazing Incidence ◽  
Md Simulations ◽  
X Ray Diffraction ◽  
X Ray ◽  
Spontaneous Formation ◽  
Rational Explanation ◽  
Dynamics Simulations

Fully atomistic molecular-dynamics (MD) simulations of perfluoroalkylalkane molecules at the surface of water show the spontaneous formation of aggregates whose size and topography closely resemble the experimentally observed hemimicelles for this system. Furthermore, the grazing incidence X-ray diffraction (GIXD) pattern calculated from the simulation trajectories reproduces the experimental GIXD spectra previously obtained, fully validating the MD simulation results. The detailed analysis of the internal structure of the aggregates obtained by the MD simulations supports a definite rational explanation for the spontaneous formation, stability, size, and shape of perfluoroalkylalkane hemimicelles at the surface of water.

scholarly journals On the Structure in Aqueous Superconcentrated Calcium Nitrate

1981 ◽  
Vol 36 (8) ◽  
pp. 831-835 ◽  
Author(s):  
R. Caminiti ◽  
A. Musinu ◽  
G. Paschina ◽  
G. Piccaluga ◽  
G. Pinna
Keyword(s):  
Experimental Data ◽  
Calcium Ions ◽  
Calcium Nitrate ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
Crystalline Hydrates ◽  
Oxygen Atoms

Abstract Liquid hydrous calcium nitrate of composition Ca(NO3)2 · 3.5 H2O was investigated by X-ray diffraction. Experimental data were interpreted in terms of geometrical models suggested by the structure of the crystalline hydrates Ca (NO3)2 · 3H2O and Ca(NO3)2 · 4H2O, in which calcium ions are coordinated to nine oxygen atoms, partly coming from water molecules, partly from NO3-ions.

X-Ray Diffraction and Sims Studies of Mbe Grown Doping Superlattices in Silicon

1987 ◽  
Vol 102 ◽  
Author(s):  
G T Brown ◽  
S J Barnett ◽  
G W Blackmore ◽  
S J Courtney ◽  
D C Houghton
Keyword(s):  
Experimental Data ◽  
Reasonable Agreement ◽  
Simulated Data ◽  
Dopant Distribution ◽  
X Ray Diffraction ◽  
Double Crystal ◽  
X Ray ◽  
B Doping ◽  
Good Agreement ◽  
Superlattice Period

ABSTRACTSi-Si(B) doping superlattices (pipi structures) were grown by MBE and studied using double crystal x-ray diffraction and SIMS. Detailed analysis of the complex x-ray rocking curves required comparison of experimental data with theoretically simulated data. It is demonstrated that this technique is sensitive to irregularities in the dopant composition, dopant distribution and superlattice period. The B concentration profile is shown to spread well into the intrinsic layers and the extent and magnitude of the dopant distribution has been quantified. A comparison of this data with SIMS showed good agreement for the distribution of B and reasonable agreement for the peak values of B concentration.

scholarly journals Interpreting Disordered PXRD Structures using Molecular Dynamics

2014 ◽  
Vol 70 (a1) ◽  
pp. C1569-C1569
Author(s):  
Kristoffer Johansson ◽  
Xiaozhou Li ◽  
Andrew Bond ◽  
Jacco van de Streek
Keyword(s):  
Molecular Dynamics ◽  
Structural Information ◽  
Supplementary Information ◽  
Rational Approach ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
X Ray Diffraction ◽  
X Ray ◽  
Crystal Properties ◽  
Solid Form

A central topic in the formulation of solid medicinal products is the identification of a suitable solid form of an active compound to obtain optimal physicochemical properties. To this end, disorder may be important for relevant crystal properties like stability. For example, disorder may account for more than 10% of the crystal volume. A rational approach to solid-form selection is typically based on structural information at atomic resolution. In practice, pharmaceutical compounds are not always well-behaved and especially in the study of polymorphs or compounds with flexible groups it can be challenging to obtain crystals suitable for single-crystal X-ray diffraction. Powder X-ray diffraction (PXRD) is a popular alternative, but it generally requires supplementary information like molecular connectivity in simple cases or computational models to solve larger structures. Computational modeling has come a long way and accurate and reliable structures of pharmaceutically relevant compounds can indeed be obtained using laboratory PXRD measurements and quantum-mechanical calculations [1]. The major limitation of quantum mechanical calculations, however, is that they do not consider time nor temperature but only static structures at zero temperature. Thus, these methods cannot model phenomena related to disorder. The molecular dynamics (MD) method can add temperature as well as time and spatial resolution to a model and has in recent years developed to be a scalable, reliable and increasingly available technique. As more and more groups from academia as well as industry employ MD in their work, the development will increase to gain momentum in the coming years. We use MD in a high-performance setting to study crystal properties that are relevant for pharmaceutical research. Using a combination of models from first principles and MD we are able to study highly disordered structures and polymorphs on the basis of PXRD data.

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