scholarly journals Inclusion complexes of β-cyclodextrin with tricyclic drugs: an X-ray diffraction, NMR and molecular dynamics study

2017 ◽  
Vol 13 ◽  
pp. 714-719 ◽  
Author(s):  
Franca Castiglione ◽  
Fabio Ganazzoli ◽  
Luciana Malpezzi ◽  
Andrea Mele ◽  
Walter Panzeri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Inclusion Complexes ◽  
Water Solution ◽  
Md Simulations ◽  
Conformational Transitions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Fused Ring ◽  
Explicit Water

Tricyclic fused-ring cyclobenzaprine (1) and amitriptyline (2) form 1:1 inclusion complexes with β-cyclodextrin (β-CD) in the solid state and in water solution. Rotating frame NOE experiments (ROESY) showed the same geometry of inclusion for both 1/β-CD and 2/β-CD complexes, with the aromatic ring system entering the cavity from the large rim of the cyclodextrin and the alkylammonium chain protruding out of the cavity and facing the secondary OH rim. These features matched those found in the molecular dynamics (MD) simulations in solution and in the solid state from single-crystal X-ray diffraction of 1/β-CD and 2/β-CD complexes. The latter complex was found in a single conformation in the solid state, whilst the MD simulations in explicit water reproduced the conformational transitions observed experimentally for the free molecule.

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.

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.

Study of Molecular Dynamics and the Solid State Phase Transition Mechanism for Unsymmetrical Thiopyrophosphate Using X-ray Diffraction, DFT Calculations and NMR Spectroscopy

2006 ◽  
Vol 110 (2) ◽  
pp. 761-771 ◽  
Author(s):  
Marek J. Potrzebowski ◽  
Grzegorz D. Bujacz ◽  
Anna Bujacz ◽  
Sebastian Olejniczak ◽  
Paweł Napora ◽  
...  
Keyword(s):  
Phase Transition ◽  
Molecular Dynamics ◽  
Solid State ◽  
Nmr Spectroscopy ◽  
Dft Calculations ◽  
X Ray Diffraction ◽  
X Ray ◽  
Transition Mechanism

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.

EM observation on poly(β-alanine) crystal formed by the thermal solid State polymerization

1990 ◽  
Vol 48 (4) ◽  
pp. 858-859
Author(s):  
Hirokazu Kimura ◽  
Hiroshi Sakabe ◽  
Hitoshi Morita ◽  
Takashi Itoh ◽  
Takashi Konishi
Keyword(s):  
Electron Microscopy ◽  
Solid State ◽  
Single Crystal ◽  
Single Crystals ◽  
Water Solution ◽  
Aminocaproic Acid ◽  
X Ray Diffraction ◽  
X Ray ◽  
Transmission Electron ◽  
Solid State Polymerization

It is well known that several ω-amino acids are polymerized in the solid state. A single crystal of ε-aminocaproic acid has been reported to be polymerized in the solid state to be the biaxially oriented nylon 6. We also reported in the previous paper that the thermal solid state polymerization of glycine single crystal produced poly(glycine-I) crystal.In this paper,structure of poly(β-alanine) polymerized in the solid state is investigated by means of scanning electron microscopy (SEM).transmission electron microscopy (TEM) and X-ray diffraction.Commercial β-alanine (Nakarai Tesque,Inc.,Kyoto) was recrystallized three times from the distilled-water solution (lg/ml) at 80°C. The single crystal continued to grow gradually during 24 hr. The obtained single crystals with rhombic habit had clear cleavage planes. These single crystals about 10 mm in size were used as the original specimens. The polymerization procedure was carried out on the single crystals at temperatures between 140 and 170°C in an evacuated and subsequently sealed tube.

Effect of water on the structure of a prototype ionic liquid

2016 ◽  
Vol 18 (34) ◽  
pp. 23474-23481 ◽  
Author(s):  
Oleg Borodin ◽  
David L. Price ◽  
Bachir Aoun ◽  
Miguel A. González ◽  
Justin B. Hooper ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Md Simulations ◽  
High Energy ◽  
X Ray Diffraction ◽  
X Ray ◽  
Effect Of Water ◽  
Influence Of Water

The influence of water on the structure of a prototype ionic liquid (IL) 1-octyl-3-methylimidazolium tetrafluoroborate (C8mimBF4) is examined in the IL-rich regime using high-energy X-ray diffraction (HEXRD) and molecular dynamics (MD) simulations.

Dynamics of Chloromethanes in Cryptophane-E Inclusion Complexes:  A2H Solid-State NMR and X-ray Diffraction Study

2005 ◽  
Vol 109 (20) ◽  
pp. 4442-4451 ◽  
Author(s):  
Oleg Petrov ◽  
Zdeněk Tošner ◽  
Ingeborg Csöregh ◽  
Jozef Kowalewski ◽  
Dick Sandström
Keyword(s):  
Solid State ◽  
Diffraction Study ◽  
Inclusion Complexes ◽  
Solid State Nmr ◽  
X Ray Diffraction ◽  
X Ray

The Collagenic Molecular Structural Unit of Solid State Complexes

1971 ◽  
Vol 29 ◽  
pp. 478-479
Author(s):  
Kenneth M. Richter ◽  
John A. Schilling
Keyword(s):  
Molecular Weight ◽  
Solid State ◽  
Structural Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Naoh Treatment

The structural unit of solid state collagen complexes has been reported by Porter and Vanamee via EM and by Cowan, North and Randall via x-ray diffraction to be an ellipsoidal unit of 210-270 A. length by 50-100 A. diameter. It subsequently was independently demonstrated by us in dog tendon, dermis, and induced complexes. Its detailed morphologic, dimensional and molecular weight (MW) aspects have now been determined. It is pear-shaped in long profile with m diameters of 57 and 108 A. and m length of 263 A. (Fig. 1, tendon, KMnO4 fixation, Na-tungstate; Fig. 2a, schematic of unit in long, C, and x-sectional profiles of its thin, xB, and bulbous, xA portions; Fig. 2b, tendon essentially unmodified by ether and 0.4 N NaOH treatment, Na-tungstate). The unit consists of a uniquely coild cable, c, of ṁ 22.9 A. diameter and length of 2580-3316 A. The cable consists of three 2nd-strands, s, each of m 10.6 A.

TEM studies of solid-state reactions in sputter-deposited Nb/Al multilayer thin films

1996 ◽  
Vol 54 ◽  
pp. 1020-1021
Author(s):  
F. Ma ◽  
S. Vivekanand ◽  
K. Barmak ◽  
C. Michaelsen
Keyword(s):  
Thin Films ◽  
Solid State ◽  
Stoichiometric Composition ◽  
Analytical Electron Microscopy ◽  
Grain Structure ◽  
Solid State Reactions ◽  
Multilayer Thin Films ◽  
X Ray Diffraction ◽  
X Ray ◽  
Sputter Deposited

Solid state reactions in sputter-deposited Nb/Al multilayer thin films have been studied by transmission and analytical electron microscopy (TEM/AEM), differential scanning calorimetry (DSC) and X-ray diffraction (XRD). The Nb/Al multilayer thin films for TEM studies were sputter-deposited on (1102)sapphire substrates. The periodicity of the films is in the range 10-500 nm. The overall composition of the films are 1/3, 2/1, and 3/1 Nb/Al, corresponding to the stoichiometric composition of the three intermetallic phases in this system.Figure 1 is a TEM micrograph of an as-deposited film with periodicity A = dA1 + dNb = 72 nm, where d's are layer thicknesses. The polycrystalline nature of the Al and Nb layers with their columnar grain structure is evident in the figure. Both Nb and Al layers exhibit crystallographic texture, with the electron diffraction pattern for this film showing stronger diffraction spots in the direction normal to the multilayer. The X-ray diffraction patterns of all films are dominated by the Al(l 11) and Nb(l 10) peaks and show a merging of these two peaks with decreasing periodicity.

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