Self-assembled Materials Containing Complementary Nucleobase Molecular Recognition

2008 ◽  
Vol 1094 ◽  
Author(s):  
Wirasak Smitthipong ◽  
Arkadiusz Chworos ◽  
Brian Lin ◽  
Thorsten Neumann ◽  
Surekha Gajria ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Mechanical Properties ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
X Ray ◽  
Transparent Films ◽  
X Ray Scattering ◽  
Counter Ions ◽  
Self Assembled ◽  
Cationic Amphiphile

AbstractHere we report the nucleic acid/cationic amphiphile based-materials in which we exchange the counter-ions of the polyanionic backbone of the nucleic acids with the cationic amphiphiles to form self-assembled transparent films with the thickness of several microns. Predominantly, single stranded poly(A), poly(U) and double stranded poly(AU) were employed for these studies. Small-angle X-ray scattering (SAXS) experiments suggested lamellar-like structure for all the film samples. However, the molecule length as well as the molecular structure of nucleic acids can affect the topology and mechanical properties of these films. Complementary base-paring of poly(AU) is reported here with comparison to poly(A) and poly(U) complexes.

Comparative Studies on Photoelasticity of Elastomers and Plastomers

1948 ◽  
Vol 21 (4) ◽  
pp. 790-798
Author(s):  
Wilfried Heller ◽  
Hans Oppenheimer
Keyword(s):  
Mechanical Properties ◽  
Film Structure ◽  
Polymer Chains ◽  
X Ray Diffraction ◽  
Photoelastic Method ◽  
Double Refraction ◽  
X Ray ◽  
Transparent Films ◽  
X Ray Scattering

Abstract Transparent films of elastomers and plastomers were found to differ sufficiently in their photoelastic behavior to make stress double refraction a useful criterion of the prospective mechanical properties of a given material. The stress double refraction in such films is mostly an effect of deformation, of orientation, or of both deformation and orientation of polymer chains. In such polymers, however, which crystallize under stress, a large part of the optical effect may be due to oriented crystallization. In addition to its practical value as a testing method for polymers, the photoelastic method offers, therefore, particularly in combination with simultaneous investigations of mechanical properties, the prospect of correlating mechanical properties of a polymer film with its internal structure, and of correlating changes in both qualities on exposure of the film to different degrees of stress. Although results obtained on such films, by means of x-ray diffraction or x-ray scattering and electron-diffraction, are, in general, easier to interpret, the photoelastic method has the considerable advantage of making possible a quantitative follow-up of rapid changes in film structure, e.g., of relaxations.

scholarly journals Martini bead form factors for nucleic acids and their application in the refinement of protein–nucleic acid complexes against SAXS data

2019 ◽  
Vol 52 (2) ◽  
pp. 394-402 ◽  
Author(s):  
Cristina Paissoni ◽  
Alexander Jussupow ◽  
Carlo Camilloni
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Computational Cost ◽  
Form Factors ◽  
Dynamics Simulation ◽  
Saxs Data ◽  
X Ray ◽  
Atomic Structures ◽  
X Ray Scattering ◽  
Protein Nucleic Acid

The use of small-angle X-ray scattering (SAXS) in combination with molecular dynamics simulation is hampered by its heavy computational cost. The calculation of SAXS from atomic structures can be speeded up by using a coarse-grain representation of the structure. Following the work of Niebling, Björling & Westenhoff [J. Appl. Cryst. (2014), 47, 1190–1198], the Martini bead form factors for nucleic acids have been derived and then implemented, together with those previously determined for proteins, in the publicly available PLUMED library. A hybrid multi-resolution strategy has also been implemented to perform SAXS restrained simulations at atomic resolution by calculating the virtual positions of the Martini beads on the fly and using them for the calculation of SAXS. The accuracy and efficiency of the method are demonstrated by refining the structure of two protein–nucleic acid complexes. Instrumental for this result is the use of metainference, which allows the consideration and alleviation of the approximations at play in the present SAXS calculations.

scholarly journals Vibrational resonant inelastic X-ray scattering in liquid acetic acid: a ruler for molecular chain lengths

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Viktoriia Savchenko ◽  
Iulia Emilia Brumboiu ◽  
Victor Kimberg ◽  
Michael Odelius ◽  
Pavel Krasnov ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Acetic Acid ◽  
Molecular Chain ◽  
X Ray ◽  
X Ray Scattering ◽  
Localized Excitations ◽  
Vibrational Excitations ◽  
Chain Lengths ◽  
X Ray Absorption ◽  
Ray Scattering

AbstractQuenching of vibrational excitations in resonant inelastic X-ray scattering (RIXS) spectra of liquid acetic acid is observed. At the oxygen core resonance associated with localized excitations at the O–H bond, the spectra lack the typical progression of vibrational excitations observed in RIXS spectra of comparable systems. We interpret this phenomenon as due to strong rehybridization of the unoccupied molecular orbitals as a result of hydrogen bonding, which however cannot be observed in x-ray absorption but only by means of RIXS. This allows us to address the molecular structure of the liquid, and to determine a lower limit for the average molecular chain length.

scholarly journals Neutron and X-ray scattering for biophysics and biotechnology: examples of self-assembled lipid systems

Soft Matter ◽  
2009 ◽  
Vol 5 (14) ◽  
pp. 2694 ◽  
Author(s):  
Thad A. Harroun ◽  
Norbert Kučerka ◽  
Mu-Ping Nieh ◽  
John Katsaras
Keyword(s):  
X Ray ◽  
X Ray Scattering ◽  
Self Assembled ◽  
Ray Scattering

Molecular structure of poly(3-alkyl-thiophenes) investigated by calorimetry and grazing incidence X-ray scattering

2012 ◽  
Vol 97 ◽  
pp. 109-118 ◽  
Author(s):  
Jose Abad ◽  
Nieves Espinosa ◽  
Pilar Ferrer ◽  
Rafael García-Valverde ◽  
Carmen Miguel ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Grazing Incidence ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

scholarly journals Vibrational Resonant Inelastic X-Ray Scattering Inliquid Acetic Acid: A Ruler for Molecular Chain Lengths

2020 ◽  
Author(s):  
Viktoriia Savchenko ◽  
Iulia-Emilia Brumboiu ◽  
Victor Kimberg ◽  
Michael Odelius ◽  
Pavel Krasnov ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonding ◽  
Acetic Acid ◽  
Molecular Chain ◽  
X Ray ◽  
X Ray Scattering ◽  
Localized Excitations ◽  
Vibrational Excitations ◽  
Chain Lengths ◽  
Ray Scattering

Abstract Quenching of vibrational excitations in resonant inelastic X-ray scattering (RIXS) spectra of liquid acetic acid is observed. At the oxygen core resonance associated with localized excitations at the O-H bond, the spectra lack the typical progressionof vibrational excitations observed in RIXS spectra of comparable systems. We interpret this phenomenon as due to strong rehybridization of the unoccupied molecular orbitals as a result of hydrogen bonding. This allows us to address the molecular structure of the liquid, and to determine a lower limit for the average molecular chain length.

scholarly journals Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data

2020 ◽  
Vol 124 (25) ◽  
pp. 5186-5200 ◽  
Author(s):  
Milka Doktorova ◽  
Norbert Kučerka ◽  
Jacob J. Kinnun ◽  
Jianjun Pan ◽  
Drew Marquardt ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Small Angle ◽  
Fluid Phase ◽  
Scattering Data ◽  
Joint Analysis ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Influence of the Molecular Structure and Morphology of Self-Assembled 1,3,5-Benzenetrisamide Nanofibers on their Mechanical Properties

Small ◽  
2012 ◽  
Vol 8 (16) ◽  
pp. 2563-2570 ◽  
Author(s):  
Daniel Kluge ◽  
Julia C. Singer ◽  
Jens W. Neubauer ◽  
Frank Abraham ◽  
Hans-Werner Schmidt ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Mechanical Properties ◽  
Structure And Morphology ◽  
Self Assembled
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