scholarly journals A study of vibrational dynamics of poly (a-n-butyl-b-l-aspartate) (panbla)

2009 ◽  
Vol 3 (1) ◽  
pp. 7-18
Author(s):  
Mahendra Singh ◽  
◽  
Anuj Kumar ◽  
Naresh Kumar ◽  
Poonam Tandon ◽  
...  
Keyword(s):  
Normal Modes ◽  
Internal Symmetry ◽  
Dynamical Behaviour ◽  
Least Square ◽  
X Ray Diffraction ◽  
Molecular Mechanics Calculations ◽  
Vibrational Dynamics ◽  
X Ray ◽  
Hexagonal Form ◽  
Tetragonal Form

Poly(-N-butyl--L-aspartate) (PANBLA) is nylon-3 derivative in which an alcoxycarbonyl group has been stereoregularly attached to -carbon of the repeating unit. Like poly(-isobutyl--L-aspartate) (PAIBLA) exists in two helical forms, namely hexagonal form (13/4 helix) and tetragonal form (4/1 helix), were characterized by X-ray diffraction. The hexagonal form appears to be poorly crystalline and it could not be obtained well oriented. On the other hand tetragonal form turns to be highly crystalline. Both molecular mechanics calculations and the linked-atom least square (LALS) methodology using X-ray diffraction data have revealed that an antiparallel packing of 13/4 helices with a right handed (2R) scheme of hydrogen bonds is most favourable for hexagonal form of PANBLA. Regarding tetragonal form the above techniques favour a parallel arrangement of 4/1 helices according to right handed 4R model. IR dichroism studies also support the above results. Although the vibrational dynamics of both forms of PAIBLA has been studied, no such study has been performed for PANBLA. In the present communication the vibrational dynamics of PANBLA in tetragonal form (4/1 helix) has been studied through the dispersion of normal modes. The effect of side chain nature on the dynamical behaviour has also been analyzed. Apart from detailed assignments of modes, various characteristic features of dispersion curves have been explained as arising due to internal symmetry in energy momentum space. Finally, the density of states has been used to calculate heat capacity of this polymer.

Preliminary X-ray diffraction studies of the tetragonal form of native horse-spleen apoferritin

1996 ◽  
Vol 52 (3) ◽  
pp. 594-596 ◽  
Author(s):  
T. Granier ◽  
B. Gallois ◽  
A. Dautant ◽  
B. Langois d'Estaintot ◽  
G. Précigoux
Keyword(s):  
X Ray Diffraction ◽  
X Ray ◽  
Tetragonal Form

The Peak Resolution of Diffuse X-Ray Diffraction Pattern of Tibetan Medicine

2012 ◽  
Vol 562-564 ◽  
pp. 1959-1963
Author(s):  
Xin Wen Duan ◽  
Yuan Liu ◽  
Cheng Xi Hu ◽  
Yong De Li
Keyword(s):  
Least Square Method ◽  
Least Square ◽  
Tibetan Medicine ◽  
X Ray Diffraction ◽  
Composite Function ◽  
Xrd Pattern ◽  
X Ray ◽  
Signal Processing Method ◽  
Peak Resolution ◽  
Diffraction Peaks

Modern signal processing method is employed to peak resolution for four kinds of classical Tibetan Medicine X-ray diffraction patterns.Characterizing crystal diffraction peaks with Guass-Cauchy composite function, and combining with seventh polynomial characterizing the non-crystalline peak, the nonlinear least square method are adopted for peak resolution of Tibetan medicine XRD pattern. The result shows good handling effects of peak resolution.

scholarly journals Measuring and modeling diffuse scattering in protein X-ray crystallography

2016 ◽  
Vol 113 (15) ◽  
pp. 4069-4074 ◽  
Author(s):  
Andrew H. Van Benschoten ◽  
Lin Liu ◽  
Ana Gonzalez ◽  
Aaron S. Brewster ◽  
Nicholas K. Sauter ◽  
...  
Keyword(s):  
Diffuse Scattering ◽  
Structure Refinement ◽  
Normal Modes ◽  
Coarse Grained ◽  
X Ray Diffraction ◽  
Diffuse Intensity ◽  
X Ray ◽  
Protein Motions ◽  
X Ray Crystallography ◽  
Standard Data

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.

scholarly journals Preparation of red and grey elemental selenium for food fortification

2021 ◽  
Author(s):  
B. Khandsuren ◽  
J. Prokisch
Keyword(s):  
Electron Microscope ◽  
Sodium Selenite ◽  
Food Science ◽  
Elemental Selenium ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hexagonal Form ◽  
Transmission Electron ◽  
Particle Size Analyzer ◽  
Wide Range

AbstractIn recent years, the importance of nanomaterials in food science, medicine, etc. has been increasing quickly. Herein, organic and inorganic red selenium nanoparticles synthesised by the reduction of sodium selenite with chemical and biological reducing agents. Grey hexagonal form in aqueous and powder was assembled at a high temperature of 85 °C for 10 min. Also, selenium enriched yogurt powder was made that contained about 2,000 mg kg−1 selenium, 93.8% of which is in nano form with a size of 50–500 nm. The synthesised nanoparticles were characterised by Dynamic Light Scattering Particle Size Analyzer (DLS), X-ray Diffraction Analysis (XRD), Scanning Electron Microscope (SEM) and Transmission Electron Microscope (TEM). The prepared SeNPs could be promising additive for a wide range of applications.

Coordination Chemistry of N-(2-Hydroxybenzyl)-(S)-amino Acids. Absolute Configuration of LAMBDA-mer-R,R-[Co(ohb-(S)-Ala)2]- Anion

1997 ◽  
Vol 62 (8) ◽  
pp. 1205-1213 ◽  
Author(s):  
Svetlana Pakhomova ◽  
Jan Ondráček ◽  
František Jursík
Keyword(s):  
Absolute Configuration ◽  
Diffraction Method ◽  
Cd Spectroscopy ◽  
X Ray Diffraction ◽  
Aromatic Rings ◽  
Molecular Mechanics Calculations ◽  
X Ray ◽  
Bond Network ◽  
Twist Boat ◽  
C Nmr

The crystal and molecular structure of the Ag[Co(ohb-(S)-Ala)2] . 5 H2O have been determined by X-ray diffraction method. The crystals are hexagonal with a = b = 9.039(0.002) Å, c = 24.896(0.006) Å, space group P3221, and Z = 3. Each Ag+ counterion coordinated by one water molecule which is a part of hydrogen bond network, is bonded to aromatic rings. The anion adopts LAMBDA-mer absolute configuration. Mer geometry is in accord with the molecular mechanics calculations. Since CD spectroscopy does not reflect configurational chirality, the absolute configuration has been determined by the X-ray structure analysis and assigned using chirality descriptors. The arrangements at the chiral centers are R for both N atoms. The two five-membered rings each assume envelope conformation with C1 and C2 atoms exceptionally deviated (0.378(7) and 1.210(7) Å) from the N-Co-O plane. Both six-membered rings have delta twist boat conformations. The complex described has been also characterized by the electronic and 13C NMR spectroscopies.

Kristallstrukturen, Schwingungsspektren und Normalkoordinatenanalysen von Tetrahalogenooxalatoosmaten (IV), [OsX4(ox)]2-, X = Cl, Br, I / Crystal Structures, Vibrational Spectra and Normal Coordinate Analyses of Tetrahalogenooxalatoosmates (IV), [OsX4(ox)]2-, X = Cl, Br, I

1997 ◽  
Vol 52 (3) ◽  
pp. 315-322 ◽  
Author(s):  
W. Preetz ◽  
A. Krull
Keyword(s):  
Crystal Structures ◽  
Normal Modes ◽  
Force Constants ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Normal Coordinate ◽  
Valence Force ◽  
Space Group ◽  
X Ray ◽  
Modes Of Vibration

Abstract The crystal structures of [(C5H5N)2CH2][OsCl4(ox)] (monoclinic, space group I2/m, a = 10.260(5), b = 13.841(5), c = 12.273(5) Å, β = 92.050(5)°, Z = 4), [(C5H5N)2CH2][OsBr4(ox)]·H2O(monoclinic, space group P21/n, a = 11.666(3),b = 11.591(5), c = 14.926(2) Å, β = 102.45(2)°, Z = 4) and [P(C6H5)4]2 [OsI4(ox)]·2CH2Cl2 (triclinic, space group P1̄, a = 14.597(2), b = 11.9185(9), c = 22.5624(14) Å, α = 80.284(8), β = 78.903(8), γ = 69.432(8)°, Z = 2) have been determined by single crystal X-ray diffraction analysis. The IR and Raman spectra of the three complexes were measured at room temperature. Using the molecular parameters of the X-ray determinations normal coordinate analyses based on a modified valence force field have been performed and the normal modes of vibration are assigned. With a set of 25 force constants and taking into account the innerligand vibrations a good agreement between observed and calculated frequencies has been achieved. The valence force constants of the X-Os-X axis are fd(OsCl) = 1.77, fd(OsBr) = 1.48, fd(OsI) = 1.0 mdyn/Å, of the X′-Os-O• axes are fd(OsCl′) = 1.88, fd(OsBr′) = 1.6, fd(OsI′) =1.1 mdyn/Å and fd(OsO•) ranges from 2.7 to 2.8 mdyn/Å.

Variable-temperature studies of the 4-isopropylphenol crystal structure from X-ray diffraction. Comparison of thermal expansion and molecular dynamics with spectroscopic results

2002 ◽  
Vol 58 (4) ◽  
pp. 684-689 ◽  
Author(s):  
Grażyna Wójcik ◽  
Jolanta Holband
Keyword(s):  
Thermal Expansion ◽  
Inelastic Neutron Scattering ◽  
Variable Temperature ◽  
Normal Modes ◽  
Low Frequency ◽  
Inelastic Neutron ◽  
X Ray Diffraction ◽  
X Ray ◽  
Thermal Expansion Coefficients ◽  
Scattering Spectra

Crystalline 4-isopropylphenol, C9H12O, an optically non-linear material, was studied by X-ray diffraction in order to determine its structure at several temperatures in the 95–300 K range. The thermal expansion coefficients have been calculated from the lattice parameters' dependence on temperature. The rigid-body analysis of the anisotropic displacement parameters including the correlation with the internal motion of large amplitude provided the values of the molecular translation and libration tensors at the temperatures studied and was used to characterize the torsional motion of the isopropyl group. The calculated normal modes and internal torsion frequency were compared with the wave numbers at the maximum of bands in the low-frequency Raman scattering, FTIR and inelastic neutron scattering spectra.

The combustion synthesis of the ferroelectric material, BaTiO3, studied by time-resolved X-ray diffraction

1999 ◽  
Vol 14 (2) ◽  
pp. 111-113 ◽  
Author(s):  
E. M. Larson ◽  
Joe Wong ◽  
J. B. Holt ◽  
P. A. Waide ◽  
B. Rupp
Keyword(s):  
Combustion Synthesis ◽  
Ferroelectric Material ◽  
Bragg Diffraction ◽  
Cubic Phase ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
Tetragonal Form ◽  
Diffraction Peaks ◽  
The Common

The combustion synthesis of the common ferroelectric material, BaTiO3, was developed using the stoichiometry: BaO2+0.2 Ti+0.8 TiO2→BaTiO3+0.3 O2. An adiabatic temperature, Tad, of the reaction was calculated from known thermodynamic data to be 1917 °C. Real time chemical changes in the formation of BaTiO3 during the reaction have been monitored using time-resolved X-ray diffraction with synchrotron radiation as the X-ray source. A time resolution of 250 ms was achieved. The combustion synthesis of BaTiO3 was followed by observing the intensities of reactant and product Bragg diffraction peaks in order to qualitatively identify the phases present. Because BaTiO3 forms initially as a cubic phase, X-ray diffraction of the product was monitored for a period of 20 min after the reaction to observe the phase transformation to the tetragonal form. This transformation is evident in these post-reaction scans as the cubic 110 and 220 peaks are split to the tetragonal 101/110 and 202/220 ones, respectively.

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