A general hydrogen bonding definition based on three-dimensional spatial distribution functions and its extension to quantitative structural analysis of solutions and general intermolecular bonds

2019 ◽  
Vol 281 ◽  
pp. 225-235 ◽  
Author(s):  
Jan Dočkal ◽  
Martin Svoboda ◽  
Martin Lísal ◽  
Filip Moučka
Keyword(s):  
Hydrogen Bonding ◽  
Spatial Distribution ◽  
Structural Analysis ◽  
Three Dimensional ◽  
Distribution Functions

Modified polyoxometalate: a novel monocapped bi-supporting and reduced α-Keggin structure {PMo12O40[Cu(2,2′-bpy)]}[Cu(2,2′-bpy)(en)(H2O)]2

2019 ◽  
Vol 75 (10) ◽  
pp. 1344-1352
Author(s):  
Yu-Kun Lu ◽  
Ya-Ping Li ◽  
Ling-Yu Yang ◽  
Wen-Hong Wang ◽  
Yuan Pan ◽  
...  
Keyword(s):  
Methylene Blue ◽  
Hydrogen Bonding ◽  
Structural Analysis ◽  
Organic Pollutant ◽  
Three Dimensional ◽  
Supramolecular Network ◽  
Stacking Interactions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Π Stacking

A novel modified polyoxometalate, {PMo12O40[Cu(2,2′-bpy)]}[Cu(2,2′-bpy)(en)(H2O)]2 [2,2′-bpy is 2,2′-bipyridyl (C10H8N2) and en is ethylenediamine (C2H8N2)], has been synthesized hydrothermally and structurally characterized by elemental analysis, TG, IR, XPS and single-crystal X-ray diffraction. The structural analysis reveals that the compound contains the reduced Keggin polyanion [PMo12O40]6− as the parent unit, which is monocapped by [Cu(2,2′-bpy)]2+ fragments via four bridging O atoms on an {Mo4O4} pit and bi-supported by two [Cu(2,2′-bpy)(en)(H2O)]2+ coordination cations simultaneously. There exist strong intramolecular π–π stacking between the capping and supporting units, which play a stabilizing role during the crystallization of the compound. Adjacent POM clusters are further aggregated to form a three-dimensional supramolecular network through noncovalent forces, hydrogen bonding and π–π stacking interactions. In addition, the photocatalytic properties were investigated in detail, and the results indicated that the compound can be used as a photocatalyst towards the decomposition of the organic pollutant methylene blue (MB).

scholarly journals Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michela Quadrini
Keyword(s):  
Hydrogen Bonding ◽  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Structural Effect ◽  
Biological Processes ◽  
Structural Pattern ◽  
Rna Molecules

Abstract RNA molecules play crucial roles in various biological processes. Their three-dimensional configurations determine the functions and, in turn, influences the interaction with other molecules. RNAs and their interaction structures, the so-called RNA–RNA interactions, can be abstracted in terms of secondary structures, i.e., a list of the nucleotide bases paired by hydrogen bonding within its nucleotide sequence. Each secondary structure, in turn, can be abstracted into cores and shadows. Both are determined by collapsing nucleotides and arcs properly. We formalize all of these abstractions as arc diagrams, whose arcs determine loops. A secondary structure, represented by an arc diagram, is pseudoknot-free if its arc diagram does not present any crossing among arcs otherwise, it is said pseudoknotted. In this study, we face the problem of identifying a given structural pattern into secondary structures or the associated cores or shadow of both RNAs and RNA–RNA interactions, characterized by arbitrary pseudoknots. These abstractions are mapped into a matrix, whose elements represent the relations among loops. Therefore, we face the problem of taking advantage of matrices and submatrices. The algorithms, implemented in Python, work in polynomial time. We test our approach on a set of 16S ribosomal RNAs with inhibitors of Thermus thermophilus, and we quantify the structural effect of the inhibitors.

scholarly journals Do galactic bars depend on environment?: an information theoretic analysis of Galaxy Zoo 2

2020 ◽  
Vol 501 (1) ◽  
pp. 994-1001
Author(s):  
Suman Sarkar ◽  
Biswajit Pandey ◽  
Snehasish Bhattacharjee
Keyword(s):  
Spatial Distribution ◽  
Mutual Information ◽  
Local Density ◽  
Statistical Significance ◽  
Distribution Functions ◽  
Cumulative Distribution ◽  
Host Galaxy ◽  
Data Sets ◽  
Data Set ◽  
Information Theoretic

ABSTRACT We use an information theoretic framework to analyse data from the Galaxy Zoo 2 project and study if there are any statistically significant correlations between the presence of bars in spiral galaxies and their environment. We measure the mutual information between the barredness of galaxies and their environments in a volume limited sample (Mr ≤ −21) and compare it with the same in data sets where (i) the bar/unbar classifications are randomized and (ii) the spatial distribution of galaxies are shuffled on different length scales. We assess the statistical significance of the differences in the mutual information using a t-test and find that both randomization of morphological classifications and shuffling of spatial distribution do not alter the mutual information in a statistically significant way. The non-zero mutual information between the barredness and environment arises due to the finite and discrete nature of the data set that can be entirely explained by mock Poisson distributions. We also separately compare the cumulative distribution functions of the barred and unbarred galaxies as a function of their local density. Using a Kolmogorov–Smirnov test, we find that the null hypothesis cannot be rejected even at $75{{\ \rm per\ cent}}$ confidence level. Our analysis indicates that environments do not play a significant role in the formation of a bar, which is largely determined by the internal processes of the host galaxy.

Element-specific structural analysis of Si/B4C using resonant X-ray reflectivity

2015 ◽  
Vol 48 (3) ◽  
pp. 786-796 ◽  
Author(s):  
Maheswar Nayak ◽  
P. C. Pradhan ◽  
G. S. Lodha
Keyword(s):  
Thin Film ◽  
Spatial Distribution ◽  
Structural Analysis ◽  
Chemical Changes ◽  
X Ray ◽  
Buried Interfaces ◽  
Smooth Interface ◽  
Specific Composition ◽  
Applied Fields ◽  
Spatial Modulations

Element-specific structural analysis at the buried interface of a low electron density contrast system is important in many applied fields. The analysis of nanoscaled Si/B4C buried interfaces is demonstrated using resonant X-ray reflectivity. This technique combines information about spatial modulations of charges provided by scattering, which is further enhanced near the resonance, with the sensitivity to electronic structure provided by spectroscopy. Si/B4C thin-film structures are studied by varying the position of B4C in Si layers. Measured values of near-edge optical properties are correlated with the resonant reflectivity profile to quantify the element-specific composition. It is observed that, although Si/B4C forms a smooth interface, there are chemical changes in the sputtered B4C layer. Nondestructive quantification of the chemical changes and the spatial distribution of the constituents is reported.

scholarly journals Three-Dimensional Spatial Distribution of Synapses in the Neocortex: A Dual-Beam Electron Microscopy Study

2013 ◽  
Vol 24 (6) ◽  
pp. 1579-1588 ◽  
Author(s):  
Angel Merchán-Pérez ◽  
José-Rodrigo Rodríguez ◽  
Santiago González ◽  
Víctor Robles ◽  
Javier DeFelipe ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Spatial Distribution ◽  
Three Dimensional ◽  
Microscopy Study ◽  
Electron Microscopy Study ◽  
Beam Electron ◽  
Dual Beam

Coupled Sea Ice-Ocean Model of the Arctic Ocean

1998 ◽  
Vol 120 (2) ◽  
pp. 77-84 ◽  
Author(s):  
I. V. Polyakov ◽  
I. Yu. Kulakov ◽  
S. A. Kolesov ◽  
N. Eu. Dmitriev ◽  
R. S. Pritchard ◽  
...  
Keyword(s):  
Arctic Ocean ◽  
Three Dimensional ◽  
Coupled Model ◽  
Ocean Model ◽  
Distribution Functions ◽  
Constitutive Law ◽  
Prognostic Models ◽  
The Arctic ◽  
The Arctic Ocean ◽  
Ocean Layer

A fully prognostic coupled ice-ocean model is described. The ice model is based on the elastic-plastic constitutive law with ice mass and compactness described by distribution functions. The ice thermodynamics model is applied individually to each ice thickness category. Advection of the ice partial mass and concentrations is parameterized by a fourth-order algorithm that conserves monotonicity of the solution. The ocean is described as a three-dimensional time-dependent baroclinic model with free surface. The coupled model is applied to establish the Arctic Ocean seasonal climatology using fully prognostic models for ice and ocean. Results reflect the importance of the ice melting/freezing in the formation of the thermohaline structure of the upper ocean layer.

Elastomers Based on Polycyclic Bisphenol Polycarbonates

1966 ◽  
Vol 39 (4) ◽  
pp. 1008-1018
Author(s):  
K. P. Perry ◽  
W. J. Jackson ◽  
J. R. Caldwell
Keyword(s):  
Hydrogen Bonding ◽  
Bisphenol A ◽  
Methylene Chloride ◽  
Three Dimensional ◽  
Pyridine Solution ◽  
Designed Experiment ◽  
Spun Fibers

Abstract Polycarbonate elastomers were prepared by the addition of phosgene to a pyridine solution of poly (tetramethylene ether) glycol and bisphenols containing norbornane-type groups. These elastomers do not contain the classical “tie-down” points—crosslinks, hydrogen bonding, or crystallinity—which, heretofore, have been considered necessary for good elastomer properties. This work introduces a new concept in elastomer chemistry : bulky, three-dimensional groups are effective tie-down points. Most of the elastomers were prepared with 4,4′- (2-norbornylidene) bis(2,6-dichlorophenol). For comparison, several elastomers with bisphenol-A were also prepared. A statistically designed experiment was carried out to determine the effect of composition variables on the properties of these elastomers. The properties were determined on films cast from methylene chloride and, in many cases, on wet-spun fibers. These elastomers have elongations of 400–600 per cent and instantaneous elastic recoveries up to 100.

Three-dimensional structural analysis by the integrated force method

1996 ◽  
Vol 58 (5) ◽  
pp. 869-886 ◽  
Author(s):  
I. Kaljević ◽  
S.N. Patnaik ◽  
D.A. Hopkins
Keyword(s):  
Structural Analysis ◽  
Three Dimensional ◽  
Force Method ◽  
Integrated Force Method

scholarly journals One-loop matching for spin-dependent quasi-TMDs

2020 ◽  
Vol 2020 (9) ◽  
Author(s):  
Markus A. Ebert ◽  
Stella T. Schindler ◽  
Iain W. Stewart ◽  
Yong Zhao
Keyword(s):  
Spin Structure ◽  
Wilson Line ◽  
Three Dimensional ◽  
Distribution Functions ◽  
Longitudinal Momentum ◽  
Loop Order ◽  
Parton Distribution Functions ◽  
Transverse Momentum Dependent ◽  
Unique Probe ◽  
Transverse Position

Abstract Transverse momentum dependent parton distribution functions (TMDPDFs) provide a unique probe of the three-dimensional spin structure of hadrons. We construct spin-dependent quasi-TMDPDFs that are amenable to lattice QCD calculations and that can be used to determine spin-dependent TMDPDFs. We calculate the short-distance coefficients connecting spin-dependent TMDPDFs and quasi-TMDPDFs at one-loop order. We find that the helicity and transversity distributions have the same coefficient as the unpolarized TMDPDF. We also argue that the same is true for pretzelosity and that this spin universality of the matching will hold to all orders in αs. Thus, it is possible to calculate ratios of these distributions as a function of longitudinal momentum and transverse position utilizing simpler Wilson line paths than have previously been considered.

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