scholarly journals Factors Impacting σ- and π-Hole Regions as Revealed by the Electrostatic Potential and Its Source Function Reconstruction: The Case of 4,4′-Bipyridine Derivatives

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4409
Author(s):  
Carlo Gatti ◽  
Alessandro Dessì ◽  
Roberto Dallocchio ◽  
Victor Mamane ◽  
Sergio Cossu ◽  
...  
Keyword(s):  
Electron Density ◽  
Electrostatic Potential ◽  
Source Function ◽  
Noncovalent Interactions ◽  
Conformational Search ◽  
Atomic Group ◽  
Group Contributions ◽  
Conformational Freedom ◽  
Molecular Patterns ◽  
The Impact

Positive electrostatic potential (V) values are often associated with σ- and π-holes, regions of lower electron density which can interact with electron-rich sites to form noncovalent interactions. Factors impacting σ- and π-holes may thus be monitored in terms of the shape and values of the resulting V. Further precious insights into such factors are obtained through a rigorous decomposition of the V values in atomic or atomic group contributions, a task here achieved by extending the Bader–Gatti source function (SF) for the electron density to V. In this article, this general methodology is applied to a series of 4,4′-bipyridine derivatives containing atoms from Groups VI (S, Se) and VII (Cl, Br), and the pentafluorophenyl group acting as a π-hole. As these molecules are characterized by a certain degree of conformational freedom due to the possibility of rotation around the two C–Ch bonds, from two to four conformational motifs could be identified for each structure through conformational search. On this basis, the impact of chemical and conformational features on σ- and π-hole regions could be systematically evaluated by computing the V values on electron density isosurfaces (VS) and by comparing and dissecting in atomic/atomic group contributions the VS maxima (VS,max) values calculated for different molecular patterns. The results of this study confirm that both chemical and conformational features may seriously impact σ- and π-hole regions and provide a clear analysis and a rationale of why and how this influence is realized. Hence, the proposed methodology might offer precious clues for designing changes in the σ- and π-hole regions, aimed at affecting their potential involvement in noncovalent interactions in a desired way.

scholarly journals Structural genomics approach to investigate deleterious impact of nsSNPs in conserved telomere maintenance component 1

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arunabh Choudhury ◽  
Taj Mohammad ◽  
Nikhil Samarth ◽  
Afzal Hussain ◽  
Md. Tabish Rehman ◽  
...  
Keyword(s):  
Noncovalent Interactions ◽  
Md Simulations ◽  
Telomere Maintenance ◽  
Nucleotide Polymorphisms ◽  
Telomeric Dna ◽  
Congenital Diseases ◽  
Ob Fold ◽  
Significant Conformational Change ◽  
The Stability ◽  
The Impact

AbstractConserved telomere maintenance component 1 (CTC1) is an important component of the CST (CTC1-STN1-TEN1) complex, involved in maintaining the stability of telomeric DNA. Several non-synonymous single-nucleotide polymorphisms (nsSNPs) in CTC1 have been reported to cause Coats plus syndrome and Dyskeratosis congenital diseases. Here, we have performed sequence and structure analyses of nsSNPs of CTC1 using state-of-the-art computational methods. The structure-based study focuses on the C-terminal OB-fold region of CTC1. There are 11 pathogenic mutations identified, and detailed structural analyses were performed. These mutations cause a significant disruption of noncovalent interactions, which may be a possible reason for CTC1 instability and consequent diseases. To see the impact of such mutations on the protein conformation, all-atom molecular dynamics (MD) simulations of CTC1-wild-type (WT) and two of the selected mutations, R806C and R806L for 200 ns, were carried out. A significant conformational change in the structure of the R806C mutant was observed. This study provides a valuable direction to understand the molecular basis of CTC1 dysfunction in disease progression, including Coats plus syndrome.

Measurement of Dysprosium Stark Width and the Electron Impact Width Parameter

2018 ◽  
Vol 73 (2) ◽  
pp. 203-213 ◽  
Author(s):  
Jhonatha R. dos Santos ◽  
Jonas Jakutis Neto ◽  
N. Rodrigues ◽  
M.G. Destro ◽  
José W. Neri ◽  
...  
Keyword(s):  
Electron Density ◽  
Impact Parameter ◽  
Plasma Temperature ◽  
Spectral Lines ◽  
Emission Lines ◽  
Spectroscopic Methods ◽  
Species Concentration ◽  
The Impact ◽  
Stark Width

In this work, we suggest a methodology to determine the impact parameter for neutral dysprosium emission lines from the characterization of the plasma generated by laser ablation in a sealed chamber filled with argon. The procedure is a combination of known consistent spectroscopic methods for plasma temperature determination, electron density, and species concentration. With an electron density of 3.1 × 1018 cm–3 and temperature close to 104 K, we estimated the impact electron parameter for nine spectral lines of the neutral dysprosium atom. The gaps in the impact parameter data in the literature, mainly for heavy elements, stress the importance of the proposed method.

scholarly journals A comparison of Galactic electron density models using PyGEDM

2021 ◽  
Vol 38 ◽  
Author(s):  
D. C. Price ◽  
C. Flynn ◽  
A. Deller
Keyword(s):  
Electron Density ◽  
Large Scale ◽  
Galactic Halo ◽  
Application Programming Interface ◽  
Dispersion Measure ◽  
Radio Pulsars ◽  
Distribution Models ◽  
Distance Measurements ◽  
Application Programming ◽  
The Impact

Abstract Galactic electron density distribution models are crucial tools for estimating the impact of the ionised interstellar medium on the impulsive signals from radio pulsars and fast radio bursts. The two prevailing Galactic electron density models (GEDMs) are YMW16 (Yao et al. 2017, ApJ, 835, 29) and NE2001 (Cordes & Lazio 2002, arXiv e-prints, pp astro–ph/0207156). Here, we introduce a software package PyGEDM which provides a unified application programming interface for these models and the YT20 (Yamasaki & Totani 2020, ApJ, 888, 105) model of the Galactic halo. We use PyGEDM to compute all-sky maps of Galactic dispersion measure (DM) for YMW16 and NE2001 and compare the large-scale differences between the two. In general, YMW16 predicts higher DM values towards the Galactic anticentre. YMW16 predicts higher DMs at low Galactic latitudes, but NE2001 predicts higher DMs in most other directions. We identify lines of sight for which the models are most discrepant, using pulsars with independent distance measurements. YMW16 performs better on average than NE2001, but both models show significant outliers. We suggest that future campaigns to determine pulsar distances should focus on targets where the models show large discrepancies, so future models can use those measurements to better estimate distances along those line of sight. We also suggest that the Galactic halo should be considered as a component in future GEDMs, to avoid overestimating the Galactic DM contribution for extragalactic sources such as FRBs.

On the transfer of theoretical multipole parameters for restoring static electron density and revealing and treating atomic anharmonic motion. Features of chemical bonding in crystals of an isocyanuric acid derivative

2021 ◽  
Vol 77 (6) ◽  
Author(s):  
Sergey A. Shteingolts ◽  
Julia K. Voronina ◽  
Liliya F. Saifina ◽  
Marina M. Shulaeva ◽  
Vyacheslav E. Semenov ◽  
...  
Keyword(s):  
Electron Density ◽  
Acid Derivative ◽  
Noncovalent Interactions ◽  
Initial Guess ◽  
Atomic Motion ◽  
Total Probability ◽  
Electronic Temperature ◽  
Covalent Bonds ◽  
Isocyanuric Acid ◽  
Static Electron

The crystal and electronic structure of an isocyanuric acid derivative was studied by high-resolution single-crystal X-ray diffraction within the Hansen–Coppens multipole formalism. The observed deformation electron density shows signs of thermal smearing. The experimental picture meaningfully assigned to the consequences of unmodelled anharmonic atomic motion. Straightforward simultaneous refinement of all parameters, including Gram–Charlier coefficients, resulted in more significant distortion of apparent static electron density, even though the residual density became significantly flatter and more featureless. Further, the method of transferring multipole parameters from the model refined against theoretical structure factors as an initial guess was employed, followed by the subsequent block refinement of Gram–Charlier coefficients and the other parameters. This procedure allowed us to appropriately distinguish static electron density from the contaminant smearing effects of insufficiently accounted atomic motion. In particular, some covalent bonds and the weak π...π interaction between isocyanurate moieties were studied via the mutual penetration of atomic-like kinetic and electrostatic potential φ-basins with complementary atomic ρ-basins. Further, local electronic temperature was applied as an advanced descriptor for both covalent bonds and noncovalent interactions. Total probability density function (PDF) of nuclear displacement showed virtually no negative regions close to and around the atomic nuclei. The distribution of anharmonic PDF to a certain extent matched the residual electron density from the multipole model before anharmonic refinement. No signs of disordering of the sulfonyl group hidden in the modelled anharmonic motion were found in the PDF.

scholarly journals Noncovalent Bonds, Spectral and Thermal Properties of Substituted Thiazolo[2,3-b][1,3]thiazinium Triiodides

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 506 ◽  
Author(s):  
Irina Yushina ◽  
Natalya Tarasova ◽  
Dmitry Kim ◽  
Vladimir Sharutin ◽  
Ekaterina Bartashevich
Keyword(s):  
Electron Density ◽  
Noncovalent Interactions ◽  
Material Design ◽  
Spectroscopic Properties ◽  
Structural Features ◽  
Halogen Bonds ◽  
X Ray Diffraction ◽  
Raman Spectroscopic ◽  
Pairwise Interactions ◽  
Noncovalent Bonds

The interrelation between noncovalent bonds and physicochemical properties is in the spotlight due to the practical aspects in the field of crystalline material design. Such study requires a number of similar substances in order to reveal the effect of structural features on observed properties. For this reason, we analyzed a series of three substituted thiazolo[2,3-b][1,3]thiazinium triiodides synthesized by an iodocyclization reaction. They have been characterized with the use of X-ray diffraction, Raman spectroscopy, and thermal analysis. Various types of noncovalent interactions have been considered, and an S…I chalcogen bond type has been confirmed using the electronic criterion based on the calculated electron density and electrostatic potential. The involvement of triiodide anions in the I…I halogen and S…I chalcogen bonding is reflected in the Raman spectroscopic properties of the I–I bonds: identical bond lengths demonstrate different wave numbers of symmetric triiodide vibration and different values of electron density at bond critical points. Chalcogen and halogen bonds formed by the terminal iodine atom of triiodide anion and numerous cation…cation pairwise interactions can serve as one of the reasons for increased thermal stability and retention of iodine in the melt under heating.

Treatment of metastatic bladder cancer

2017 ◽  
Author(s):  
Fabio Calabrò ◽  
Cora N. Sternberg
Keyword(s):  
Bladder Cancer ◽  
Urothelial Cancer ◽  
Clinical Investigation ◽  
Good Prognosis ◽  
New Drugs ◽  
Urothelial Bladder Cancer ◽  
Urothelial Bladder ◽  
Molecular Patterns ◽  
The Impact

Although bladder cancer is considered a chemosensitive malignancy, the prognosis of patients with metastatic disease is poor, with a median survival of approximately 12–14 months in good prognosis patients and with cure in only a minority. The addition of new drugs to the standard cisplatin-based regimens has not improved these outcomes. In this chapter, we highlight the role of chemotherapy and the impact of the new targeted agents in the treatment of metastatic bladder carcinoma. A better understanding of the underlying biology and the molecular patterns of urothelial bladder cancer has led to clinical investigation of several therapeutic targets. To date, these agents have yet to demonstrate an improvement in overall survival. Urothelial cancer is extremely sensitive to checkpoint inhibition with both anti PD-1 and anti PDL1 antibodies. The future seems brighter with the advent of these new therapies.

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