scholarly journals A computational analysis of the apparent nido vs. hypho conflict: are we dealing with six- or eight-vertex open-face diheteroboranes?

2015 ◽  
Vol 44 (26) ◽  
pp. 11819-11826 ◽  
Author(s):  
João Pedro F. Nunes ◽  
Josef Holub ◽  
David W. H. Rankin ◽  
Derek A. Wann ◽  
Drahomír Hnyk
Keyword(s):  
Electronic Structures ◽  
Computational Analysis ◽  
Computational Studies ◽  
Open Face

Computational studies have been undertaken to investigate the electronic structures of six hetero-substituted borane cages, concluding that hypho-7,8-[S2B6H9]− is the only true hypho species in this series.

Accessing pyrrolones and pyridinones: controlling 5-exo and 6-endo ring closures in heterocyclic alkynylamides

2017 ◽  
Vol 95 (4) ◽  
pp. 415-423 ◽  
Author(s):  
Genesis Infante ◽  
Sara Eisler
Keyword(s):  
Intramolecular Cyclization ◽  
Computational Analysis ◽  
Experimental Results ◽  
Computational Studies ◽  
Cyclization Reactions ◽  
Theoretical Predictions ◽  
Insight Into

Competitive 5-exo and 6-endo anionic intramolecular cyclization reactions in heterocyclic alkynylamides were explored via experimental and computational analysis. The 5-exo-dig cyclization pathway is usually disfavoured in heterocyclic systems, and 6-endo products are often both the kinetic and thermodynamic products. However, we’ve found that it is possible to shift selectivity toward the 5-exo-dig pyrrolone products away from the less strained pyridinone products that are produced via the 6-endo-dig cyclization. Parameters such as identity of heteroatom, heteroatom positioning within the heterocycle, and functionality on the alkyne were investigated and, in many cases, were found to strongly influence product ratios. A series of computational studies was performed to provide further insight into the 5-exo-dig and 6-endo-dig pathways in these heterocyclic systems. Theoretical predictions were found to reproduce experimental results, highlighting the predictive capabilities of the computations in determining preferred products.

scholarly journals Computational studies on eukaryotic transmembrane β-barrel proteins

2018 ◽  
Author(s):  
Ahmed F. Roumia ◽  
Margarita C. Theodoropoulou ◽  
Konstantinos D. Tsirigos ◽  
Pantelis G. Bagos
Keyword(s):  
Computational Analysis ◽  
Markov Models ◽  
Outer Membrane Proteins ◽  
Computational Studies ◽  
Cellular Functions ◽  
Pfam Database ◽  
Eukaryotic Proteins ◽  
Transport Of Ions ◽  
First Time

Transmembrane β-barrel proteins perform multiple cellular functions such as passive transport of ions and allowing the flux of molecules. Also, they act as enzymes, transporters, receptors and virulence factors. Even though, in the last few years, several families of eukaryotic β-barrel outer membrane proteins (OMPs) have been discovered, the computational characterization of these families is far from complete. The PFAM database includes only very few characteristic profiles for these families and, in most cases, the profile Hidden Markov Models where trained using both prokaryotic and eukaryotic proteins. Here, we present, for the first time, a comprehensive computational analysis of eukaryotic transmembrane β- barrels. Ten characteristic pHMMs were build that can discriminate eukaryotic β-barrels from other classes of β-barrel proteins (globular and bacterial) and are, also, capable of discriminating between mitochondrial and chloroplastic ones. Specifically, we built six new pHMMs for the chloroplastic β-barrel families not included in the PFAM database and, also, updated the profile for MDM10 family (PF12519) and divided the porin family (PF01459) into two separated families VDAC and TOM40. We hope that all the pHMMs presented here will be used for the detection and characterization of eukaryotic OMPs in newly discovered proteomes.

scholarly journals CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language

GigaScience ◽  
2019 ◽  
Vol 8 (7) ◽  
Author(s):  
Michael Kotliar ◽  
Andrey V Kartashov ◽  
Artem Barski
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Computational Analysis ◽  
Computational Studies ◽  
Cloud Environment ◽  
Sequencing Data ◽  
Massive Growth ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Version 2.0 ◽  
The Common ◽  
Computational Research

Abstract Background Massive growth in the amount of research data and computational analysis has led to increased use of pipeline managers in biomedical computational research. However, each of the >100 such managers uses its own way to describe pipelines, leading to difficulty porting workflows to different environments and therefore poor reproducibility of computational studies. For this reason, the Common Workflow Language (CWL) was recently introduced as a specification for platform-independent workflow description, and work began to transition existing pipelines and workflow managers to CWL. Findings Herein, we present CWL-Airflow, a package that adds support for CWL to the Apache Airflow pipeline manager. CWL-Airflow uses CWL version 1.0 specification and can run workflows on stand-alone MacOS/Linux servers, on clusters, or on a variety of cloud platforms. A sample CWL pipeline for processing of chromatin immunoprecipitation sequencing data is provided. Conclusions CWL-Airflow will provide users with the features of a fully fledged pipeline manager and the ability to execute CWL workflows anywhere Airflow can run—from a laptop to a cluster or cloud environment. CWL-Airflow is available under Apache License, version 2.0 (Apache-2.0), and can be downloaded from https://barski-lab.github.io/cwl-airflow, https://scicrunch.org/resolver/RRID:SCR_017196.

Photophysical and theoretical studies of peripherally halogenated octaphenoxyphthalocyanines

RSC Advances ◽  
2015 ◽  
Vol 5 (72) ◽  
pp. 58854-58864 ◽  
Author(s):  
Saad Makhseed ◽  
Basma Ghazal ◽  
Amr Mohamed Abdelmoniem ◽  
Veronika Novakova ◽  
Petr Zimcik
Keyword(s):  
Singlet Oxygen ◽  
Electronic Structures ◽  
Heavy Atom ◽  
Experimental Results ◽  
Quantum Yields ◽  
Theoretical Studies ◽  
Computational Studies ◽  
Two Dimensional ◽  
Heavy Atom Effect ◽  
Atom Effect

Computational studies validated the experimental results and revealing details about the electronic structures of novel halogenated phthalocyanines. Fluorescence and singlet oxygen quantum yields analysis revealed two-dimensional heavy atom effect.

scholarly journals THE AUTHORSHIP OF THE HISTORIA AUGUSTA: TWO NEW COMPUTATIONAL STUDIES

2016 ◽  
Vol 59 (2) ◽  
pp. 140-157 ◽  
Author(s):  
JUSTIN A. STOVER ◽  
MIKE KESTEMONT
Keyword(s):  
Principal Components ◽  
Computational Analysis ◽  
Computational Studies ◽  
Multiple Authorship ◽  
Established Method ◽  
Method Of Principal Components ◽  
Authorship Verification ◽  
Simple Alternative ◽  
Historia Augusta ◽  
Components Analysis

Abstract The case of the Historia Augusta, a collection of imperial biographies from Hadrian to Carus supposedly written by six different authors, provided the impetus for the introduction of computational methods into the Echtheitskritik of ancient authors in 1979. After a flurry of studies in the 1990s, interest waned, particularly because most of those studies seemed to support conclusions incompatible with the scholarly consensus on the question. In the paper, we approach this question with the new tool of authorship verification – one of the most promising approaches in forensic stylometry today – as well as the established method of principal components analysis to demonstrate that there is no simple alternative between single and multiple authorship, and that the results of a computational analysis are in fact compatible with the results obtained from historical, literary, and philological analysis.

scholarly journals Synthesis, Photophysical, and Computational Studies of a Bridged IrΙΙΙ-PtΙΙ Heterodimetallic Complex

Crystals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 236
Author(s):  
Si-Hai Wu ◽  
Dian-Xue Ma ◽  
Zhong-Liang Gong ◽  
Junjie Ma ◽  
Jiang-Yang Shao ◽  
...  
Keyword(s):  
Excited State ◽  
Electronic Structures ◽  
Theoretical Calculations ◽  
Excitation Wavelength ◽  
Computational Studies ◽  
Ambient Conditions ◽  
Excited State Lifetime ◽  
X Ray ◽  
Experimental Findings ◽  
Single Emission

An IrIII-PtII heterodimetallic complex [(ppy)2Ir(dapz)PtCl2]Cl (4), together with the corresponding monometallic complexes [(dapz)PtCl2] (2) and [(ppy)2Ir(dapz)]Cl (3) was designed and prepared, where dapz is 2,5-di(N-methyl-N′-(pyrid-2-yl)amino)pyrazine and ppy is 2-phenylpyridine, respectively. Single-crystal X-ray analysis was carried out for complex 4, displaying the intermolecular Pt∙∙∙Pt and aromatic plane∙∙∙plane distances of 3.839 and 3.886 Å, respectively. The monometallic complex 2 exhibits a single emission maximum at 432 nm with a shorter excited-state lifetime (τ) of 6 ns, while complex 3 exhibits an emission band at 454 nm with a longer excited-state lifetime of 135 ns in CH3CN (N2-saturated) under ambient conditions. In contrast, the heterodimetallic complex 4 displays intriguing excitation wavelength-dependent dual singlet and triplet emissions. Theoretical calculations of the electronic structures and absorption spectra of these complexes were carried out to assist the interpretation of these experimental findings.

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