EPR and modelling studies of hydrogen-abstraction reactions relevant to polyolefin cross-linking and grafting chemistryElectronic supplementary information (ESI) available: computed 3D structures of the transition states of hydrogen abstraction from 2,4-dimethylpentane by tert-butoxyl radical. “1 ry24dmp.pdb”: H-abstraction from the methyl group (to generate a primary radical). “2ry24dmp.pdb”: H-abstraction from the central methylene group (to generate a secondary radical). “3 ry24dmp.pdb”: H-abstraction from the methine group (to generate a tertiary radical). See http://www.rsc.org/suppdata/ob/b2/b212543a/

2003 ◽  
Vol 1 (7) ◽  
pp. 1181-1190 ◽  
Author(s):  
Susana Camara ◽  
Bruce C. Gilbert ◽  
Robert J. Meier ◽  
Martin van Duin ◽  
Adrian C. Whitwood
Keyword(s):  
Hydrogen Abstraction ◽  
Transition States ◽  
Supplementary Information ◽  
Cross Linking ◽  
Methyl Group ◽  
Primary Radical ◽  
3D Structures ◽  
Modelling Studies ◽  
Secondary Radical ◽  
Methylene Group

A Reinvestigation of the Deceptively Simple Reaction of Toluene with ●OH, and the Fate of the Benzyl Radical. I. a Combined Thermodynamic and Kinetic Study on the Competition Between ●OH Addition and Hydrogen Abstraction Reactions.

2019 ◽  
Author(s):  
Zoi Salta ◽  
Agnie M. Kosmas ◽  
Marc E. Segovia ◽  
Martina Kieninger ◽  
Oscar Ventura ◽  
...  
Keyword(s):  
Density Functional ◽  
Room Temperature ◽  
Hydrogen Abstraction ◽  
Reaction Rates ◽  
Composite Model ◽  
Alternative Mechanism ◽  
Radical Intermediate ◽  
Experimental Conditions ◽  
Methyl Group ◽  
Benzyl Radical

This work reports density functional and composite model chemistry calculations performed on the reactions of toluene with the hydroxyl radical. Both experimentally observed H-abstraction from the methyl group and possible additions to the phenyl ring were investigated. Reaction enthalpies and heights of the barriers suggest that H-abstraction is more favorable than ●OH addition to the ring. The calculated reaction rates at room temperature and the radical-intermediate product fractions support this view. This is somehow contradictory with the fact that, under most experimental conditions, cresols are observed in a larger concentration than benzaldehyde. Since the accepted mechanism for benzaldehyde formation involves H-abstraction, a contradiction arises that begs for an explanation. In this first part of our work we give the evidences that support the preference of hydrogen abstraction over ●OH addition and suggest an alternative mechanism which shows that cresols can actually arise also from the former reaction and not only from the latter.

A Reinvestigation of the Deceptively Simple Reaction of Toluene with ●OH, and the Fate of the Benzyl Radical. I. a Combined Thermodynamic and Kinetic Study on the Competition Between ●OH Addition and Hydrogen Abstraction Reactions.

2019 ◽  
Author(s):  
Zoi Salta ◽  
Agnie M. Kosmas ◽  
Marc E. Segovia ◽  
Martina Kieninger ◽  
Oscar Ventura ◽  
...  
Keyword(s):  
Density Functional ◽  
Room Temperature ◽  
Hydrogen Abstraction ◽  
Reaction Rates ◽  
Composite Model ◽  
Alternative Mechanism ◽  
Radical Intermediate ◽  
Experimental Conditions ◽  
Methyl Group ◽  
Benzyl Radical

This work reports density functional and composite model chemistry calculations performed on the reactions of toluene with the hydroxyl radical. Both experimentally observed H-abstraction from the methyl group and possible additions to the phenyl ring were investigated. Reaction enthalpies and heights of the barriers suggest that H-abstraction is more favorable than ●OH addition to the ring. The calculated reaction rates at room temperature and the radical-intermediate product fractions support this view. This is somehow contradictory with the fact that, under most experimental conditions, cresols are observed in a larger concentration than benzaldehyde. Since the accepted mechanism for benzaldehyde formation involves H-abstraction, a contradiction arises that begs for an explanation. In this first part of our work we give the evidences that support the preference of hydrogen abstraction over ●OH addition and suggest an alternative mechanism which shows that cresols can actually arise also from the former reaction and not only from the latter.

The photochemical reactivity of some benzoylthiophenes. IV. The effect of an adjacent methyl group on the excited state reactivity of 3-benzoylthiophene

1978 ◽  
Vol 56 (15) ◽  
pp. 1970-1984 ◽  
Author(s):  
D. R. Arnold ◽  
C. P. Hadjiantoniou
Keyword(s):  
Hydrogen Abstraction ◽  
Thiophene Ring ◽  
Emission Spectra ◽  
Photochemical Reactions ◽  
Triplet States ◽  
Photochemical Reactivity ◽  
Methyl Group ◽  
State Diagrams ◽  
Phosphorescence Emission ◽  
Intramolecular Hydrogen

The electronic absorption and phosphorescence emission spectra and the photochemical reactivity of several methyl-3-benzoylthiophenes (2- and 4-methyl-3-benzoylthiophene (1, 2), 2,5-dimethyl-3-benzoylthiophene (3), and 3-(2-methylbenzoyl)thiophene (4)) have been studied. Partial state diagrams have been constructed. The lowest energy absorption in hexane solution in every case is the carbonyl n → π* transition. The two lowest triplet states of these ketones are close in energy and, in fact, the nature of the emitting triplet (n,π* or π,π*) depends upon the position of methyl substitution and upon the solvent. The photochemical reactions studied include intramolecular hydrogen abstraction (revealed by deuterium exchange in the adjacent methyl group upon irradiation in perdeuteriomethanol solution), photocycloaddition of dimethyl acetylenedicarboxylate to the thiophene ring, and photocycloaddition of isobutylene to the carbonyl group. Generalizations, potentially useful for predicting photochemical reactivity of these and other aromatic ketones are summarized.

FREE RADICALS OF BIOLOGICAL INTEREST: PART II. ELECTRON SPIN RESONANCE (ESR) SPECTRA OF 2537 A IRRADIATED AMINO ACIDS

1967 ◽  
Vol 45 (12) ◽  
pp. 1831-1839 ◽  
Author(s):  
W. F. Forbes ◽  
P. D. Sullivan
Keyword(s):  
Amino Acids ◽  
Electron Spin Resonance ◽  
Electron Spin ◽  
Hydrogen Abstraction ◽  
Esr Spectra ◽  
Side Chain ◽  
Biological Interest ◽  
Spin Resonance ◽  
Cyclohexadienyl Radical ◽  
Secondary Radical

Polycrystalline amino acids, when irradiated with 2537 Å light, afford a variety of electron spin resonance signals. These signals are generally stable at room temperature for relatively long periods of time. For a number of the spectra obtained, there is evidence that more than one radical species contributes to the observed spectra. The signals obtained frequently differ from those obtained on exposure to ionizing radiation. The postulated species formed can often be visualized as being formed by effective hydrogen abstraction from the alkyl-substituted tertiary carbon atom or from the —OH, —SH or —NH group contained in the side chain. For L-phenylalanine a secondary radical is obtained, which is ascribed to a cyclohexadienyl radical.

scholarly journals Deep-learning with synthetic data enables automated picking of cryo-EM particle images of biological macromolecules

2019 ◽  
Author(s):  
Ruijie Yao ◽  
Jiaqiang Qian ◽  
Qiang Huang
Keyword(s):  
Deep Learning ◽  
Single Particle ◽  
Feature Matching ◽  
Synthetic Data ◽  
Supplementary Information ◽  
Particle Analysis ◽  
Biological Macromolecules ◽  
Low Contrast ◽  
3D Structures ◽  
Particle Images

Abstract Motivation Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique for determining 3D structures of biological macromolecules at near-atomic resolution. However, this approach requires picking huge numbers of macromolecular particle images from thousands of low-contrast, high-noisy electron micrographs. Although machine-learning methods were developed to get rid of this bottleneck, it still lacks universal methods that could automatically picking the noisy cryo-EM particles of various macromolecules. Results Here, we present a deep-learning segmentation model that employs fully convolutional networks trained with synthetic data of known 3D structures, called PARSED (PARticle SEgmentation Detector). Without using any experimental information, PARSED could automatically segment the cryo-EM particles in a whole micrograph at a time, enabling faster particle picking than previous template/feature-matching and particle-classification methods. Applications to six large public cryo-EM datasets clearly validated its universal ability to pick macromolecular particles of various sizes. Thus, our deep-learning method could break the particle-picking bottleneck in the single-particle analysis, and thereby accelerates the high-resolution structure determination by cryo-EM. Availability and implementation The PARSED package and user manual for noncommercial use are available as Supplementary Material (in the compressed file: parsed_v1.zip). Supplementary information Supplementary data are available at Bioinformatics online.

Ambident Heterocyclic Reactivity: Alkylation of 4-Substituted and 2,4-Disubstituted Benzimidazoles

1994 ◽  
Vol 47 (8) ◽  
pp. 1523 ◽  
Author(s):  
MR Haque ◽  
M Rasmussen
Keyword(s):  
Hydrogen Bonding ◽  
Transition State ◽  
Electrostatic Field ◽  
Transition States ◽  
Alkyl Halides ◽  
Methyl Group ◽  
Site Selectivity ◽  
Leaving Group ◽  
Standard Set ◽  
Specific Association

The N1/N3-alkylation patterns of 4-amino-, 4-methyl- and 4-nitro-benzimidazole anions, and their 2-methyl analogues, with a standard set of primary alkyl halides (in dimethylformamide, 30°) have been determined and compared. The observed regioselectivities are dominated by proximal effects-electrostatic field, non-bonded steric and in some cases specific association (hydrogen bonding)-the interplay of which is critically dependent on the (variable) geometries of the SN2 transition states involved, in particular on the N---C distance of the developing N-alkyl bonds. The presence of a symmetrically placed 2-methyl group produces an enhanced N1/N3 site selectivity, very sensitive to the loose-tight nature of the transition state. Halide leaving group effects on butylation regioselectivities of 2-unsubstituted, 2-ethoxy-, 2-methyl- and 2-chloro-4-methylbenzimidazole anions, whilst small, are consistent with a Bell-Evans-Polanyi analysis of SN2 transition state variations, with the earlier transition states of CH3(CH2)3I leading to reduced regioselectivities.

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