Heavy-Atom Tunneling Processes during Denitrogenation of 2,3-Diazabicyclo[2.2.1]hept-2-ene and Ring Closure of Cyclopentane-1,3-diyl Diradical. Stereoselectivity in Tunneling and Matrix Effect

2020 ◽  
Vol 85 (14) ◽  
pp. 8881-8892 ◽  
Author(s):  
Sujan K. Sarkar ◽  
Ephrath Solel ◽  
Sebastian Kozuch ◽  
Manabu Abe
Keyword(s):  
Matrix Effect ◽  
Heavy Atom ◽  
Ring Closure

Spin-forbidden heavy-atom tunneling in the ring-closure of triplet cyclopentane-1,3-diyl

2021 ◽  
Author(s):  
Luís P. Viegas ◽  
Cláudio Manaia Nunes ◽  
Rui Fausto
Keyword(s):  
Heavy Atom ◽  
Ring Closure ◽  
Quantum Mechanical ◽  
Quantum Mechanical Tunneling

In 1975, Buchwalter and Closs reported one of the first examples of heavy-atom quantum mechanical tunneling (QMT) by studying the ring closure of triplet cyclopentane-1,3-diyl to singlet bicyclo[2.1.0]pentane in cryogenic...

scholarly journals Dimerization reactions of aryl selenophen-2-yl-substituted thiocarbonyl S-methanides as diradical processes: a computational study

2017 ◽  
Vol 13 ◽  
pp. 410-416 ◽  
Author(s):  
Michael L McKee ◽  
Grzegorz Mlostoń ◽  
Katarzyna Urbaniak ◽  
Heinz Heimgartner
Keyword(s):  
Computational Methods ◽  
Computational Study ◽  
Heavy Atom ◽  
Ring Closure ◽  
Reactive Intermediate

An intriguing stepwise diradical mechanism of the dimerization of the reactive intermediate (thiocarbonyl S-methanide) appearing in the reaction of phenyl selenophen-2-yl thioketone with diazomethane was studied by means of computational methods. The preferred formation of the unusual macroheterocycle, competitive with the 1,3-ring closure leading to a thiirane and the head-to-head dimerization yielding a 1,4-dithiane derivative, respectively, was explained based on the analysis of the structure of the favored conformer of the intermediate, delocalized diradical species. The influence of selenium as a ‘heavy atom’ for stabilization of this intermediate has been emphasized.

Isomorphous replacement in electron diffraction of wet crystals of rat hemoglobin

1983 ◽  
Vol 41 ◽  
pp. 446-447
Author(s):  
William F. Tivol ◽  
Murray Vernon King ◽  
D. F. Parsons
Keyword(s):  
Electron Diffraction ◽  
Heavy Atom ◽  
Isomorphous Substitution ◽  
X Ray Diffraction ◽  
Salt Solutions ◽  
X Ray ◽  
Isomorphous Replacement ◽  
Structure Factors ◽  
Diffraction Structure ◽  
The Mean

Feasibility of isomorphous substitution in electron diffraction is supported by a calculation of the mean alteration of the electron-diffraction structure factors for hemoglobin crystals caused by substituting two mercury atoms per molecule, following Green, Ingram & Perutz, but with allowance for the proportionality of f to Z3/4 for electron diffraction. This yields a mean net change in F of 12.5%, as contrasted with 22.8% for x-ray diffraction.Use of the hydration chamber in electron diffraction opens prospects for examining many proteins that yield only very thin crystals not suitable for x-ray diffraction. Examination in the wet state avoids treatments that could cause translocation of the heavy-atom labels or distortion of the crystal. Combined with low-fluence techniques, it enables study of the protein in a state as close to native as possible.We have undertaken a study of crystals of rat hemoglobin by electron diffraction in the wet state. Rat hemoglobin offers a certain advantage for hydration-chamber work over other hemoglobins in that it can be crystallized from distilled water instead of salt solutions.

A Base Specific Single Heavy Atom Stain for Electron Microscopy

1972 ◽  
Vol 30 ◽  
pp. 184-185
Author(s):  
J. P. Langmore ◽  
N. R. Cozzarelli ◽  
A. V. Crewe
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
High Resolution ◽  
Elastic Scattering ◽  
Heavy Atom ◽  
High Vacuum ◽  
Heavy Atoms ◽  
Large Movement ◽  
Base Sequencing ◽  
Scanning Electron

A system has been developed to allow highly specific derivatization of the thymine bases of DNA with mercurial compounds wich should be visible in the high resolution scanning electron microscope. Three problems must be completely solved before this staining system will be useful for base sequencing by electron microscopy: 1) the staining must be shown to be highly specific for one base, 2) the stained DNA must remain intact in a high vacuum on a thin support film suitable for microscopy, 3) the arrangement of heavy atoms on the DNA must be determined by the elastic scattering of electrons in the microscope without loss or large movement of heavy atoms.

Correction of the contrast transfer function to determine the radial density distribution of frozen-hydrated tobacco mosaic virus

1992 ◽  
Vol 50 (1) ◽  
pp. 536-537
Author(s):  
Michael F. Smith ◽  
John P. Langmore
Keyword(s):  
Transfer Function ◽  
Phase Contrast ◽  
Heavy Atom ◽  
Biological Molecules ◽  
Frequency Compensation ◽  
Contrast Transfer Function ◽  
High Background ◽  
Low Contrast ◽  
Radial Density Distribution ◽  
Excellent Preservation

The purpose of image reconstruction is to determine the mass densities within molecules by analysis of the intensities within images. Cryo-EM offers this possibility by virtue of the excellent preservation of internal structure without heavy atom staining. Cryo-EM images, however, have low contrast because of the similarity between the density of biological material and the density of vitreous ice. The images also contain a high background of inelastic scattering. To overcome the low signal and high background, cryo-images are typically recorded 1-3 μm underfocus to maximize phase contrast. Under those conditions the image intensities bear little resemblance to the object, due to the dependence of the contrast transfer function (CTF) upon spatial frequency. Compensation (i.e., correction) for the CTF is theoretically possible, but implementation has been rare. Despite numerous studies of molecules in ice, there has never been a quantitative evaluation of compensated images of biological molecules of known structure.

Direct STEM ADF imaging of gold on silicon (111)

1989 ◽  
Vol 47 ◽  
pp. 472-473
Author(s):  
P. Xu ◽  
E. J. Kirkland ◽  
J. Silcox
Keyword(s):  
Film Growth ◽  
Heavy Atom ◽  
High Vacuum ◽  
Dark Field ◽  
Thin Metal Film ◽  
Base Pressure ◽  
Ultra High Vacuum ◽  
Specimen Preparation ◽  
Dark Field Imaging ◽  
Wide Range

Many studies of thin metal film growth and the formation of metal-semiconductor contacts have been performed using a wide range of experimental methods. STEM annular dark field imaging could be an important complement since it may allow direct imaging of a single heavy atom on a thin silicon substrate. This would enable studies of the local atomic arrangements and defects in the initial stage of metal silicide formation.Preliminary experiments were performed in an ultra-high vacuum VG HB501A STEM with a base pressure of 1 × 10-10 mbar. An antechamber directly attached to the microscope for specimen preparation has a base pressure of 2×l0-10 mbar. A thin single crystal membrane was fabricated by anodic etching and subsequent reactive etching. The specimen was cleaned by the Shiraki method and had a very thin oxide layer left on the surface. 5 Å of gold was deposited on the specimen at room temperature from a tungsten filament coil monitored by a quartz crystal monitor.

High resolution mapping of nucleic acid containing complexes in vitro and in situ

1996 ◽  
Vol 54 ◽  
pp. 48-49
Author(s):  
D. P. Bazett-Jones ◽  
M. J. Hendzel
Keyword(s):  
Nucleic Acid ◽  
High Resolution ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Heavy Atom ◽  
Regulation Of Transcription ◽  
High Exposure ◽  
Resolution Mapping ◽  
Tata Sequence

Structural analysis of combinations of nucleosomes and transcription factors on promoter and enhancer elements is necessary in order to understand the molecular mechanisms responsible for the regulation of transcription initiation. Such complexes are often not amenable to study by high resolution crystallographic techniques. We have been applying electron spectroscopic imaging (ESI) to specific problems in molecular biology related to transcription regulation. There are several advantages that this technique offers in studies of nucleoprotein complexes. First, an intermediate level of spatial resolution can be achieved because heavy atom contrast agents are not necessary. Second, mass and stoichiometric relationships of protein and nucleic acid can be estimated by phosphorus detection, an element in much higher proportions in nucleic acid than protein. Third, wrapping or bending of the DNA by the protein constituents can be observed by phosphorus mapping of the complexes. Even when ESI is used with high exposure of electrons to the specimen, important macromolecular information may be provided. For example, an image of the TATA binding protein (TBP) bound to DNA is shown in the Figure (top panel). It can be seen that the protein distorts the DNA away from itself and much of its mass sits off the DNA helix axis. Moreover, phosphorus and mass estimates demonstrate whether one or two TBP molecules interact with this particular promoter TATA sequence.

Refinement of light atoms in heavy atom structures*

1971 ◽  
Vol 133 (133) ◽  
pp. 150-167 ◽  
Author(s):  
Effi Huber-Buser
Keyword(s):  
Heavy Atom ◽  
Light Atoms
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