scholarly journals Conformational impact of structural modifications in 2-fluorocyclohexanone

2017 ◽  
Vol 13 ◽  
pp. 1781-1787 ◽  
Author(s):  
Francisco A Martins ◽  
Josué M Silla ◽  
Matheus P Freitas
Keyword(s):  
Structural Changes ◽  
Conformational Equilibrium ◽  
Chemical Shifts ◽  
Conformational Stability ◽  
Three Dimensional ◽  
Building Blocks ◽  
Intramolecular Interactions ◽  
Coupling Constants ◽  
Structural Modifications ◽  
Gauche Effect

2-Haloketones are building blocks that combine physical, chemical and biological features of materials and bioactive compounds, while organic fluorine plays a fundamental role in the design of performance organic molecules. Since these features are dependent on the three-dimensional chemical structure of a molecule, simple structural modifications can affect its conformational stability and, consequently, the corresponding physicochemical/biological property of interest. In this work, structural changes in 2-fluorocyclohexanone were theoretically studied with the aim at finding intramolecular interactions that induce the conformational equilibrium towards the axial or equatorial conformer. The interactions evaluated were hydrogen bonding, hyperconjugation, electrostatic and steric effects. While the gauche effect, originated from hyperconjugative interactions, does not appear to cause some preferences for the axial conformation of organofluorine heterocycles, more classical effects indeed rule the conformational equilibrium of the compounds. Spectroscopic parameters (NMR chemical shifts and coupling constants), which can be useful to determine the stereochemistry and the interactions operating in the series of 2-fluorocyclohexanone derivatives, were also calculated.

scholarly journals Analysis of the structural variability of topologically associated domains as revealed by Hi-C

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Natalie Sauerwald ◽  
Akshat Singhal ◽  
Carl Kingsford
Keyword(s):  
Structural Changes ◽  
Chromosome Structure ◽  
Three Dimensional ◽  
Replication Timing ◽  
Building Blocks ◽  
Structural Features ◽  
Genetic Sequence ◽  
Experimental Variation ◽  
Topologically Associated Domains ◽  
Integral Role

Abstract Three-dimensional chromosome structure plays an integral role in gene expression and regulation, replication timing, and other cellular processes. Topologically associated domains (TADs), building blocks of chromosome structure, are genomic regions with higher contact frequencies within the region than outside the region. A central question is the degree to which TADs are conserved or vary between conditions. We analyze 137 Hi-C samples from 9 studies under 3 measures to quantify the effects of various sources of biological and experimental variation. We observe significant variation in TAD sets between both non-replicate and replicate samples, and provide initial evidence that this variability does not come from genetic sequence differences. The effects of experimental protocol differences are also measured, demonstrating that samples can have protocol-specific structural changes, but that TADs are generally robust to lab-specific differences. This study represents a systematic quantification of key factors influencing comparisons of chromosome structure, suggesting significant variability and the potential for cell-type-specific structural features, which has previously not been systematically explored. The lack of observed influence of heredity and genetic differences on chromosome structure suggests that factors other than the genetic sequence are driving this structure, which plays an important role in human disease and cellular functioning.

A Proton Magnetic Resonance Study of the Effect of 2′-O-Methylation on Ribonucleoside Conformation

1973 ◽  
Vol 51 (7) ◽  
pp. 1099-1106 ◽  
Author(s):  
Frank E. Hruska ◽  
Alan Mak ◽  
Harwant Singh ◽  
David Shugar
Keyword(s):  
Proton Magnetic Resonance ◽  
Molecular Conformation ◽  
Chemical Shifts ◽  
Three Dimensional ◽  
Coupling Constants ◽  
Dimensional Structure ◽  
Aqueous Environment ◽  
Magnetic Resonance Study ◽  
Proton Magnetic Resonance Study ◽  
Methyl Derivatives

The 100- and 220- MHz p.m.r. spectra of uridine, cytidine, and their 2′-O-methyl derivatives are obtained in aqueous solution at several temperatures. The experimental chemical shifts and coupling constants are discussed in terms of the overall molecular conformation. The conclusion is reached that 2′-O-methylation has little effect upon the three-dimensional structure of a nucleoside at the monomer level in an aqueous environment.

CYCLOHEXANE COMPOUNDS: IV. NUCLEAR MAGNETIC RESONANCE SPECTRA OF SOME DERIVATIVES OF THE STEREOISOMERIC 3-AMINO-1,2-CYCLOHEXANEDIOLS

1963 ◽  
Vol 41 (9) ◽  
pp. 2331-2338 ◽  
Author(s):  
F. A. L. Anet ◽  
R. A. B. Bannard ◽  
L. D. Hall
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Room Temperature ◽  
Conformational Equilibrium ◽  
Chemical Shifts ◽  
Chloroform Solution ◽  
Coupling Constants ◽  
Order Analysis ◽  
First Order ◽  
Nuclear Magnetic Resonance Spectra ◽  
Derivatives Of

The n.m.r. spectra of 1α-methoxy-2β-hydroxy-3α-aminocyclohexane, 1α-methoxy-2α-hydroxy-3β-aminocyclohexane, their N-acetyl and O,N-diacetyl derivatives, ethoxy analogues, and 3α-amino-1α,2β-cyclohexanediol and 3β-amino-1α,2β-cyclohexanediol triacetates were measured in chloroform solution. From the chemical shifts of the O- and/or N-acetyl methyl protons it was possible to assign conformations to all the substituted derivatives and in most cases the assignments thus made were confirmed by first-order analysis of the multiplet pattern from the methine protons. In all cases, the conformations found were those predicted on simple conformational grounds and no evidence for a conformational equilibrium at room temperature was obtained from the coupling constants. In general, the coupling constants for the methine protons followed the pattern predicted by the Karplus equation. Acetylation of the 1α-alkoxy-2α-hydroxy-3β-aminocyclohexanes with acetic anhydride gave both the O,N-diacetyl derivative and the O,N,N-triacetyl derivative.

The conformational equilibrium in [13C-1-methyl]-cis-1,4-dimethylcyclohexane

1980 ◽  
Vol 58 (23) ◽  
pp. 2709-2713 ◽  
Author(s):  
Harold Booth ◽  
Jeremy Ramsey Everett
Keyword(s):  
Conformational Equilibrium ◽  
Chemical Shifts ◽  
Relaxation Times ◽  
Lattice Relaxation ◽  
Coupling Constants ◽  
Spin Lattice Relaxation ◽  
Spin Lattice ◽  
Nuclear Overhauser ◽  
In Cis ◽  
C Nmr

The conformational equilibrium in [13C-1-methyl]-cis-1,4-dimethylcyclohexane has been assessed by (a) direct integration of signals due to equatorial and axial methyl carbons in the 13C nmr spectrum at 172 K and (b) by measurement of the 13C chemical shifts of C-1 and C-4 in the spectrum at 300 K. It is concluded that a 13C isotope effect on the position of the degenerate equilibrium in cis-1,4-dimethylcyclohexane is either nonexistent, or is too small to be detected by methods of analyses employed. The 13C nmr data incidental to the study (chemical shifts, coupling constants, spin–lattice relaxation times, nuclear Overhauser enhancements, and 1-bond isotope shifts) are recorded for the title compound and its trans-isomer.

scholarly journals Analysis of the structural variability of topologically associated domains as revealed by Hi-C

2018 ◽  
Author(s):  
Natalie Sauerwald ◽  
Akshat Singhal ◽  
Carl Kingsford
Keyword(s):  
Structural Changes ◽  
Chromosome Structure ◽  
Three Dimensional ◽  
Replication Timing ◽  
Building Blocks ◽  
Cellular Processes ◽  
Experimental Variation ◽  
Topologically Associated Domains ◽  
Integral Role ◽  
To Come

AbstractThree-dimensional chromosome structure plays an integral role in gene expression and regulation, replication timing, and other cellular processes. Topologically associating domains (TADs), one of the building blocks of chromosome structure, are genomic regions with higher contact frequencies within the region than outside the region. A central question is the degree to which TADs are conserved or vary between conditions. We analyze a set of 137 Hi-C samples from 9 different studies under 3 measures in order to quantify the effects of various sources of biological and experimental variation. We observe significant variation in TAD sets between both non-replicate and replicate samples, and show that this variability does not seem to come from genetic sequence differences. The effects of experimental protocol differences are also measured, demonstrating that samples can have protocol-specific structural changes, but that TADs are generally robust to lab-specific differences. This study represents a systematic quantification of the key factors influencing comparisons of chromosome structure.

scholarly journals Mechanical adaptation of brachiopod shells via hydration-induced structural changes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Johannes Ihli ◽  
Anna S. Schenk ◽  
Sabine Rosenfeldt ◽  
Klaus Wakonig ◽  
Mirko Holler ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Structural Changes ◽  
Molecular Level ◽  
Organic Matrix ◽  
Building Blocks ◽  
Hierarchical Organization ◽  
Mechanical Adaptation ◽  
X Ray ◽  
Structural Modifications ◽  
Complementary Set

AbstractThe function-optimized properties of biominerals arise from the hierarchical organization of primary building blocks. Alteration of properties in response to environmental stresses generally involves time-intensive processes of resorption and reprecipitation of mineral in the underlying organic scaffold. Here, we report that the load-bearing shells of the brachiopod Discinisca tenuis are an exception to this process. These shells can dynamically modulate their mechanical properties in response to a change in environment, switching from hard and stiff when dry to malleable when hydrated within minutes. Using ptychographic X-ray tomography, electron microscopy and spectroscopy, we describe their hierarchical structure and composition as a function of hydration to understand the structural motifs that generate this adaptability. Key is a complementary set of structural modifications, starting with the swelling of an organic matrix on the micron level via nanocrystal reorganization and ending in an intercalation process on the molecular level in response to hydration.

Application of stereological analysis of cell volume to isolated myocytes in culture with and without adrenergic innervation

1990 ◽  
Vol 48 (3) ◽  
pp. 416-417
Author(s):  
Jane K. Rosenthal ◽  
Dianne L. Atkins ◽  
William J. Marvin ◽  
Penny A. Krumm
Keyword(s):  
Cardiac Myocytes ◽  
Structural Changes ◽  
Three Dimensional ◽  
Adrenergic Innervation ◽  
Culture Cell ◽  
Serial Sections ◽  
Newborn Rats ◽  
Primary Culture Cell ◽  
Biological Studies ◽  
Cell Volumes

To comprehend structural changes in cardiac myocytes accompanying adrenergic innervation, it is essential that a three dimensional analysis be performed. To date, biological studies which utilize stereological methods have been limited to cells in tissue and in organs. Our laboratory has utilized current stereological techniques for measuring absolute volumes of individual myocytes in primary culture. Cell volumes are calculated for two distinct groups of cells at 96 hours in culture: isolated myocytes and myocytes innervated with adrenergic neurons (Figure 1).Cardiac myocytes are cultured from the ventricular apices of newborn rats. Cells are plated directly onto tissue culture dishes with or without preplated explants from the paravertebral thoracolumbar sympathetic chain. On day four cultures are photographed and marked for one-to-one cell location. Following conventional fixation and embeddment in eponate-12, the cells are relocated and mounted for microtomy. The cells are completely sectioned at 120nm in their parallel orientation to the surface of the dish (Figure 2). Serial sections are collected on formvar coated slotted grids and are recorded in sequence.

Going Beyond 3-D Imaging: Automated 3-D Montaged image Analysis of Cytological Specimens

1996 ◽  
Vol 54 ◽  
pp. 282-283
Author(s):  
Badrinath Roysam ◽  
Hakan Ancin ◽  
Douglas E. Becker ◽  
Robert W. Mackin ◽  
Matthew M. Chestnut ◽  
...  
Keyword(s):  
Image Analysis ◽  
Structural Changes ◽  
Sampling Methods ◽  
Spatial Clustering ◽  
Three Dimensional ◽  
Field Of View ◽  
Cell Counting ◽  
Depth Of Field ◽  
Tissue Cell ◽  
Tissue Organization

This paper summarizes recent advances made by this group in the automated three-dimensional (3-D) image analysis of cytological specimens that are much thicker than the depth of field, and much wider than the field of view of the microscope. The imaging of thick samples is motivated by the need to sample large volumes of tissue rapidly, make more accurate measurements than possible with 2-D sampling, and also to perform analysis in a manner that preserves the relative locations and 3-D structures of the cells. The motivation to study specimens much wider than the field of view arises when measurements and insights at the tissue, rather than the cell level are needed.The term “analysis” indicates a activities ranging from cell counting, neuron tracing, cell morphometry, measurement of tracers, through characterization of large populations of cells with regard to higher-level tissue organization by detecting patterns such as 3-D spatial clustering, the presence of subpopulations, and their relationships to each other. Of even more interest are changes in these parameters as a function of development, and as a reaction to external stimuli. There is a widespread need to measure structural changes in tissue caused by toxins, physiologic states, biochemicals, aging, development, and electrochemical or physical stimuli. These agents could affect the number of cells per unit volume of tissue, cell volume and shape, and cause structural changes in individual cells, inter-connections, or subtle changes in higher-level tissue architecture. It is important to process large intact volumes of tissue to achieve adequate sampling and sensitivity to subtle changes. It is desirable to perform such studies rapidly, with utmost automation, and at minimal cost. Automated 3-D image analysis methods offer unique advantages and opportunities, without making simplifying assumptions of tissue uniformity, unlike random sampling methods such as stereology.12 Although stereological methods are known to be statistically unbiased, they may not be statistically efficient. Another disadvantage of sampling methods is the lack of full visual confirmation - an attractive feature of image analysis based methods.

Conformational characterization of nucleosome structure by Electron Microscopy

1993 ◽  
Vol 51 ◽  
pp. 194-195
Author(s):  
Gregory J. Czarnota
Keyword(s):  
Electron Microscopy ◽  
Structural Changes ◽  
Physiological State ◽  
Gene Activation ◽  
Three Dimensional ◽  
Macromolecular Complex ◽  
Ultrastructural Studies ◽  
Ionic Environment ◽  
Nucleosome Structure ◽  
Dimensional Reconstruction

Chromatin structure at the fundamental level of the nucleosome is important in vital cellular processes. Recent biochemical and genetic analyses show that nucleosome structure and structural changes are very active participants in gene expression, facilitating or inhibiting transcription and reflecting the physiological state of the cell. Structural states and transitions for this macromolecular complex, composed of DNA wound about a heterotypic octamer of variously modified histone proteins, have been measured by physico-chemical techniques and by enzyme-accessibility and are recognized to occur with various post-translational modifications, gene activation, transformation and with ionic-environment. In spite of studies which indicate various forms of nucleosome structure, all current x-ray and neutron diffraction studies have consistently resulted in only one structure, suggestive of a static conformation. In contrast, two-dimensional electron microscopy studies and three-dimensional reconstruction techniques have yielded different structures. These fundamental differences between EM and other ultrastructural studies have created a long standing quandary, which I have addressed and resolved using spectroscopic electron microscopy and statistical analyses of nucleosome images in a study of nucleosome structure with ionic environment.

Sign in / Sign up

Export Citation Format

Share Document