Glycosylation under Thermodynamic Control: Synthesis of the Di- and the Hexasaccharide Fragments of the O-SP ofVibrio Cholerae O:1 Serotype Ogawa from Fully Functionalized Building Blocks

2007 ◽  
Vol 2007 (6) ◽  
pp. 988-1000 ◽  
Author(s):  
Roberto Adamo ◽  
Pavol Kováč
Keyword(s):  
Building Blocks ◽  
Control Synthesis ◽  
Thermodynamic Control

scholarly journals Controlling Supramolecular Plasticity through Stoichiometry

2019 ◽  
Author(s):  
David Komaromy ◽  
Theodora Tiemersma-Wegman ◽  
Johan Kemmink ◽  
Giuseppe Portale ◽  
Friso Aalbers ◽  
...  
Keyword(s):  
Binding Energy ◽  
Building Block ◽  
Systems Approach ◽  
Building Blocks ◽  
Supramolecular Assemblies ◽  
Energy Landscapes ◽  
Complex Energy ◽  
Thermodynamic Control ◽  
One To One

In this manuscript we describe how, by taking a systems approach, complex energy landscapes of supramolecular assemblies can be navigated using stoichiometry to control, with remarkable selectivity, which assembly gets populated. The perhaps counterintuitive finding is that it is not necessarily the assembly that, in a one-to-one comparison, is the most stable that wins the competition for common building blocks, even though the system is under thermodynamic control. Instead, an individually less stable assembly may completely dominate the system. This domination is possible when the building block stoichiometry in the system matches the stoichiometry of this specific assembly, allowing the system to maximize binding energy by making a large number of assemblies of moderate stability as opposed to a small number of more stable assemblies. <br>

Gene action in development

1970 ◽  
Vol 176 (1044) ◽  
pp. 347-366 ◽  
Keyword(s):  
Basal Body ◽  
Spatial Relations ◽  
Building Blocks ◽  
Control Synthesis ◽  
Basal Bodies ◽  
Cell Organelles ◽  
Negative Results ◽  
Molecular Building Blocks

This paper deals with processes occurring in the assembly of genic products into cell organelles and structures, especially with processes determining the initiation, location, orientation and number of cortical structures in the ciliated protozoan, Paramecium aurelia . The examples analysed experimentally are: ciliary basal bodies and their associated structures, the repeating unit territory of cortical structure, the pattern of path directions of the rows of basal bodies and unit territories, the distribution in the cortex of two different kinds of unit territories, and the ingestatory apparatus (vestibule and gullet). Among the processes that appear to occur are homonucleation, heteronucleation, and allosteric transitions, as found by others in the in vitro assembly of bacterial flagella, bacterial viruses, and the parts of ciliary microtubules and their appendages. In Paramecium , new basal bodies can arise only in one position and orientation, close and at right angles to an existing basal body at a specified spot. Unit territories reproduce by forming additional parts and subdividing. The information for the positioning and orientation of the developing parts of the unit territory is located within the unit itself and, when experimentally altered, reproduces in the altered orientation which cannot be corrected by genic action. This hereditary aspect of development is determined by an unbroken chain of self-reproducing arrangements of cortical parts. Search for DNA in the cortex gave negative results. Analysis of the hereditary determination of initiation, location, and orientation of the gullet gave results similar to those on the basal body and unit territory. Analysis of the hereditary determination of the path of the rows of unit territories and basal bodies and of the distribution of the two kinds of unit territories showed developmental and genetic control by spatial relations to the vestibule-gullet. Thus, for all corticaltra its examined, development is hereditarily determined by existing and self-reproducing cortical arrangements: the genes (or DNA) doubtless control synthesis of the molecular building blocks, but not their site of assembly or the position, orientation and number of assemblies. The flatworm Stenostomum also shows hereditary developmental control by self-perpetuating structural arrangements, two variations from normal (two kinds of doublet worms) reproducing true to type during asexual reproduction. Whether similar processes occur in the inheritance of the developmentally decisive organization of the amphibian egg is still an open question The processes described in this paper constitute but one of many options available for hereditary control of development.

scholarly journals Low-Cost Unattended Design of Miniaturized 4 × 4 Butler Matrices with Nonstandard Phase Differences

Sensors ◽  
2021 ◽  
Vol 21 (3) ◽  
pp. 851
Author(s):  
Adrian Bekasiewicz ◽  
Slawomir Koziel
Keyword(s):  
High Performance ◽  
Low Cost ◽  
Computational Cost ◽  
Numerical Algorithms ◽  
Building Blocks ◽  
Mobile Systems ◽  
Fine Tuning ◽  
Control Synthesis ◽  
Primary Concern ◽  
Phase Differences

Design of Butler matrices dedicated to Internet of Things and 5th generation (5G) mobile systems—where small size and high performance are of primary concern—is a challenging task that often exceeds capabilities of conventional techniques. Lack of appropriate, unified design approaches is a serious bottleneck for the development of Butler structures for contemporary applications. In this work, a low-cost bottom-up procedure for rigorous and unattended design of miniaturized 4 × 4 Butler matrices is proposed. The presented approach exploits numerical algorithms (governed by a set of suitable objective functions) to control synthesis, implementation, optimization, and fine-tuning of the structure and its individual building blocks. The framework is demonstrated using two miniaturized matrices with nonstandard output-port phase differences. Numerical results indicate that the computational cost of the design process using the presented framework is over 80% lower compared to the conventional approach. The footprints of optimized matrices are only 696 and 767 mm2, respectively. Small size and operation frequency of around 2.6 GHz make the circuits of potential use for mobile devices dedicated to work within a sub-6 GHz 5G spectrum. Both structures have been benchmarked against the state-of-the-art designs from the literature in terms of performance and size. Measurements of the fabricated Butler matrix prototype are also provided.

scholarly journals Metal Cyamelurates: Structural Diversity Caused by Kinetic and Thermodynamic Controls

2021 ◽  
Author(s):  
Albina S. Isbjakowa ◽  
Vladimir V Chernyshev ◽  
Victor A Tafeenko ◽  
Leonid A Aslanov
Keyword(s):  
Reaction Times ◽  
Structural Diversity ◽  
Building Blocks ◽  
Weak Acid ◽  
Crystal Nucleation ◽  
Kinetic Control ◽  
Thermodynamic Control ◽  
Structural Types ◽  
Copper Aluminum ◽  
Manganese Magnesium

Abstract The kinetic control of chemical reactions makes it possible both to isolate metastable substances with properties different from those of thermodynamically stable phases, and to obtain information useful for studying the crystal nucleation and further transformations of metastable phases into stable ones. Metal cyamelurates are suitable subjects for kinetic control in synthesis due to their easy crystallization and short reaction times. In this work cobalt, manganese, magnesium, copper, aluminum, chromium, calcium and lead cyamelurates were obtained and their crystal structures were determined. Most syntheses at room temperature take place under kinetic control, and this often leads to a mixture of phases. KM(C6N7O3)·5H2O (M=Co(II), Mn(II)) powders consisted of one crystalline compound. An increase in temperature leads to thermodynamic control, which is proved by registration of Mn(C6N7O3H)·5H2O and KMg(C6N7O3)·5H2O crystalline phases. It was possible to isolate Ca(C6 N7O3H)·6H2O and Pb(C6N7O3H)·3H2O from the mixture by washing samples with a weak acid solution. As a result of the work, five different structural types were obtained, including KCu(C6N7O3)∙2H2O and KM(C6N7O3H) 2 ·6H2O (M=Al, Cr(III)). Despite the diversity of salts obtained as a result of thermodynamic or kinetic control, practically the same building blocks form the crystal structure of cyamelurates. The hypothesis of nucleation in a colloidal micelle with electric double layer can be applied to the compounds listed above.

scholarly journals Controlling Supramolecular Plasticity through Stoichiometry

2019 ◽  
Author(s):  
David Komaromy ◽  
Theodora Tiemersma-Wegman ◽  
Johan Kemmink ◽  
Giuseppe Portale ◽  
Friso Aalbers ◽  
...  
Keyword(s):  
Binding Energy ◽  
Building Block ◽  
Systems Approach ◽  
Building Blocks ◽  
Supramolecular Assemblies ◽  
Energy Landscapes ◽  
Complex Energy ◽  
Thermodynamic Control ◽  
One To One

In this manuscript we describe how, by taking a systems approach, complex energy landscapes of supramolecular assemblies can be navigated using stoichiometry to control, with remarkable selectivity, which assembly gets populated. The perhaps counterintuitive finding is that it is not necessarily the assembly that, in a one-to-one comparison, is the most stable that wins the competition for common building blocks, even though the system is under thermodynamic control. Instead, an individually less stable assembly may completely dominate the system. This domination is possible when the building block stoichiometry in the system matches the stoichiometry of this specific assembly, allowing the system to maximize binding energy by making a large number of assemblies of moderate stability as opposed to a small number of more stable assemblies. <br>

scholarly journals DNA functionalization by dynamic chemistry

2016 ◽  
Vol 12 ◽  
pp. 2136-2144 ◽  
Author(s):  
Zeynep Kanlidere ◽  
Oleg Jochim ◽  
Marta Cal ◽  
Ulf Diederichsen
Keyword(s):  
Deoxyribonucleic Acid ◽  
Solid Phase ◽  
Building Blocks ◽  
Thermodynamic Control ◽  
Dna Templates ◽  
Phase Synthesis ◽  
Dynamic Combinatorial Chemistry ◽  
Dna Oligonucleotides ◽  
Reversible Reactions ◽  
Modified Nucleobases

Dynamic combinatorial chemistry (DCC) is an attractive method to efficiently generate libraries of molecules from simpler building blocks by reversible reactions under thermodynamic control. Here we focus on the chemical modification of DNA oligonucleotides with acyclic diol linkers and demonstrate their potential for the deoxyribonucleic acid functionalization and generation of libraries of reversibly interconverting building blocks. The syntheses of phosphoramidite building blocks derived from D-threoninol are presented in two variants with protected amino or thiol groups. The threoninol building blocks were successfully incorporated via automated solid-phase synthesis into 13mer oligonucleotides. The amino group containing phosphoramidite was used together with complementary single-strand DNA templates that influenced the Watson–Crick base-pairing equilibrium in the mixture with a set of aldehyde modified nucleobases. A significant fraction of all possible base-pair mismatches was obtained, whereas, the highest selectivity (over 80%) was found for the guanine aldehyde templated by the complementary cytosine containing DNA. The elevated occurrence of mismatches can be explained by increased backbone plasticity derived from the linear threoninol building block as a cyclic deoxyribose analogue.

Photochemical Evolution of Interstellar/Precometary Organic Material

1997 ◽  
Vol 161 ◽  
pp. 23-47 ◽  
Author(s):  
Louis J. Allamandola ◽  
Max P. Bernstein ◽  
Scott A. Sandford
Keyword(s):  
Origin Of Life ◽  
Building Blocks ◽  
Complex Species ◽  
Infrared Observations ◽  
Interstellar Ice ◽  
Polycyclic Aromatic ◽  
Ultraviolet Photolysis ◽  
The Origin Of Life ◽  
Simple Molecules ◽  
Complex Organic

AbstractInfrared observations, combined with realistic laboratory simulations, have revolutionized our understanding of interstellar ice and dust, the building blocks of comets. Since comets are thought to be a major source of the volatiles on the primative earth, their organic inventory is of central importance to questions concerning the origin of life. Ices in molecular clouds contain the very simple molecules H2O, CH3OH, CO, CO2, CH4, H2, and probably some NH3and H2CO, as well as more complex species including nitriles, ketones, and esters. The evidence for these, as well as carbonrich materials such as polycyclic aromatic hydrocarbons (PAHs), microdiamonds, and amorphous carbon is briefly reviewed. This is followed by a detailed summary of interstellar/precometary ice photochemical evolution based on laboratory studies of realistic polar ice analogs. Ultraviolet photolysis of these ices produces H2, H2CO, CO2, CO, CH4, HCO, and the moderately complex organic molecules: CH3CH2OH (ethanol), HC(= O)NH2(formamide), CH3C(= O)NH2(acetamide), R-CN (nitriles), and hexamethylenetetramine (HMT, C6H12N4), as well as more complex species including polyoxymethylene and related species (POMs), amides, and ketones. The ready formation of these organic species from simple starting mixtures, the ice chemistry that ensues when these ices are mildly warmed, plus the observation that the more complex refractory photoproducts show lipid-like behavior and readily self organize into droplets upon exposure to liquid water suggest that comets may have played an important role in the origin of life.

Laboratory and in-situ analysis of comet dust

1988 ◽  
Vol 46 ◽  
pp. 8-9
Author(s):  
D.E. Brownlee ◽  
A.L. Albee
Keyword(s):  
Electron Microscopy ◽  
Solar System ◽  
Laboratory Study ◽  
Isotopic Analysis ◽  
Building Blocks ◽  
Sem Analysis ◽  
Early Solar System ◽  
Cometary Material ◽  
Comet Dust

Comets are primitive, kilometer-sized bodies that formed in the outer regions of the solar system. Composed of ice and dust, comets are generally believed to be relic building blocks of the outer solar system that have been preserved at cryogenic temperatures since the formation of the Sun and planets. The analysis of cometary material is particularly important because the properties of cometary material provide direct information on the processes and environments that formed and influenced solid matter both in the early solar system and in the interstellar environments that preceded it.The first direct analyses of proven comet dust were made during the Soviet and European spacecraft encounters with Comet Halley in 1986. These missions carried time-of-flight mass spectrometers that measured mass spectra of individual micron and smaller particles. The Halley measurements were semi-quantitative but they showed that comet dust is a complex fine-grained mixture of silicates and organic material. A full understanding of comet dust will require detailed morphological, mineralogical, elemental and isotopic analysis at the finest possible scale. Electron microscopy and related microbeam techniques will play key roles in the analysis. The present and future of electron microscopy of comet samples involves laboratory study of micrometeorites collected in the stratosphere, in-situ SEM analysis of particles collected at a comet and laboratory study of samples collected from a comet and returned to the Earth for detailed study.

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