scholarly journals Non-Kolbe electrolysis of N-protected-α-amino acids: a standardized method for the synthesis of N-protected (1-methoxyalkyl)amines

RSC Advances ◽  
2022 ◽  
Vol 12 (4) ◽  
pp. 2107-2114
Author(s):  
A. Walęcka-Kurczyk ◽  
J. Adamek ◽  
K. Walczak ◽  
M. Michalak ◽  
A. Październiok-Holewa
Keyword(s):  
Amino Acids ◽  
Electrochemical Method ◽  
Kolbe Electrolysis ◽  
Standardized Method ◽  
User Friendly

A high-yielding, standardized, electrochemical method for the synthesis of N-protected (1-methoxyalkyl)amines using commercially available, user-friendly kit – not only for “electro-curious” chemists.

scholarly journals TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
David Ferro-Costas ◽  
Irea Mosquera-Lois ◽  
Antonio Fernández-Ramos
Keyword(s):  
Amino Acids ◽  
Electronic Structure ◽  
Energy Surface ◽  
Random Search ◽  
Torsional Potential ◽  
Complete Work ◽  
Chemical Knowledge ◽  
Validation Tests ◽  
User Friendly

AbstractIn this work, we introduce , a user-friendly software written in Python 3 and designed to find all the torsional conformers of flexible acyclic molecules in an automatic fashion. For the mapping of the torsional potential energy surface, the algorithm implemented in combines two searching strategies: preconditioned and stochastic. The former is a type of systematic search based on chemical knowledge and should be carried out before the stochastic (random) search. The algorithm applies several validation tests to accelerate the exploration of the torsional space. For instance, the optimized structures are stored and this information is used to prevent revisiting these points and their surroundings in future iterations. operates with a dual-level strategy by which the initial search is carried out at an inexpensive electronic structure level of theory and the located conformers are reoptimized at a higher level. Additionally, the program takes advantage of conformational enantiomerism, when possible. As a case study, and in order to exemplify the effectiveness and capabilities of this program, we have employed to locate the conformers of the twenty proteinogenic amino acids in their neutral canonical form. has produced a number of conformers that roughly doubles the amount of the most complete work to date. Graphical Abstract

scholarly journals Estimation of biomass composition from genomic and transcriptomic information

2016 ◽  
Vol 13 (2) ◽  
pp. 1-14 ◽  
Author(s):  
Sophia Santos ◽  
Isabel Rocha
Keyword(s):  
Experimental Data ◽  
Amino Acids ◽  
Metabolic Model ◽  
Good Alternative ◽  
Biomass Composition ◽  
Biomass Equation ◽  
Transcriptomic Data ◽  
Balance Analysis ◽  
User Friendly ◽  
Genome Information

SummaryGiven the great potential impact of the growing number of complete genome-scale metabolic network reconstructions of microorganisms, bioinformatics tools are needed to simplify and accelerate the course of knowledge in this field. One essential component of a genomescale metabolic model is its biomass equation, whose maximization is one of the most common objective functions used in Flux Balance Analysis formulations. Some components of biomass, such as amino acids and nucleotides, can be estimated from genome information, providing reliable data without the need of performing lab experiments. In this work a java tool is proposed that estimates microbial biomass composition in amino acids and nucleotides, from genome and transcriptomic information, using as input files sequences in FASTA format and files with transcriptomic data in the csv format. This application allows to obtain the results rapidly and is also a user-friendly tool for users with any or little background in informatics (http://darwin.di.uminho.pt/biomass/). The results obtained using this tool are fairly close to experimental data, showing that the estimation of amino acid and nucleotide compositions from genome information and from transcriptomic data is a good alternative when no experimental data is available.

scholarly journals When Second Best Is Good Enough: Another Probabilistic Look at Saturation Mutagenesis

2011 ◽  
Vol 78 (1) ◽  
pp. 258-262 ◽  
Author(s):  
Yuval Nov
Keyword(s):  
Amino Acids ◽  
Computer Program ◽  
Saturation Mutagenesis ◽  
Library Size ◽  
Second Best ◽  
Randomization Scheme ◽  
Design Requirements ◽  
User Friendly ◽  
New Criteria

ABSTRACTWe developed new criteria for determining the library size in a saturation mutagenesis experiment. When the number of all possible distinct variants is large, any of the top-performing variants (e.g., any of the top three) is likely to meet the design requirements, so the probability that the library contains at least one of them is a sensible criterion for determining the library size. By using a criterion of this type, one may significantly reduce the library size and thus save costs and labor while minimally compromising the quality of the best variant discovered. We present the probabilistic tools underlying these criteria and use them to compare the efficiencies of four randomization schemes: NNN, which uses all 64 codons; NNB, which uses 48 codons; NNK, which uses 32 codons; and MAX, which assigns equal probabilities to each of the 20 amino acids. MAX was found to be the most efficient randomization scheme and NNN the least efficient. TopLib, a computer program for carrying out the related calculations, is available through a user-friendly Web server.

Torsiflex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids

2021 ◽  
Author(s):  
David Ferro-Costas ◽  
Irea Mosquera-Lois ◽  
Antonio Fernandez-Ramos
Keyword(s):  
Amino Acids ◽  
Electronic Structure ◽  
Energy Surface ◽  
Random Search ◽  
Torsional Potential ◽  
Complete Work ◽  
Chemical Knowledge ◽  
Validation Tests ◽  
User Friendly

Abstract In this work, we introduce TorsiFlex, a user-friendly software written in Python 3 and designed to find all the torsional conformers of flexible acyclic molecules in an automatic fashion. For the mapping of the torsional potential energy surface, the algorithm implemented in TorsiFlex combines two searching strategies: preconditioned and stochastic. The former is a type of systematic search based on chemical knowledge and should be carried out before the stochastic (random) search. The algorithm applies several validation tests to accelerate the exploration of the torsional space. For instance, the optimized structures are stored and this information is used to prevent revisiting these points and their surroundings in future iterations. TorsiFlex operates with a dual-level strategy by which the initial search is carried out at an inexpensive electronic structure level of theory and the located conformers are reoptimized at a higher level. Additionally, the program takes advantage of conformational enantiomerism, when possible. As a case study, and in order to exemplify the effectiveness and capabilities of this program, we have employed TorsiFlex to locate the conformers of the twenty proteinogenic amino acids in their neutral canonical form. TorsiFlex has produced a number of conformers that roughly doubles the amount of the most complete work to date.

Protein Stability Determination (PSD): A Tool for Proteomics Analysis

2018 ◽  
Vol 14 (1) ◽  
pp. 70-77
Author(s):  
Anindya Sundar Panja ◽  
Akash Nag ◽  
Bidyut Bandopadhyay ◽  
Smarajit Maiti
Keyword(s):  
Amino Acids ◽  
Protein Stability ◽  
Protein Sequence ◽  
Graphical Interface ◽  
Functional Stability ◽  
Proteomics Data ◽  
Sequence Determination ◽  
Bioinformatics Tool ◽  
Proteomics Analysis ◽  
User Friendly

Background:Protein Stability Determination (PSD) is a sequence-based bioinformatics tool which was developed by utilizing a large input of datasets of protein sequences in FASTA format. The PSD can be used to analyze the meta-proteomics data which will help to predict and design thermozyme and mesozyme for academic and industrial purposes. The PSD also can be utilized to analyze the protein sequence and to predict whether it will be stable in thermophilic or in the mesophilic environment. </P><P> Method and Results: This tool which is supported by any operating system is designed in Java and it provides a user-friendly graphical interface. It is a simple programme and can predict the thermostability nature of proteins with >90% accuracy. The PSD can also predict the nature of constituent amino acids i.e. acidic or basic and polar or nonpolar etc.Conclusion:PSD is highly capable to determine the thermostability status of a protein of hypothetical or unknown peptides as well as meta-proteomics data from any established database. The utilities of the PSD driven analyses include predictions on the functional assignment to a protein. The PSD also helps in designing peptides having flexible combinations of amino acids for functional stability. PSD is freely available at https://sourceforge.net/projects/protein-sequence-determination.

Electrochemical approach to trifluoroacetamide synthesis from 1,1,1-trichloro-2,2,2-trifluoroethane (CFC-113a) catalyzed by B12 complex

2021 ◽  
pp. A-H
Author(s):  
Mohammad Moniruzzaman ◽  
Yoshio Yano ◽  
Toshikazu Ono ◽  
Yoshio Hisaeda ◽  
Hisashi Shimakoshi
Keyword(s):  
Electrochemical Method ◽  
Room Temperature ◽  
Synthetic Approach ◽  
One Pot ◽  
Mild Conditions ◽  
Electrochemical Approach ◽  
User Friendly

One-pot synthetic approach to produce trifluoroacetamide has been developed using an electrochemical method with the B[Formula: see text] complex as a catalyst under mild conditions, in open air at room temperature. Thirty examples of trifluoroacetamide were synthesized from 1,1,1-trichloro-2,2,2-trifluoroethane (CFC-113a) in moderate to good yields. This user-friendly strategy is compatible with a broad range of trifluoroacetamide syntheses.

Homochirality as the Signature of Extra-Terrestrial Life

1997 ◽  
Vol 161 ◽  
pp. 505-510
Author(s):  
Alexandra J. MacDermott ◽  
Laurence D. Barron ◽  
Andrè Brack ◽  
Thomas Buhse ◽  
John R. Cronin ◽  
...  
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Optical Rotation ◽  
Physical Origin ◽  
Natural Choice ◽  
Rosetta Mission ◽  
Terrestrial Life ◽  
Subsurface Layers ◽  
Solar System Bodies ◽  
Origin Of Homochirality

AbstractThe most characteristic hallmark of life is its homochirality: all biomolecules are usually of one hand, e.g. on Earth life uses only L-amino acids for protein synthesis and not their D mirror images. We therefore suggest that a search for extra-terrestrial life can be approached as a Search for Extra- Terrestrial Homochirality (SETH). The natural choice for a SETH instrument is optical rotation, and we describe a novel miniaturized space polarimeter, called the SETH Cigar, which could be used to detect optical rotation as the homochiral signature of life on other planets. Moving parts are avoided by replacing the normal rotating polarizer by multiple fixed polarizers at different angles as in the eye of the bee. We believe that homochirality may be found in the subsurface layers on Mars as a relic of extinct life, and on other solar system bodies as a sign of advanced pre-biotic chemistry. We discuss the chiral GC-MS planned for the Roland lander of the Rosetta mission to a comet and conclude with theories of the physical origin of homochirality.

Hydrogen Cyanide Polymers from the Impact of Comet P/Shoemaker-Levy 9 on Jupiter

1997 ◽  
Vol 161 ◽  
pp. 179-187
Author(s):  
Clifford N. Matthews ◽  
Rose A. Pesce-Rodriguez ◽  
Shirley A. Liebman
Keyword(s):  
Amino Acids ◽  
Solar System ◽  
Hydrogen Cyanide ◽  
Nitrogen Heterocycles ◽  
Laboratory Studies ◽  
Heterogeneous Solids ◽  
The Many ◽  
Comet Halley ◽  
The Impact ◽  
By Products

AbstractHydrogen cyanide polymers – heterogeneous solids ranging in color from yellow to orange to brown to black – may be among the organic macromolecules most readily formed within the Solar System. The non-volatile black crust of comet Halley, for example, as well as the extensive orangebrown streaks in the atmosphere of Jupiter, might consist largely of such polymers synthesized from HCN formed by photolysis of methane and ammonia, the color observed depending on the concentration of HCN involved. Laboratory studies of these ubiquitous compounds point to the presence of polyamidine structures synthesized directly from hydrogen cyanide. These would be converted by water to polypeptides which can be further hydrolyzed to α-amino acids. Black polymers and multimers with conjugated ladder structures derived from HCN could also be formed and might well be the source of the many nitrogen heterocycles, adenine included, observed after pyrolysis. The dark brown color arising from the impacts of comet P/Shoemaker-Levy 9 on Jupiter might therefore be mainly caused by the presence of HCN polymers, whether originally present, deposited by the impactor or synthesized directly from HCN. Spectroscopic detection of these predicted macromolecules and their hydrolytic and pyrolytic by-products would strengthen significantly the hypothesis that cyanide polymerization is a preferred pathway for prebiotic and extraterrestrial chemistry.

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