One-Step Synthesis of Labeled Sugar Nucleotides for ProteinO-GlcNAc Modification Studies by Chemical Function Analysis of an Archaeal Protein

Rahman M. Mizanur; Firoz A. Jaipuri; Nicola L. Pohl

doi:10.1021/ja044117p

An electron localization function analysis of the molecular mechanism and the C–O bond formation in the [3+2] cycloaddition reaction involving zwitterionic type between a nitrone and an electron deficient ethyne

Progress in Reaction Kinetics and Mechanism ◽

10.1177/1468678319825742 ◽

2019 ◽

Vol 45 ◽

pp. 146867831982574

Author(s):

Abdelilah Benallou ◽

Habib El Alaoui El Abdallaoui ◽

Hocine Garmes

Keyword(s):

Electron Density ◽

Function Analysis ◽

Bond Formation ◽

Cycloaddition Reaction ◽

Intrinsic Reaction Coordinate ◽

Dimethyl Acetylenedicarboxylate ◽

Central Carbon ◽

One Step ◽

Free Activation Energy ◽

Step Mechanism

The mechanistic nature of a [3+2] cycloaddition reaction involving zwitterionic species has been investigated, and the changes of electron density related to the O–C and C–C bond formation along the intrinsic reaction coordinate have been characterized. This polar [3+2] cycloaddition reaction, which takes place through a non-concerted two-stage one-step mechanism, proceeds with a moderate Gibbs free activation energy of 21 kcal mol−1. The reaction begins by the creation of a pseudoradical centre at the central carbon, first on the dimethyl acetylenedicarboxylate, and second on the nitrone framework. This immediately favours the formation of the first O–C single bond by donation of some electron density of the oxygen atom lone pairs, which represents the most attractive centre in this cycloaddition reaction.

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One-Step Synthesis of Sugar Nucleotides

The Journal of Organic Chemistry ◽

10.1021/acs.joc.0c01943 ◽

2020 ◽

Vol 85 (23) ◽

pp. 15645-15651

Author(s):

Atsushi Miyagawa ◽

Sanami Toyama ◽

Ippei Ohmura ◽

Shun Miyazaki ◽

Takeru Kamiya ◽

...

Keyword(s):

Sugar Nucleotides ◽

One Step

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The Molecular Mechanism of the Formation of Four-Membered Cyclic Nitronates and Their Retro (3 + 2) Cycloaddition: A DFT Mechanistic Study

Molecules ◽

10.3390/molecules26164786 ◽

2021 ◽

Vol 26 (16) ◽

pp. 4786

Author(s):

Agnieszka Kącka-Zych

Keyword(s):

Density Functional ◽

Function Analysis ◽

Population Analysis ◽

Density Functional Theory Method ◽

Mechanistic Study ◽

Functional Theory ◽

Tert Butyl ◽

The Density Functional Theory ◽

One Step ◽

Butyl Ketone

In the present work, the formation of the four-membered cyclic nitronates and the retro (3 + 2) cycloaddition (retro-32CA) reaction of the 4H-[1,2]oxazete 2-oxide were studied using the density functional theory method at the MPWB1K/6-311G(d,p) theoretical level. The electronic structure of 3-tert-butyl-4,4-dimethyl-1,2-dinitro-pent-2-ene was known through electron localization function analysis, natural population analysis, and molecular electrostatic potential analysis. The formation of 4,4-di-tert-butyl-3-nitromethyl-4H-[1,2]oxazete 2-oxide proceeds through a one-step mechanism. The mechanism of the retro-32CA leading to di-tert-butyl ketone and nitrile oxide derivative should be described as an asynchronous two-stage one-step process. The bonding evolution theory study was carried out to clarify the mechanisms of the formation of 4H-[1,2]oxazete 2-oxide and their retro-32CA.

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Fourth-order iterative method without calculating the higher derivatives for nonlinear equation

Journal of Algorithms & Computational Technology ◽

10.1177/1748302619887686 ◽

2019 ◽

Vol 13 ◽

pp. 174830261988768

Author(s):

Shengfeng Li

Keyword(s):

Iterative Method ◽

Continued Fraction ◽

Function Analysis ◽

Root Finding ◽

The Third ◽

Higher Derivatives ◽

One Step ◽

And Performance ◽

Derivatives Of ◽

Third Derivative

In this paper, we present firstly several one-step iterative methods including classical Newton’s method and Halley’s method for root-finding problem based on Thiele’s continued fraction. Secondly, by using approximants of the second derivative and the third derivative, we obtain an improved iterative method, which is not only two-step iterative method but also avoids calculating the higher derivatives of the function. Analysis of its convergence shows that the order of convergence of the modified iterative method is four for a simple root of the equation. Finally, to illustrate the efficiency and performance of the proposed method, we give some numerical experiments and comparison.

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An Interactive Minicomputer Program for the Indexing and Simulation of Electron Diffraction Patterns

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100092670 ◽

1976 ◽

Vol 34 ◽

pp. 542-543

Author(s):

R.P. Goehner ◽

W.T. Hatfield ◽

Prakash Rao

Keyword(s):

Electron Diffraction ◽

Real Time ◽

Pattern Analysis ◽

Flow Diagram ◽

Hard Copy ◽

Time Analysis ◽

Real Time Analysis ◽

Transmission Electron ◽

One Step ◽

Diffraction Patterns

Computer programs are now available in various laboratories for the indexing and simulation of transmission electron diffraction patterns. Although these programs address themselves to the solution of various aspects of the indexing and simulation process, the ultimate goal is to perform real time diffraction pattern analysis directly off of the imaging screen of the transmission electron microscope. The program to be described in this paper represents one step prior to real time analysis. It involves the combination of two programs, described in an earlier paper(l), into a single program for use on an interactive basis with a minicomputer. In our case, the minicomputer is an INTERDATA 70 equipped with a Tektronix 4010-1 graphical display terminal and hard copy unit.A simplified flow diagram of the combined program, written in Fortran IV, is shown in Figure 1. It consists of two programs INDEX and TEDP which index and simulate electron diffraction patterns respectively. The user has the option of choosing either the indexing or simulating aspects of the combined program.

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Nutrient-regulated gene expression in eukaryotes

Biochemical Society Symposium ◽

10.1042/bss0730085 ◽

2006 ◽

Vol 73 ◽

pp. 85-96 ◽

Cited By ~ 8

Author(s):

Richard J. Reece ◽

Laila Beynon ◽

Stacey Holden ◽

Amanda D. Hughes ◽

Karine Rébora ◽

...

Keyword(s):

Gene Expression ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Transcriptional Control ◽

Direct Interaction ◽

Signalling Pathways ◽

A Cell ◽

One Step ◽

Higher Eukaryotes ◽

Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

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Sensory and Cognitive Components of Auditory Processing in Individuals With Tinnitus

American Journal of Audiology ◽

10.1044/2019_aja-19-0011 ◽

2019 ◽

Vol 28 (4) ◽

pp. 834-842

Author(s):

Harini Vasudevan ◽

Hari Prakash Palaniswamy ◽

Ramaswamy Balakrishnan

Keyword(s):

Selective Attention ◽

Auditory Processing ◽

Function Analysis ◽

Event Related Potential ◽

Oscillatory Activity ◽

Default Mode ◽

Auditory Selective Attention ◽

Cognitive Components ◽

Mode Function ◽

Related Potentials

Purpose The main purpose of the study is to explore the auditory selective attention abilities (using event-related potentials) and the neuronal oscillatory activity in the default mode network sites (using electroencephalogram [EEG]) in individuals with tinnitus. Method Auditory selective attention was measured using P300, and the resting state EEG was assessed using the default mode function analysis. Ten individuals with continuous and bothersome tinnitus along with 10 age- and gender-matched control participants underwent event-related potential testing and 5 min of EEG recording (at wakeful rest). Results Individuals with tinnitus were observed to have larger N1 and P3 amplitudes along with prolonged P3 latency. The default mode function analysis revealed no significant oscillatory differences between the groups. Conclusion The current study shows changes in both the early sensory and late cognitive components of auditory processing. The change in the P3 component is suggestive of selective auditory attention deficit, and the sensory component (N1) suggests an altered bottom-up processing in individuals with tinnitus.

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