Does Ionic Screening Lower Activation Barriers for Conformational Transitions in Proteins?

2018 ◽  
Vol 122 (50) ◽  
pp. 11817-11826 ◽  
Author(s):  
Jan M. Antosiewicz ◽  
Maciej Długosz
Keyword(s):  
Conformational Transitions ◽  
Activation Barriers ◽  
Lower Activation

scholarly journals Acid-Catalyzed Esterification of Betaines: Theoretical Exploration of the Impact of the Carbon Chain Length on the Reaction Mechanism

Physchem ◽  
2021 ◽  
Vol 1 (3) ◽  
pp. 288-296
Author(s):  
Richail Dubien Moulandou-Koumba ◽  
Frédéric Guégan ◽  
Jean-Maurille Ouamba ◽  
Samuel N’Sikabaka ◽  
Gilles Frapper
Keyword(s):  
Chain Length ◽  
Acid Catalysis ◽  
Carbon Chain ◽  
Carbon Chain Length ◽  
Sugar Production ◽  
Activation Barriers ◽  
Lower Activation ◽  
Fine Chemistry ◽  
Acid Catalyzed ◽  
The Impact

Betaine derivatives, especially esters, are compounds of interest for the development of a more sustainable fine chemistry, as they are widely available from biomass and currently produced as side-products from various industries (among which, sugar production). In this publication, we studied the impact of carbon chain length on three considered reaction mechanisms for the esterification of (CH3)3N(CH2)nCO2 betaine (n = 1, 2, 3) with glycerol under acid catalysis. DFT calculations show that the mechanism proposed by Bachmann–Frapper et al. may also be active here, but it can interestingly be seen as an avatar of the former proposition by Watson. Conversely, Ingold’s proposition is in this case too energetically prevented. Overall, lower activation barriers and higher reaction exergonicity are reported, suggesting esterification of longer carbon-chain based betaines is more readily achieved.

Tropane-Based Dispirocyclic Oxiranes and Spirocyclic Ketones

Synthesis ◽  
2021 ◽  
Author(s):  
Alexander Shivanyuk ◽  
Andrii Gerasov ◽  
Rodion Boiko ◽  
Grygoriy Dolgonos ◽  
Aleksandr Mandzhulo ◽  
...  
Keyword(s):  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Oxirane Ring ◽  
Activation Barriers ◽  
Lower Activation

AbstractThe Prilezhaev epoxidation of N-Boc-protected 3-cyclobutylidenetropane 1a affords a 1:2 mixture of compounds 2a and 2b, in which tropane and cyclobutane fragments are spiro-connected to the oxirane ring in endo- and exo-fashion, respectively. The exo-isomer 2b is obtained in 89% yield and 97% selectivity via the dioxirane oxidation of 1a. BF3-catalyzed isomerization of exo-oxirane 2b results in a 1:1 mixture of the spirocyclic ketones endo 3a and exo 3b containing spiro-connected tropane and cyclopentanone rings, while endo-epoxide 2a gives exclusively endo-ketone 3a. Prilezhaev and dioxirane epoxidations of N-Boc-protected 3-cyclopropylidenetropane 1b affords a mixture of endo- and exo-oxiranes 2c and 2d. Compounds 2c and 2d are not isolated in individual forms since they isomerize into a mixture of spirocyclic ketones endo 3c and exo 3d. Removal of the Boc groups from ketones 3a–d gives the corresponding hydrochlorides of aminoketones 4a–d in quantitative yields. Quantum chemical calculations predict that the rearrangement of endo-epoxides into the corresponding endo-ketones involving BF3-containing intermediates has by 4.4–7.9 kcal/mol lower activation barriers than the respective conversion of the exo-epoxides into exo-ketones. The cyclopropyl-containing dispiroepoxides 2c and 2d are predicted to interconvert faster into the corresponding ketones compared to their less strained cyclobutyl counterparts 2a and 2b.

Optimization of GaN/AlGaN Quantum Wells for Ultraviolet Emitters

2003 ◽  
Vol 798 ◽  
Author(s):  
A. Hangleiter ◽  
D. Fuhrmann ◽  
M. Greve ◽  
U. Rossow
Keyword(s):  
Quantum Wells ◽  
Thermal Activation ◽  
Internal Quantum Efficiency ◽  
Excitation Power ◽  
Temperature Dependent ◽  
Activation Barriers ◽  
Quantum Well Structures ◽  
Lower Activation ◽  
Nm Range

ABSTRACTWe have studied GaN/AlGaN and GaInN/GaN quantum well structures grown on sapphire and SiC substrates using low-pressure MOVPE. The emission wavelength of the GaN/AlGaN QW's was varied in the 320–400 nm range and that of the GaInN/GaN QW's in the 390–480 nm range, by adjusting the QW width. Using temperature dependent resonant-excitation photoluminescence measurements we have determined the internal quantum efficiency (IQE) and analyzed its temperature dependence. For the GaN/AlGaN QW's we achieve a reasonable IQE of in excess of 5 % only at fairly high excitation power, while GaInN/GaN QW's provide IQE's of up to 46 % at rather low power density, indicating a much stronger role of defects for the former. While thermal activation energies are dominated by intrinsic mechanisms for GaInN/GaN QW's, lower activation barriers evident from the GaN/AlGaN data also hint at a more import role of defects.

Exploring the peri-, chemo-, and regioselectivity of addition of technetium metal oxides of the type TcO3L (L = Cl–, O–, OCH3, CH3) to substituted ketenes: a DFT computational study

2016 ◽  
Vol 94 (5) ◽  
pp. 523-532
Author(s):  
Issahaku Ahmed ◽  
Richard Tia ◽  
Evans Adei
Keyword(s):  
Density Functional Theory ◽  
Oxidation State ◽  
Density Functional ◽  
Computational Study ◽  
Density Functional Theory Calculations ◽  
High Activation ◽  
Functional Theory ◽  
Activation Barriers ◽  
Lower Activation ◽  
Zwitterionic Intermediate

The addition of TcO3L (L = Cl, O–, OCH3, CH3) to substituted ketenes along various addition pathways was studied with density functional theory calculations to explore the peri-, chemo-, and regioselectivity of the reactions. In the reactions of TcO3L with dimethyl ketene, the results show that for L = O– and CH3, [1 + 1] addition to form a triplet zwitterionic intermediate is the preferred first step; for L = Cl, the [3 + 2]C=C addition across the O–Tc–Cl bond is the preferred first step and for L = OCH3 the [3 + 2]C=C addition across the O–Tc–OCH3 bond is the preferred first step. In the reactions of TcO3Cl with substituted ketenes, [1 + 1] addition to form a triplet zwitterionic intermediate is the preferred first step for X = Ph, CN, and Cl; the [3 + 2]C=C addition across the O–Tc–O bond of the complex is the preferred first step for X = H, while the [3 + 2]C=C addition across the O–Tc–CH3 bond is the preferred first step. Reactions involving a change in the oxidation state of metal have high activation barriers, while reactions that do not involve a change in oxidation state have low activation barriers. Reactions of ketenes with TcO3L complexes have lower activation barriers for the preferred addition pathways than those of the ReO3L complexes reported in the literature. Thus, the TcO3L complexes may be better catalysts for the activation of the C=C bonds of substituted ketenes than the reported ReO3L complexes.

Conformational Transitions in Escherichia coli Ribosomal RNAs as Visualized by Dedicated STEM

1988 ◽  
Vol 46 ◽  
pp. 176-177
Author(s):  
J.S. Wall ◽  
V. Maridiyan ◽  
S. Tumminia ◽  
J. Hairifeld ◽  
M. Boublik
Keyword(s):  
Ionic Strength ◽  
Three Dimensional ◽  
Conformational Transitions ◽  
Dark Field ◽  
Dimensional Structure ◽  
Ribosomal Rnas ◽  
Field Mode ◽  
Freeze Dried ◽  
High Resolution Images ◽  
Low Ionic Strength

The high contrast in the dark-field mode of dedicated STEM, specimen deposition by the wet film technique and low radiation dose (1 e/Å2) at -160°C make it possible to obtain high resolution images of unstained freeze-dried macromolecules with minimal structural distortion. Since the image intensity is directly related to the local projected mass of the specimen it became feasible to determine the molecular mass and mass distribution within individual macromolecules and from these data to calculate the linear density (M/L) and the radii of gyration.2 This parameter (RQ), reflecting the three-dimensional structure of the macromolecular particles in solution, has been applied to monitor the conformational transitions in E. coli 16S and 23S ribosomal RNAs in solutions of various ionic strength.In spite of the differences in mass (550 kD and 1050 kD, respectively), both 16S and 23S RNA appear equally sensitive to changes in buffer conditions. In deionized water or conditions of extremely low ionic strength both appear as filamentous structures (Fig. la and 2a, respectively) possessing a major backbone with protruding branches which are more frequent and more complex in 23S RNA (Fig. 2a).

How Certain Are the Reported Ionic Conductivities of Thiophosphate-Based Solid Electrolytes? an Interlaboratory Study

2020 ◽  
Author(s):  
Saneyuki Ohno ◽  
Tim Bernges ◽  
Johannes Buchheim ◽  
Marc Duchardt ◽  
Anna-Katharina Hatz ◽  
...  
Keyword(s):  
Standard Deviation ◽  
Ionic Conductivity ◽  
Relative Standard Deviation ◽  
Solid Electrolytes ◽  
Ionic Conductivities ◽  
Ionic Conductors ◽  
Energy Storage Devices ◽  
Activation Barriers ◽  
Storage Devices ◽  
Relative Standard

<p>Owing to highly conductive solid ionic conductors, all-solid-state batteries attract significant attention as promising next-generation energy storage devices. A lot of research is invested in the search and optimization of solid electrolytes with higher ionic conductivity. However, a systematic study of an <i>interlaboratory reproducibility</i> of measured ionic conductivities and activation energies is missing, making the comparison of absolute values in literature challenging. In this study, we perform an uncertainty evaluation via a Round Robin approach using different Li-argyrodites exhibiting orders of magnitude different ionic conductivities as reference materials. Identical samples are distributed to different research laboratories and the conductivities and activation barriers are measured by impedance spectroscopy. The results show large ranges of up to 4.5 mScm<sup>-1</sup> in the measured total ionic conductivity (1.3 – 5.8 mScm<sup>-1</sup> for the highest conducting sample, relative standard deviation 35 – 50% across all samples) and up to 128 meV for the activation barriers (198 – 326 meV, relative standard deviation 5 – 15%, across all samples), presenting the necessity of a more rigorous methodology including further collaborations within the community and multiplicate measurements.</p>

Quasi-Barrierless Submolecular Motion in Mechanically Interlocked Carbon Nanotubes

2020 ◽  
Author(s):  
Julia Villalva ◽  
Belén Nieto-Ortega ◽  
Manuel Melle-Franco ◽  
Emilio Pérez
Keyword(s):  
Density Functional ◽  
Close Contact ◽  
Tight Binding ◽  
Energetic Cost ◽  
Molecular Fragments ◽  
Activation Barriers ◽  
Flat Surfaces ◽  
Different Types ◽  
Atomically Flat ◽  
Derivatives Of

The motion of molecular fragments in close contact with atomically flat surfaces is still not fully understood. Does a more favourable interaction imply a larger barrier towards motion even if there are no obvious minima? Here, we use mechanically interlocked rotaxane-type derivatives of SWNTs (MINTs) featuring four different types of macrocycles with significantly different affinities for the SWNT thread as models to study this problem. Using molecular dynamics, we find that there is no direct correlation between the interaction energy of the macrocycle with the SWNT and its ability to move along or around it. Density functional tight-binding calculations reveal small (<2.5 Kcal·mol-1) activation barriers, the height of which correlates with the commensurability of the aromatic moieties in the macrocycle with the SWNT. Our results show that macrocycles in MINTs rotate and translate freely around and along SWNTs at room temperature, with an energetic cost lower than the rotation around the C−C bond in ethane.<br>

Exploring the Influence of Substitution on the Structure and Transport Properties in the Sodium Superionic Conductor Na11+xSn2+x(Sb1−yPy)1−xS12

2020 ◽  
Author(s):  
Marvin Kraft ◽  
Lara Gronych ◽  
Theodosios Famprikis ◽  
Saneyuki Ohno ◽  
Wolfgang Zeier
Keyword(s):  
Electrochemical Impedance ◽  
Structural Phase ◽  
Ionic Transport ◽  
Sodium Ion ◽  
Ionic Conductors ◽  
Temperature Dependent ◽  
Activation Barriers ◽  
Rietveld Refinements ◽  
High Performing ◽  
The Given

<p>Sulfidic sodium ion conductors are currently investigated for the possible use in all-solid-state sodium ion batteries. The design of high performing electrolytes in terms of temperature-dependent ionic transport is based upon the fundamental understanding of structure – transport relationships within the given structural phase boundaries inherent to the investigated materials class. In this work, the Na<sup>+</sup> superionic structural family of Na<sub>11</sub>Sn<sub>2</sub>PS<sub>12</sub> is explored by using the systematic antimony substitution with phosphorous in Na<sub>11+<i>x</i></sub>Sn<sub>2+<i>x</i></sub>(Sb<sub>1-<i>y</i></sub>P<i><sub>y</sub></i>)<sub>1-<i>x</i></sub>S<sub>12</sub>. A combination of Rietveld refinements against X-ray synchrotron diffraction data with electrochemical impedance spectroscopy is used to monitor the changes in the anionic framework, the Na<sup>+</sup> substructure and the ionic transport. A new simplified descriptor for the average Na<sup>+</sup> diffusion pathways, the average Na<sup>+</sup> polyhedral volume is introduced, which is used to correlate the contraction of the overall lattice and the found activation barriers in the system. This study exemplifies how substitution affects diffusion pathways in ionic conductors and widens the knowledge about the related structural motifs and their influence on the ionic transport in this novel class of ionic conductors.</p>

Stereospecific 1,3-H Transfer of Indenols Proceeds via Persistent Ion-Pairs Anchored By NH···Pi Interactions

2018 ◽  
Author(s):  
David Ascough ◽  
Fernanda Duarte ◽  
Robert Paton
Keyword(s):  
Computational Analysis ◽  
Ion Pairs ◽  
Ion Pair ◽  
Hydrogen Atom Transfer ◽  
Polar Solvents ◽  
Chirality Transfer ◽  
Activation Barriers ◽  
Sense And Avoid ◽  
Phase Dynamics ◽  
Pi Interactions

The base-catalyzed rearrangement of arylindenols is a rare example of a suprafacial [1,3]-hydrogen atom transfer. The mechanism has been proposed to proceed via sequential [1,5]-sigmatropic shifts, which occur in a selective sense and avoid an achiral intermediate. A computational analysis using quantum chemistry casts serious doubt on these suggestions: these pathways have enormous activation barriers and in constrast to what is observed experimentally, they overwhelmingly favor a racemic product. Instead we propose that a suprafacial [1,3]-prototopic shift occurs in a two-step deprotonation/reprotonation sequence. This mechanism is favored by 15 kcal mol<sup>-1</sup> over that previously proposed. Most importantly, this is also consistent with stereospecificity since reprotonation occurs rapidly on the same p-face. We have used explicitly-solvated molecular dynamics studies to study the persistence and condensed-phase dynamics of the intermediate ion-pair formed in this reaction. Chirality transfer is the result of a particularly resilient contact ion-pair, held together by electrostatic attraction and a critical NH···p interaction which ensures that this species has an appreciable lifetime even in polar solvents such as DMSO and MeOH.

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