scholarly journals Experimental Determination of Activation Energies for Covalent Bond Formation via Ion/Ion Reactions and Competing Processes

2021 ◽  
Author(s):  
Melanie Cheung See Kit ◽  
Samantha O. Shepherd ◽  
James S. Prell ◽  
Ian K. Webb
Keyword(s):  
Experimental Determination ◽  
Bond Formation ◽  
Covalent Bond ◽  
Activation Energies ◽  
Covalent Bond Formation

scholarly journals Experimental Determination of Activation Energies for Covalent Bond Formation via Ion/Ion Reactions and Competing Processes

2021 ◽  
Author(s):  
Melanie Cheung See Kit ◽  
Samantha O. Shepherd ◽  
James Prell ◽  
Ian Webb
Keyword(s):  
Gas Phase ◽  
Collisional Activation ◽  
Collision Cross Section ◽  
Bond Formation ◽  
Protein Structures ◽  
Covalent Bond ◽  
Activation Energies ◽  
Supporting Evidence ◽  
Simple Modification ◽  
Covalent Bond Formation

The combination of ion/ion chemistry with commercially available ion mobility/mass spectrometry systems has allowed rich structural information to be obtained for gaseous protein ions. Recently, the simple modification of such an instrument with an electrospray reagent source has allowed three-dimensional gas-phase interrogation of protein structures through covalent and non-covalent interactions coupled with collision cross section measurements. However, the energetics of these processes have not yet been studied quantitatively. In this work, previously developed Monte Carlo simulations of ion temperatures inside traveling wave ion guides are used to characterize the energetics of the transition state of activated ubiquitin cation/reagent anion long-lived complexes formed via ion/ion reactions. The ΔH<sup>‡</sup> and ΔS<sup>‡</sup> of major processes observed from collisional activation of long-lived gas phase ion/ion complexes, namely collision induced unfolding (CIU), covalent bond formation, or neutral loss of the anionic reagent via intramolecular proton transfer, were determined. Covalent bond formation via ion/ion complexes was found to be significantly lower energy compared to unfolding and bond cleavage. ΔG<sup>‡</sup> of activation of all three processes lie between 55 and 75 kJ/mol, easily accessible with moderate collisional activation. Bond formation is favored over reagent loss at lower activation energies, whereas reagent loss becomes competitive at higher collision energies. Though ΔG<sup>‡</sup> are between CIU of a precursor ion and covalent bond formation of its ion/ion product complex are comparable, our data suggest covalent bond formation does not require extensive isomerization, supporting evidence from previous structural studies that these ion/ion reactions measure compact gas phase structures.

In-situ determination of amine/epoxy and carboxylic/epoxy exothermic heat of reaction on surface of modified carbon nanotubes and structural verification of covalent bond formation

2018 ◽  
Vol 436 ◽  
pp. 495-504 ◽  
Author(s):  
Juliana C. Neves ◽  
Vinícius G. de Castro ◽  
Ana L.S. Assis ◽  
Amanda G. Veiga ◽  
Maria Luiza M. Rocco ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Bond Formation ◽  
Covalent Bond ◽  
Heat Of Reaction ◽  
Covalent Bond Formation ◽  
Modified Carbon Nanotubes

scholarly journals Experimental Determination of Activation Energies for Covalent Bond Formation via Ion/Ion Reactions and Competing Processes

2021 ◽  
Author(s):  
Melanie Cheung See Kit ◽  
Samantha O. Shepherd ◽  
James Prell ◽  
Ian Webb
Keyword(s):  
Gas Phase ◽  
Collisional Activation ◽  
Collision Cross Section ◽  
Bond Formation ◽  
Protein Structures ◽  
Covalent Bond ◽  
Activation Energies ◽  
Supporting Evidence ◽  
Simple Modification ◽  
Covalent Bond Formation

The combination of ion/ion chemistry with commercially available ion mobility/mass spectrometry systems has allowed rich structural information to be obtained for gaseous protein ions. Recently, the simple modification of such an instrument with an electrospray reagent source has allowed three-dimensional gas-phase interrogation of protein structures through covalent and non-covalent interactions coupled with collision cross section measurements. However, the energetics of these processes have not yet been studied quantitatively. In this work, previously developed Monte Carlo simulations of ion temperatures inside traveling wave ion guides are used to characterize the energetics of the transition state of activated ubiquitin cation/reagent anion long-lived complexes formed via ion/ion reactions. The ΔH<sup>‡</sup> and ΔS<sup>‡</sup> of major processes observed from collisional activation of long-lived gas phase ion/ion complexes, namely collision induced unfolding (CIU), covalent bond formation, or neutral loss of the anionic reagent via intramolecular proton transfer, were determined. Covalent bond formation via ion/ion complexes was found to be significantly lower energy compared to unfolding and bond cleavage. ΔG<sup>‡</sup> of activation of all three processes lie between 55 and 75 kJ/mol, easily accessible with moderate collisional activation. Bond formation is favored over reagent loss at lower activation energies, whereas reagent loss becomes competitive at higher collision energies. Though ΔG<sup>‡</sup> are between CIU of a precursor ion and covalent bond formation of its ion/ion product complex are comparable, our data suggest covalent bond formation does not require extensive isomerization, supporting evidence from previous structural studies that these ion/ion reactions measure compact gas phase structures.

scholarly journals Chemical Investigations Into the Biosynthesis of the Gymnastatin and Dankastatin Alkaloids

2021 ◽  
Author(s):  
Bingqi Tong ◽  
Bridget Belcher ◽  
Daniel Nomura ◽  
Thomas Maimone
Keyword(s):  
Natural Products ◽  
Protein Function ◽  
Bond Formation ◽  
Covalent Bond ◽  
Fungal Strain ◽  
Fertile Ground ◽  
Covalent Bond Formation

Electrophilic natural products have provided fertile ground for understanding how nature inhibits protein function using covalent bond formation. The fungal strain Gymnascella dankaliensis has provided an especially interesting collection of...

Material Adhesion through Direct Covalent Bond Formation Assisted by Noncovalent Interactions

2021 ◽  
Author(s):  
Motofumi Osaki ◽  
Tomoko Sekine ◽  
Hiroyasu Yamaguchi ◽  
Yoshinori Takashima ◽  
Akira Harada
Keyword(s):  
Noncovalent Interactions ◽  
Bond Formation ◽  
Covalent Bond ◽  
Covalent Bond Formation

scholarly journals Mechanism of Covalent Binding of Ibrutinib to Bruton’s Tyrosine Kinase revealed by QM/MM Calculations

2020 ◽  
Author(s):  
Angus Voice ◽  
Gary Tresadern ◽  
Rebecca Twidale ◽  
Herman Van Vlijmen ◽  
Adrian Mulholland
Keyword(s):  
Tyrosine Kinase ◽  
Covalent Binding ◽  
Bond Formation ◽  
Covalent Bond ◽  
Covalent Modification ◽  
Mechanistic Study ◽  
Bruton’S Tyrosine Kinase ◽  
Bruton's Tyrosine Kinase ◽  
Covalent Inhibitors ◽  
Covalent Bond Formation

<p>Ibrutinib is the first covalent inhibitor of Bruton’s tyrosine kinase (BTK) to be used in the treatment of B-cell cancers. Understanding the mechanism of covalent inhibition is crucial for the design of safer and more selective covalent inhibitors that target BTK. There are questions surrounding the precise mechanism of covalent bond formation in BTK as there is no appropriate active site residue that can act as a base to deprotonate the cysteine thiol prior to covalent bond formation. To address this, we have investigated several mechanistic pathways of covalent modification of C481 in BTK by ibrutinib using QM/MM reaction simulations. The lowest energy pathway we identified involves a direct proton transfer from C481 to the acrylamide warhead in ibrutinib, followed by covalent bond formation to form an enol intermediate. There is a subsequent rate-limiting keto-enol tautomerisation step (DG<sup>‡</sup>=10.5 kcal mol<sup>-1</sup>) to reach the inactivated BTK/ibrutinib complex. Our results represent the first mechanistic study of BTK inactivation by ibrutinib to consider multiple mechanistic pathways. These findings should aid in the design of covalent drugs that target BTK and related proteins. </p>

Supramolecular Assembly-Enabled Homochiral Polymerization of Short (dA)n Oligonucleotides

2021 ◽  
Author(s):  
Sreejith Mangalath ◽  
Suneesh C Karunakaran ◽  
Gary Newnam ◽  
Gary Schuster ◽  
Nicholas Hud
Keyword(s):  
Supramolecular Chemistry ◽  
Bond Formation ◽  
Supramolecular Assembly ◽  
Covalent Bond ◽  
Complex Mixtures ◽  
Covalent Bond Formation

A goal of supramolecular chemistry is to create covalent polymers of precise composition and stereochemistry from complex mixtures by the reversible assembly of specific monomers prior to covalent bond formation....

scholarly journals Light‐Controlled Orthogonal Covalent Bond Formation at Two Different Wavelengths

2019 ◽  
Vol 58 (22) ◽  
pp. 7470-7474 ◽  
Author(s):  
Jan P. Menzel ◽  
Florian Feist ◽  
Bryan Tuten ◽  
Tanja Weil ◽  
James P. Blinco ◽  
...  
Keyword(s):  
Bond Formation ◽  
Covalent Bond ◽  
Covalent Bond Formation
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