A Theoretical Approach to Demystify the Role of Copper Salts and O2 in the Mechanism of C-N Bond Cleavage and Nitrogen Transfer

C≡N bond scission accomplished by protonation, reductive cleavage and metathesis techniques are well-known to execute nitrogen transfer reactions. Herein, we have conducted an extensive computational study, using DFT and molecular dynamics simulations, to unravel the mechanistic pathways traversed in CuCN and CuBr2 promoted splitting of coordinated cyanide anion under a dioxygen atmosphere, which enables nitrogen transfer to various aldehydes. Our detailed electronic structure analysis using ab initio multi-reference CASSCF calculations reveal that both the promoters facilitate radical pathways, in agreement with the experimental findings. This is a unique instance of oxygen activation initiated by single electron transfer from the nitrile carbon, while the major driving force is the operation of the CuII/I redox cycle. Our study reveals that the copper salts act as the “electron pool” in this unique nitrogen transfer reaction forming aryl nitrile from aryl aldehydes.

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Computational investigation on the role of C-Terminal of human albumin on the dimerization of Aβ1-42 peptide

Biointerface Research in Applied Chemistry ◽

10.33263/briac101.944955 ◽

2020 ◽

Vol 10 (1) ◽

pp. 4944-4955 ◽

Cited By ~ 1

Keyword(s):

Computational Study ◽

Binding Free Energy ◽

Conformational Dynamics ◽

Human Albumin ◽

Potential Of Mean Force ◽

Amber Force Field ◽

Aβ Aggregation ◽

The Difference ◽

Dynamics Simulations

Alzheimer’s disease (AD) is characterized by the presence of Amyloid-beta (Aβ) peptide, which has the propensity to fold into β-sheets under stress forming aggregated amyloid plaques. Nowadays many studies have focused on the development of novel, specific therapeutic strategies to slow down Aβ aggregation or control preformed aggregates. Albumin, the most abundant protein in the cerebrospinal fluid, was reported to bind Aβ impeding its aggregation. Recently, it has been reported that C-terminal (CTerm) of Human Albumin binds with Aβ1-42, impairs Aβ aggregation and promotes disassembly of Aβ aggregates protecting neurons. In this computational study, we have investigated the effect of CTerm on the conformational dynamics and the aggregation propensity of Aβ1-42 peptide. We have performed molecular dynamics simulations on the Aβ1-42-Aβ1-42 homodimer and Aβ1-42-CTerm of albumin heterodimer using the AMBER force field ff99SBildn. From the Potential of mean force (PMF) study and Binding free energy (BFE) analysis, we observed the association of Aβ1-42 peptide monomer with itself in the form of homodimer to be stronger than its association with the CTerm in the heterodimer complex. The difference in the number of residues in the Aβ1-42 peptide monomer (42 AAs) and CTerm (35 AAs) may be probable reason for the difference in association between the monomeric units in corresponding homodimer and heterodimer complexes. But even then CTerm shows a significant effect on the dimerization of Aβ1-42 peptide. Our findings therefore suggest that CTerm can be used for the disassembly of Aβ1-42 peptide monomer.

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Computational study on the mechanism of metal-free photochemical borylation of aryl halides

10.22541/au.162550161.13972740/v1 ◽

2021 ◽

Author(s):

Chenhao Tu ◽

Nana Ma ◽

Qingli Xu ◽

Wenyue Guo ◽

Lanxin Zhou ◽

...

Keyword(s):

Density Functional ◽

Uv Light ◽

Computational Study ◽

Halogen Bond ◽

Bond Cleavage ◽

Aryl Halides ◽

Homolytic Cleavage ◽

Functional Theory ◽

Aryl Radicals

C-radical borylation is an significant approach for the construction of carbon−boron bond. Photochemical borylation of aryl halides successfully applied this strategy. However, precise mechanisms, such as the generation of aryl radicals and the role of base additive(TMDAM) and water, remain controversy in these reactions. In this study, photochemical borylation of aryl halides has been researched by density functional theory (DFT) calculations. Indeed, the homolytic cleavage of the C−X bond under irradiation with UV-light is a key step for generation of aryl radicals. Nevertheless, the generation of aryl radicals may also undergo the process of single electron transfer and the heterolytic carbon-halogen bond cleavage sequence, and the latter is favorable during the reaction.

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On the Lack of Beneficial Role of Rh Towards C-C Bond Cleavage During Low Temperature Ethanol Electrooxidation on Pt-Rh Nanoalloys

10.26434/chemrxiv.6281264.v1 ◽

2018 ◽

Author(s):

Justyna Piwowar ◽

Adam Lewera

Keyword(s):

Low Temperature ◽

Electrode Potential ◽

Ethanol Oxidation ◽

Bond Cleavage ◽

Ethanol Electrooxidation ◽

Co Stripping ◽

Beneficial Role ◽

Bond Scission ◽

Oxidation Of Ethanol

Numerous reports in scientific literature claim the increased activity of Rh-containing systems towards C-C bond scission in electrocatalytic oxidation of ethanol at ambient temperatures. Due to the claimed C-C bond breaking ability, Rh-containing systems are intensively investigated and widely recognized as the most promising candidates as anode materials for ethanol-feed low temperature fuel cells. This study aims at verifying the claim of beneficial role of Rh towards C-C bond scission during low temperature ethanol electrooxidation on Pt-Rh nanoparticles. We determined that the surface-normalized amounts of CO2 produced during ethanol oxidation are comparable on Pt, Rh and Pt-Rh nanoalloys, and smaller than CO2 amounts obtained on exactly the same electrode from oxidation of monolayer of adsorbed CO. The whole amount of CO2 detected during ethanol oxidation, regardless of Rh presence, or lack of thereof, seems to come exclusively from oxidation of submonolayer of COads produced during dissociative adsorption of ethanol at low electrode potential, and its subsequent oxidation at sufficiently high electrode potential. Our work suggest that Rh-containing alloys are not more active towards C-C bond scission than pure Pt, and on both metals the mechanism of oxidation of ethanol to CO2 proceeds via the submonolayer of COads, which limits the quantity of CO2 produced from ethanol at room temperature to negligible amount. The higher activity of Rh-containing materials towards C-C bond scission claimed in literature was determined to be due to overinterpretation of selectivity data. To characterized the samples we used techniques like XPS, TEM, and cyclic voltammetry. For drove a conclusions we compere amount of CO2 detected in DEMS during ethanol oxidation reaction and so called CO stripping experiment.

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Computational study of the dissolution of cellulose into single chains: the role of the solvent and agitation

Cellulose ◽

10.1007/s10570-021-04382-9 ◽

2022 ◽

Author(s):

Eivind Bering ◽

Jonathan Ø. Torstensen ◽

Anders Lervik ◽

Astrid S. de Wijn

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Hydrophobic Interactions ◽

Computational Study ◽

Pure Water ◽

Solvent Mixture ◽

Dissolution Mechanism ◽

Dynamics Simulations ◽

External Forces

Abstract We investigate the dissolution mechanism of cellulose using molecular dynamics simulations in both water and a mixture solvent consisting of water with Na$$^+$$ + , OH$$^-$$ - and urea. As a first computational study of its kind, we apply periodic external forces that mimic agitation of the suspension. Without the agitation, the bundles do not dissolve, neither in water nor solvent. In the solvent mixture the bundle swells with significant amounts of urea entering the bundle, as well as more water than in the bundles subjected to pure water. We also find that the mixture solution stabilizes cellulose sheets, while in water these immediately collapse into bundles. Under agitation the bundles dissolve more easily in the solvent mixture than in water, where sheets of cellulose remain that are bound together through hydrophobic interactions. Our findings highlight the importance of urea in the solvent, as well as the hydrophobic interactions, and are consistent with experimental results. Graphical abstract

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On the Lack of Beneficial Role of Rh Towards C-C Bond Cleavage During Low Temperature Ethanol Electrooxidation on Pt-Rh Nanoalloys

10.26434/chemrxiv.6281264 ◽

2018 ◽

Author(s):

Justyna Piwowar ◽

Adam Lewera

Keyword(s):

Low Temperature ◽

Electrode Potential ◽

Ethanol Oxidation ◽

Bond Cleavage ◽

Ethanol Electrooxidation ◽

Co Stripping ◽

Beneficial Role ◽

Bond Scission ◽

Oxidation Of Ethanol

Numerous reports in scientific literature claim the increased activity of Rh-containing systems towards C-C bond scission in electrocatalytic oxidation of ethanol at ambient temperatures. Due to the claimed C-C bond breaking ability, Rh-containing systems are intensively investigated and widely recognized as the most promising candidates as anode materials for ethanol-feed low temperature fuel cells. This study aims at verifying the claim of beneficial role of Rh towards C-C bond scission during low temperature ethanol electrooxidation on Pt-Rh nanoparticles. We determined that the surface-normalized amounts of CO2 produced during ethanol oxidation are comparable on Pt, Rh and Pt-Rh nanoalloys, and smaller than CO2 amounts obtained on exactly the same electrode from oxidation of monolayer of adsorbed CO. The whole amount of CO2 detected during ethanol oxidation, regardless of Rh presence, or lack of thereof, seems to come exclusively from oxidation of submonolayer of COads produced during dissociative adsorption of ethanol at low electrode potential, and its subsequent oxidation at sufficiently high electrode potential. Our work suggest that Rh-containing alloys are not more active towards C-C bond scission than pure Pt, and on both metals the mechanism of oxidation of ethanol to CO2 proceeds via the submonolayer of COads, which limits the quantity of CO2 produced from ethanol at room temperature to negligible amount. The higher activity of Rh-containing materials towards C-C bond scission claimed in literature was determined to be due to overinterpretation of selectivity data. To characterized the samples we used techniques like XPS, TEM, and cyclic voltammetry. For drove a conclusions we compere amount of CO2 detected in DEMS during ethanol oxidation reaction and so called CO stripping experiment.

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Computational Study of the Dissolution of Cellulose into Single Chains: the Role of the Solvent and Agitation

10.21203/rs.3.rs-679922/v1 ◽

2021 ◽

Author(s):

Eivind Bering ◽

Jonathan Torstensen ◽

Anders Lervik ◽

Astrid S. de Wijn

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Hydrophobic Interactions ◽

Computational Study ◽

Pure Water ◽

Solvent Mixture ◽

Dissolution Mechanism ◽

Dynamics Simulations ◽

External Forces

Abstract We investigate the dissolution mechanism of cellulose using molecular dynamics simulations in both water and a mixture solvent consisting of water with Na + , OH - and urea. As a first computational study of its kind, we apply periodic external forces that mimic agitation of the suspension. Without the agitation, the bundles do not dissolve, neither in water nor solvent. In the solvent mixture the bundle swells up with significant amounts of urea entering the bundle, as well as more water than in the bundles subjected to pure water. We also find that the mixture solution stabilizes cellulose sheets, while in water these immediately collapse into bundles. Under agitation the bundles dissolve more easily in the solvent mixture than in water, where sheets of cellulose remain that are bound together through hydrophobic interactions. Our findings highlight the importance of urea in the solvent, as well as the hydrophobic interactions, and are consistent with experimental results.

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A Theoretical and Computational Study of Superlubricity and the Role of the Roughness Exponent

World Tribology Congress III, Volume 2 ◽

10.1115/wtc2005-63868 ◽

2005 ◽

Author(s):

Martin H. Mu¨ser ◽

Carlos Campana

Keyword(s):

Friction Velocity ◽

Computational Study ◽

Absolute Magnitude ◽

Flat Surfaces ◽

Coulomb’S Friction ◽

Fractal Surfaces ◽

Elastic Interactions ◽

Roughness Exponent ◽

Dynamics Simulations

Superlubricity can only be achieved if the intra-bulk elastic interactions dominate interfacial shear forces at every single length-scale in a contact. Otherwise, there will be some type of plucking motion which will lead to friction-velocity relationships akin of Coulomb’s friction law. For nominally flat surfaces, it has been predicted theoretically and demonstrated experimentally that plucking motion and hence kinetic friction can be avoided under certain circumstances. We present theoretical arguments, why these findings may extend to fractal surfaces. The theories are checked by molecular dynamics simulations. It turns out that the roughness exponent and the absolute magnitude of the roughness both play a crucial role in determining whether there can be superlubricity.

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A computational study of the interface interaction between SARS-CoV-2 RBD and ACE2 from human, cat, dog and ferret.

10.22541/au.161539677.73493964/v1 ◽

2021 ◽

Author(s):

William Sote ◽

Eduardo Franca ◽

Aline Hora ◽

Moacyr Comar

Keyword(s):

Animal Species ◽

Computational Study ◽

Infection Process ◽

Point Of View ◽

Cellular Receptor ◽

Angiotensin Converting Enzyme 2 ◽

Dynamics Simulations ◽

Key Residues ◽

Total Impact

The total impact of the worldwide COVID-19 pandemic is still emerging, changing all relationships as a result, including those with pet animals. In the infection process, the use of Angiotensin-converting enzyme 2 (ACE2) as a cellular receptor to the spike protein of the new coronavirus is a fundamental step. In this sense, understanding which residue plays what role in the interaction between SARS-CoV-2 spike glycoprotein and ACE2 from cats, dogs, and ferrets is an important guide for helping to choose which animal model can be used to study the pathology of COVID-19 and if there are differences between these interactions and those occurring in the human system. Hence, trying to help to answer these questions, we performed classical molecular dynamics simulations to evaluate, from an atomistic point of view, the interactions in these systems. Our results show that there are significant differences in the interacting residues between the systems from different animal species, and the role of ACE2 key residues are different in each system and can assist in the search for different inhibitors for each animal.

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The Role of Hydrophobicity in the Stability and pH-Switchability of (RXDX)4 and Coumarin-RXDX Conjugate β-Sheets

10.26434/chemrxiv.11493060 ◽

2020 ◽

Author(s):

Ryan Weber ◽

Martin McCullagh

Keyword(s):

Biological Imaging ◽

Ph Sensing ◽

Hydrophobic Residue ◽

Ideal Candidate ◽

Self Assembling ◽

Sensing Applications ◽

Β Sheets ◽

The Stability ◽

Dynamics Simulations

pH-switchable, self-assembling materials are of interest in biological imaging and sensing applications. Here we propose that combining the pH-switchability of RXDX (X=Ala, Val, Leu, Ile, Phe) peptides and the optical properties of coumarin creates an ideal candidate for these materials. This suggestion is tested with a thorough set of all-atom molecular dynamics simulations. We first investigate the dependence of pH-switchabiliy on the identity of the hydrophobic residue, X, in the bare (RXDX)4 systems. Increasing the hydrophobicity stabilizes the fiber which, in turn, reduces the pH-switchabilty of the system. This behavior is found to be somewhat transferable to systems in which a single hydrophobic residue is replaced with a coumarin containing amino acid. In this case, conjugates with X=Ala are found to be unstable and both pHs while conjugates with X=Val, Leu, Ile and Phe are found to form stable β-sheets at least at neutral pH. The (RFDF)4-coumarin conjugate is found to have the largest relative entropy value of 0.884 +/- 0.001 between neutral and acidic coumarin ordering distributions. Thus, we posit that coumarin-(RFDF)4 containing peptide sequences are ideal candidates for pH-sensing bioelectronic materials.

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