scholarly journals Theoretical insights into C–H bond activation of methane by transition metal clusters: the role of anharmonic effects

2021 ◽  
Author(s):  
Preeti Bhumla ◽  
Manish Kumar ◽  
Saswata Bhattacharya
Keyword(s):  
Free Energy ◽  
Md Simulation ◽  
Bond Activation ◽  
Integration Method ◽  
Excess Free Energy ◽  
Configurational Entropy ◽  
Transition Metal Clusters ◽  
Vibrational Free Energy ◽  
Free Energy Contribution

To incorporate the anharmonicity in the vibrational free energy contribution to the configurational entropy, we evaluate the excess free energy of clusters numerically by a thermodynamic integration method with ab initio molecular dynamics (aiMD) simulation inputs.

scholarly journals Exploring the Free Energy Landscape and Thermodynamics of Protein-Protein Association: HIV-1 Integrase Multimerization Induced by an Allosteric Inhibitor

2020 ◽  
Author(s):  
C. Tse ◽  
L. Wickstrom ◽  
M. Kvaratskhelia ◽  
E. Gallicchio ◽  
R. Levy ◽  
...  
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Critical Role ◽  
Configurational Entropy ◽  
Umbrella Sampling ◽  
Free Energy Landscape ◽  
Drug Induced ◽  
Protein Association ◽  
Hiv 1

AbstractWe report the free energy landscape and thermodynamics of the protein-protein association responsible for the drug-induced multimerization of HIV-1 integrase (IN). Allosteric HIV-1 integrase inhibitors (ALLINIs) promote aberrant IN multimerization by bridging IN-IN intermolecular interactions. However, the thermodynamic driving forces and kinetics of the multimerization remain largely unknown. Here we explore the early steps in the IN multimerization by using umbrella sampling and unbiased molecular dynamics simulations in explicit solvent. In direct simulations, the two initially separated dimers spontaneously associate to form near-native complexes that resemble the crystal structure of the aberrant tetramer. Most strikingly, the effective interaction of the protein-protein association is very short-ranged: the two dimers associate rapidly within tens of nanoseconds when their binding surfaces are separated by d ≤ 4.3 Å (less than two water diameters). Beyond this distance, the oligomerization kinetics appears to be diffusion controlled with a much longer association time. The free energy profile also captured the crucial role of ALLINI in promoting multimerization, and explained why several CTD mutations are remarkably resistant to the drug-induced multimerization. The results also show that at small separation the protein-protein binding process contains two consecutive phases with distinct thermodynamic signatures. First, inter-protein water molecules are expelled to the bulk resulting in a small increase in entropy, as the solvent entropy gain from the water release is nearly cancelled by the loss of side chain entropies as the two proteins approach each other. At shorter distances, the two dry binding surfaces adapt to each other to optimize their interaction energy at the expense of further protein configurational entropy loss. While the binding interfaces feature clusters of hydrophobic residues, overall, the protein-protein association in this system is driven by enthalpy and opposed by entropy.Statement of SignificanceElucidating the energetics and thermodynamic aspects of protein-protein association is important for understanding this fundamental biophysical process. This study provided a more complete physical picture of the protein-protein association responsible for the drug-induced HIV-1 integrase multimerization. The results captured the critical role of the inhibitor, and accounted for the effects of mutations on the protein association. Remarkably, the effective range of the protein-protein attractive funnel is found to be very short, at less than two layers of water, despite the fact that the two binding partners carry opposite net charges. Lastly, entropy/enthalpy decomposition shows that the solvent release from the inter-protein region into the bulk is more than offset by the loss of the solute configurational entropy due to complexation.

Metal-Metal Cooperative Bond Activation by Heterobimetallic Alkyl, Aryl, and Acetylide PtII/CuI Complexes

2020 ◽  
Author(s):  
Shubham Deolka ◽  
Orestes Rivada Wheelaghan ◽  
Sandra Aristizábal ◽  
Robert Fayzullin ◽  
Shrinwantu Pal ◽  
...  
Keyword(s):  
Alkyl Group ◽  
Bond Activation ◽  
Bond Cleavage ◽  
Terminal Alkyne ◽  
Alkyl Aryl ◽  
Metal Metal ◽  
The Stability ◽  
Selective Formation ◽  
Organoplatinum Compounds

We report selective formation of heterobimetallic PtII/CuI complexes that demonstrate how facile bond activation processes can be achieved by altering reactivity of common organoplatinum compounds through their interaction with another metal center. The interaction of the Cu center with Pt center and with a Pt-bound alkyl group increases the stability of PtMe2 towards undesired rollover cyclometalation. The presence of the CuI center also enables facile transmetalation from electron-deficient tetraarylborate [B(ArF)4]- anion and mild C-H bond cleavage of a terminal alkyne, which was not observed in the absence of an electrophilic Cu center. The DFT study indicates that the role of Cu center acts as a binding site for alkyne substrate, while activating its terminal C-H bond.

scholarly journals Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Sensen Zhang ◽  
Baolei Yuan ◽  
Jordy Homing Lam ◽  
Jun Zhou ◽  
Xuan Zhou ◽  
...  
Keyword(s):  
Md Simulation ◽  
Potential Role ◽  
Md Simulations ◽  
Full Length ◽  
Inflammasome Activation ◽  
Simulation Studies ◽  
Cryo Electron Microscopy ◽  
Gating Mechanism ◽  
Atp Efflux

AbstractPannexin1 (PANX1) is a large-pore ATP efflux channel with a broad distribution, which allows the exchange of molecules and ions smaller than 1 kDa between the cytoplasm and extracellular space. In this study, we show that in human macrophages PANX1 expression is upregulated by diverse stimuli that promote pyroptosis, which is reminiscent of the previously reported lipopolysaccharide-induced upregulation of PANX1 during inflammasome activation. To further elucidate the function of PANX1, we propose the full-length human Pannexin1 (hPANX1) model through cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulation studies, establishing hPANX1 as a homo-heptamer and revealing that both the N-termini and C-termini protrude deeply into the channel pore funnel. MD simulations also elucidate key energetic features governing the channel that lay a foundation to understand the channel gating mechanism. Structural analyses, functional characterizations, and computational studies support the current hPANX1-MD model, suggesting the potential role of hPANX1 in pyroptosis during immune responses.

TBAI Catalyzed Electrochemical C-H Bond Activation of 2-arylated-N-methoxyamides for the Synthesis of Phenanthridinones

Synlett ◽  
2021 ◽  
Author(s):  
Kripa Subramanian ◽  
Subhash L. Yedage ◽  
Kashish Sethi ◽  
Bhalchandra M. Bhanage
Keyword(s):  
Electrochemical Method ◽  
Bond Activation ◽  
Supporting Electrolyte ◽  
Bioactive Compound ◽  
Reaction Conditions ◽  
Redox Catalyst ◽  
Synthetic Utility ◽  
One Step ◽  
Constant Potential

An electrochemical method for the synthesis of phenanthridinones via constant potential electrolysis (CPE) mediated by <i>n</i>-Bu<sub>4</sub>NI (TBAI) has been reported. The protocol is metal and oxidant free and proceeds with 100% current efficiency. Here TBAI plays the dual role of the redox catalyst as well as supporting electrolyte. The intramolecular C-H activation proceeds under mild reaction conditions and short reaction time via electrochemically generated amidyl radicals. The reaction has been scaled up to gram level showing its practicability and the synthetic utility and applicability of the protocol has been demonstrated by the direct one-step synthesis of the bioactive compound Phenaglaydon.

Topography of the Free Energy Landscape on the Claisen-Schmidt Condensation: Solvent and Temperature Effect in the Rate-Controlling Step

2021 ◽  
Author(s):  
Nayara Dantas Coutinho ◽  
Hugo Gontijo Machado ◽  
Valter Henrique Carvalho-Silva ◽  
Wender A. Silva
Keyword(s):  
Free Energy ◽  
Temperature Effect ◽  
Strong Influence ◽  
Aldol Condensation ◽  
Energy Landscape ◽  
Bond Formation ◽  
Free Energy Landscape ◽  
Rate Controlling Step ◽  
Formation Step

Recent studies have assigned hydroxide elimination and C=C bond formation step in base-promoted aldol condensation the role of having a strong influence in the overall rate reaction, in contrast to...

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