Modelling the Hydrolysis of Iron-Sulfur Clusters

2019 ◽  
Author(s):  
Murilo H. Teixeira ◽  
Felipe Curtolo ◽  
Sofia R. G. Camilo ◽  
Martin J. Field ◽  
Peng Zheng ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Density Functional ◽  
Catalytic Efficiency ◽  
Implicit Solvent ◽  
Hybrid Functional ◽  
Iron Sulfur ◽  
The Stability ◽  
Dynamics Simulations ◽  
High Level ◽  
Hydrolysis Of

<div>Iron-sulfur (FeS) clusters are essential metal cofactors involved in a wide variety of biological functions. Their catalytic efficiency, biosynthesis and regulation depend on FeS stability in aqueous solution. Here, molecular modelling is used to investigate the hydrolysis of an oxidized (ferric) mononuclear FeS cluster by bare dissociation and water substitution mechanisms in neutral and acidic solution. First, approximate electronic structure descriptions of FeS reactions by density functional theory are validated against high-level wave-function CCSD(T) calculations. Solvation contributions are evaluated by an all-atom model with hybrid quantum chemical/molecular mechanical (QM/MM) potentials and enhanced sampling molecular dynamics simulations. The free energy profile obtained for FeS cluster hydrolysis indicates the hybrid functional M06 together with an implicit solvent correction capture the most important aspects of FeS cluster reactivity in aqueous solution. Then, 20 reaction channels leading to two consecutive Fe--S bond ruptures were explored with this calibrated model. For all protonation states, nucleophilic substitution with concerted bond breaking and forming to iron is the preferred mechanism, both kinetic and thermodynamically. In neutral solution, proton transfer from water to the sulfur leaving group is also concerted. Dissociative reactions show higher barriers and will not be relevant for FeS reactivity when exposed to solvent. These hydrolysis mechanisms may help to explain the stability and catalytic mechanisms of FeS clusters of multiple sizes and proteins</div><div><br></div>

Modelling the Hydrolysis of Iron-Sulfur Clusters

2019 ◽  
Author(s):  
Murilo H. Teixeira ◽  
Felipe Curtolo ◽  
Sofia R. G. Camilo ◽  
Martin J. Field ◽  
Peng Zheng ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Density Functional ◽  
Catalytic Efficiency ◽  
Implicit Solvent ◽  
Hybrid Functional ◽  
Iron Sulfur ◽  
The Stability ◽  
Dynamics Simulations ◽  
High Level ◽  
Hydrolysis Of

<div>Iron-sulfur (FeS) clusters are essential metal cofactors involved in a wide variety of biological functions. Their catalytic efficiency, biosynthesis and regulation depend on FeS stability in aqueous solution. Here, molecular modelling is used to investigate the hydrolysis of an oxidized (ferric) mononuclear FeS cluster by bare dissociation and water substitution mechanisms in neutral and acidic solution. First, approximate electronic structure descriptions of FeS reactions by density functional theory are validated against high-level wave-function CCSD(T) calculations. Solvation contributions are evaluated by an all-atom model with hybrid quantum chemical/molecular mechanical (QM/MM) potentials and enhanced sampling molecular dynamics simulations. The free energy profile obtained for FeS cluster hydrolysis indicates the hybrid functional M06 together with an implicit solvent correction capture the most important aspects of FeS cluster reactivity in aqueous solution. Then, 20 reaction channels leading to two consecutive Fe--S bond ruptures were explored with this calibrated model. For all protonation states, nucleophilic substitution with concerted bond breaking and forming to iron is the preferred mechanism, both kinetic and thermodynamically. In neutral solution, proton transfer from water to the sulfur leaving group is also concerted. Dissociative reactions show higher barriers and will not be relevant for FeS reactivity when exposed to solvent. These hydrolysis mechanisms may help to explain the stability and catalytic mechanisms of FeS clusters of multiple sizes and proteins</div><div><br></div>

Schiff base equilibria. II. Beryllium complexes of N-n-butylsalicylideneimine and the hydrolysis of the Be2+ ion

1965 ◽  
Vol 18 (5) ◽  
pp. 651 ◽  
Author(s):  
RW Green ◽  
PW Alexander
Keyword(s):  
Aqueous Solution ◽  
Schiff Base ◽  
Complex Formation ◽  
Distribution Coefficient ◽  
Dilute Aqueous Solution ◽  
The Stability ◽  
Ph Range ◽  
Hydrolysis Of ◽  
Beryllium Complexes ◽  
Equilibria In Aqueous Solution

The Schiff base, N-n-butylsalicylideneimine, extracts more than 99.8% beryllium into toluene from dilute aqueous solution. The distribution of beryllium has been studied in the pH range 5-13 and is discussed in terms of the several complex equilibria in aqueous solution. The stability constants of the complexes formed between beryllium and the Schiff base are log β1 11.1 and log β2 20.4, and the distribution coefficient of the bis complex is 550. Over most of the pH range, hydrolysis of the Be2+ ion competes with complex formation and provides a means of measuring the hydrolysis constants. They are for the reactions: Be(H2O)42+ ↔ 2H+ + Be(H2O)2(OH)2, log*β2 - 13.65; Be(H2O)42+ ↔ 3H+ + Be(H2O)(OH)3-, log*β3 -24.11.

scholarly journals Ab initio thermodynamics of liquid and solid water

2019 ◽  
Vol 116 (4) ◽  
pp. 1110-1115 ◽  
Author(s):  
Bingqing Cheng ◽  
Edgar A. Engel ◽  
Jörg Behler ◽  
Christoph Dellago ◽  
Michele Ceriotti
Keyword(s):  
Machine Learning ◽  
Thermodynamic Properties ◽  
Ab Initio ◽  
Density Functional ◽  
Machine Learning Techniques ◽  
Intermediate Step ◽  
Hybrid Functional ◽  
Learning Techniques ◽  
The Stability ◽  
Comprehensive Framework

Thermodynamic properties of liquid water as well as hexagonal (Ih) and cubic (Ic) ice are predicted based on density functional theory at the hybrid-functional level, rigorously taking into account quantum nuclear motion, anharmonic fluctuations, and proton disorder. This is made possible by combining advanced free-energy methods and state-of-the-art machine-learning techniques. The ab initio description leads to structural properties in excellent agreement with experiments and reliable estimates of the melting points of light and heavy water. We observe that nuclear-quantum effects contribute a crucial 0.2 meV/H2O to the stability of ice Ih, making it more stable than ice Ic. Our computational approach is general and transferable, providing a comprehensive framework for quantitative predictions of ab initio thermodynamic properties using machine-learning potentials as an intermediate step.

scholarly journals Thermodynamic Study of Hydrolysis Reactions in Aqueous Solution fromAb InitioPotential and Molecular Dynamics Simulations

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
S. Tolosa ◽  
A. Hidalgo ◽  
J. A. Sansón
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Free Energy ◽  
Reaction Mechanism ◽  
Molecular Dynamics Simulations ◽  
Infinite Dilution ◽  
Theoretical Study ◽  
Water Model ◽  
Dynamics Simulations ◽  
Hydrolysis Of

A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described usingab initiosolute-solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3) via concerted and water-assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activation energies.

Phosphorane lifetime and stereo-electronic effects along the alkaline hydrolysis of phosphate esters

2016 ◽  
Vol 18 (27) ◽  
pp. 18255-18267 ◽  
Author(s):  
Eufrásia S. Pereira ◽  
Júlio C. S. Da Silva ◽  
Tiago A. S. Brandão ◽  
Willian R. Rocha
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Alkaline Hydrolysis ◽  
Electrostatic Interactions ◽  
Phosphate Esters ◽  
Electronic Effects ◽  
Important Intermediate ◽  
Dynamics Simulations ◽  
Phosphate Diesters ◽  
Hydrolysis Of

Ab initio molecular dynamics simulations revealed that phosphorane, an important intermediate in the hydrolysis of phosphate diesters, has a lifetime of ∼1 ps in aqueous solution. QTAIM and EDA analyses along the reaction coordinate show that the hydrolysis reaction of phosphate esters is driven mainly by electrostatic interactions.

scholarly journals Tissue-Nonspecific Alkaline Phosphatase (TNAP) as the Enzyme Involved in the Degradation of Nucleotide Analogues in the Ligand Docking and Molecular Dynamics Approaches

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1104
Author(s):  
Rafal Madaj ◽  
Bartlomiej Gostynski ◽  
Roza Pawlowska ◽  
Arkadiusz Chworos
Keyword(s):  
Molecular Dynamics ◽  
Alkaline Phosphatase ◽  
Electrostatic Interactions ◽  
Thermodynamic Integration ◽  
Ligand Docking ◽  
In Silico Studies ◽  
Tissue Nonspecific Alkaline Phosphatase ◽  
The Stability ◽  
Dynamics Simulations ◽  
Hydrolysis Of

Tissue-nonspecific alkaline phosphatase (TNAP) is known to be involved in the degradation of extracellular ATP via the hydrolysis of pyrophosphate (PPi). We investigated, using three different computational methods, namely molecular docking, thermodynamic integration (TI) and conventional molecular dynamics (MD), whether TNAP may also be involved in the utilization of β,γ-modified ATP analogues. For that, we analyzed the interaction of bisphosphonates with this enzyme and evaluated the obtained structures using in silico studies. Complexes formed between pyrophosphate, hypophosphate, imidodiphosphate, methylenediphosphonic acid monothiopyrophosphate, alendronate, pamidronate and zoledronate with TNAP were generated and analyzed based on ligand docking, molecular dynamics and thermodynamic integration. The obtained results indicate that all selected ligands show high affinity toward this enzyme. The forming complexes are stabilized through hydrogen bonds, electrostatic interactions and van der Waals forces. Short- and middle-term molecular dynamics simulations yielded very similar affinity results and confirmed the stability of the protein and its complexes. The results suggest that certain effectors may have a significant impact on the enzyme, changing its properties.

scholarly journals Direct Non-adiabatic Simulations of the Photoinduced Charge Transfer Dynamics

2020 ◽  
Author(s):  
Sharma Yamijala ◽  
Pengfei Huo
Keyword(s):  
Charge Transfer ◽  
Density Functional ◽  
Time Dependent ◽  
Photoinduced Charge Transfer ◽  
Molecular Systems ◽  
Classical Path ◽  
Charge Transfer Dynamics ◽  
Dynamics Simulations ◽  
High Level ◽  
Photoinduced Charge

We apply direct non-adiabatic dynamics simulations to investigate photoinduced charge transfer reactions. Our approach is based on the mixed quantum-classical fewest switches surface hopping (FSSH) method that treats the transferring electron through time-dependent density functional theory and the nuclei classically. The photoinduced excited state is modeled as a transferring single-electron that initially occupies the LUMO of the donor molecule/moiety. This single-particle electronic wavefunction is then propagated quantum mechanically by solving the time-dependent Schr\"odinger equation in the basis of the instantaneous molecular orbitals (MOs) of the entire system. The non-adiabatic transitions among electronic states are modeled using the FSSH approach within the classical-path approximation. We apply this approach to simulate the photoinduced charge transfer dynamics in a few well-characterized molecular systems. Our results are in excellent agreement with both the experimental measurements and high-level (yet expensive) theoretical results.

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