Theoretical study on the aging and reactivation mechanism of tabun-inhibited acetylcholinesterase by using the quantum mechanical / molecular mechanical method

2012 ◽  
Vol 90 (4) ◽  
pp. 376-383 ◽  
Author(s):  
Yanwei Li ◽  
Likai Du ◽  
Yueming Hu ◽  
Xiaomin Sun ◽  
Jingtian Hu
Keyword(s):  
Energy Barrier ◽  
Single Point ◽  
Geometry Optimization ◽  
Stationary Points ◽  
Nucleophilic Attack ◽  
Quantum Mechanical ◽  
Organophosphorous Compound ◽  
Hlö 7 ◽  
Reactivation Mechanism ◽  
The Military

The organophosphorous compound tabun is highly neurotoxic because of its irreversible inhibition on acetylcholinesterase (AChE). It is wildly used as a warfare agent in the military. In this work, the aging and reactivation mechanism of tabun-inhibited AChE were studied by using the quantum mechanical / molecular mechanical (QM/MM) method. Geometry optimization of the stationary points were performed at the B3LYP/6–31G(d) level. Single-point energies were computed at the B3LYP/6–311++G(d,p) level. On the basis of the QM/MM results, a conclusion that the C–O bond scission is caused by water attack on the ethoxy group in the aging mechanism can be drawn. The reactivation process initialed by the antidotes CH2NO– or HLÖ-7 consists of three elemental steps, the nucleophilic attack on the P atom by the antidote, the dephosphorylation process, and the decomposition of the antidote–tabun complex. The highest energy barriers of the aging reaction, CH2NO–-induced reactivation, and HLÖ-7-induced reactivation are 19.9, 20.0, and 14.8 kcal/mol (1 cal = 4.184 J), respectively. The relative lower overall energy barrier of HLÖ-7-induced reactivation compared with that of the aging reaction indicates that HLÖ-7 is able to reactivate tabun-inhibited AChE. In addition, whether a newly designed antidote is able to reactivate tabun-inhibited AChE can be examined by the inequation X < 19.9 kcal/mol,where X means the highest energy barrier of the reactivation reaction of the newly designed antidote.

scholarly journals An Insight into the Interaction Between α-Ketoamide-Based Inhibitor and Coronavirus Main Protease: A Detailed in Silico Study

2020 ◽  
Author(s):  
Snehasis Banerjee
Keyword(s):  
Single Point ◽  
Cysteine Proteases ◽  
Nbo Analysis ◽  
Noncovalent Interaction ◽  
Keto Group ◽  
Stationary Points ◽  
Nucleophilic Attack ◽  
Enzyme Active Site ◽  
Main Protease ◽  
Reversible Covalent

<div> <p>The search for therapeutic drugs that can neutralize the effects of COVID-2019 (SARS-CoV-2) infection is the main focus of current research. The coronavirus main protease (M<sub>pro</sub>) is an attractive target for anti-coronavirus drug design. Further, α-ketoamide is proved to be very effective as a reversible covalent-inhibitor against cysteine proteases. Herein, we report on the non-covalent to the covalent adduct formation mechanism of α‑ketoamide-based inhibitor with the enzyme active site amino acids by QM/SQM model (QM= quantum mechanical, SQM= semi-empirical QM). To uncover the mechanism, we focused on two approaches: a concerted and a stepwise fashion. The concerted pathway proceeds <i>via</i> deprotonation of the thiol of cysteine (here, Cys<sub>145</sub> SgH) and simultaneous reversible nucleophilic attack of sulfur onto the α-ketoamide warhead. In this work, we propose three plausible concerted pathways. On the contrary, in a traditional two-stage pathway, the first step is proton transfer from Cys<sub>145</sub> SgH to His<sub>41</sub> Nd forming an ion pair, and consecutively, in the second step, the thiolate ion attacks the a-keto group to form a thiohemiketal. In this reaction, we find that the stability of the tetrahedral intermediate oxyanion/hydroxyl hole plays an important role. Moreover, as the α-keto group has two faces <i>Si</i> or <i>Re</i> for the nucleophilic attack, we considered both possibilities of attack leading to S- and R-thiohemiketal. We computed the structural, electronic, and energetic parameters of all stationary points including transition states <i>via</i> ONIOM methodology at B3LYP/6-31G(d):PM6 level. Furthermore, to get more accurate results, we also calculated the single-point dispersion-corrected energy profile by using ωB97X-D/6-31G(d,p):PM6 level. Additionally, to characterize covalent, weak noncovalent interaction (NCI) and hydrogen-bonds, we applied NCI-reduced density gradient (NCI-RDG) methods along with Bader’s Quantum Theory of Atoms-in-Molecules (QTAIM) and natural bonding orbital (NBO) analysis.</p> </div> <br>

scholarly journals An Insight into the Interaction Between α-Ketoamide-Based Inhibitor and Coronavirus Main Protease: A Detailed in Silico Study

2020 ◽  
Author(s):  
Snehasis Banerjee
Keyword(s):  
Single Point ◽  
Cysteine Proteases ◽  
Nbo Analysis ◽  
Noncovalent Interaction ◽  
Keto Group ◽  
Stationary Points ◽  
Nucleophilic Attack ◽  
Enzyme Active Site ◽  
Main Protease ◽  
Reversible Covalent

<div> <p>The search for therapeutic drugs that can neutralize the effects of COVID-2019 (SARS-CoV-2) infection is the main focus of current research. The coronavirus main protease (M<sub>pro</sub>) is an attractive target for anti-coronavirus drug design. Further, α-ketoamide is proved to be very effective as a reversible covalent-inhibitor against cysteine proteases. Herein, we report on the non-covalent to the covalent adduct formation mechanism of α‑ketoamide-based inhibitor with the enzyme active site amino acids by QM/SQM model (QM= quantum mechanical, SQM= semi-empirical QM). To uncover the mechanism, we focused on two approaches: a concerted and a stepwise fashion. The concerted pathway proceeds <i>via</i> deprotonation of the thiol of cysteine (here, Cys<sub>145</sub> SgH) and simultaneous reversible nucleophilic attack of sulfur onto the α-ketoamide warhead. In this work, we propose three plausible concerted pathways. On the contrary, in a traditional two-stage pathway, the first step is proton transfer from Cys<sub>145</sub> SgH to His<sub>41</sub> Nd forming an ion pair, and consecutively, in the second step, the thiolate ion attacks the a-keto group to form a thiohemiketal. In this reaction, we find that the stability of the tetrahedral intermediate oxyanion/hydroxyl hole plays an important role. Moreover, as the α-keto group has two faces <i>Si</i> or <i>Re</i> for the nucleophilic attack, we considered both possibilities of attack leading to S- and R-thiohemiketal. We computed the structural, electronic, and energetic parameters of all stationary points including transition states <i>via</i> ONIOM methodology at B3LYP/6-31G(d):PM6 level. Furthermore, to get more accurate results, we also calculated the single-point dispersion-corrected energy profile by using ωB97X-D/6-31G(d,p):PM6 level. Additionally, to characterize covalent, weak noncovalent interaction (NCI) and hydrogen-bonds, we applied NCI-reduced density gradient (NCI-RDG) methods along with Bader’s Quantum Theory of Atoms-in-Molecules (QTAIM) and natural bonding orbital (NBO) analysis.</p> </div> <br>

scholarly journals A theoretical study on the mechanism of the reaction between azacyclopropenylidene and oxirane

2015 ◽  
Vol 80 (1) ◽  
pp. 53-62
Author(s):  
Ying Jing ◽  
Xiaojun Tan
Keyword(s):  
Energy Surface ◽  
Theoretical Study ◽  
Single Point ◽  
Geometry Optimization ◽  
Vibrational Analysis ◽  
Membered Ring ◽  
Reaction Pathways ◽  
Stationary Points ◽  
Energy Property ◽  
Mechanism Of The Reaction

The reaction mechanism between azacyclopropenylidene and oxirane has been systematically investigated employing the second-order M?ller-Plesset perturbation theory (MP2) method to better understand the azacyclopropenylidene reactivity with three-membered ring compound oxirane. Geometry optimization, vibrational analysis, and energy property for the involved stationary points on the potential energy surface have been calculated. Energies of all the species are also further corrected by CCSD(T)/6-311+G* single-point calculations. Our calculational results show that there are two possible reaction pathways. From the kinetic viewpoint, the first pathway is primary. From the viewpoint of thermodynamics, the second is dominating.

scholarly journals Theoretical Investigation of the Size Effect on the Oxygen Adsorption Energy of Coinage Metal Nanoparticles

2021 ◽  
Author(s):  
Amir H. Hakimioun ◽  
Elisabeth M. Dietze ◽  
Bart D. Vandegehuchte ◽  
Daniel Curulla-Ferre ◽  
Lennart Joos ◽  
...  
Keyword(s):  
Particle Size ◽  
Size Effect ◽  
Adsorption Energy ◽  
Single Point ◽  
Finite Size ◽  
Geometry Optimization ◽  
Oxygen Adsorption ◽  
Finite Size Effect ◽  
Full Geometry Optimization ◽  
Coinage Metal

AbstractThis study evaluates the finite size effect on the oxygen adsorption energy of coinage metal (Cu, Ag and Au) cuboctahedral nanoparticles in the size range of 13 to 1415 atoms (0.7–3.5 nm in diameter). Trends in particle size effects are well described with single point calculations, in which the metal atoms are frozen in their bulk position and the oxygen atom is added in a location determined from periodic surface calculations. This is shown explicitly for Cu nanoparticles, for which full geometry optimization only leads to a constant offset between relaxed and unrelaxed adsorption energies that is independent of particle size. With increasing cluster size, the adsorption energy converges systematically to the limit of the (211) extended surface. The 55-atomic cluster is an outlier for all of the coinage metals and all three materials show similar behavior with respect to particle size. Graphic Abstract

scholarly journals A QM/MM Study of Acylphosphatase Reveals the Nucleophilic-Attack and Ensuing Carbonyl-Assisted Catalytic Mechanisms

2020 ◽  
Author(s):  
zheng zhao ◽  
Phil bourne ◽  
Hao Hu ◽  
Huanyu Chu
Keyword(s):  
Energy Barrier ◽  
Potential Energy Surfaces ◽  
Catalytic Mechanism ◽  
Interaction Networks ◽  
Nucleophilic Attack ◽  
Reaction Coordinates ◽  
Transition State Stabilization ◽  
Catalytic Mechanisms ◽  
Energy Surfaces

Acylphosphatase is one of the vital enzymes in many organs/tissues to catalyze an acylphosphate molecule into carboxylate and phosphate. Here we use a combined <i>ab initio</i> QM/MM approach to reveal the catalytic mechanism of the benzoylphosphate-bound acylphosphatase system. Using a multi-dimensional reaction-coordinates-driving scheme, we obtained a detailed catalytic process including one nucleophilic-attack and then an ensuing carbonyl-shuttle catalytic mechanism by calculating two-dimensional potential energy surfaces. We also obtained an experiment-agreeable energy barrier and validated the role of the key amino acid Asn38. Additionally, we qualified the transition state stabilization strategy based on the amino acids-contributed interaction networks revealed in the enzymatic environment. This study provided usefule insights into the underlying catalytic mechanism to contribute to disease-involved research.

scholarly journals A Hidden Side of the Conformational Mobility of the Quercetin Molecule Caused by the Rotations of the O3H, O5H and O7H Hydroxyl Groups: In Silico Scrupulous Study

Symmetry ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 230 ◽  
Author(s):  
Ol’ha O. Brovarets’ ◽  
Dmytro M. Hovorun
Keyword(s):  
Energy Barrier ◽  
Conformational Dynamics ◽  
Point Symmetry ◽  
Quantum Mechanical ◽  
Hydroxyl Groups ◽  
Free Energy Barrier ◽  
Quantum Mechanical Theory ◽  
Conformational Transformations ◽  
Orthogonal Orientation ◽  
Conformational Rearrangements

In this study at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of quantum-mechanical theory it was explored conformational variety of the isolated quercetin molecule due to the mirror-symmetrical hindered turnings of the O3H, O5H and O7H hydroxyl groups, belonging to the A and C rings, around the exocyclic C–O bonds. These dipole active conformational transformations proceed through the 72 transition states (TSs; C1 point symmetry) with non-orthogonal orientation of the hydroxyl groups relatively the plane of the A or C rings of the molecule (HO7C7C8/HO7C7C6 = ±(89.9–93.3), HO5C5C10 = ±(108.9–114.4) and HO3C3C4 = ±(113.6–118.8 degrees) (here and below signs ‘±’ corresponds to the enantiomers)) with Gibbs free energy barrier of activation ΔΔGTS in the range 3.51–16.17 kcal·mol−1 under the standard conditions (T = 298.1 K and pressure 1 atm): ΔΔGTSO7H (3.51–4.27) < ΔΔGTSO3H (9.04–11.26) < ΔΔGTSO5H (12.34–16.17 kcal mol−1). Conformational dynamics of the O3H and O5H groups is partially controlled by the intramolecular specific interactions O3H…O4, C2′/C6′H…O3, O3H…C2′/C6′, O5H…O4 and O4…O5, which are flexible and cooperative. Dipole-active interconversions of the enantiomers of the non-planar conformers of the quercetin molecule (C1 point symmetry) is realized via the 24 TSs with C1 point symmetry (HO3C3C2C1 = ±(11.0–19.1), HC2′/C6′C1′C2 = ±(0.6–2.9) and C3C2C1′C2′/C3C2C1′C6′ = ±(1.7–9.1) degree; ΔΔGTS = 1.65–5.59 kcal·mol−1), which are stabilized by the participation of the intramolecular C2′/C6′H…O1 and O3H…HC2′/C6′ H-bonds. Investigated conformational rearrangements are rather quick processes, since the time, which is necessary to acquire thermal equilibrium does not exceed 6.5 ns.

Dual-level direct dynamics study on the hydrogen abstraction reaction of fluorine atom with 1,1-difluoro-1-chloroethane

2011 ◽  
Vol 89 (11) ◽  
pp. 1396-1402 ◽  
Author(s):  
Li Wang ◽  
Song Liu ◽  
Hongqing He ◽  
Jinglai Zhang
Keyword(s):  
Reaction Path ◽  
Hydrogen Abstraction ◽  
Single Point ◽  
Minimum Energy ◽  
State Theory ◽  
Stationary Points ◽  
Kinetic Properties ◽  
Direct Dynamics ◽  
Wide Range ◽  
Major Reaction

The kinetic properties of the reaction of F atoms with CH2H′CF2Cl are investigated by a dual-level direct dynamics method. Optimized geometries and frequencies of all the stationary points and extra points along the minimum-energy path (MEP) are obtained at the MPW1K/6–311+G(d,p) level of theory. Two complexes with energy less than that of the reactants are located in the two reactant paths, respectively. The energy profiles of two reactions are refined with the interpolated single-point energies (ISPE) method at the G3(MP2)/MPW1K level. The rate constants are evaluated using the canonical variational transition state theory (CVT) with a small-curvature tunneling correction (SCT) over a wide range of temperature 200–2000 K. Agreement between the calculated CVT/SCT rate constant and the experimental value is good at 295 K. Our calculations show that the reaction path CH2H′CF2Cl + F → CH2CF2Cl + H′F (Ra) is the major reaction path below 400 K. Moreover, the contribution of CH2H′CF2Cl + F → CHH′CF2Cl + HF (Rb) to the whole reaction increases with the temperature increasing and exceeds path Ra to be the major reaction path.

The search for stationary points on a quantum mechanical/molecular mechanical potential-energy surface

2002 ◽  
Vol 107 (3) ◽  
pp. 147-153 ◽  
Author(s):  
Xavier Prat-Resina ◽  
Mireia Garcia-Viloca ◽  
Gerald Monard ◽  
Angels González-Lafont ◽  
José M. Lluch ◽  
...  
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Energy Surface ◽  
Stationary Points ◽  
Quantum Mechanical

Metal hydride reductions of unsymmetrical cyclic anhydrides. The importance of the antiperiplanar effect on the regioselectivity of these reactions

1982 ◽  
Vol 60 (10) ◽  
pp. 1192-1198 ◽  
Author(s):  
Margaret M. Kayser ◽  
Georges Wipff
Keyword(s):  
Carbonyl Group ◽  
Metal Hydride ◽  
Lower Energy ◽  
Succinic Anhydride ◽  
Chair Conformation ◽  
Nucleophilic Attack ◽  
Quantum Mechanical ◽  
Mechanical Study ◽  
Quantum Mechanical Study ◽  
Experimental Findings

A quantum mechanical study by the SCF abinitio method of the interaction of H− with methylsuccinic and 2,2-dimethylsuccinic anhydrides (naked and in the presence of a cation) suggests that nonperpendicular rearside attack cannot be the factor responsible for the regioselectivity of hydride transfer to the more sterically hindered carbonyl group. In this model, the nucleophilic attack at the less hindered carbonyl group is calculated to be of lower energy (with or without cation). Deformation of the planar succinic anhydride ring to the quasi-chair conformation is energetically favoured as it allows the nucleophile to attack both carbonyl functions antiperiplanar to a quasi axial C—H or C—C bond. The attack antiperiplanar to the C—CH3 bond is lower in energy than the attack antiperiplanar to the C—H bond suggesting that the reduction will occur at the sterically more hindered carbonyl group which is in agreement with the experimental findings.

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