Potential Energy Surface
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Lulu Zhang ◽  
Juan Zhao ◽  
Dong Liu ◽  
Wei Wang ◽  
Daguang Yue ◽  

Relaxed triangular plot of the new PES in hyperspherical coordinates.

J. Espinosa-Garcia

In this paper we study the gas-phase hydrogen abstraction reaction between fluorine atoms and silane in a three-step process: potential energy surface, kinetics and dynamics. Firstly, we developed for the...

2022 ◽  
Meiling Xu ◽  
Yinwei Li ◽  
Yanming Ma

Pressure, a fundamental thermodynamic variable, can generate two essential effects on materials. First, pressure can create new high-pressure phases via modification of the potential energy surface. Second, pressure can produce...

2021 ◽  
Vol 23 ◽  
Saumya Kapoor ◽  
Gurudutt Dubey ◽  
Samima Khatun ◽  
Prasad V. Bharatam

Background: Remdesivir (GS-5734) has emerged as a promising drug during the challenging times of COVID-19 pandemic. Being a prodrug, it undergoes several metabolic reactions before converting to its active triphosphate metabolite. It is important to establish the atomic level details and explore the energy profile of the prodrug to drug conversion process. Methods: In this work, Density Functional Theory (DFT) calculations were performed to explore the entire metabolic path. Further, the potential energy surface (PES) diagram for the conversion of prodrug remdesivir to its active metabolite was established. The role of catalytic triad of Hint1 phosphoramidase enzyme in P-N bond hydrolysis was also studied on a model system using combined molecular docking and quantum mechanics approach. Results: The overall energy of reaction is 11.47 kcal/mol exergonic and the reaction proceeds through many steps requiring high activation energies. In the absence of a catalyst, the P-N bond breaking step requires 41.78 kcal/mol, which is reduced to 14.26 kcal/mol in a catalytic environment. Conclusion: The metabolic pathways of model system of remdesivir (MSR) were completely explored completely and potential energy surface diagrams at two levels of theory, B3LYP/6-311++G(d, p) and B3LYP/6-31+G(d), were established and compared. The results highlight the importance of an additional water molecule in the metabolic reaction. The P-N bond cleavage step of the metabolic process requires the presence of an enzymatic environment.

2021 ◽  
Dominika VIGLASKA ◽  
Xiao-Gang Wang ◽  
David Tew

In this paper we report rovibrational energy levels, transition frequencies, and intensities computed for H2O-HF using a new ab initio potential energy surface and compare with available experimental data. We use the rigid monomer approximation. A G4 symmetry-adapted Lanczos algorithm and an uncoupled product basis are employed. The rovibrational levels are computed up to J = 4. The new analytic 9-D potential is �t to 39771 counterpoise corrected CCSD(T)(F12*)/augcc- pVTZ energies and reduces to the sum of uncoupled H2O and HF potentials in the dissociation limit. On the new potential better agreement with experiment is obtained by re-assigning the R(1) transitions of two vibrational states.

2021 ◽  
Kaisheng Song ◽  
Jun Li

Ion-neutral molecular reactions play key roles in the field of ion related chemistry. As a prototypical multi-channel ion-molecular reaction, the reaction H2 + NH2- → NH3 + H- has been studied for decades. In this work, we develop a globally accurate potential energy surface (PES) for the title system H2 + NH2- based on nearly hundreds of thousands points over a wide dynamically relevant region. The permutational invariants polynomials neural network (PIP-NN) method is used for fitting and the total root mean squared error (RMSE) is extremely small, only 0.026 kcal mol-1. Extensive dynamical and rate coefficient calculations are carried out on this new PIP-NN PES by the quasi-classical trajectory (QCT) method. The calculated rate coefficients for H2 / D2 + NH2- agree well with the experimental results that show a inverse temperature dependence from 50 to 300 K, consistent with the capture nature of this barrierless reaction. A significant kinetic isotope effect has been well reproduced by the QCT computations. In addition, we report a unique phenomenon of significant reactivity suppression by exciting the rotational mode of H2, particular at low collision energies. Further analysis shows that the excitation of rotational mode of H2 would prevent the formation of the reactant complex and thus suppress reactivity.

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