Stabilization of resonance states by an asymptotic Coulomb potential

Адамсон, С. О.; Kharlampidi, D. D.; Dementiev, A. I.

doi:10.1063/1.2821102

Cited by 15 publications

(6 citation statements)

References 26 publications

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“…Metadynamics is part of the family of adaptive bias methods, where a history-dependent bias is modified over time to ideally achieve a fully diffusive behavior on the chosen reaction coordinate. Among other methods in this family, − we discuss metadynamics here because of its widespread use and availability in the computational drug discovery community. , In the first version of metadynamics, constrained and coarse-grained simulations were used . Later, a continuous version emerged .…”

Section: Enhanced Sampling Methodsmentioning

confidence: 99%

Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation

2020

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Computational studies play an increasingly important role in chemistry and biophysics, mainly thanks to improvements in hardware and algorithms. In drug discovery and development, computational studies can reduce the costs and risks of bringing a new medicine to market. Computational simulations are mainly used to optimize promising new compounds by estimating their binding affinity to proteins. This is challenging due to the complexity of the simulated system. To assess the present and future value of simulation for drug discovery, we review key applications of advanced methods for sampling complex free-energy landscapes at near nonergodicity conditions and for estimating the rate coefficients of very slow processes of pharmacological interest. We outline the statistical mechanics and computational background behind this research, including methods such as steered molecular dynamics and metadynamics. We review recent applications to pharmacology and drug discovery and discuss possible guidelines for the practitioner. Recent trends in machine learning are also briefly discussed. Thanks to the rapid development of methods for characterizing and quantifying rare events, simulation’s role in drug discovery is likely to expand, making it a valuable complement to experimental and clinical approaches.

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Section: Enhanced Sampling Methodsmentioning

confidence: 99%

Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation

2020

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“…These include methods that explicitly solve the scattering problem , as well as approaches that involve modifications of standard quantum chemical methods. Examples of the latter include the complex scaling, − complex absorbing potential (CAP), − and stabilization methods. ,,,− In addition, one can add a perturbation to the system to convert the TA to a bound state and then extrapolate to zero perturbation. − …”

Section: Introductionmentioning

confidence: 99%

Assessment of Various Electronic Structure Methods for Characterizing Temporary Anion States: Application to the Ground State Anions of N₂, C₂H₂, C₂H₄, and C₆H₆

et al. 2014

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The theoretical characterization of temporary anions is an especially challenging problem. In the present study we assess the performance of several electronic structure methods when used in conjunction with the stabilization method to characterize temporary anion states. The ground state anions of N2, C2H2, C2H4, and C6H6 are used as the test systems, with the most extensive testing being done for N2. For the (2)Πg anion state of N2(-) the ADC(2), EOM-MP2, and EOM-CCSD methods give values of the resonance parameters in excellent agreement with the results of prior high-level calculations. For the hydrocarbon systems, the EOM-MP2 method consistently provides excellent agreement with the EOM-CCSD results for the test systems, whereas the ADC(2) considerably underestimates the widths for ethylene and benzene. Several density functional theory (DFT) approaches are tested and, although none performs as well as the EOM-MP2 method, it is found that inclusion of Hartree-Fock exchange greatly improves the results. Of the DFT-based methods, time-dependent DFT with standard correlation functionals and use of Hartree-Fock exchange provides the best performance for N2(-) over the range of bond lengths considered and is also found to give reasonable values of the resonance parameters of the three hydrocarbon molecules.

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“…The investigation of continuum and resonant states is an important subject in quantum physics. For the theoretical determination of resonant parameters (the energy and the width), in addition to many approaches which are based on the connection of the unbound states (including resonances and antibound or virtual states) and the poles of the S matrix, several bound-state-like methods have been developed, e.g., the complex scaling method (CSM) [1][2][3][4][5][6][7][8][9], the complex absorbing potential (CAP) method [10,11], the analytical continuation in the coupling constant (ACCC) approach [12][13][14][15][16][17][18][19][20] and the real stabilization method (RSM) [21][22][23][24][25][26][27][28][29][30].…”

Section: Introductionmentioning

confidence: 99%

A spherical-box approach for resonances in the presence of the Coulomb interaction

Zhou¹,

Meng²,

Zhao³

2009

J. Phys. B: At. Mol. Opt. Phys.

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The spherical-box approach is extended to calculate the resonance parameters and the real part of the wavefunction for single particle resonances in a potential containing the long-range Coulomb interaction. A model potential is taken to demonstrate the ability and accuracy of this approach. The calculated resonance parameters are compared with available results from other methods. It is shown that in the presence of the Coulomb interaction, the spherical-box approach works well for not so broad resonances. In particular, for very narrow resonances, the present method gives resonance parameters to a very high precision.

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Stabilization of resonance states by an asymptotic Coulomb potential

Cited by 15 publications

References 26 publications

Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation

Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation

Assessment of Various Electronic Structure Methods for Characterizing Temporary Anion States: Application to the Ground State Anions of N₂, C₂H₂, C₂H₄, and C₆H₆

A spherical-box approach for resonances in the presence of the Coulomb interaction

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Stabilization of resonance states by an asymptotic Coulomb potential

Cited by 15 publications

References 26 publications

Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation

Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation

Assessment of Various Electronic Structure Methods for Characterizing Temporary Anion States: Application to the Ground State Anions of N2, C2H2, C2H4, and C6H6

A spherical-box approach for resonances in the presence of the Coulomb interaction

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Product

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Assessment of Various Electronic Structure Methods for Characterizing Temporary Anion States: Application to the Ground State Anions of N₂, C₂H₂, C₂H₄, and C₆H₆