FFLUX: Transferability of polarizable machine‐learned electrostatics in peptide chains

Fletcher, Timothy L.; Popelier, Paul L. A.

doi:10.1002/jcc.24775

Cited by 20 publications

(23 citation statements)

References 41 publications

(57 reference statements)

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“…DFT-based first-principles calculations of ELNES and partial density of states (PDOS) are performed using the Cambridge Serial Total Energy Package (CASTEP) within the generalized gradient approximation (GGA) using the Perdew-Burke-Enzerhof (PBE) functional (Perdew et al, 1996). The Broyden-Fletcher-Goldfrab-Shanno (BFGS) geometry optimization scheme has been used (Broyden, 1970;Fletcher, 1970;Goldfarb, 1970;Shanno, 1970). All atoms were fully relaxed until the magnitude of the force on each atom converged to less than 0.01 eV Å À1 and the energy change per atom converged to less than 5 Â 10 À7 eV atom À1 , yielding optimized structures using the virtual crystal approximation (Bellaiche & Vanderbilt, 2000;Sen & Ghosh, 2016).…”

Section: Theory and Computational Methodologymentioning

confidence: 99%

Doping site identification in 112 iron pnictides through a first-principles core-electron spectroscopic study

Ghosh

2019

J Synchrotron Radiat

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Density functional theory based first‐principles core‐electron spectroscopic studies on iron‐based superconducting 112 materials are presented. The existence of an extra As zigzag chain structure along with Fe–As planes in 112 materials is emphasised. Doping on an As site belonging to a chain by Sb is found to enhance the superconducting transition temperature. This is also shown from calculations with enhanced density of states when doped on chain‐As. Therefore, As site identification in 112 is crucial. Theoretically computed As K‐edge absorption spectra of two different types of As atoms for Ca0.85La0.15FeAs2 show a distinctly different nature. The sensitivities of As K‐edge absorption spectra in the presence and absence of the `core‐hole effect' are presented for future possible identification of the same experimentally. In both cases absorption spectra contain several features, the origins of which are thoroughly described in terms of site projected density of states results.

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Section: Theory and Computational Methodologymentioning

confidence: 99%

Doping site identification in 112 iron pnictides through a first-principles core-electron spectroscopic study

Ghosh

2019

J Synchrotron Radiat

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“…The interaction energy, V AB corr , of each atom with itself (A = B) or with one of the other atoms (A ≠ B) is obtained from the 2PDM via a 6D quadrature integration. The 3D ESP [51] approach was more recently developed with the intent of ultimate implementation in our polarizable multipolar [52] topological force field FFLUX [53][54][55][56][57], since 3D ESP is faster and more accurate when compared to the 6D approach. The master equation for the 3D ESP integration is given just below, where any derivation details are not repeated here but can be found in the selfcontained account of ref.…”

Section: Iqa Dynamic Electron Correlation Energymentioning

confidence: 99%

Contributions of IQA electron correlation in understanding the chemical bond and non-covalent interactions

2020

Self Cite

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The quantum topological energy partitioning method Interacting Quantum Atoms (IQA) has been applied for over a decade resulting in an enlightening analysis of a variety of systems. In the last three years we have enriched this analysis by incorporating into IQA the two-particle density matrix obtained from Møller-Plesset (MP) perturbation theory. This work led to a new computational and interpretational tool to generate atomistic electron correlation and thus topologically based dispersion energies. Such an analysis determines the effects of electron correlation within atoms and between atoms, which covers both bonded and non-bonded "throughspace" atom-atom interactions within a molecule or molecular complex. A series of papers published by us and other groups shows that the behavior of electron correlation is deeply ingrained in structural chemistry. Some concepts that were shown to be connected to bond correlation are bond order, multiplicity, aromaticity, and hydrogen bonding. Moreover, the concepts of covalency and ionicity were shown not to be mutually excluding but to both contribute to the stability of polar bonds. The correlation energy is considerably easier to predict by machine learning (kriging) than other IQA terms. Regarding the nature of the hydrogen bond, correlation energy presents itself in an almost contradicting way: there is much localized correlation energy in a hydrogen bond system, but its overall effect is null due to internal cancelation. Furthermore, the QTAIM delocalization index has a connection with correlation energy. We also explore the role of electron correlation in protobranching, which provides an explanation for the extra stabilization present in branched alkanes compared to their linear counterparts. We hope to show the importance of understanding the true nature of the correlation energy as the foundation of a modern representation of dispersion forces for ab initio, DFT, and force field calculations.

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“…We use 16 × 16 × 1, 16 × 16 × 1, and 8 × 16 × 1 k-points for the 1H, 1T and 1T MoS 2 , respectively. To obtain optimized atomic configurations of MoS 2 monolayers, the atomic positions and cell vectors are fully relaxed using the Broyden-Fretcher-Goldfarb-Shanno minimization method [22][23][24][25] until all the Hellmann-Feynman forces and all components of the stress are less than 5 × 10 −4 Ry/a.u. and 5 × 10 −2 GPa, respectively.…”

Section: Calculation Detailsmentioning

confidence: 99%

Two-dimensional MoS₂ electromechanical actuators

Hung¹,

Nugraha²,

Saito³

2018

J. Phys. D: Appl. Phys.

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We investigate electromechanical properties of two-dimensional MoS 2 monolayers in the 1H, 1T, and 1T structures as a function of charge doping by using density functional theory. We find isotropic elastic moduli in the 1H and 1T structures, while the 1T structure exhibits an anisotropic elastic modulus. Moreover, the 1T structure is shown to have a negative Poisson's ratio, while Poisson's ratios of the 1H and 1T are positive. By charge doping, the monolayer MoS 2 shows a reversibly strain and work density per cycle ranging from −0.68% to 2.67% and from 4.4 to 36.9 MJ/m 3 , respectively, making them suitable for applications in electromechanical actuators. Stress generated is also examined in this work and we find that 1T and 1T MoS 2 monolayers relatively have better performance than 1H MoS 2 monolayer. We argue that such excellent electromechanical performance originate from the electrical conductivity of the metallic 1T and semimetallic 1T structures high Young's modulus of about 150 − 200 GPa. arXiv:1711.00188v1 [cond-mat.mtrl-sci] 1 Nov 2017 Two-dimensional MoS 2 electromechanical actuators

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FFLUX: Transferability of polarizable machine‐learned electrostatics in peptide chains

Cited by 20 publications

References 41 publications

Doping site identification in 112 iron pnictides through a first-principles core-electron spectroscopic study

Doping site identification in 112 iron pnictides through a first-principles core-electron spectroscopic study

Contributions of IQA electron correlation in understanding the chemical bond and non-covalent interactions

Two-dimensional MoS₂ electromechanical actuators

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FFLUX: Transferability of polarizable machine‐learned electrostatics in peptide chains

Cited by 20 publications

References 41 publications

Doping site identification in 112 iron pnictides through a first-principles core-electron spectroscopic study

Doping site identification in 112 iron pnictides through a first-principles core-electron spectroscopic study

Contributions of IQA electron correlation in understanding the chemical bond and non-covalent interactions

Two-dimensional MoS2 electromechanical actuators

Contact Info

Product

Resources

About

Two-dimensional MoS₂ electromechanical actuators