A fast charge‐Dependent atom‐pairwise dispersion correction for DFTB3

Petraglia, Riccardo; Steinmann, Stephan N.; Corminbœuf, Clémence

doi:10.1002/qua.24887

Cited by 16 publications

(24 citation statements)

References 78 publications

(123 reference statements)

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“…The conformations of dithiacyclophane (Fig. ), previously investigated by two of the authors, perfectly illustrates this aspect. This highly flexible molecule was originally found to possess several low‐lying conformers featuring both π‐stacked (structure 1 , meta‐stable) and open conformations (structure 2 , lower in energy) using accurate electronic structure methods.…”

Section: Resultssupporting

confidence: 74%

“…This highly flexible molecule was originally found to possess several low‐lying conformers featuring both π‐stacked (structure 1 , meta‐stable) and open conformations (structure 2 , lower in energy) using accurate electronic structure methods. Not surprisingly, Born–Oppenheimer MD simulations performed at both the DFT (i.e., PBE) and DFTB3 levels were shown to be highly sensitive to the inclusion of a dispersion correction . As might be expected, in the absence of van der Waals corrections, the π‐stacked conformation readily converted into the open conformers (on a scale as fast as 250 fs), whereas the stacked meta‐stable conformer persisted for a few picoseconds in the dispersion‐corrected trajectories.…”

Section: Resultsmentioning

confidence: 79%

“…S2) than those in Refs. [38] and [39] remained, for most of the time, trapped in its original stacked conformational region without identifying the thermodynamically more important region associated with the new conformation …”

Section: Resultsmentioning

confidence: 99%

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Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry

et al. 2015

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Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a multitude of molecular conformations exists on incredibly complex potential energy surfaces (PES). Here, we borrow a computational technique originally conceived to be used in the context of biological simulations, together with empirical force fields, and apply it to organic chemical problems. Replica‐exchange molecular dynamics (REMD) permits thorough exploration of the PES. We combined REMD with density functional tight binding (DFTB), thereby establishing the level of accuracy necessary to analyze small molecular systems. Through the study of four prototypical problems: isomer identification, reaction mechanisms, temperature‐dependent rotational processes, and catalysis, we reveal new insights and chemistry that likely would be missed using static electronic structure computations. The REMD‐DFTB methodology at the heart of this study is powered by i‐PI, which efficiently handles the interface between the DFTB and REMD codes. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

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Section: Resultssupporting

confidence: 74%

Section: Resultsmentioning

confidence: 79%

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Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry

et al. 2015

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“…The correction of noncovalent interactions can be described with multiple empirical approaches. The implemented variations for dispersion correction are the following: Slater‐Kirkwood, Lennard‐Jones, DFT‐D2, DFT‐D3, DFT‐ ulg , and dDMC . Note that dDMC is not fully empirical but charge dependent collection.…”

Section: Dc‐dftb Modelmentioning

confidence: 99%

Dcdftbmd: Divide‐and‐Conquer Density Functional Tight‐Binding Program for Huge‐System Quantum Mechanical Molecular Dynamics Simulations

Nishimura

Nakai

2019

J Comput Chem

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Dcdftbmd is a Fortran 90/95 program that enables efficient quantum mechanical molecular dynamics (MD) simulations using divide‐and‐conquer density functional tight‐binding (DC‐DFTB) method. Based on the remarkable performance of previous massively parallel DC‐DFTB energy and gradient calculations for huge systems, the code has been specialized to MD simulations. Recent implementations and modifications including DFTB extensions, improved computational speed in the DC‐DFTB computational steps, algorithms for efficient initial guess charge prediction, and free energy calculations via metadynamics technique have enhanced the capability to obtain atomistic insights in novel applications to nanomaterials and biomolecules. The energy, structure, and other molecular properties are also accessible through the single‐point calculation, geometry optimization, and vibrational frequency analysis. The available functionalities are outlined together with efficiency tests and simulation examples. © 2019 Wiley Periodicals, Inc.

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“…30,31 Precalculated and tabulated C 6 (dipole−dipole) coefficients are used to calculate pairwiseadditive dispersion energies in these methods. The C 6…”

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confidence: 99%

Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding

Mortazavi

Brandenburg

Maurer

et al. 2018

J. Phys. Chem. Lett.

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Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko−Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction. ■ INTRODUCTIONStability and structure prediction of molecular materials from first-principles electronic structure calculations bears significance to a wide range of problems ranging from pharmaceutical activity of drugs to optical properties of modern organic materials.1−3 The rugged and complex energy landscapes of molecular crystals give rise to the phenomenon of polymorphismthe ability of molecules to form different crystalpacking motifswhich is a crucial aspect in drug design, food chemistry, and organic semiconductor materials.4−7 Polymorphic materials exhibit many energetically close-lying minima, which can easily coexist and transform into each other at time scales that are inaccessible by conventional molecular dynamic simulations. Rigorous computational polymorph screening followed by correct stability ranking is therefore a crucial aspect for molecular crystal structure prediction (CSP). 8−11In recent years, DFT methods have become more reliable in predicting and ranking polymorphic systems due to the incorporation of efficient dispersion correction methods that, 9,12−15 at the same time, ensure computational feasibility. 10,16−19 In particular, the inclusion of beyond-pairwise dispersion interactions through the many-body dispersion (MBD) method coupled to semilocal DFT functionals has proven to be successful in this context. 10,15,20 To address larger length and time scales and more efficient structure prediction, several approximate electronic structure methods have been highly successful including semiempirical quantum chemical methods such as AM1, PM7, or the DFT-based densityfunctional tight binding (DFTB). 21−23 DFTB has been significantly improved recently, particularly in its description of charge polarization via third-order charge fluctuation corrections (DFTB3) 24,25 or its description of hydrogen bonding.26 Nevertheless, several shortcomings still persist that prohibit its use as standard tool in structure and stability prediction for molecular crystals. 22,2...

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A fast charge‐Dependent atom‐pairwise dispersion correction for DFTB3

Abstract: International audienc

Cited by 16 publications

References 78 publications

Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry

Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry

Dcdftbmd: Divide‐and‐Conquer Density Functional Tight‐Binding Program for Huge‐System Quantum Mechanical Molecular Dynamics Simulations

Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding

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