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See detailCoulomb interactions between dipolar quantum fluctuations in van der Waals bound molecules and materials
Stoehr, Martin UL; Sadhukhan, Mainak; Al-Hamdani, Yasmine S. et al

in Nature Communications (2021), 12(1), 137

Mutual Coulomb interactions between electrons lead to a plethora of interesting physical and chemical effects, especially if those interactions involve many fluctuating electrons over large spatial scales ... [more ▼]

Mutual Coulomb interactions between electrons lead to a plethora of interesting physical and chemical effects, especially if those interactions involve many fluctuating electrons over large spatial scales. Here, we identify and study in detail the Coulomb interaction between dipolar quantum fluctuations in the context of van der Waals complexes and materials. Up to now, the interaction arising from the modification of the electron density due to quantum van der Waals interactions was considered to be vanishingly small. We demonstrate that in supramolecular systems and for molecules embedded in nanostructures, such contributions can amount to up to 6 kJ/mol and can even lead to qualitative changes in the long-range van der Waals interaction. Taking into account these broad implications, we advocate for the systematic assessment of so-called Dipole-Correlated Coulomb Singles in large molecular systems and discuss their relevance for explaining several recent puzzling experimental observations of collective behavior in nanostructured materials. [less ▲]

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See detailvan der Waals Dispersion Interactions in Biomolecular Systems: Quantum-Mechanical Insights and Methodological Advances
Stoehr, Martin UL

Doctoral thesis (2020)

Intermolecular interactions are paramount for the stability, dynamics and response of systems across chemistry, biology and materials science. In biomolecules they govern secondary structure formation ... [more ▼]

Intermolecular interactions are paramount for the stability, dynamics and response of systems across chemistry, biology and materials science. In biomolecules they govern secondary structure formation, assembly, docking, regulation and functionality. van der Waals (vdW) dispersion contributes a crucial part to those interactions. As part of the long-range electron correlation, vdW interactions arise from Coulomb-coupled quantum-mechanical fluctuations in the instan- taneous electronic charge distribution and are thus inherently many-body in nature. Common approaches to describe biomolecular systems (i.e., classical molecular mechanics) fail to capture the full complexity of vdW dispersion by adapting a phenomenological, atom-pairwise formalism. This thesis explores beyond-pairwise vdW forces and the collectivity of intrinsic electronic behav- iors in biomolecular systems and discusses their role in the context of biomolecular processes and function. To this end, the many-body dispersion (MBD) formalism parameterized from density-functional tight-binding (DFTB) calculations is used. The investigation of simple molecular solvents with particular focus on water gives insights into the vdW energetics and electronic response properties in liquids and solvation as well as emergent behavior for coarse-grained models. A detailed study of intra-protein and protein–water vdW interactions highlights the role of many-body forces during protein folding and provides a funda- mental explanation for the previously observed “unbalanced” description and over-compaction of disordered protein states. Further analysis of the intrinsic electronic behaviors in explicitly solvated proteins indicates a long-range persistence of electron correlation through the aque- ous environment, which is discussed in the context of protein–protein interactions, long-range coordination and biomolecular regulation and allostery. Based on the example of a restriction enzyme, the potential role of many-body vdW forces and collective electronic behavior for the long-range coordination of enzymatic activity is discussed. Introducing electrodynamic quantum fluctuations into the classical picture of allostery opens up the path to a more holistic view on biomolecular regulation beyond the traditional focus on merely local structural modifications. Building on top of the MBD framework, which describes vdW dispersion within the interatomic dipole-limit, a practical extension to higher-order terms is presented. The resulting Dipole- Correlated Coulomb Singles account for multipolar as well as dispersion-polarization-like contri- butions beyond the random phase approximation by means of first-order perturbation theory over the dipole-coupled MBD state. It is shown that Dipole-Correlated Coulomb Singles become particularly relevant for relatively larger systems and can alter qualitative trends in the long-range interaction under (nano-)confinement. Bearing in mind the frequent presence of confinement in biomolecular systems due to cellular crowding, in ion channels or for interfacial water, this so-far neglected contribution is expected to have broad implications for systems of biological relevance. Ultimately, this thesis introduces a hybrid approach of DFTB and machine learning for the accu- rate description of large-scale systems on a robust, albeit approximate, quantum-mechanical level. The developed DFTB-NN rep approach combines the semi-empirical DFTB Hamiltonian with a deep tensor neural network model for localized many-body repulsive potentials. DFTB- NN rep provides an accurate description of energetic, structural and vibrational properties of a wide range of small organic molecules much superior to standard DFTB or machine learning. Overall, this thesis aims to extend the current view of complex (bio)molecular systems being governed by local, (semi-)classical interactions and develops methodological steps towards an advanced description and understanding including non-local interaction mechanisms enabled by quantum-mechanical phenomena such as long-range correlation forces arising from collective electronic fluctuations. [less ▲]

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See detailAccurate Many-Body Repulsive Potentials for Density-Functional Tight Binding from Deep Tensor Neural Networks
Stoehr, Martin UL; Medrano Sandonas, Leonardo UL; Tkatchenko, Alexandre UL

in Journal of Physical Chemistry Letters (2020), 11(16), 68356843

We combine density-functional tight binding (DFTB) with deep tensor neural networks (DTNN) to maximize the strengths of both approaches in predicting structural, energetic, and vibrational molecular ... [more ▼]

We combine density-functional tight binding (DFTB) with deep tensor neural networks (DTNN) to maximize the strengths of both approaches in predicting structural, energetic, and vibrational molecular properties. The DTNN is used to construct a nonlinear model for the localized many-body interatomic repulsive energy, which so far has been treated in an atom-pairwise manner in DFTB. Substantially improving upon standard DFTB and DTNN, the resulting DFTB-NNrep model yields accurate predictions of atomization and isomerization energies, equilibrium geometries, vibrational frequencies, and dihedral rotation profiles for a large variety of organic molecules compared to the hybrid DFT-PBE0 functional. Our results highlight the potential of combining semiempirical electronic-structure methods with physically motivated machine learning approaches for predicting localized many-body interactions. We conclude by discussing future advancements of the DFTB-NNrep approach that could enable chemically accurate electronic-structure calculations for systems with tens of thousands of atoms. [less ▲]

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See detailDFTB+, a software package for efficient approximate density functional theory based atomistic simulations
Hourahine, Ben; Aradi, Bálint; Blum, Volker et al

in The Journal of Chemical Physics (2020), 152(12), 124101

DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods ... [more ▼]

DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green’s functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives. [less ▲]

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See detailQuantum mechanics of proteins in explicit water: The role of plasmon-like solute-solvent interactions
Stoehr, Martin UL; Tkatchenko, Alexandre UL

in Science Advances (2019), 5(12), 0024

Quantum-mechanical van der Waals dispersion interactions play an essential role in intraprotein and protein-water interactions—the two main factors affecting the structure and dynamics of proteins in ... [more ▼]

Quantum-mechanical van der Waals dispersion interactions play an essential role in intraprotein and protein-water interactions—the two main factors affecting the structure and dynamics of proteins in water. Typically, these interactions are only treated phenomenologically, via pairwise potential terms in classical force fields. Here, we use an explicit quantum-mechanical approach of density-functional tight-binding combined with the many-body dispersion formalism and demonstrate the relevance of many-body van der Waals forces both to protein energetics and to protein-water interactions. In contrast to commonly used pairwise approaches, many-body effects substantially decrease the relative stability of native states in the absence of water. Upon solvation, the protein-water dispersion interaction counteracts this effect and stabilizes native conformations and transition states. These observations arise from the highly delocalized and collective character of the interactions, suggesting a remarkable persistence of electron correlation through aqueous environments and providing the basis for long-range interaction mechanisms in biomolecular systems. [less ▲]

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See detailTheory and practice of modeling van der Waals interactions in electronic-structure calculations
Stoehr, Martin UL; Van Voorhis, Troy; Tkatchenko, Alexandre UL

in Chemical Society Reviews (2019), 48

The accurate description of long-range electron correlation, most prominently including van der Waals (vdW) dispersion interactions, represents a particularly challenging task in the modeling of molecules ... [more ▼]

The accurate description of long-range electron correlation, most prominently including van der Waals (vdW) dispersion interactions, represents a particularly challenging task in the modeling of molecules and materials. vdW forces arise from the interaction of quantum-mechanical fluctuations in the electronic charge density. Within (semi-)local density functional approximations or Hartree–Fock theory such interactions are neglected altogether. Non-covalent vdW interactions, however, are ubiquitous in nature and play a key role for the understanding and accurate description of the stability, dynamics, structure, and response properties in a plethora of systems. During the last decade, many promising methods have been developed for modeling vdW interactions in electronic-structure calculations. These methods include vdW-inclusive Density Functional Theory and correlated post-Hartree–Fock approaches. Here, we focus on the methods within the framework of Density Functional Theory, including non-local van der Waals density functionals, interatomic dispersion models within many-body and pairwise formulation, and random phase approximation-based approaches. This review aims to guide the reader through the theoretical foundations of these methods in a tutorial-style manner and, in particular, highlight practical aspects such as the applicability and the advantages and shortcomings of current vdW-inclusive approaches. In addition, we give an overview of complementary experimental approaches, and discuss tools for the qualitative understanding of non-covalent interactions as well as energy decomposition techniques. Besides representing a reference for the current state-of-the-art, this work is thus also designed as a concise and detailed introduction to vdW-inclusive electronic structure calculations for a general and broad audience. [less ▲]

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