Structure Optimisation of Large Transition‐Metal Complexes with Extended Tight‐Binding Methods

Bursch, Markus; Neugebauer, Hagen; Grimme, Stefan

doi:10.1002/anie.201904021

Cited by 89 publications

(95 citation statements)

References 70 publications

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“…For each binding mode, the electrostatic binding energies in solution were calculated by using the density functional tight-binding (DFTB) level of theory [ 35 ]. The binding energies were then correlated with the experimental free binding energies ∆G exp (derived from the experimental K I values).…”

Section: Resultsmentioning

confidence: 99%

“…In order to reduce the computational burden of the subsequent geometry optimizations, we generated reduced ligand-receptor complexes, selecting only the residues around 10 Å from the ligand, and capping the incomplete residues by adding H atoms. The following reduced ligand-receptor complexes hCA IX/ a , hCA IX/ b , hCA IX/ 1 , hCA IX/ 2 , hCA XII/ a , hCA XII/ b , hCA XII/ 1 , hCA XII/ 2 , and the free reduced receptors, hCA IX and hCA XII, were optimized in water using density functional tight-binding (DFTB) theory as implemented in XTB software [ 35 , 36 ], adopting the GFN2-xTB method [ 37 ]. The coordinates of the backbone atoms were kept frozen in the optimization calculations.…”

Section: Methodsmentioning

confidence: 99%

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Dual Carbonic Anhydrase IX/XII Inhibitors and Carbon Monoxide Releasing Molecules Modulate LPS-Mediated Inflammation in Mouse Macrophages

et al. 2021

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Low concentrations of carbon monoxide (CO) were reported to exhibit anti-inflammatory effects when administered in cells by suitable chemotypes such as CO releasing molecules (CO-RMs). In addition, the pH-modulating abilities of specific carbonic anhydrase isoforms played a crucial role in different models of inflammation and neuropathic pain. Herein, we report a series of chemical hybrids consisting of a Carbonic Anhydrase (CA) inhibitor linked to a CO-RM tail (CAI/CO-RMs). All compounds and their precursors were first tested in vitro for their inhibition activity against the human CA I, II, IX, and XII isoforms as well their CO releasing properties, aiming at corroborating the data by means of molecular modelling techniques. Then, their impact on metabolic activity modulation of RAW 264.7 mouse macrophages for 24 and 48 h was assessed with or without lipopolysaccharide (LPS) stimulation. The compounds were shown to counteract the inflammatory stimulus as also indicated by the reduced tumor necrosis factor alpha (TNF-α) release after treatment. All the biological results were compared to those of N-acetylcysteine (NAC) as a reference antioxidant compound. Within the series, two CAI/CO-RM hybrids (1 and 2), bearing both the well-known scaffold able to inhibit CAs (acesulfame) and the cobalt-based CO releasing portion, induced a higher anti-inflammatory effect up to 48 h at concentrations lower than NAC.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Dual Carbonic Anhydrase IX/XII Inhibitors and Carbon Monoxide Releasing Molecules Modulate LPS-Mediated Inflammation in Mouse Macrophages

et al. 2021

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“…Fortransition-metal complexes,the quality of theoretical structures is tested on the challenging TMG145 benchmark set [48] (for structural examples,s ee Figure 5E). Thep erformance of GFN-FF is compared to UFF and GFN2-xTB with reference to high-quality DFT-optimized structures (TPSSh-D3(BJ)-ATM/def2-TZVPP).…”

Section: Forschungsartikelmentioning

confidence: 99%

Robust Atomistic Modeling of Materials, Organometallic, and Biochemical Systems

Spicher

Grimme

2020

Angewandte Chemie

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Modern chemistry seems to be unlimited in molecular size and elemental composition. Metal‐organic frameworks or biological macromolecules involve complex architectures and a large variety of elements. Yet, a general and broadly applicable theoretical method to describe the structures and interactions of molecules beyond the 1000‐atom size regime semi‐quantitatively is not self‐evident. For this purpose, a generic force field named GFN‐FF is presented, which is completely newly developed to enable fast structure optimizations and molecular‐dynamics simulations for basically any chemical structure consisting of elements up to radon. The freely available computer program requires only starting coordinates and elemental composition as input from which, fully automatically, all potential‐energy terms are constructed. GFN‐FF outperforms other force fields in terms of generality and accuracy, approaching the performance of much more elaborate quantum‐mechanical methods in many cases.

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“…However, the chemical diversity of the structures in the TMC32 benchmark set is rather limited and hence we decided to extend this cross-check. The recently published TMG145 benchmark set 117 will be used for a more detailed examination of transition metal complex geometries. This set is intended to estimate the quality of bond lengths and angles in transition metal complexes by comparing them against reference structures at the TPSSh-D3(BJ)-ATM/def2-TZVPP 92,118-121 level of theory.…”

Section: Molecular Structuresmentioning

confidence: 99%

A Robust Non-Self-Consistent Tight-Binding Quantum Chemistry Method for large Molecules

Pracht

Caldeweyher²,

Ehlert³

et al. 2019

Preprint

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106

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We propose a semiempirical quantum chemical method, designed for the fast calculation of molecular Geometries, vibrational Frequencies and Non-covalent interaction energies (GFN) of systems with up to a few thousand atoms. Like its predecessors GFN-xTB and GFN2-xTB, the new method termed GFN0-xTB is parameterized for all elements up to radon (Z = 86) and mostly shares well-known density functional tight-binding approximations as well as basis set and integral approximations. The main new feature is the avoidance of the self-consistent charge iterations leading to speed-ups of a factor of 2-20 depending on the size and electronic complexity of the system. This is achieved by including only quantum mechanical contributions up to first-order which are incorporated similar to the previous versions without any pair-specific parameterization. The essential electrostatic electronic interaction is treated by a classical electronegativity equilibration charge model yielding atomic partial charges that enter the electronic Hamiltonian indirectly. Furthermore, the atomic charge-dependent D4 dispersion correction is included to account for long range London correlation effects. Formulas for analytical total energy gradients with respect to nuclear displacements are derived and implemented in the xtb code allowing numerically very precise structure optimizations. The neglect of self-consistent energy terms not only leads to a large gain in computational speed but also can increase robustness in electronically difficult situations because ill-convergence or artificial charge-transfer (CT) is avoided. The comparison of GFN0-xTB and GFN/GFN2-xTB allows dissection of quantum electronic polarization and CT effects thereby improving our understanding of chemical bonding. Compared the the most sophisticated multipole-based GFN2-xTB model (which approaches DFT accuracy for the target properties closely), GFN0-xTB performs slightly worse for non-covalent interactions and molecular structures, while very good results are observed for conformational energies. Vibrational frequencies are obtained less accurately than with GFN/GFN2-xTB but they may still be useful for various purposes like estimating relative thermostatistical reaction energies. Most exceptional is the fact that even relatively complicated transition metal complex structures can be accurately optimized with a non-self-consistent quantum approach. The new method bridges the gap between force-fields and traditional semiempirical methods with its excellent computational cost to accuracy ratio and is intended to explore the chemical space of large molecular systems and solids.

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Structure Optimisation of Large Transition‐Metal Complexes with Extended Tight‐Binding Methods

Cited by 89 publications

References 70 publications

Dual Carbonic Anhydrase IX/XII Inhibitors and Carbon Monoxide Releasing Molecules Modulate LPS-Mediated Inflammation in Mouse Macrophages

Dual Carbonic Anhydrase IX/XII Inhibitors and Carbon Monoxide Releasing Molecules Modulate LPS-Mediated Inflammation in Mouse Macrophages

Robust Atomistic Modeling of Materials, Organometallic, and Biochemical Systems

A Robust Non-Self-Consistent Tight-Binding Quantum Chemistry Method for large Molecules

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