Biomolecular Structure Information from High-Speed Quantum Mechanical Electronic Spectra Calculation

Seibert, Jakob; Bannwarth, Christoph; Grimme, Stefan

doi:10.1021/jacs.7b05833

Cited by 41 publications

(44 citation statements)

References 39 publications

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“…Due to their robust and extensive parametrization for all elements Z=1-86, the GFNn-xTB methods are well suited for a broad range of applications, e.g., in structure optimizations of metal organic complexes 67,68 or in high temperature MD simulations of electron impact mass spectra. 69 One of the most dominant fields of application for the GFN methods is structural sampling and exploration of chemical space, [70][71][72][73] where structures are generated and pre-ranked and subsequently passed to a higher level of theory (e.g., a DFT treatment within a multilevel ansatz).…”

Section: Introductionmentioning

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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Section: Introductionmentioning

confidence: 99%

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

Pracht

Caldeweyher²,

Ehlert³

et al. 2019

Preprint

Self Cite

106

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“…-glucose 1cis-1-ethyl-2-methylcyclohexane (2) n-decane (2) tri-alanine 3-Ionone (4) Guaiol (5) Rivaroxaban (6) Capecitabine 7Oseltamivir (9) Abiraterone (10) Pacritinib (11) Etoposide 12Macrocarpal A (13) Grubbs cat. 14Paclitaxel 15Bisacridine-peptide (16) Nonactin (17) Vinblastine (18) Ledipasvir (19) Everolimus (20) Adocobalmin+ (21) Vancomycin (22) Figure 4: Molecular starting structures in the conformer search benchmark.…”

Section: Nanoreactormentioning

confidence: 99%

“…As such, it has been successfully used in structure optimizations of organometallic complexes 15,16 and structural sampling. 7,[17][18][19] Apart from that, the method performed well in high-temperature molecular dynamics (MD) simulations of electron impact mass spectra. 20 Very recently, it is has been extended by including multipole electrostatic as well as one-center exchange-correlation terms leading to higher accuracy (at lower empiricism) specifically for non-covalent interactions and conformational energies.…”

Section: Introductionmentioning

confidence: 99%

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Exploration of Chemical Compound, Conformer, and Reaction Space with Meta-Dynamics Simulations Based on Tight-Binding Quantum Chemical Calculations

Grimme

2019

Preprint

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The semi-empirical tight-binding based quantum chemistry method GFN2-xTB is used in the framework of meta-dynamics (MTD) to globally explore chemical compound, conformer, and reaction space. The approach us used for three common problems, i.e., conformer search, chemical reaction space exploration in a virtual nanoreactor, and for guessing reaction paths. <div>For typical conformational search problems of drug-like organic molecules, the new MTD(RMSD) algorithm yields lower energy structures and more complete conformer ensembles at reduced computational effort compared with its already well performing predecessor.<br><br></div>

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“…[2][3][4][5] One limitation of this kind of simulations is that their computational complexity renders them impractical when the system size goes beyond 10 4 atoms. [6,7] In physics and engineering, the transfer matrix (T-matrix) approach [8] is a very common tool for computing the electromagnetic responses of single and composite objects. The T-matrix of an object is equivalent to its scattering matrix and contains all the information about its electromagnetic response.…”

Section: Introductionmentioning

confidence: 99%

Computation of Electromagnetic Properties of Molecular Ensembles

et al. 2020

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We outline a methodology for efficiently computing the electromagnetic response of molecular ensembles. The methodology is based on the link that we establish between quantumchemical simulations and the transfer matrix (T-matrix) approach, a common tool in physics and engineering. We exemplify and analyze the accuracy of the methodology by using the time-dependent Hartree-Fock theory simulation data of a single chiral molecule to compute the T-matrix of a crosslike arrangement of four copies of the molecule, and then computing the circular dichroism of the cross. The results are in very good agreement with full quantum-mechanical calculations on the cross. Importantly, the choice of computing circular dichroism is arbitrary: Any kind of electromagnetic response of an object can be computed from its T-matrix. We also show, by means of another example, how the methodology can be used to predict experimental measurements on a molecular material of macroscopic dimensions. This is possible because, once the T-matrices of the individual components of an ensemble are known, the electromagnetic response of the ensemble can be efficiently computed. This holds for arbitrary arrangements of a large number of molecules, as well as for periodic or aperiodic molecular arrays. We identify areas of research for further improving the accuracy of the method, as well as new fundamental and technological research avenues based on the use of the T-matrices of molecules and molecular ensembles for quantifying their degrees of symmetry breaking. We provide T-matrix-based formulas for computing traditional chiro-optical properties like (oriented) circular dichroism, and also for quantifying electromagnetic duality and electromagnetic chirality. The formulas are valid for light-matter interactions of arbitrarily-high multipolar orders.

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Biomolecular Structure Information from High-Speed Quantum Mechanical Electronic Spectra Calculation

Cited by 41 publications

References 39 publications

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

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

Exploration of Chemical Compound, Conformer, and Reaction Space with Meta-Dynamics Simulations Based on Tight-Binding Quantum Chemical Calculations

Computation of Electromagnetic Properties of Molecular Ensembles

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