A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+

Kromann, Jimmy C.; Christensen, Anders S.; Steinmann, Casper; Korth, Martin; Jensen, Jan H.

doi:10.7717/peerj.449

Cited by 53 publications

(47 citation statements)

References 31 publications

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“…A general similarity between all SQM methods is parameterization, which, if conducted carefully, can minimize accuracy issues for special purpose applications. [30][31][32][33][34][35][36] Among the most frequently used Hartree-Fock based zero-differential overlap (ZDO) methods are PM6, [37][38][39][40][41][42] -used for the computation of ground state structures and energies [43][44][45][46] -and OM2, [47][48][49][50][51] which is extensively applied in excited state dynamics studies. [52][53][54][55][56] Over the past decades, density functional tight binding (DFTB) methods, [57][58][59][60][61][62][63][64][65][66] as derived from DFT, have found more attention, whereat in recent years the extended tightbinding (xTB) family of methods has been developed.…”

Section: Introductionmentioning

confidence: 99%

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

Pracht

Caldeweyher²,

Ehlert³

et al. 2019

Preprint

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

106

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“…The structures are geometry optimized using PM6-D3H+ (Kromann et al, 2014) using the PCM solvation model (Tomasi et al, 2005;Steinmann et al, 2013) and the CHARMM22/CMAP force field (Mackerell, 2004) using the GB/SA solvation model (Qiu et al, 1997) with the 1UBQ (Vijay- Kumar et al, 1987) and 2OED (Ulmer et al, 2003) structures as starting points. The PM6-D3H+ optimizations are done using the GAMESS program (Schmidt et al, 1993) with a convergence criterion of 5 × 10 −4 atomic units, while the CHARMM22/CMAP optimizations are done using TINKER (Ponder and Richards, 1987) with the default convergence criterion of 0.01 kcal/mole/Å.…”

Section: Nmr Calculations and Protein Structures Usedmentioning

confidence: 99%

ProCS15: A DFT-based chemical shift predictor for backbone and C β atoms in proteins

Larsen

Bratholm

Christensen

et al. 2015

Preprint

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We present ProCS15: A program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values below 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms respectively. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each protein. The maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7 -1.1, 0.2 -0.4, and 1.8 -2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively.

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“…For these systems, the trans-chalcone 1 molecule was flipped on itself to adopt the three other available conformation in the groove with respect to the peroxide and the N-terminal (see figure 4A, B, C and D). The four supramolecular complexes were then energy minimized without constraints using the PM6-D3H+ method 25 implemented in the GAMESS software. 26 Analysis of the resulting supramolecular complexes showed that only the conformation depicted in figure 4A presented a reactive conformation with respect to the peroxide with a distance of 2.5A and angle of 98 degree close to the dunitz angle.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Revisiting the Juliá–Colonna enantioselective epoxidation: supramolecular catalysis in water

et al. 2017

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We describe an efficient epoxidation process leading to chiral epoxyketones using the reusable homo-oligopeptide poly-l-leucine (PLL) in pure water, without any organic co-solvent. A range of substituted epoxyketones can be accessed with good conversions and high enantioselectivities. Based on the experimental results and computational studies, we propose a mechanism that demonstrates the importance of both the α-helical structure and the presence of a hydrophobic groove of the homo-oligopeptide catalyst for reactivity and selectivity.

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A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+

Cited by 53 publications

References 31 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

ProCS15: A DFT-based chemical shift predictor for backbone and C β atoms in proteins

Revisiting the Juliá–Colonna enantioselective epoxidation: supramolecular catalysis in water

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