Lennard–Jones parameters for the combined QM/MM method using the B3LYP/6‐31G*/AMBER potential

Freindorf, Marek; Shao, Yihan; Furlani, Thomas R.; Kong, Jing

doi:10.1002/jcc.20264

Cited by 85 publications

(90 citation statements)

References 46 publications

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“…Several attempts have been made to cure this problem by using special van der Waals parameters for the QM system. 49,50,51,52 The effect of the scaling (column scal in Table 3) is appreciably larger than that of the polarisation, 19 kJ/mol for set 1 and 9 kJ/mol for set 2.…”

Section: Energy Contributionsmentioning

confidence: 93%

On the Convergence of QM/MM Energies

Söderhjelm

Ryde

2011

J. Chem. Theory Comput.

202

282

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We have studied the convergence of QM/MM calculations with respect to the size of the QM system. We study a proton transfer between a first-sphere cysteine ligand and a secondsphere histidine group in [Ni,Fe] hydrogenase and use a 446-atom model of the protein, treated purely with QM methods as reference. We have tested 12 different ways to redistribute charges close to the junctions (to avoid overpolarisation of the QM system), but once the junctions are moved away from the active site, there is little need to redistribute the charges. We have tested 13 different variants of QM/MM approaches, including two schemes to correct errors caused by the truncation of the QM system. However, we see little gain from such correction schemes; on the contrary they are sensitive to the charge-redistribution scheme and may cause large errors if charges are close to the junctions. In fact, the best results were obtained with a mechanical embedding approach that does not employ any correction scheme and ignores polarisation. It gives a mean unsigned error for 40 QM systems of different sizes of 7 kJ/mol with a maximum error of 28 kJ/mol. The errors can be significantly decreased if bonds between the QM and MM system (junctions) are moved one residue away from all active-site residues. Then, most QM/MM variants give mean unsigned errors of 5-9 kJ/mol, maximum errors of 16-35 kJ/mol, and only 5-7 residues give an error of over 5 kJ/mol. In general, QM/MM calculations converge faster with system size than pure QM calculations.

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Section: Energy Contributionsmentioning

confidence: 93%

On the Convergence of QM/MM Energies

Söderhjelm

Ryde

2011

J. Chem. Theory Comput.

202

282

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“…The LJ parameters for the quantum region were taken from Ref. 67, where the parameters have been re-fitted for use in a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme at the B3LYP(6-31G*)/AMBER/TIP3P level of theory. The calculations were performed using a development version of the Dalton program.…”

Section: Frequency Calculationsmentioning

confidence: 99%

Molecular quantum mechanical gradients within the polarizable embedding approach—Application to the internal vibrational Stark shift of acetophenone

List

Beerepoot

Olsen

et al. 2015

The Journal of Chemical Physics

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We present an implementation of analytical quantum mechanical molecular gradients within the polarizable embedding (PE) model to allow for efficient geometry optimizations and vibrational analysis of molecules embedded in large, geometrically frozen environments. We consider a variational ansatz for the quantum region, covering (multiconfigurational) self-consistent-field and Kohn-Sham density functional theory. As the first application of the implementation, we consider the internal vibrational Stark effect of the C==O group of acetophenone in different solvents and derive its vibrational linear Stark tuning rate using harmonic frequencies calculated from analytical gradients and computed local electric fields. Comparisons to PE calculations employing an enlarged quantum region as well as to a non-polarizable embedding scheme show that the inclusion of mutual polarization between acetophenone and water is essential in order to capture the structural modifications and the associated frequency shifts observed in water. For more apolar solvents, a proper description of dispersion and exchange-repulsion becomes increasingly important, and the quality of the optimized structures relies to a larger extent on the quality of the Lennard-Jones parameters. C 2015 AIP Publishing LLC. [http://dx

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“…Unfortunately, there are no fixed values for these parameters which would be universally applicable in a wide scope of situations. Even for the same systems different authors choose different parameters (see e.g., [99][100][101]). Some arbitrariness in the choice of the vdW correction seems to be a general problem of the hybrid approaches.…”

Section: Potential Energy Surface For Glycine Hexapeptide With the Shmentioning

confidence: 99%

“…Note, that these energies depend strongly on the set of the chosen constants. For example, the vdW energy correction calculated with a set of constants suggested in [101] for conformation 2 is equal to 0.0076 eV, resulting in the relative error of 7.5 %. These estimates demonstrate that the vdW polarization energy plays an important role giving the relative error to the calculated energies of the order of about 5-10 %.…”

Section: Potential Energy Surface For Glycine Hexapeptide With the Shmentioning

confidence: 99%

Theory of Phase Transitions in Polypeptides and Proteins

Yakubovich¹

2011

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Lennard–Jones parameters for the combined QM/MM method using the B3LYP/6‐31G*/AMBER potential

Cited by 85 publications

References 46 publications

On the Convergence of QM/MM Energies

On the Convergence of QM/MM Energies

Molecular quantum mechanical gradients within the polarizable embedding approach—Application to the internal vibrational Stark shift of acetophenone

Theory of Phase Transitions in Polypeptides and Proteins

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