Fully polarizable QM/MM calculations: An application to the nonbonded iodine-oxygen interaction in dimethyl-2-iodobenzoylphosphonate

Gooding, Stuart R.; Winn, Peter J.; Maurer, Richard I.; Ferenczy, György G.; Miller, John R.; Harris, Jayne E.; Griffiths, D. Vaughan; Reynolds, Christopher A.

doi:10.1002/(sici)1096-987x(20000430)21:6<478::aid-jcc6>3.0.co;2-d

Cited by 16 publications

(16 citation statements)

References 23 publications

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“…Elsewhere we have shown that electrostatic noncomplementarities can exist among well-docked structures and that they can be alleviated by use of induced charges. 45,74 This factor contributes to the improvement in docking seen for a number of the difficult cases presented in Tables 1 and 2. Thus, Figure 4 Polarization does not improve every case studied here and this is to be expected because other effects that have been ignored here (as is often the case in state-of-the-art docking 75 ) may be equally important.…”

Section: Discussionmentioning

confidence: 96%

Assessing the Role of Polarization in Docking

et al. 2008

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We describe a strategy for including ligand and protein polarization in docking that is based on the conversion of induced dipoles to induced charges. Induced charges have a distinct advantage in that they are readily implemented into a number of different computer programs, including many docking programs and hybrid QM/MM programs; induced charges are also more readily interpreted. In this study, the ligand was treated quantum mechanically to avoid parametrization issues and was polarized by the target protein, which was treated as a set of point charges. The induced dipole at a given target atom, due to polarization by the ligand and neighboring residues, was reformulated as induced charges at the given atom and its bonded neighbors, and these were allowed to repolarize the ligand in an iterative manner. The final set of polarized charges was evaluated in docking using AutoDock 4.0 on 12 protein-ligand systems against the default empirical Gasteiger charges, and against nonpolarized and partially polarized potential-derived charges. One advantage of AutoDock is that the best rmsd structure can be identified not only from the lowest energy pose but also from the largest cluster of poses. Inclusion of polarization does not always lead to the lowest energy pose having a lower rmsd, because docking is designed by necessity to be rapid rather than accurate. However, whenever an improvement in methodology, corresponding to a more thorough treatment of polarization, resulted in an increased cluster size, then there was also a corresponding decrease in the rmsd. The options for implementing polarization within a purely classical docking framework are discussed.2008112

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Section: Discussionmentioning

confidence: 96%

Assessing the Role of Polarization in Docking

et al. 2008

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“…Gaussian03 [26] was used to carry out a QM optimisation on a water monomer at the [27,28], and Stone's GDMA 1.3 program [29] was used to convert the charge distribution into a multipole series, which was then converted into potential derived point charges using the mulfit methodology [21,22,[30][31][32]. Both the protein and the water charges are derived from correlated wavefunctions and therefore suitable for polarization calculations [32].…”

Section: Methodsmentioning

confidence: 99%

“…where E is the field, and α is the isotropic atomic polarizability, taken from Miller and Savchik [34]. These dipoles were then expressed as induced charges using the mulfit technology, described above [21,22,[30][31][32]. These new induced charges were added to the permanent charges to generate a new QM/MM system, and in accordance with previous work [8] this process was iterated four times, bringing the system very close to convergence.…”

Section: Methodsmentioning

confidence: 99%

“…However, in these models electronic polarization is included in the QM model of the ligand but it is not incorporated into the MM model of the enzyme. Noting the importance of electrostatic effects in this system, [16,20] here we apply the method of induced charges [8,[21][22][23] (IC) to incorporate polarization into a QM/MM(IC) model of the chorismate mutase reaction, with the aim of demonstrating the feasibility of studying the effect of enzyme polarization on transition state stabilization.…”

Section: Introductionmentioning

confidence: 99%

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The effect of MM polarization on the QM/MM transition state stabilization: application to chorismate mutase

Illingworth¹,

Parkes²,

Snell³

et al. 2008

Mol. Phys.

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Registro de acceso restringido Este recurso no está disponible en acceso abierto por política de la editorial. No obstante, se puede acceder al texto completo desde la Universitat Jaume I o si el usuario cuenta con suscripción. Registre d'accés restringit Aquest recurs no està disponible en accés obert per política de l'editorial. No obstant això, es pot accedir al text complet des de la Universitat Jaume I o si l'usuari compta amb subscripció. Restricted access item This item isn't open access because of publisher's policy. The full--text version is only available from Jaume I University or if the user has a running suscription to the publisher's contents.

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“…Early approaches to the PE method involved simple iterations over an electrostatic embedding scheme where the inducible dipoles could be back-polarized by point charges fit to the electronic density until the system converged. [11][12][13][14] A related approximation to the polarizable embedding was introduced with the LICHEM interface, which couples generic QM and MM software using a partially self-consistent polarization scheme, compromising some accuracy for a more generalized interface and grater computational efficiency. 15,16 By solving the QM equations and the MM polarization equations in a fully coupled fashion, some recent approaches adopt a more intimate coupling between the electron density in the QM region and the polarization in the MM region, with the latter being modeled by inducible point dipoles (IPD), [17][18][19][20][21][22][23][24][25] fluctuating charges, [26][27][28][29][30][31] Drude oscillators., [32][33][34][35][36][37] or using a response kernel.…”

Section: Introductionmentioning

confidence: 99%

A Many-Body, Fully Polarizable Approach to QM/MM Simulations

Lambros¹,

Lipparini²,

Cisneros³

et al. 2020

Preprint

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<div> <div> <div> <p>We present a new development in quantum mechanics/molecular mechanics (QM/MM) methods by replacing conventional MM models with data-driven many-body (MB) representations rigorously derived from high-level QM calculations. The new QM/MM approach builds on top of mutually polarizable QM/MM schemes developed for polarizable force fields with inducible dipoles and uses permutationally invariant polynomials to effectively account for quantum- mechanical contributions (e.g., exchange-repulsion, and charge transfer and penetration) that are difficult to describe by classical expressions adopted by conventional MM models. Us- ing the many-body MB-pol and MB-DFT potential energy functions for water, which include explicit 2-body and 3-body terms fitted to reproduce the corresponding CCSD(T) and PBE0 2- body and 3-body energies for water, we demonstrate a smooth energetic transition as molecules are transferred between QM and MM regions, without the need of a transition layer. By effectively elevating the accuracy of both the MM region and the QM/MM interface to that of the QM region, the new QM/MB-MM approach achieves an accuracy comparable to that obtained with a fully QM treatment of the entire system. </p> </div> </div> </div>

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Fully polarizable QM/MM calculations: An application to the nonbonded iodine-oxygen interaction in dimethyl-2-iodobenzoylphosphonate

Cited by 16 publications

References 23 publications

Assessing the Role of Polarization in Docking

Assessing the Role of Polarization in Docking

The effect of MM polarization on the QM/MM transition state stabilization: application to chorismate mutase

A Many-Body, Fully Polarizable Approach to QM/MM Simulations

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