Molecular Electrostatic Potentials from Invariom Point Charges

Wandtke, Claudia M.; Lübben, Jens; Dittrich, Birger

doi:10.1002/cphc.201600213

Cited by 6 publications

(6 citation statements)

References 80 publications

(153 reference statements)

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“…Originally, point charges from the restrained fitting to electrostatic potential (RESP) methodology (Bayly et al, 1993) were used. Recently, we have shown that charges from the semiempirical Austin model 1 with bond charge correction (AM1-BCC) method (Jakalian et al, 2002) and from the Invariom Point Charges database (Wandtke et al, 2016) might also be used in the aug-PROmol method of electrostatic energy estimations (Bojarowski et al, 2018).…”

Section: Figurementioning

confidence: 99%

Extension of the transferable aspherical pseudoatom data bank for the comparison of molecular electrostatic potentials in structure–activity studies

Kumar

Gruza

Bojarowski

et al. 2019

Acta Crystallogr A Found Adv

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The transferable aspherical pseudoatom data bank, UBDB2018, is extended with over 130 new atom types present in small and biological molecules of great importance in biology and chemistry. UBDB2018 can be applied either as a source of aspherical atomic scattering factors in a standard X-ray experiment (d min ' 0.8 Å ) instead of the independent atom model (IAM), and can therefore enhance the final crystal structure geometry and refinement parameters; or as a tool to reconstruct the molecular charge-density distribution and derive the electrostatic properties of chemical systems for which 3D structural data are available. The extended data bank has been extensively tested, with the focus being on the accuracy of the molecular electrostatic potential computed for important drug-like molecules, namely the HIV-1 protease inhibitors. The UBDB allows the reconstruction of the reference B3LYP/6-31G** potentials, with a root-mean-squared error of 0.015 e bohr À1 computed for entire potential grids which span values from ca 200 e bohr À1 to ca À0.1 e bohr À1 and encompass both the inside and outside regions of a molecule. UBDB2018 is shown to be applicable to enhancing the physical meaning of the molecular electrostatic potential descriptors used to construct predictive quantitative structure-activity relationship/quantitative structure-property relationship (QSAR/QSPR) models for drug discovery studies. In addition, it is suggested that electron structure factors computed from UBDB2018 may significantly improve the interpretation of electrostatic potential maps measured experimentally by means of electron diffraction or single-particle cryo-EM methods.

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Section: Figurementioning

confidence: 99%

Extension of the transferable aspherical pseudoatom data bank for the comparison of molecular electrostatic potentials in structure–activity studies

Kumar

Gruza

Bojarowski

et al. 2019

Acta Crystallogr A Found Adv

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“…The proposed aug‐PROmol model is based on densities having a solid physical basis, although there is still room for improvement. The procedure of obtaining RESP charges can be revised or tabulated point charges can be used . The Clementi‐Roetti basis set can be replaced by a more accurate one, which includes relativistic effects or electron correlation .…”

Section: Figurementioning

confidence: 99%

“…The procedure of obtaining RESP charges can be revisedo rt abulated point charges can be used. [57] The Clementi-Roetti basis set can be replaced by am ore accurate one, which includes relativistic effects or electron correlation. [58] The values for k parameters can be optimized to account for condensed phase hydrogen atoms as the currently used value of k was optimized for the hydrogen atoms of an isolated hydrogen molecule.…”

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confidence: 99%

A Universal and Straightforward Approach to Include Penetration Effects in Electrostatic Interaction Energy Estimation

2016

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To compensate for the lack of the explicit treatment of charge penetration in classical force fields, we propose a new charge-distribution model based on a promolecule augmented with point charges (aug-PROmol). It relies on a superposition of spherical atomic electron densities obtained for each chemical element from SCF energy optimized atomic orbitals. Atomic densities are further rescaled by partial point charges computed from fits to the molecular electrostatic potential. Aug-PROmol was tested on the S66 benchmark dataset extended to nonequilibrium geometries (J. Chem. Theory Comput., 2011, 7, 3466). The model does not need any additional parametrization other than point charges. Despite its simplicity, aug-PROmol approximates the electrostatic energy with good agreement (RMSE=0.76 kcal mol(-1) to DFT-SAPT with B3LYP/aug-cc-pVTZ).

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“…Values for RESP point charges were taken from our previous publication . Tabulated point charges were taken from the Invariom Point Charges (IPC) database, which is closely related to the Generalized Invariom Database . For the IPC database construction, charges were obtained by restrained fitting to electrostatic potential at the B3LYP/aug-cc-pVTZ − level of theory.…”

Section: Methods and Materialsmentioning

confidence: 99%

“…For the IPC database construction, charges were obtained by restrained fitting to electrostatic potential at the B3LYP/aug-cc-pVTZ − level of theory. For further information please see ref . For point charges from a semiempirical model we applied the Austin Model 1 with Bond Charge Correction (AM1-BCC) .…”

Section: Methods and Materialsmentioning

confidence: 99%

Universal Method for Electrostatic Interaction Energies Estimation with Charge Penetration and Easily Attainable Point Charges

Bojarowski

Kumar

Wandtke

et al. 2018

J. Chem. Theory Comput.

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Our new model of electron density augmented by point charges (aug-PROmol) provides an estimation of electrostatic interaction energies including penetration effects (ChemPhysChem 2016, 17, 2455–2460). In this paper we prove that it can be applied using sources of point charges other than those from direct restrained fitting to electrostatic potential (RESP). We used a newly established databank of tabulated invariom point charges and a widely known semiempirical method. Both sources perform equivalently to the basic aug-PROmol method as well as to reference energies at the DFT-SAPT/aug-cc-pVTZ level of theory. This is possible due to the universal character of the penetration model included in the aug-PROmol. Aug-PROmol may become a basis for development of new nonbonded terms in force fields or a high success rate scoring function.

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Molecular Electrostatic Potentials from Invariom Point Charges

Cited by 6 publications

References 80 publications

Extension of the transferable aspherical pseudoatom data bank for the comparison of molecular electrostatic potentials in structure–activity studies

Extension of the transferable aspherical pseudoatom data bank for the comparison of molecular electrostatic potentials in structure–activity studies

A Universal and Straightforward Approach to Include Penetration Effects in Electrostatic Interaction Energy Estimation

Universal Method for Electrostatic Interaction Energies Estimation with Charge Penetration and Easily Attainable Point Charges

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