Variable van der Waals Radii Derived From a Hybrid Gaussian Charge Distribution Model for Continuum-Solvent Electrostatic Calculations
-
Renlong Ye
Abstract
We introduce a hybrid Gaussian charge distribution model (HGM) that partitions the molecular electron density into overlapping spherical atomic domains. The semi-empirical HGM consists of atom-centered spherical Gaussian functions and discrete point charges, which are optimized to reproduce the electrostatic potential on the molecular surface as well as the number of electrons in atom-centered and certain off-atom-centered spherical regions as closely as possible. In contrast, our previous Gaussian charge distribution model [J. Chem. Phys. 129, 014509 (2008)] contained only spherical Gaussian functions and was not required to reproduce the number of electrons in off-atom-centered regions. Variable van der Waals (vdW) radii fluctuating around the Bondi radii are derived from the HGM based on the isodensity contour concept and further employed to define the molecular cavity in our quantum mechanical/Poisson–Boltzmann/surface area model as well as the polarizable continuum model. The variable vdW radii produce more accurate solvation free energies for 31 neutral molecules than the Bondi radii for both continuum solvent models (CSM) consistently. Moreover, for H atoms, the linear dependence of the atomic radii on the atomic partial charges is identified.
Supplementary material
the online version of this article (DOI: 10.1515/zpch-2015-0746) provides supplementary material for authorized users.
Acknowledgement
BZ gratefully acknowledges the financial support from “the Fundamental Research Funds for the Central Universities”, No. 30915011314. CFW acknowledges the support from a University of Missouri Research Board Award. We appreciate the useful comments from Dr. Norman Hamer to improve the manuscript.
©2016 Walter de Gruyter Berlin/Boston
Artikel in diesem Heft
- Frontmatter
- Preface
- Congratulations to Michael Springborg
- Fourier Space Uncoupled Hartree–Fock Polarizabilities of One-Dimensionally Periodic Systems. Polyethylene and Polysilane Revisited
- Construction of Constrained Dipole Oscillator Strength Distributions
- Incremental DF-LCCSD(T) Calculations for a Water Molecule Inside and Outside Armchair Carbon Nanotubes
- An Efficient Unrestricted PCM-Elongation Method for Large High-Spin Polymer/Dendrimer Systems
- Variable van der Waals Radii Derived From a Hybrid Gaussian Charge Distribution Model for Continuum-Solvent Electrostatic Calculations
- Natural Extension of Hartree–Fock Through Extremal 1-Fermion Information: Overview and Application to the Lithium Atom
- Direct Piezoelectric Tensor of 3D Periodic Systems through a Coupled Perturbed Hartree–Fock/Kohn–Sham Method
- Intensive Atomization Energy: Re-Thinking a Metric for Electronic Structure Theory Methods
- The VES Hypothesis and Protein Conformational Changes
- Understanding the Electronic Structure of Graphene Quantum Dot-Fullerene Nanohybrids for Photovoltaic Applications
- A First-Principles Study of Metal-Decorated Graphene Nanoribbons for Hydrogen Storage
- Defect Effects on the Interfacial Interactions between a (5, 5) Carbon Nanotube and an Al (111) Surface
- Structural Insight into Self Assembly of Sophorolipids: A Molecular Dynamics Simulation Study
- The Role of Mutations at the Side Door on the Thermal Stability and Structural Flexibility of the pnbCE Enzyme
- Electric (Hyper) Polarizability of the Hypofluorous Acid (HOF) from High-Level ab initio Calculations with Especially Designed Purpose-Oriented Basis Sets
- Conformational and Vibrational Analysis of 2-, 3- and 4-Pyridinecarbonyl Chloride Using DFT
- Spectral Properties of α and β L Rhamno-Indigo Molecules and Activities Prediction Through NBO Analysis. A DFT Study
- Solid State Structure Prediction Through DFT Calculations and 13C NMR Measurements: Case Study of Spiro-2,4-dithiohydantoins
- Eu2+-Containing Luminescent Perovskite-Type Hydrides Studied by Electron Paramagnetic Resonance
- Mn Adsorption on the GaAs(111)–(2×2)B Surface: First Principles Studies
- Charge and Compositional Effects on the 2D–3D Transition in Octameric AgAu Clusters
- Diversity Characterization of Binary Clusters by Means of a Generalized Distance
- First Principle Investigation of (Bi2O3)n Clusters With n = 6 − 9
- The Role of Aluminum Substitution on the Stability of Substituted Polyhedral Oligomeric Silsesquioxanes
- Ab-Initio Investigation of Nowotny Chimney Ladder Silicide Os2Si3 Using the Modified BJ Potential
- Surface Plasmon Assisted Two-Photon Ionization of Noble and Alkali Metal Clusters
- Temperature Dependence of Stability of Copper Clusters
- Detecting and Quantifying Geometric Features in Large Series of Cluster Structures
Artikel in diesem Heft
- Frontmatter
- Preface
- Congratulations to Michael Springborg
- Fourier Space Uncoupled Hartree–Fock Polarizabilities of One-Dimensionally Periodic Systems. Polyethylene and Polysilane Revisited
- Construction of Constrained Dipole Oscillator Strength Distributions
- Incremental DF-LCCSD(T) Calculations for a Water Molecule Inside and Outside Armchair Carbon Nanotubes
- An Efficient Unrestricted PCM-Elongation Method for Large High-Spin Polymer/Dendrimer Systems
- Variable van der Waals Radii Derived From a Hybrid Gaussian Charge Distribution Model for Continuum-Solvent Electrostatic Calculations
- Natural Extension of Hartree–Fock Through Extremal 1-Fermion Information: Overview and Application to the Lithium Atom
- Direct Piezoelectric Tensor of 3D Periodic Systems through a Coupled Perturbed Hartree–Fock/Kohn–Sham Method
- Intensive Atomization Energy: Re-Thinking a Metric for Electronic Structure Theory Methods
- The VES Hypothesis and Protein Conformational Changes
- Understanding the Electronic Structure of Graphene Quantum Dot-Fullerene Nanohybrids for Photovoltaic Applications
- A First-Principles Study of Metal-Decorated Graphene Nanoribbons for Hydrogen Storage
- Defect Effects on the Interfacial Interactions between a (5, 5) Carbon Nanotube and an Al (111) Surface
- Structural Insight into Self Assembly of Sophorolipids: A Molecular Dynamics Simulation Study
- The Role of Mutations at the Side Door on the Thermal Stability and Structural Flexibility of the pnbCE Enzyme
- Electric (Hyper) Polarizability of the Hypofluorous Acid (HOF) from High-Level ab initio Calculations with Especially Designed Purpose-Oriented Basis Sets
- Conformational and Vibrational Analysis of 2-, 3- and 4-Pyridinecarbonyl Chloride Using DFT
- Spectral Properties of α and β L Rhamno-Indigo Molecules and Activities Prediction Through NBO Analysis. A DFT Study
- Solid State Structure Prediction Through DFT Calculations and 13C NMR Measurements: Case Study of Spiro-2,4-dithiohydantoins
- Eu2+-Containing Luminescent Perovskite-Type Hydrides Studied by Electron Paramagnetic Resonance
- Mn Adsorption on the GaAs(111)–(2×2)B Surface: First Principles Studies
- Charge and Compositional Effects on the 2D–3D Transition in Octameric AgAu Clusters
- Diversity Characterization of Binary Clusters by Means of a Generalized Distance
- First Principle Investigation of (Bi2O3)n Clusters With n = 6 − 9
- The Role of Aluminum Substitution on the Stability of Substituted Polyhedral Oligomeric Silsesquioxanes
- Ab-Initio Investigation of Nowotny Chimney Ladder Silicide Os2Si3 Using the Modified BJ Potential
- Surface Plasmon Assisted Two-Photon Ionization of Noble and Alkali Metal Clusters
- Temperature Dependence of Stability of Copper Clusters
- Detecting and Quantifying Geometric Features in Large Series of Cluster Structures
