A “critical” appraisal of electrostatic charge models for molecules

Gadre, Shridhar R.; Pundlik, Savita S.; Shrivastava, Indira H.

doi:10.1007/bf02840752

Cited by 11 publications

(1 citation statement)

References 32 publications

(34 reference statements)

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“…These point charges polarize the QM electron density. However, the electrostatic potential due to the external atoms is not accurately described by a collection of point charges. − One important correction is to include the charge penetration effect. As a point charge approaches a frozen atom, it sees more and more of the positive nuclear charge because the shielding of the nuclear charge by its electron density decreases.…”

Section: New Methods For Electrostatic Embedding and Fragment Boundariesmentioning

confidence: 99%

Quantum Mechanical Fragment Methods Based on Partitioning Atoms or Partitioning Coordinates

Wang

Yang

et al. 2014

Acc. Chem. Res.

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Conspectus The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches. First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches. Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine atoms for capping dangling bonds, and we have shown that they can greatly improve the accuracy. Finally we present a new approach that goes beyond QM/MM by combining the convenience of molecular mechanics with the accuracy of fitting a potential function to electronic structure calculations on a specific system. To make the latter practical for systems with a large number of degrees of freedom, we developed a method to interpolate between local internal-coordinate fits to the potential energy. A key issue for the application to large systems is that rather than assigning the atoms or monomers to fragments, we assign the internal coordinates to reaction, secondary, and tertiary sets. Thus, we make a partition in coordinate space rather than atom space. Fits to the local dependence of the potential energy on tertiary coordinates are arrayed along a preselected reaction coordinate at a sequence of geometries called anchor points; the potential energy function is called an anchor points reactive potential. Electrostatically embedded fragment methods and the anc...

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Section: New Methods For Electrostatic Embedding and Fragment Boundariesmentioning

confidence: 99%

Quantum Mechanical Fragment Methods Based on Partitioning Atoms or Partitioning Coordinates

Wang

Yang

et al. 2014

Acc. Chem. Res.

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Transferable atom equivalent multicentered multipole expansion method

et al. 2003

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The transferability of atomic and functional group properties is an implicit concept in chemistry. The work presented here describes the use of Transferable Atom Equivalents (TAE) to represent molecular electrostatic potential fields through the use of integrated atomic multipole moments that are associated with each TAE atom type used in the reconstruction. TAE molecular surface distributions of electrostatic potentials are compared with analytical ab initio and empirical (Gasteiger) partial charge reference models for several conformations of test peptides. Surface electrostatic potential distributions computed using TAE multipole representations were found to converge at the octopole level, with incremental improvement observed when hexadecapoles were included. Molecular electrostatic potential fields that were produced using the TAE method were observed to be responsive to conformational changes and to compare well with ab initio reference distributions. Generation of TAE atom types and their associated multipoles does not involve fitting to sample electrostatic potential fields, but rather utilizes integrated AIM atomic electron density distributions within representative chemical environments. The RECON program was used for TAE reconstruction. RECON is capable of processing 5,000 drug-sized molecules or 25 proteins per minute per 1.7 GHz P4 Linux processor.

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Prelude to molecular dynamics: Topography‐driven gaussian charge models

Albuquerque

Shirsat

2018

Int J of Quantum Chemistry

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A new strategy to develop Gaussian charge models (GCMs) for molecules like ammonia, water, ethene, hydrogen sulfide, formaldehyde and benzene is presented. These molecular models comprising of positive point charges and negative Gaussian charge distributions (GCDs), which represent nuclei and continuous electron charge distribution, are found to correctly represent the ab initio Molecular Electrostatic Potential (MESP) and reproduce its essential topographical features of corresponding molecules. The models use optimized parameters: positive charges at nuclei, negative charges on GCDs, Gaussian exponent and centers. The Potential Energy Surface (PES) of water dimer has been explored using water GCMs. A good agreement has been found between PES obtained using GCMs and wave function. The Gaussian models correctly predict structure of benzene‐water complex. It is thus recommended to use GCMs for molecular dynamic simulations.

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A “critical” appraisal of electrostatic charge models for molecules

Cited by 11 publications

References 32 publications

Quantum Mechanical Fragment Methods Based on Partitioning Atoms or Partitioning Coordinates

Quantum Mechanical Fragment Methods Based on Partitioning Atoms or Partitioning Coordinates

Transferable atom equivalent multicentered multipole expansion method

Prelude to molecular dynamics: Topography‐driven gaussian charge models

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