Ligand atom partial charges assignment for complementary electrostatic potentials

1992 ◽  
Vol 6 (5) ◽  
pp. 461-474 ◽  
Author(s):  
S. L. Chan ◽  
P. L. Chau ◽  
J. M. Goodman
Keyword(s):  
Electrostatic Potentials ◽  
Ligand Atom ◽  
Partial Charges

Message Passing Neural Networks for Partial Charge Assignment to Metal-Organic Frameworks

2020 ◽  
Author(s):  
Ali Raza ◽  
Arni Sturluson ◽  
Cory Simon ◽  
Xiaoli Fern
Keyword(s):  
Electronic Structure ◽  
Message Passing ◽  
Gas Adsorption ◽  
Metal Organic Frameworks ◽  
Computational Cost ◽  
Electronic Structure Calculations ◽  
High Fidelity ◽  
Partial Charges ◽  
Metal Organic ◽  
Structure Calculations

Virtual screenings can accelerate and reduce the cost of discovering metal-organic frameworks (MOFs) for their applications in gas storage, separation, and sensing. In molecular simulations of gas adsorption/diffusion in MOFs, the adsorbate-MOF electrostatic interaction is typically modeled by placing partial point charges on the atoms of the MOF. For the virtual screening of large libraries of MOFs, it is critical to develop computationally inexpensive methods to assign atomic partial charges to MOFs that accurately reproduce the electrostatic potential in their pores. Herein, we design and train a message passing neural network (MPNN) to predict the atomic partial charges on MOFs under a charge neutral constraint. A set of ca. 2,250 MOFs labeled with high-fidelity partial charges, derived from periodic electronic structure calculations, serves as training examples. In an end-to-end manner, from charge-labeled crystal graphs representing MOFs, our MPNN machine-learns features of the local bonding environments of the atoms and learns to predict partial atomic charges from these features. Our trained MPNN assigns high-fidelity partial point charges to MOFs with orders of magnitude lower computational cost than electronic structure calculations. To enhance the accuracy of virtual screenings of large libraries of MOFs for their adsorption-based applications, we make our trained MPNN model and MPNN-charge-assigned computation-ready, experimental MOF structures publicly available.<br>

Bonded Force Constant Derivation of Lysine-Arginine Cross-linked Advanced Glycation End-Products

2018 ◽  
Author(s):  
Anthony Nash ◽  
Nora H de Leeuw ◽  
Helen L Birch
Keyword(s):  
Molecular Dynamics ◽  
Force Constant ◽  
Computational Study ◽  
Force Constants ◽  
Quantum Mechanical ◽  
Advanced Glycation ◽  
Partial Charges ◽  
Cross Links ◽  
Complete Set ◽  
Dynamics Simulations

<div> <div> <div> <p>The computational study of advanced glycation end-product cross- links remains largely unexplored given the limited availability of bonded force constants and equilibrium values for molecular dynamics force fields. In this article, we present the bonded force constants, atomic partial charges and equilibrium values of the arginine-lysine cross-links DOGDIC, GODIC and MODIC. The Hessian was derived from a series of <i>ab initio</i> quantum mechanical electronic structure calculations and from which a complete set of force constant and equilibrium values were generated using our publicly available software, ForceGen. Short <i>in vacuo</i> molecular dynamics simulations were performed to validate their implementation against quantum mechanical frequency calculations. </p> </div> </div> </div>

A Graphical Method to Study Electrostatic Potentials of 25 nm Channel Length DG SOI MOSFETs

2018 ◽  
Vol 10 (4) ◽  
pp. 04027-1-04027-4
Author(s):  
M. Djerioui ◽  
◽  
M. Hebali ◽  
D. Chalabi ◽  
A. Saidane ◽  
...  
Keyword(s):  
Graphical Method ◽  
Channel Length ◽  
Electrostatic Potentials

Some Approximate Atomic and Molecular Energy Formulas

2003 ◽  
Vol 68 (1) ◽  
pp. 61-74 ◽  
Author(s):  
Peter Politzer ◽  
Abraham F. Jalbout ◽  
Ping Jin
Keyword(s):  
Density Functional ◽  
Electrostatic Potentials ◽  
Hartree Fock ◽  
Chemical Potentials ◽  
Approximate Formulas

We have tested several approximate formulas that relate atomic and molecular energies to the electrostatic potentials at the nuclei, V0 and V0,A, respectively. They are based upon the assumption that the chemical potentials can be neglected relative to V0 and V0,A. Exact, Hartree-Fock and density-functional values were used for the latter. The results are overall encouraging; the errors in the energies generally decrease markedly as the nuclear charges Z increase and the assumptions become more valid. Improvement is needed, however, in fitting the V0 and V0,A to Z.

A comparison of different electrostatic potentials on prediction accuracy in CoMFA and CoMSIA studies

2010 ◽  
Vol 45 (4) ◽  
pp. 1544-1551 ◽  
Author(s):  
Keng-Chang Tsai ◽  
Yu-Chen Chen ◽  
Nai-Wan Hsiao ◽  
Chao-Li Wang ◽  
Chih-Lung Lin ◽  
...  
Keyword(s):  
Prediction Accuracy ◽  
Electrostatic Potentials

Accurately Reproducing Ab Initio Electrostatic Potentials with Multipoles and Fragmentation

2009 ◽  
Vol 113 (39) ◽  
pp. 10527-10533 ◽  
Author(s):  
Hai-Anh Le ◽  
Adrian M. Lee ◽  
Ryan P. A. Bettens
Keyword(s):  
Ab Initio ◽  
Electrostatic Potentials
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